Tables with rowspan (693)

elife-00306-v1.xml

10.7554/eLife.00306.008

Table 1.

Early oxidation targets in yeast

DOI: http://dx.doi.org/10.7554/eLife.00306.008

Gene (Cys)	Protein	Loc.	2% glucose (standard)					0.5% glucose (CR)
Gene (Cys)	Protein	Loc.	D0	D1	D2	D3	D4	D0	D1	D2	D3	D4	D5	D7
CCT4 (399)	T-complex protein 1 subunit delta	C	12	24	58	87	86	12	14	13	11	39	72	82
ARO2 (221)*	Chorismate synthase	C	13	13	31	71	74				nd
CDC48 (115)	Cell division control protein 48	ER, C	12	29	55	75	93	13	15	14	28	62	68	90
CCT8 (336)	T-complex protein 1 subunit theta	C	47	40	77	76	89				nd
TRR (142;145)	Thioredoxin reductase	C/M	33	33	65	77	82	34	39	42	44	73	80	86
UBC4 (108)	Ubiquitin-conjugating enzyme E2 4	N	19	23	48	70	81	20	15	22	24	49	73	88
YCR090C (124)	UPF0587 protein	C, N	34	39	67	76	88				nd
LYS2 (614)	L-aminoadipate-semialdehyde DH	C	15	22	49	79	86	14	11	12	48	56	74	81
YDJ1 (185;188)*	Homologue of DnaJ	C	46	46	82	89	75	45	44	51	70	73	83	88
MES1 (353)	Methionyl-tRNA synthetase	C	23	34	64	86	82	20	21	31	61	78	80	98
OLA1 (43)	Uncharacterized GTP-binding protein	C	17	12	46	91	83	20	10	22	29	53	78	88
PAA1 (51;55)	Polyamine N-acetyltransferase 1	C	26	36	53	48	61	18	15	25	52	61	71	83
PRB1 (36)	Cerevisin	V	18	23	57	91	94	12	14	26	23	77	80	88
PUT2 (162)	δ-1-pyrroline-5-carboxylate DH	M	12	10	35	60	66				nd
RPL10 (49)	60S protein L10	C	15	15	31	73	89	21	17	28	23	59	80	90
RPL42B (74)*	60S protein L42	C	15	22	49	86	86	15	19	25	49	54	77	93
RPS11B (58)	40S protein S11	C	18	17	37	77	81	14	17	27	25	36	83	86
RPS22B (72)	40S protein S22-B	C	13	9	34	62	72	32	29	36	32	41	72	79
SES1 (413;414)*	Seryl-tRNA synthetase	C	22	23	55	66	79	20	19	17	43	65	71	81
HEM1 (386)	5-aminolevulinate synthase	M	13	21	58	77	88				nd
IDP1 (398)	Isocitrate dehydrogenase 1	M	18	19	41	61	85	16	18	32	25	49	81	80
KGD1 (983)	2-oxoglutarate dehydrogenase E1	M	25	21	49	57	84	18	18	19	16	57	54	70
FAS2 (917)	Fatty acid synthase subunit alpha	C, M	22	16	30	62	86	14	8	15	59	81	87	72
ERG13 (300)	Hydroxymethylglutaryl-CoA synthase	ER	17	38	47	80	91	16	18	30	44	55	70	84
FUS2 (371)	Nuclear fusion protein FUS2	N	18	33	57	68	80	9	18	12	20	31	64	91
LAP4 (202)	Vacuolar aminopeptidase 1	V	19	38	45	83	86	25	35	27	22	39	61	81
PYC2 (218)	Pyruvate carboxylase 2	C	11	28	46	81	93	13	11	22	47	66	77	81
TEF1 (409)*	Elongation factor 1-alpha	C	13	38	40	62	70	18	30	17	26	36	57	68
GapDH(150;154)†	Glyceraldehyde-3-P Dehydrogenase	C	26	22	28	70	81	24	22	21	26	28	72	87

Peroxide sensitive (Brandes et al. 2011).

†

Follows the general oxidation pattern.

All cluster D and E proteins thiols whose oxidation kinetics significantly preceded the general oxidation trend are listed. Thiol oxidation states, which are at least 2-fold higher as compared to day 0 or at least 1.5 fold higher as compared to day 0 and exceeding a total oxidation of 60% are shaded. Standard deviations can be found in Figure 1—Source data 1.

elife-00425-v1.xml

10.7554/eLife.00425.005

Table 1.

ROIs with corresponding Talairach coordinates (mean x, y, and z centre of mass and standard deviations) and sizes

DOI: http://dx.doi.org/10.7554/eLife.00425.005

ROI name	Tailarach coordinates						ROI size
ROI name	x	y	z	std x	std y	std z	mm³	Nr voxels
Parieto-frontal ROIs
L Superior parieto-occipital cortex (SPOC)	−8	−75	29	2.4	2.9	3.6	1469	54
L Posterior intraparietal sulcus (pIPS)	−22	−68	45	3.4	3.7	4.1	1640	61
L Middle intraparietal sulcus (midIPS)	−32	−56	46	4.4	4	3.9	1943	72
L Posterior anterior intraparietal sulcus (post. aIPS)	−42	−49	43	3.6	4.3	3.9	2290	85
L Anterior intraparietal sulcus (aIPS)	−42	−40	42	4.2	4.3	4.2	2067	77
L Supramarginal gyrus (SMG)	−56	−35	33	3.7	3.7	4	1479	55
L Motor cortex	−38	−29	48	4.3	4.3	4.3	2407	89
L Dorsal premotor (PMd) cortex	−26	−14	52	4.2	3.8	4.1	2135	79
L Ventral premotor (PMv) cortex	−52	3	15	3.3	3.8	3.1	1460	54
L Somatosensory (SS) cortex	−39	−40	48	2.8	2.8	2.9	1592	59
Localizer-defined ROIs
L tool-anterior intraparietal sulcus (t-aIPS)	−41	−42	46	3.3	3.4	4.2	1038	38
L Posterior middle temporal gyrus (pMTG)	−53	−57	−3	4.1	3.1	3.3	621	23
L Extrastriate body area (EBA)	−49	−72	1	2.8	3.6	3.7	851	32

Mean ROI sizes across subjects from ACPC data (in mm³ and functional voxels). Std = standard deviation.

elife-00669-v1.xml

10.7554/eLife.00669.014

Table 3.

The values of the parameters of the Model 1 best fits shown in Figure 2

DOI: http://dx.doi.org/10.7554/eLife.00669.014

	Model 1
	WT early night (panel F)	WT normal night (panel F)	WT late night(panel F)	cca1/lhy early night (panel H)	cca1/lhy normal night (panel H)	WT low light level (panel J)	WT normal light level (panel J)
ρ₀ (mg g⁻¹ FW) within 10% of the measured value	8.5	11.0	11.7	4.2	5.1	3.6	6.1
γ (0.7–3.0)	1.8	1.8	1.9	1.2	1.2	1.5	1.3
(βk_ST1)⁻¹ (1.5–5.0) hr	5.0	5.0	5.0	1.6	1.7	2.1	1.5
t_r (9.0–12.0) hr	9.0	Any value in the specified range	Any value in the specified range	11.7	11.7	Any value in the specified range	Any value in the specified range
t₀ (−5.0–5.0) hr for the cca1/lhy data, t₀ = 0 for WT	0.0	0.0	0.0	−4.2	−2.5	0.0	0.0

With each parameter the range used in the best fit search is indicated.

WT: wild-type plants.

elife-00669-v1.xml

10.7554/eLife.00669.015

Table 4.

The values of the parameters of the Model 2 best fits shown in Figure 2

DOI: http://dx.doi.org/10.7554/eLife.00669.015

	Model 2
	WT early night (panel G)	WT normal night (panel G)	WT late night (panel G)	cca1/lhy early night (panel I)	cca1/lhy normal night (panel I)	WT low light level (panel K)	WT normal light level (panel K)
ρ₀ (mg g⁻¹ FW) within 10% of the measured value	8.3	11.0	12.1	4.2	5.1	3.5	5.8
γ (0.7–3.0)	1.1	1.0	1.1	1.3	1.2	1.2	0.9
t_r1 (9.0–12.0) hr	11.0	12.0	12.0	11.0	11.4	10.5	10.2
t_r2 (20.0–23.0) hr	20.1	20.0	20.0	21.8	21.4	21.4	22.5
t₀ (−5.0–5.0) hr for the cca1/lhy data, t₀ = 0 for WT	0.0	0.0	0.0	−2.4	−1.3	0.0	0.0

With each parameter the range used in the best fit search is indicated.

WT: wild-type plants.

elife-00669-v1.xml

10.7554/eLife.00669.016

Table 5.

The values of the parameters of the Model 1 best fits shown in Figure 3

DOI: http://dx.doi.org/10.7554/eLife.00669.016

	Model 1
	Panel A	Panel B	Panel C	Panel D
ρ₀ (mg g⁻¹ FW) within 10% of the measured value	5.4	9.0	7.7	4.2
γ (0.7–3.0)	2.4	1.4	1.1	1.0
(βk_ST1)⁻¹ (1.5–5.0) hr	5.0	2.6	2.1	2.0
t_r (9.0–12.0) hr	9.0	9.0	10.3	12.0
t₀ (−5.0—5.0) hr	4.3	3.3	2.4	−0.5

With each parameter the range used in the best fit search is indicated.

elife-00669-v1.xml

10.7554/eLife.00669.017

Table 6.

The values of the parameters of the Model 2 best fits shown in Figure 3—figure supplement 2

DOI: http://dx.doi.org/10.7554/eLife.00669.017

	Model 2
	Panel A	Panel B	Panel C	Panel D
ρ₀ (mg g⁻¹ FW) within 10% of the measured value	5.5	9.1	7.7	4.2
γ (0.7–3.0)	1.5	1.3	0.7	0.7
t_r1 (9.0–12.0) hr	12.0	9.0	9.0	9.0
t_r2 (20.0–23.0) hr	20.0	20.9	22.1	22.1
t₀ (−5.0–5.0) hr	5.0	5.0	2.4	0.0

With each parameter the range used in the best fit search is indicated.

elife-00747-v1.xml

10.7554/eLife.00747.007

Table 1.

Probability of treatment failure for combination therapy in patients

DOI: http://dx.doi.org/10.7554/eLife.00747.007

Patient	Primary tumor type	Number of metastases	Total tumor burden (number of cells)	Probability of treatment failure
Patient	Primary tumor type	Number of metastases	Total tumor burden (number of cells)	Monotherapy	Dual therapy: n₁₂ = 1	Dual therapy: n₁₂ = 0
N1	Pancreas	18	2.6 × 10¹¹	1	1	0.283
N2	Colon	25	2.3 × 10¹¹	1	1	0.26
N3	Melanoma	26	1.7 × 10¹¹	1	1	0.203
N4	Melanoma	30	1.4 × 10¹¹	1	1	0.172
N5	Colon	21	1.0 × 10¹¹	1	1	0.128
N6	Melanoma	8	9.8 × 10¹⁰	1	1	0.12
N7	Colon	25	9.1 × 10¹⁰	1	1	0.112
N8	Pancreas	8	7.4 × 10¹⁰	1	1	0.092
N9	Pancreas	23	6.4 × 10¹⁰	1	1	0.08
N10	Pancreas	5	5.5 × 10¹⁰	1	1	0.069
N11	Colon	14	5.4 × 10¹⁰	1	1	0.068
N12	Rectal	23	4.8 × 10¹⁰	1	1	0.061
N13	Melanoma	9	4.1 × 10¹⁰	1	1	0.052
N14	Pancreas	13	4.1 × 10¹⁰	1	1	0.051
N15	Pancreas	8	3.3 × 10¹⁰	1	1	0.042
N16	Melanoma	7	2.2 × 10¹⁰	1	1	0.028
N17	Melanoma	10	2.1 × 10¹⁰	1	1	0.027
N18	Colon	4	2.0 × 10¹⁰	1	1	0.026
N19	Melanoma	9	1.8 × 10¹⁰	1	1	0.023
N20	Colon	3	1.6 × 10⁹	1	0.881	0.002
N21	Melanoma	21	1.3 × 10⁹	1	0.828	0.002
N22	Pancreas	1	8.5 × 10⁸	1	0.677	0.001

For monotherapy, we assume that 50 point mutations (n = 50) can in principle confer resistance to the drug. With dual therapy, we assume that 50 point mutations can in principle confer resistance to each drug individually (n₁ = n₂ = 50). Two scenarios are modeled: in the first, there is one mutation that can in principle confer resistance to both drugs (i.e., cross-resistance, n₁₂ = 1). In the other case, there are no possible mutations that can confer resistance to both drugs (n₁₂ = 0). Parameter values: birth rate, b = 0.14, death rate, d = 0.13, death rate for sensitive cells during treatment, d′ = 0.17, point mutation rate u = 10⁻⁹.

Colon: colonic adenocarcinoma; Rectal: rectal adenocarcinoma; Pancreas: pancreatic ductal adenocarcinoma.

elife-00747-v1.xml

10.7554/eLife.00747.011

Table 2.

Simulation results for the probability of treatment failure when resistance is costly

DOI: http://dx.doi.org/10.7554/eLife.00747.011

Dual therapy:		Number of cells	Birth rate	Probability of treatment failure
n₁ = n₂	n₁₂	Number of cells	Birth rate	c = 0%	c = 1%	c = 5%	c = 10%
50	0	10⁹	0.14	0.0	0.0	0.0	0.0
50	0	10⁹	1	0.01	0.01	0.01	0.0
50	1	10⁹	0.14	0.74	0.73	0.72	0.7
50	1	10⁹	1	0.74	0.74	0.72	0.7
50	0	10¹¹	0.14	0.12	0.11	0.08	0.06
50	0	10¹¹	1	0.53	0.51	0.42	0.32
50	1	10¹¹	0.14	1.0	1.0	1.0	1.0
50	1	10¹¹	1	1.0	1.0	1.0	1.0

Each resistance mutation reduces the net growth rate by a factor c via a decrease of the birth rate b. Parameter values are death rate, d = b − 0.01, death rate for sensitive cells during treatment, d’ = b + 0.03, point mutation rate, u = 10⁻⁹. The simulation results are averages over 10⁶ runs per parameter combination.

elife-00801-v1.xml

10.7554/eLife.00801.008

Table 2.

Cortical areas showing significantly less average activation for trained than untrained sequences. The opposite contrast did not result in any significant areas

DOI: http://dx.doi.org/10.7554/eLife.00801.008

Area	Area (cm²)	P_cluster	Peak t₍₁₅₎	MNI
Area	Area (cm²)	P_cluster	Peak t₍₁₅₎	X	Y	Z
Left hemisphere
PMd	7.72	<0.002	6.02	−27	−1	48
OPJ	1.43	<0.002	6.74	−10	−67	59
IPS	0.16	0.020	7.55	−42	−43	40
Right hemisphere
PMd	0.14	0.020	4.25	37	16	51
IPS	0.13	0.028	5.28	19	−49	61
IPS	0.27	<0.002	5.48	29	−52	49

Table shows the result of a surface-based random effects analysis (N = 16). The uncorrected threshold was p<0.002, t(15) > 3.39, and P_cluster is the p-value corrected for multiple comparisons over the whole cortical surface using the area of the cluster (Worsley et al., 1996). The coordinates reflect the location of the cluster’s peak in MNI space.

elife-00857-v1.xml

10.7554/eLife.00857.011

Table 2.

Detailed list of the active BAF compounds

DOI: http://dx.doi.org/10.7554/eLife.00857.011

Compound	Molecular formula	Molecular weight*	Sources/companies	Purity	Rescuing percentage§ (%)		ZINC entry code¶	SMILES string
Compound	Molecular formula	Molecular weight*	Sources/companies	Purity	PC12	Hela	ZINC entry code¶	SMILES string
BAF1	C₂₀H₈Br₄O₅	647.9	Sigma-Aldrich	∼99%	38 ± 11	44 ± 7	ZINC04261875	c1ccc2c(c1)C(=O)OC23c4ccc(c(c4Oc5c3ccc(c5Br)O)Br)O
BAF4	C₂₄H₁₆N₂O₆	428.4	Aldrich	≥95%	85 ± 18	88 ± 22	ZINC13346907	c1cc(c(cc1O)O)c2cc3c(cc2N)oc-4cc(=O)c(cc4n3)c5ccc(cc5O)O
BAF8	C₁₇H₁₄N₂O₅S	358.4	Sigma-Aldrich	≥90%	26 ± 12	23 ± 11	ZINC12358966	Cc1ccc(c(c1)/N=N/c2c3ccccc3c(cc2O)S(=O)(=O)[O-])O
BAF11	C₂₀H₁₃N₂O₅S	393.5	NCI plated 2007	†	51 ± 11	48 ± 12	ZINC04521479	c1ccc2c(c1)ccc(c2O)/N=N/c3c4ccccc4c(cc3O)S(=O)(=O)[O-]
BAF12	C₁₃H₈Br₃NO	433.9	NCI plated 2007	†	19 ± 6	38 ± 6	ZINC12428965	c1cc(ccc1/N=C/c2cc(cc(c2O)Br)Br)Br
BAF26	C₁₇H₁₀O₄	278.3	Aldrich	‡	60 ± 21	46 ± 23	ZINC05770717	c12c(cc(cc1)C(=O)C=O)Cc1c2ccc(c1)C(=O)C=O
BAF30	C₁₄H₈O₅	256.2	Aldrich	‡	37 ± 18	18 ± 13	ZINC03870461	c1cc2c(cc1O)C(=O)c3c(ccc(c3O)O)C2=O
BAF31	C₁₉H₂₁NO₃	311.4	Sigma	≥98%	92 ± 22	84 ± 12	ZINC03874841	CCCN1CCC2=C3C1CC4=C(C3=CC(=C2)O)C(=C(C=C4)O)O

BAFs 1, 4, 8, 11, 12 are from the first round. BAFs 26, 30, 31 are from the second round.

Molecular weight (anhydrous basis) excluding the salt and water molecules.

†

With the standard of NCI free compound library.

‡

Analytical data for Aldrich^CPR products are not available.

Rescue percentage is a scaled cell survival rate.

Entry code for the ZINC database (http://zinc.docking.org).

elife-00857-v1.xml

10.7554/eLife.00857.016

Table 4.

Student’s t-test and p value analysis suggests that BAFs reduce the cytotoxicity of Aβ fibers significantly

DOI: http://dx.doi.org/10.7554/eLife.00857.016

	Average of cell viability (n = 4)	SD(σ)	Comparison to Aβ fiber alone
	Average of cell viability (n = 4)	SD(σ)	t value	p value
HeLa cell line
Aβ fiber alone	0.40	0.05	/	/
BAF1	0.66	0.04	8.4	5E-05
BAF4	0.93	0.13	7.4	1E-4
BAF8	0.54	0.06	3.3	1E-2
BAF11	0.69	0.07	6.6	2E-04
BAF12	0.63	0.04	7.6	1E-04
BAF26	0.68	0.14	3.8	5E-3
BAF30	0.51	0.08	2.3	4E-2
BAF31	0.91	0.07	11.5	7E-06
PC12 cell line
Aβ fiber alone	0.37	0.07	/	/
BAF1	0.61	0.07	4.9	1E-3
BAF4	0.90	0.11	8.0	7E-05
BAF8	0.53	0.07	3.2	1E-2
BAF11	0.69	0.07	6.5	2E-4
BAF12	0.49	0.04	2.9	2E-2
BAF26	0.74	0.13	5.0	1E-3
BAF30	0.60	0.11	3.5	8E-3
BAF31	0.95	0.14	7.4	1E-4

The Student’s T-test and p-value are based on the comparison to Aβ fiber alone.

elife-00857-v1.xml

10.7554/eLife.00857.022

Table 5.

Predicted binding energy and experimental measurement of the binding of two BAFs and orange G against both Aβ_16–21 (KLVFFA) and full-length Aβ fibers

DOI: http://dx.doi.org/10.7554/eLife.00857.022

	Binding to KLVFFA fiber		Binding to Aβ fiber
	Predicted binding energy (kcal/mol)	NMR Kd (µM)	Predicted binding energy (kcal/mol)	NMR peak reduction (%)
BAF1	−8	12	−10	8
BAF8	−12	24	−12	13
orange G	−8	43	−9	6

The determination of the binding parameters with KLVFFA fiber is detailed in Table 6.

elife-01071-v1.xml

10.7554/eLife.01071.021

Table 7.

Quantification of centriole/centrosome numbers in dCPAP or dSTIL mutant larval brain cells expressing the indicated WT or mutant constructs

DOI: http://dx.doi.org/10.7554/eLife.01071.021

Genotype	Number of brains	Total number of cells	Cells with centrosome number (%)
Genotype	Number of brains	Total number of cells	0	1	2	3
WT	12	944	2.1	2.6	95.2	0.0
dCPAP	8	661	95.2	4.2	0.6	0.0
dCPAP_WT-GFP	9	715	2.8	6.3	90.5	0.4
dCPAP_ΔC-GFP	13	1147	95.1	3.8	1.0	0.0
dCPAP_MC1-GFP	11	968	64.9	30.1	4.8	0.3
dCPAP_MC2-GFP	17	1053	43.5	42.2	14.1	0.3
dCPAP_MC3-GFP	16	1870	4.5	13.3	81.9	0.3
dCPAP_MC1-3-GFP	11	888	90.1	8.0	1.8	0.1
dCPAP_E792V-GFP	9	1015	13.7	31.1	54.8	0.4
dSTIL¹⁶⁹	9	846	98.1	1.9	0.0	0.0
dSTIL⁷¹⁹	9	980	99.2	0.8	0.0	0.0
dSTIL_WT-GFP	6	424	5.7	9.0	85.1	0.2
dSTIL_ΔN-GFP	13	884	88.1	9.8	1.9	0.1
dSTIL_P11A-GFP	9	1008	11.0	41.0	48.0	0.0
dSTIL_R12A-GFP	9	709	7.0	31.0	62.0	0.0
dSTIL_P11AR12A-GFP	9	727	41.0	43.0	16.0	0.0

elife-01206-v1.xml

10.7554/eLife.01206.015

Table 1.

Comparison of two different intracellular EGTA concentrations on Ca²⁺ signaling and synaptic transmission. The values indicated are all in units of s. Calcium imaging measurements were performed using Fluo-4 indicator.

DOI: http://dx.doi.org/10.7554/eLife.01206.015

	Control		+ ω-conotoxin GVIA
	Ca²⁺ imaging (20% rise)	paired recording (time to peak)	Ca²⁺ imaging (20% rise)	paired recording (time to peak)
0.5 mM EGTA	0.18 ± 0.16 (4 fish, 64 boutons)	2.88 ± 0.35 (n = 8)	1.98 ± 0.84 (6 fish, 68 boutons)	4.88 ± 0.35 (n = 8)
5 mM EGTA	0.71 ± 0.47 (3 fish, 38 boutons)	3.36 ± 0.50 (n = 15)	5.42 ± 1.95 (4 fish, 56 boutons)	10.54 ± 2.37 (n = 13)

elife-01229-v1.xml

10.7554/eLife.01229.003

Table 1.

S. Typhi mutants constructed for this study

DOI: http://dx.doi.org/10.7554/eLife.01229.003

S. Typhi strain	Genotype	Minimum inhibitory concentrations (μg/ml)
S. Typhi strain	Genotype	Nalidixic acid	Norfloxacin	Ofloxacin	Ciprofloxacin	Gatifloxacin	Levofloxacin
Parent BRD948	ΔaroA, ΔaroC, ΔhtrA	1.5	0.064	0.047	0.008	0.008	0.012
DPT001	SNP in ΔaroC (codon 10)	1.5	0.064	0.047	0.008	0.008	0.012
S83Y	SNP in gyrA (codon 83)	256	0.5	0.25	0.125	0.125	0.125
S83F	SNP in gyrA (codon 83)	256	0.75	0.38	0.125	0.125	0.125
D87A	SNP in gyrA (codon 87)	48	0.75	0.19	0.094	0.064	0.064
D87N	SNP in gyrA (codon 87)	48	0.75	0.25	0.125	0.125	0.125
D87G	SNP in gyrA (codon 87)	48	0.75	0.25	0.125	0.125	0.25
S80I	SNP in parC (codon 80)	3	0.19	0.047	0.016	0.016	0.016
D87G-S80I	SNP in gyrA (codon 87) and SNP in parC (codon 80)	256	1	0.25	0.125	0.094	0.094
S83F-D87G	2 SNPs in gyrA (codons 83 and 87)	256	1	0.38	0.19	0.25	0.25
S83F-D87A	2 SNPs in gyrA (codons 83 and 87)	192	1.5	0.38	0.25	0.38	0.25
S83F-D87N	2 SNPs in gyrA (codons 83 and 87)	64	0.75	0.38	0.19	0.19	0.19
S83F-D87G-S80I	2 SNP in gyrA (codons 83 & 87) and SNP in parC (codon 80)	256	24	16	8	2	3

elife-01322-v1.xml

10.7554/eLife.01322.004

Table 1.

Summary of the mutational spectrum observed in strains derived from directed evolution of resistance to ionizing radiation

DOI: http://dx.doi.org/10.7554/eLife.01322.004

	IR-1-20							IR-2-20							IR-3-20							IR-4-20	IR-CB1000-20					IR-CB1000-30
Transitions	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C
	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B
	1	1	1	1	1	1	1	2	2	2	2	2	2	2	3	3	3	3	3	3	3	4	1	1	1	1	1	1	1	1	1
	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1
	0	1	1	1	1	2	2	0	0	0	0	0	1	1	0	0	0	0	1	1	1	0	2	2	2	2	3	0	0	0	0
	0	2	3	4	5	4	5	0	3	4	7	9	4	6	0	2	6	8	4	7	9	0	2	4	5	7	0	1	4	5	8
C → T	19	20	6	10	15	6	9	12	13	11	12	11	9	9	14	14	13	14	13	12	12	14	59	64	69	69	63	60	62	63	62
G → A	18	9	11	16	11	11	12	17	17	16	15	13	13	11	17	11	13	13	12	8	15	10	60	65	78	71	60	57	60	60	60
T → C	7	7	6	4	6	13	4	11	8	16	10	9	9	11	11	4	13	11	7	6	9	7	51	51	40	44	47	47	47	47	47
A → G	15	16	7	8	8	14	11	10	6	6	7	7	6	5	6	14	10	10	9	11	6	8	42	43	42	54	50	46	50	50	50
Transversions
G → T	4	4	1	1	1	3	5	3	4	2	3	5	4	2	5	5	4	4	4	6	4	2	10	9	7	8	6	5	6	6	6
C → A	1	1	2	1	1	5	6	5	3	6	3	3	4	6	2	4	2	1	3	4	1	6	3	2	5	5	6	4	5	5	4
A → C	1	1	2					1			1	1	2		1		1	2	2		1	1	7	4	2	2	4	4	3	3	3
T → G			1	1	1	1	1			1				1	1	1	1	2	1	2	2		2	4			1	1	1	1	1
G → C	1	1	1	2	2		1	1			1					1	1			1		1	2	1	1	2	4	3	3	3	3
C → G		1					2	3	1	1	1	1	1						1			2	1	2	1	1	2	2	2	2	2
A → T			1		2			1	1	3	1	2	1	4	3	1	1	2	1	1	1		2	2	1	2	3	3	3	3	3
T → A		1		1		1		1	1	1	1			1	1	1	3	1	1	1	2	1	3	3	2	3	3	3	3	3	2
Insertions
767bp IS1	2	1	1	1	1	1	1
Deletions	1
e14	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
93bp															1
Totals	70	63	40	46	49	56	53	66	55	64	56	53	50	51	63	57	63	61	55	53	54	53	243	251	249	265	250	236	246	247	244

The mutational spectrum of the population is inferred based on the genetic alterations observed in the subset of strains sequenced.

elife-01322-v1.xml

10.7554/eLife.01322.005

Table 2.

Summary of prominent mutational patterns observed in multiple evolved populations

DOI: http://dx.doi.org/10.7554/eLife.01322.005

			IR-1-20							IR-2-20							IR-3-20							IR-4-20	IR CB1000−+
Gene	Position	Ref.	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C		Change	Mutation
			B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B	B
			1	1	1	1	1	1	1	2	2	2	2	2	2	2	3	3	3	3	3	3	3	4
			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
			0	1	1	1	1	2	2	0	0	0	0	0	1	1	0	0	0	0	1	1	1	0
		Allele	0	2	3	4	5	4	5	0	3	4	7	9	4	6	0	2	6	8	4	7	9	0			Type
clpP	456127	A	G	G																					+	Y75C	N
clpP/clpX	456637	G															A	A	A	A	A	A	A			-	I
clpX	457803	A				G																				Y384C	N

gsiB	868947	A								G	G	G	G	G	G	G										N104S	N
gsiB	869499	T															C	C	C	C	C	C	C			L288P	N
gsiB	870075	T																						C		V480A	N

fnr	1396995	A															T	T	T	T	T	T	T		+	F185I	N

rsxB	1704735	A								G	G	G	G	G	G	G									+	K121E	N
rsxD	1707299	T															C	C	C	C	C	C	C		+	V44A	N

wcaM	2113451	T																						C	+	N156S	N
wcaK	2116031	T								C	C		C	C	C											Y132C	N
wcaC	2129153	A															G	G	G	G	G	G	G			S313S	S

yfjK	2759609	G																						A		H651Y	N
yfjK	2760683	T						C																		K293E	N
yfjK	2760809	G														A										P251S	N
yfjK	2761108	G								T	T	T	T	T	T	T										A151D	N

recA	2820924	C						A																		A289S	N
recA	2820962	T			G	G	G		G																	D276A	N
recA	2820963	C								T	T	T	T	T	T	T								T		D276N	N

nanE	3368674	C								T	T	T	T	T	T	T									+	A128T	N
nanT	3369380	A															G	G	G	G	G	G	G		+	F405S	N

dnaB	4262560	T						C																	+	L74S	N
dnaB	4262578	C								A	A	A	A	A	A	A										P80H	N
dnaB	4262935	C																						A		P199Q	N
priA	4123174	C															T	T	T	T	T	T	T			V553I	N
priC	489549	A	G	G																						L162P	N
dnaT	4599105	G			A	A	A		A																	R145C	N

Entries in red denote mutations that are present in CB2000.

elife-01370-v1.xml

10.7554/eLife.01370.010

Table 1.

Eigenvalues (in %) obtained by PCA, and the angle between restrictive subspaces

DOI: http://dx.doi.org/10.7554/eLife.01370.010

PDB ID	PIPER					RosettaDock					Discrepancy (degrees)
PDB ID	λ₁	λ₂	λ₃	λ₄	λ₅	λ₁	λ₂	λ₃	λ₄	λ₅	Discrepancy (degrees)
1AVX	59.4	32.8	6.2	1.2	0.3	67.4	15.5	13.4	3.4	0.3	5
1B6C	72.1	19.1	6.9	1.3	0.5	84.2	10.2	3.3	1.9	0.4	4
1 E6E	59.1	18.1	11.3	10.0	1.5	57.6	16.3	10.9	8.8	6.4	29
1EAW	44.3	31.7	22.2	1.0	0.9	57.9	33.0	4.6	4.0	0.4	25
1 E6J	78.7	13.5	7.1	0.3	0.3	47.6	31.5	18.7	1.2	1.0	16
1GLA	58.9	26.9	9.3	3.7	1.2	41.5	33.1	15.1	8.0	2.3	2
1IQD	74.7	13.5	7.8	3.6	0.4	58.0	26.7	12.7	1.9	0.7	13
1K74	47.8	28.0	19.0	3.6	1.5	61.0	22.0	10.5	5.2	1.2	19
1MAH	60.3	22.4	11.7	4.4	1.2	52.8	22.0	13.5	7.7	4.0	14
1N8O	56.1	23.4	13.3	6.4	0.9	66.9	22.3	10.3	0.3	0.2	20
1PPE	56.4	26.4	14.9	1.7	0.6	47.1	44.4	7.9	0.4	0.1	3
1PXV	68.3	17.0	9.6	4.3	0.8	32.1	27.2	23.6	14.5	2.7	8
1 R0R	55.0	26.8	15.3	2.7	0.2	69.3	20.2	6.7	3.0	0.9	13
2SNI	49.3	31.6	17.0	1.5	0.6	79.6	15.5	3.5	1.2	0.2	16
1KXQ	47.7	30.0	16.8	4.1	1.3	66.3	30.0	4.4	0.2	0.1	29
7CEI	44.7	28.5	20.9	4.6	1.3	47.7	27.9	18.9	3.6	1.9	19
2SIC	58.6	23.4	9.4	7.2	1.4	84.2	8.8	4.1	2.4	0.5	3
1AY7	56.9	20.3	15.0	5.4	2.4	42.1	32.5	12.6	9.2	3.7	27
1OPH	72.6	15.5	9.2	2.2	0.5	84.2	9.3	5.9	0.4	0.2	21
1UDI	64.6	18.6	12.6	2.4	1.8	51.2	27.1	14.2	6.4	1.1	33
1BUH	44.8	27.7	17.6	9.2	0.6	40.3	32.9	16.6	8.2	1.9	21
1FSK	45.0	28.0	22.1	3.5	1.4	42.6	29.7	19.9	5.8	1.9	21
1JPS	57.1	25.7	12.4	4.0	0.8	56.3	28.8	13.7	0.7	0.6	30
1DQJ	51.4	31.3	15.0	1.4	0.9	46.5	19.8	17.4	12.3	4.0	17
2B42	55.6	27.7	12.8	3.4	0.5	45.4	23.1	15.7	11.5	4.4	24
2FD6	65.1	18.1	9.9	4.6	2.2	36.4	23.9	21.0	13.7	5.0	20
2HQS	80.1	11.3	7.2	1.0	0.4	54.1	36.2	7.8	1.6	0.4	9
2I25	70.3	18.5	9.9	0.8	0.5	56.0	15.3	12.8	10.5	5.3	12
2MTA	45.8	26.1	20.5	5.2	2.5	45.5	32.2	12.2	7.4	2.7	30
1MLC	59.3	31.5	6.8	1.2	1.1	42.7	30.1	17.3	7.0	2.8	17
2HRK	57.7	31.0	9.7	0.9	0.7	61.2	16.4	10.5	8.6	3.3	30
1AHW	74.4	16.3	7.7	1.1	0.5	46.7	31.5	17.2	3.1	1.5	24
1Z5Y	66.1	18.0	8.9	5.4	1.5	57.1	32.3	9.7	0.6	0.4	29
2HLE	54.0	28.1	13.0	3.4	1.4	67.0	12.9	12.1	5.9	2.1	2
2NZ8	69.4	14.1	8.4	5.2	2.9	44.8	28.3	15.1	7.3	4.5	34
1BVN	61.4	20.3	14.3	3.6	0.4	37.2	28.5	17.8	10.0	6.5	32
1CGI	66.9	15.4	10.9	5.4	1.9	57.9	27.9	10.7	3.0	0.5	48
1GPW	53.8	20.9	14.2	6.4	4.7	46.5	26.5	17.9	5.0	4.0	27
2JEL	72.4	16.3	8.1	2.2	0.9	47.8	31.6	12.9	6.8	0.8	31
1NCA	76.7	18.8	3.0	1.2	0.4	55.9	24.3	15.6	3.2	1.0	27
2UUY	69.4	15.4	12.7	1.6	0.9	73.6	16.2	9.0	1.0	0.2	11
1KAC	48.9	34.6	13.3	2.0	1.2	53.8	19.5	15.6	6.8	4.2	30

elife-01457-v1.xml

10.7554/eLife.01457.012

Table 3.

The CDR3 sequences of bulk-sorted Vα11⁺Vβ3⁺ CD4⁺ T cells from gp250 SC mice that overlap with the published data from normal mice (Hedrick et al., 1988; McHeyzer-Williams et al., 1999)

DOI: http://dx.doi.org/10.7554/eLife.01457.012

Published CDR3α (Hedrick et al., 1988; McHeyzer-Williams et al., 1999)	Current study		Notes
	B6.K	SC	Notes
	3623	2906	Unique sequences
CAAEASSGQKLVFG	+	+	AND TCR
CAAEPSSGQKLVFG	+	+	226 TCR
CAAEASGSWQLIFG	+	+
CAAEASNTNKVVFG	+	+	5c.c7 TCR
CAAEGSNTNKVVFG	+
CAAEASAGNKLTFG	+	+
CAAASSGSWQLIFG	+	+
CAAEAGSNAKLTFG	+	+
CAAEASNNNAPRFG	+
CAAEAASLGKLQFG	+	+
CAAEASSGSWQLIFG	+	+
CAAEASNYNVLYFG	+	+
CAAEASSSFSKLVFG	+	+
CAAEASNMGYKLTFG	+	+
CAAETGGYKVVFG	+	+
CAAEANYNQGKLIFG	+	+
CAAEAGSGTYQRFG	+	+
CAGLSGSFNKLTFG	+	+
CAAEGNTGNYKYVFG		+
CAAEEGNMGYKLTFG	+	+
CAATSSGQKLVFG	+

Published CDR3β (Hedrick et al., 1988; McHeyzer-Williams et al., 1999)	Current study		Notes
	B6.K	SC	Notes
	2821	1583	Unique sequences (mean)
CASSLNSANSDY	+		AND, 5c.c7, 226 TCRs
CASSLNNANSDY	+	+
CASSLSTSQNTLYF	+
CASSLQGTNTEVFF	+	+
CASRLGQNTLYF		+
CASSLGASAETLYF		+

elife-01519-v1.xml

10.7554/eLife.01519.006

Table 1.

Crystallographic data collection and refinement statistics

DOI: http://dx.doi.org/10.7554/eLife.01519.006

	PfDTD+D-Tyr3AA	PfDTD+D-Tyr3AA
	Crystal I	Crystal II
	(PDB id: 4NBI)	(PDB id: 4NBJ)
Data Collection
Space group	C2	P2₁
Cell dimensions:
a (Å)	82.13	90.90
b (Å)	65.74	79.91
c (Å)	56.92	95.02
β (°)	93.30	93.51
Resolution range (Å)*	25.0–1.86 (1.93–1.86)	25.0–2.20 (2.28–2.20)
Total Observations	178996	449245
Unique reflections	25156 (2283)	69275 (6911)
Completeness (%)	98.3 (89.3)	100 (99.9)
R_merge (%)	7.5 (28.3)	11.8 (59.3)
<I/(σ)I>	29.4 (5.5)	17.7 (2.8)
Redundancy	7.1 (6.4)	6.5 (5.9)
Data refinement
Resolution (Å)	1.86	2.20
No. of reflections	23878	65743
R (%)	16.77	19.46
R_free (%)†	19.25	25.35
Monomers/a.u.	2	8
No. of residues	323	1289
No. of atoms	2917	10727
Protein	2595	10104
Ligand	72	248
Water	250	375
R.m.s. deviation
Bond lengths (Å)	0.007	0.010
Bond angles (°)	1.093	1.436
Mean B value (Å²)	30.33	48.11
Protein	29.09	47.69
Ligand	43.94	53.30
Water	41.29	57.16

Values in parentheses are for the highest resolution shell.

†

Throughout the refinement, 5% of the total reflections were held aside for R_free.

elife-01569-v1.xml

10.7554/eLife.01569.005

Table 1.

Summary of all clones analysed in both embryo and L3 of the same individual

DOI: http://dx.doi.org/10.7554/eLife.01569.005

	Clone #
	1		2		3		4		5		6		7		8		9		10
	E	L	E	L	E	L	E	L	E	L	E	L	E	L	E	L	E	L	E	L
−I	2	2 −I	2	2 −I	4	4 −I	2	2 −I	4	4 −I	2	2 −I	1	1 −I	4	4 −I	4	4 −I	4	4 −I
I	4	1 I’	4	1 I’	3	1 I’	3	1 I’	4	2 I’ *	4	1 I’	3	1 I’	4	1 I’	4	1 I’	4	2 I’ *
I	4	3 I	4	3 I	3	2 I	3	2 I	4	2 I	4	3 I	3	2 I	4	3 I	4	3 I	4	2 I
II	4	4 T1	3	3 T1	3	3 T1	3	3 T1	2	2 T1	2	2 T1	4	4 T1	2	2 T1	4	4 T1	2	2 T1
III	1	1 III	2	2 III	2	2 III	3	3 III	1	1 III	4	4 III	1	1 III	2	2 III	1	1 III	2	2 III
IV	4	3 IV’	4	2 IV’	3	1 IV’	2	2 IV’	4	3 IV’	1	1 IV’	4	2 IV’	3	1 IV’	3	1 IV’	3	2 IV’
IV	4	1 IV	4	2 IV	3	2 IV	2	2 IV’	4	1 IV	1	1 IV’	4	2 IV	3	2 IV	3	2 IV	3	1 IV
V	2	2 T2	2	2 T2	3	3 T2	2	2 T2	2	2 T2	3	3 T2	3	3 T2	2	2 T2	2	2 T2	2	2 T2
VI	2	2 VI	1	1 VI	1	1 VI	2	2 VI	1	1 VI	1	1 VI	2	2 VI	1	1 VI	2	2 VI	2	2 VI
VII	5	5 VII	2	2 VII	2	2 VII	1	1 VII	1	1 VII	2	2 VII	4	4 VII	1	1 VII	1	1 VII	2	2 VII
+VII	2	2 +VII	1	1 +VII	2	2 +VII	2	2 +VII	2	2 +VII	4	4 +VII	4	4 +VII	4	4 +VII	2	2 +VII	5	5 +VII

The row headers at the left show the line of cells in the embryo from which each clone originates. The numbers of cells in each clone are shown in arabic numerals. The locations of these same cells (within the lines of cells) in the larva are highlighted in bold roman numerals. Cells in lines I and IV of the embryo contribute to two separate lines of cells in the larva; within the denticulate region, apart from lines I and IV, each embryonic cell contributes to only one line of cells in the larva. Cells in line –I in the embryo never make denticles in embryo or larva, but we do not know if they contribute to two lines of cells in the larva. However, since the P compartment is made of two lines of cells in the embryo and four lines of cells in the larva, one extra row has to come from somewhere and line –I is the obvious suspect. (*) Only one these two cells showed denticles in the larva.

elife-01581-v1.xml

10.7554/eLife.01581.004

Table 1.

Stability of antisense ncRNAs

DOI: http://dx.doi.org/10.7554/eLife.01581.004

Overlap size (bp)	Overlap type				Totals
Overlap size (bp)	ORF–ORF	ORF–XUT	ORF–CUT	ORF–SUT	ORF–ncRNA	ORF–unstable ncRNA
50	700	1066	575	522	1596	1448 (91%)
100	449	1008	543	475	1507	1367 (91%)
150	216	967	508	425	1423	1306 (92%)
200	136	931	478	403	1358	1249 (92%)
250	96	893	434	380	1287	1181 (92%)
300	69	812	391	363	1189	1085 (91%)
350	62	759	335	351	1086	990 (91%)
400	54	694	292	334	992	899 (91%)
450	51	637	244	322	904	811 (90%)
500	48	591	204	302	828	741 (89%)

Number of ORFs overlapping with ORFs and various classes of ncRNAs, with various minimum size cut-offs for the overlapping region.

Totals are given for ORFs overlapping with ncRNAs and with unstable ncRNAs, including a percentage of overlapping ncRNAs that are unstable.

ncRNA: non-protein coding RNA; ORF: optical reading frame; XUT: Xrn1-sensitive unstable transcript (degraded in cytoplasm); CUT: cryptic unstable transcript (degraded by nuclear exosome); SUT: stable unannotated transcript (not known to be degraded).

elife-01604-v1.xml

10.7554/eLife.01604.006

Table 1.

Risk factors for HSV2 and HIV infection in 15–30 year old women in a population survey, Karonga District, Malawi 2007–8

DOI: http://dx.doi.org/10.7554/eLife.01604.006

	HSV2				HIV
	n/N	%	OR (95% CI)	Age adjusted	n/N	%	OR (95% CI)	Age adjusted
	n/N	%	OR (95% CI)	OR (95% CI)	n/N	%	OR (95% CI)	OR (95% CI)
All	870/3419	25.5			203/3651	5.6
Age
15–9	126/1240	10.2	1		18/1314	1.4	1
20–24	276/1072	25.8	3.1 (2.4–3.9)		64/1128	5.7	4.3 (2.6–7.4)
25–30	468/1107	42.3	6.5 (5.2–8.1)		121/1209	10.0	8.0 (4.8–13.2)
Age at menarche
<14	245/815	30.1	1	1	51/861	5.9	1	1
14	195/769	25.4	0.79 (0.63–0.99)	0.89 (0.71–1.1)	43/819	5.3	0.88 (0.60–1.3)	1.0 (0.66–1.5)
15	225/960	23.4	0.71 (0.58–0.88)	0.71 (0.57–0.89)	41/1030	4.0	0.66 (0.43–1.0)	0.68 (0.44–1.0)
≥16	157/622	25.2	0.79 (0.62–0.99)	0.69 (0.54–0.89)	51/665	7.7	1.3 (0.88–2.0)	1.2 (0.81–1.8)
Age at first sex
Never	51/639	8.0	0.21 (0.15–0.29)	0.48 (0.33–0.69)	10/684	1.5	0.23 (0.12–0.44)	0.69 (0.32–1.3)
<16	296/1014	29.2	1	1	66/1076	6.1	1	1
16–17	235/797	29.5	1.0 (0.83–1.2)	0.99 (0.80–1.2)	53/847	6.3	1.0 (0.70–1.4)	0.99 (0.68–1.5)
18+	273/930	29.4	1.0 (0.83–1.2)	0.76 (0.62–0.93)	71/1002	7.1	1.2 (0.82–1.7)	0.90 (0.63–1.3)
Marital status
Never	76/826	9.2	1	1	19/885	2.2	1	1
Current	681/2330	29.2	4.1 (3.2–5.2)	1.7 (1.3–2.3)	133/2481	5.4	2.6 (1.6–4.2)	0.78 (0.44–1.4)
Previous	113/263	43.0	7.4 (5.3–10.4)	3.4 (2.4–5.0)	51/285	17.9	9.9 (5.8–17.2)	3.2 (1.7–5.9)
Lifetime no. of partners
0	51/639	8.0	0.33 (0.24–0.46)	0.76 (0.53–1.1)	10/684	1.5	0.49 (0.25–0.98)	1.4 (0.66–3.2)
1	304/1475	20.6	1	1	46/1574	2.9	1	1
2	320/900	35.6	2.1 (1.8–2.6)	2.0 (1.7–2.4)	82/951	5.6	3.1 (2.2–4.5)	2.9 (2.0–4.2)
3	139/289	48.1	3.6 (2.7–4.6)	3.2 (2.4–4.2)	41/313	13.1	5.0 (3.2–7.8)	4.4 (2.8–6.8)
≥4	53/107	49.5	3.8 (2.5–5.6)	3.5 (2.3–5.3)	24/120	20.0	8.3 (4.9–14.2)	7.4 (4.3–12.8)
Distance from road
<1 km	410/1589	25.8	1	1	100/1595	6.3	1	1
>1 km	460/1830	25.1	0.97 (0.83–1.1)	0.94 (0.80–1.1)	62/1835	3.4	0.52 (0.38–0.72)	0.50 (0.36–0.70)
Schooling
None/Primary 1–5	101/347	29.1	1		16/378	4.2	1	1
Primary 6–7	215/889	24.2	0.78 (0.59–1.0)	0.88 (0.66–1.2)	38/945	4.0	0.95 (0.52–1.7)	1.1 (0.59–2.0)
Primary 8	271/1011	26.8	0.89 (0.68–1.2)	0.89 (0.67–1.2)	58/1069	5.4	1.3 (0.74–2.3)	1.3 (0.75–2.4)
Secondary 1–3	218/860	25.4	0.83 (0.63–1.1)	0.88 (0.65–1.2)	70/916	7.6	1.9 (1.1–3.3)	2.0 (1.2–3.6)
Secondary 4/Tertiary	36/196	18.4	0.55 (0.36–0.84)	0.42 (0.27–0.66)	18/215	8.4	2.1 (1.0–4.1)	1.8 (0.87–3.6)
Mother schooling
<=Primary	716/2861	25.0	1	1	151/3021	5.0	1	1
Secondary	80/352	22.7	0.88 (0.68–1.1)	1.0 (0.76–1.3)	30/382	7.9	1.6 (1.1–2.4)	1.8 (1.2–2.8)
Father schooling
<=Primary	517/2046	25.3	1	1	94/2158	4.4	1	1
Secondary	260/1095	23.7	0.92 (0.78–1.1)	0.96 (0.80–1.1)	81/1166	7.0	1.6 (1.2–2.2)	1.7 (1.3–2.3)
Housing quality
1 (Best)	148/662	22.4	1	1	71/732	9.7	1	1
2	149/565	26.4	1.2 (0.96–1.6)	1.2 (0.89–1.5)	32/598	5.4	0.53 (0.34–0.81)	0.48 (0.31–0.75)
3	317/1238	25.6	1.2 (0.96–1.5)	1.0 (0.96–1.3)	60/1296	4.6	0.45 (0.32–0.65)	0.38 (0.26–0.55)
4 (Worst)	227/843	26.9	1.3 (1.0–1.6)	1.2 (0.96–1.6)	38/903	4.2	0.41 (0.27–0.61)	0.37 (0.25–0.56)
Occupation
Farmer	652/2229	29.3	1	1	143/2369	6.0	1	1
In education	63/720	8.8	0.23 (0.18–0.31)	0.55 (0.40–0.76)	10/767	1.3	0.21 (0.11–0.39)	0.58 (0.28–1.2)
Not working	23/77	29.9	1.0 (0.63–1.7)	1.1 (0.66–1.9)	8/88	9.1	1.6 (0.74–3.3)	1.6 (0.77–3.5)
Other	102/272	37.5	1.5 (1.1–1.9)	1.3 (1.0–1.7)	38/293	13.0	2.3 (1.6–3.4)	2.1 (1.4–3.1)
Times of insufficient food in household in last year
No	674/2575	26.2	1	1	162/2748	5.9	1	1
Yes	166/728	22.8	0.83 (0.69–1.0)	0.83 (0.67–1.0)	39/775	5.0	0.85 (0.59–1.2)	0.85 (0.59–1.2)
Times when can’t afford soap in last year
No	519/2021	25.7	1	1	136/2166	6.3	1	1
Yes	321/1280	25.1	0.97 (0.82–1.1)	0.97 (0.82–1.1)	65/1355	4.8	0.75 (0.56–1.0)	0.75 (0.55–1.0)

OR = odds ratio

elife-01604-v1.xml

10.7554/eLife.01604.007

Table 2.

Association between age at menarche and HSV2 and HIV, adjusted for other variables, among 15–30 year-old women in Karonga District Malawi

DOI: http://dx.doi.org/10.7554/eLife.01604.007

		HSV2 (N = 3034)*			HIV (N = 3231)*
		Adjusted for age	Also adjusted for socio-economic variables	Also adjusted for behavioural variables	Adjusted for age	Also adjusted for socio-economic variables	Also adjusted for behavioural variables
		OR (95% CI)	OR (95% CI)†	OR (95% CI)‡	OR (95% CI)	OR (95% CI)†	OR (95% CI)‡
Age at menarche
	<14	1	1	1	1	1	1
	14	0.91 (0.72–1.2)	0.92 (0.73–1.2)	0.92 (0.72–1.2)	0.97 (0.63–1.5)	0.94 (0.61–1.4)	0.96 (0.62–1.5)
	15	0.73 (0.58–0.91)	0.76 (0.60–0.95)	0.77 (0.61–0.98)	0.68 (0.44–1.0)	0.64 (0.41–0.98)	0.65 (0.42–1.0)
	≥16	0.70 (0.54–0.89)	0.75 (0.58–0.97)	0.77 (0.59–1.0)	1.2 (0.79–1.8)	1.1 (0.69–1.6)	1.1 (0.70–1.7)

To allow the effects of these potential mediators to be explored fully, the analysis is restricted to individuals with no missing data for the factors included.

†

age, schooling, occupation, lack of food.

‡

age, schooling, occupation, lack of food, marital status, lifetime number of partners.

elife-01694-v1.xml

10.7554/eLife.01694.008

Table 1.

Genes differentially induced by TM between control and Lrh-1-null mice and their regulation by ATF2 and LRH-1

DOI: http://dx.doi.org/10.7554/eLife.01694.008

Gene	Known target of
Gene	ATF2	LRH-1
PLK3	✓	✓
GDF15
FGF21	*
PMM1
CRELD2		✓
NFIL3
IGSF11
GSTM2
GOT1
DPP9	✓	✓
ST5
CCBL1	✓	✓
TMEM66	✓
KRTCAP2	✓	✓
LRRC59	✓	✓
CDK2AP2	✓	✓
ST3GAL1
TES		✓
CCDC134	✓	✓
UGT1L
ACOT2	✓
PLIN5		✓
LITAF	✓
RPS13	✓
LGALS3BP
CRYM
SUPT5H	✓
B3GAT3	✓
GRN	✓
ARRDC4
SLC30A7	✓
CRELD1	✓
NT5M
ARSG
SEP15
MKNK1		✓
DDX52
EXOSC5	✓
RABAC1	✓
RPS15	✓	✓
D830014E11RIK
AVPI1	✓
RPS9	✓
CRAT		✓
BHMT2		✓
B230217C12RIK
EIF3G	✓	✓
SLC25A28		✓
HR
CCL9
ANXA4	✓	✓
SMCO4
SMOX
ARL14EP	✓
SLC39A7		✓
ICA1
ENTPD5		✓
PIWIL2
ANG	✓
MCFD2	✓	✓
SOAT2
SLC41A3	✓	✓
MFGE8
CYP4A14
D12ERTD647E

Microarray analysis was performed for control and Lrh-1^LKO mice treated with vehicle or 1 mg/kg tunicamycin for 24 hr (n = 3). Genes were screened for those induced at least 1.5 fold by TM in control mice with significantly different induction in Lrh-1^LKO mice by t-test (p<0.05). This list was filtered for those with differential expression between genotypes with TM treatment by t-test (p<0.05). Previously published genome-wide ATF2 and LRH-1 binding datasets were analyzed to identify genes with ATF2 or LRH-1 binding sites −500 to +275 bp from the TSS. Genes in our set were compared with these sets and genes that contain ATF2 or LRH-1 binding sites meeting the above criteria are marked.

No binding site for ENCODE data set but a known ATF2 direct target (Hondares et al., 2011).

elife-01879-v1.xml

10.7554/eLife.01879.004

Table 1.

Protein abundance, relative to lipids, in vacuoles or reconstituted proteoliposomes (RPL) fusion reactions

DOI: http://dx.doi.org/10.7554/eLife.01879.004

Protein	Molar ratio of lipid:protein in RPL reactions*	Molar ratio of lipid:protein on vacuoles		Ratio (RPLs/vacuoles) of molar protein:lipid ratios in std. reactions†
Protein	Molar ratio of lipid:protein in RPL reactions*	BJ3505	DKY6218
Vam7p	2 × 10³	30 × 10⁴	6.5 × 10⁴	7 × 10¹
Vam3p	2 × 10³	11 × 10⁴	22 × 10⁴	7 × 10¹
Vti1p	2 × 10³	10 × 10⁴	13 × 10⁴	5 × 10¹
Nyv1p	2 × 10³	4.3 × 10⁴	8.1 × 10⁴	3 × 10¹
Ypt7p	4 × 10³	1.9 × 10⁴	1.8 × 10⁴	0.5 × 10¹
Sec17p	7 × 10³	41 × 10⁴	13 × 10⁴	3 × 10¹
Sec18p	1 × 10³	10 × 10⁴	13 × 10⁴	10 × 10¹
Vps33p	6 × 10³	17 × 10⁴	31 × 10⁴	3 × 10¹

for SNAREs and Ypt7p, calculated, based on a 1:1000 lipid:protein ratio during reconstitution and an assumption of 50% outwardly-oriented SNAREs on proteoliposomes; for others, based on amounts of added proteins, and 0.74 mM lipids in standard proteoliposome reactions (see ‘Materials and methods’).

†

based on measured (see ‘Materials and methods’) values of 2.17 nmol lipid per µg total vacuole protein for BJ3505 vacuoles and 1.00 nmol lipid per μg total vacuole protein for DKY6218 vacuoles, and standard vacuole reactions containing 3 µg protein of each vacuole in 30 µl.

elife-01916-v1.xml

10.7554/eLife.01916.024

Table 4.

Flagella waveform transition rates

DOI: http://dx.doi.org/10.7554/eLife.01916.024

Initial	Final
Initial	Normal	Semi-coiled	Curly-1
Normal		0.28 ± 0.03 s⁻¹	0.08 ± 0.01 s⁻¹
Semi-coiled	1.6 ± 0.2 s⁻¹		0.54 ± 0.08 s⁻¹
Curly-1	1.8 ± 0.2 s⁻¹	0.04 ± 0.02 s⁻¹

Transition rates between different flagellar waveforms: normal (CCW), semi-coiled and curly-1 (both CW). Data from wild-type cells (N = 52 cells, 203 tumbles). Values are mean ± SEM.

elife-02181-v1.xml

10.7554/eLife.02181.009

Table 1.

LC-MS analysis of co-immunoprecipitation assays from ovaries and embryos

DOI: http://dx.doi.org/10.7554/eLife.02181.009

Drosophila		Human/yeast	Fandango-myc				Prp19-myc
CG	gene		ovaries		embryos		embryos
			rep1	rep2	rep1	rep2	rep1	rep2
prp19 complex
CG5519	prp19	PRP19/Prp19	+	+	+	+	+++	++
CG6905	cdc5-like	CDC5L/Cef1	+	+	+	+	+++	++
CG1796	Tango4	PLRG1/Prp46	+	+	+	+	+	+
CG4980	-	BCAS2/Snt309	–	+	-	-	+	+
CG12135	c12.1	CWC15/cwc15	+	–	–	-	–	–
Prp19 related
CG6197	Fandango	Xab2/Syf1	+++	+++	+++	+++	+	+
CG31368	–	AQR/–	+++	+++	+++	+++	+	+
CG4886	cyp33	PPIE/–	++	++	+	++	+	+
CG9667	–	ISY1/ISY1	+	+	+	+	+	+
CG8264	Bx42	SNW1/Prp45	+	+	+	+	+	+
CG14641	–	RBM22/Cwc2	–	+	+	+	+	–
CG3193	Crn	CRNKL1/Clf1	–	+	–	–	+	–
CG13892	cypl	PPIL1/-	–	–	–	+	–	–
CG1639	l(1)10Bb	BUD31/Bud31	–	–	–	–	+	–

Co-immunoprecipitations were performed using total protein extracts from the different tissues expressing Myc-tagged Fandango or Myc-tagged-Prp19. Human and yeast homologues and the different sub-complexes are shown as described in (Herold et al., 2009). (−), (+), (++), (+++) correspond to 0, 1–9, 10–19, and >20 non-repeated peptides respectively. None of the proteins shown were detected in the negative controls (for detailed LC-MS analysis see Supplementary file 1).

elife-02203-v2.xml

10.7554/eLife.02203.023

Table 3.

Light sources and filters used for wide field fluorescence imaging

DOI: http://dx.doi.org/10.7554/eLife.02203.023

Fluorophore	Light source & channel	Filter cube
Fluorophore	Light source & channel	Excitation	Beamsplitter	Emission
GFP	Colibri/LED470* Spectra-6/C§	FF01-475/28† LL01-488/1†	T495LP‡	FF01-525/50†
tdEos (red emission)	Colibri/LED555* Spectra-6/GY§	BP550/25* FF01-543/3†	FT570* FF568-Di01†	BP605/70* FF01-593/46†
tdEos (photoconversion)	Colibri/LED405* Spectra-6/V§	FF01-405/10†	59004BS‡	59004M‡

Source: *Zeiss.

†

Semrock.

‡

Chroma.

Lumencor.

elife-02206-v2.xml

10.7554/eLife.02206.004

Table 1.

Circadian periodicity analysis of the BxS RILs after photic or thermal entrainment

DOI: http://dx.doi.org/10.7554/eLife.02206.004

	Zeitgeber	Mean*	S. E	95% confidence interval
	Zeitgeber	Mean*	S. E	Lower bound	Upper bound
BxS	LD	26.702	0.035	26.633	26.771
BxS	TMP	26.269	0.034	26.202	26.335

LD-TMP		BxS
Pairwise comparisons	Mean difference (hr)	0.433
	S. E	0.047
	Significance	<0.001
Correlations	Correlation coefficient	0.86
Correlations	Significance	0.001

LD stands for photic-zeitgeber and TMP for thermal-zeitgeber.

denotes the modified population marginal mean for the 95% Confidence Interval.

S.E. denotes standard error.

LD-TMP denotes the pairwise comparisons such that TMP period is subtracted from LD period.

elife-02206-v2.xml

10.7554/eLife.02206.005

Table 2.

Statistical analysis of CCR2 circadian periodicity after the two zeitgeber protocols for BxS population

DOI: http://dx.doi.org/10.7554/eLife.02206.005

Overall model	Univariate BxS
Factor	F	P
Genotype	7.753	<0.001
Environment	36.413	<0.001
Environment*Genotype	2.183	<0.001

		Univariate LD		CV LD	Univariate TMP		CV TMP
		F	P	CV LD	F	P	CV TMP
BxS	RIL	10.387	<0.001	18.043	7.382	<0.001	16.498
BxS	TRANS (RIL)	1.513	<0.001	18.043	1.915	<0.001	16.498

F = mean sum of squares\error sum of squares. P = significance value of the F-ratio.

Genotype denotes RIL, ENVIRONMENT denotes the different entrainments, TRANS denotes independent transformants of each genotype.

denotes the testing of an interaction between two factors, whereas B(A) denotes the testing main factor A in which a factor B is nested.

CV is the coefficient of genetic variation, LD stands for photic and TMP stands for thermal entrainment.

NS denotes nonsignificance.

elife-02206-v2.xml

10.7554/eLife.02206.006

Table 3.

Localization of the main QTLs for the BxS population after photic vs thermal zeitgeber protocols

DOI: http://dx.doi.org/10.7554/eLife.02206.006

Zeitgeber	H²	Chromosome	Position	LOD score ^(*)	% expl variance	F	p value	2a
Zeitgeber	H²	Chromosome	(cM)	LOD score ^(*)	% expl variance	F	p value	(h)
LD	0.76	I	63.7	3.21	14.9	7.704	0.007	−0.614
		II	34.5	5.72	27.3	20.784	<0.001	1.003
		IV	69.9	3.89	17.1	14.003	<0.001	0.833
TMP	0.73	II	34.5	4.56	25.5	25.033	<0.001	0.988
TMP	0.73	IV	69.9	3.26	16.2	6.501	0.014	0.508

^H2 denotes broad sense heritability.

(cM) denotes centiMorgan.

(*) LOD- score threshold was determined at 2.4.

% expl variance is the percent of explained variance.

F = mean sum of squares\error sum of squares.

P denotes the significance value of the F-ratio.

2a denotes the additive effect of Bay allele when the effect of the Sha allele on period is subtracted.

(h) denotes the effect in hours.

− denotes that the Sha allele displayed longer period than that of Bay allele.

elife-02365-v2.xml

10.7554/eLife.02365.011

Table 1.

Specificity constants for the two activities of CYS-like enzymes (cysteine synthase, CYS and β-cyanoalanine synthase, CAS)

DOI: http://dx.doi.org/10.7554/eLife.02365.011

	CAS reaction			CYS reaction			CAS/CYS
	Activity (s⁻¹)	K_m (mM)	Specificity constant (mM⁻¹. s⁻¹)	Activity (s⁻¹)	K_m (mM)	Specificity constant (mM⁻¹. s⁻¹)	Ratio of specificity constants
Tetranychus urticae CAS	2.135*	0.312	6.84†	0.646*	3.17	0.203†	33.7
Arabidopsis thaliana CAS	2.66	0.14	19	2.0	8.03	0.250	76
Glycine max CAS	38.9	0.81	48	1.82	8.87	0.205	234
Glycine max CYS	0.21	0.30	0.7	57.5	3.6	15.97	0.044
Corynebacterium glutamaticum CYS	n.d	n.d	–	435*	7	62†	–
Lactobacillus casei CYS	n.d	n.d	–	89*	0.6	148†	–

n.d.: not determined.

data as V_max in µmol.min⁻¹mg⁻¹.

†

data as V_max/K_m in µmol.min⁻¹mg⁻¹mM⁻¹. CAS activity was measured with cysteine as substrate while CYS activity was measured with O-acetylserine as substrate. Data for the plants A. thaliana and G. max were obtained in Yamaguchi et al. (2000) and Yi et al. (2012), respectively, while data for the bacteria C. glutamaticum and L. casei were retrieved from Wada et al. (2004) and Bogicevic et al. (2012), respectively.

elife-02384-v2.xml

10.7554/eLife.02384.012

Table 2.

Pol V Mut affinity to 12 nt oh HP DNA

DOI: http://dx.doi.org/10.7554/eLife.02384.012

Pol V Mut	K_d (nM)
Pol V Mut	ATP	ATPγS
pol V Mut WT	nb	876 ± 52
pol V Mut E38K/K72R	nb	920 ± 112
polV Mut E38K/ΔC17	312 ± 46	469 ± 27

nb–binding not detected.

elife-02525-v2.xml

10.7554/eLife.02525.015

Table 1.

The effect of EGL3 and its two mutated forms on root epidermal cell pattern formation

DOI: http://dx.doi.org/10.7554/eLife.02525.015

Genotype	Cells in the H position		Cells in the N position
Genotype	Hair cells (%)	Non-hair cells (%)	Hair cells (%)	Non-hair cells (%)
Col-0	98.9 ± 3.3	1.1 ± 3.3	2.0 ± 4.5	98.0 ± 4.5
PEGL3::EGL3-GFP	95.8 ± 6.1	4.2 ± 6.1	1.9 ± 4.2	98.1 ± 4.2
PEGL3::EGL3^T399A-GFP	93.1 ± 6.4	6.9 ± 6.4	2.8 ± 6.0	97.2 ± 6.0
PEGL3::EGL3^T209A/T213A-GFP	85.5 ± 4.4*	14.5 ± 4.4*	1.0 ± 3.2	99.0 ± 3.2

At least 10 different 5-day-old roots were examined for each strain. Values represent means ± SD. For statistical analysis, the F test was used to determine the variance, and the two-tailed t test with equal variance or unequal variance was used to determine the significance level of the difference among the transgenic plants.

p<0.05.

elife-02725-v2.xml

10.7554/eLife.02725.003

Table 1.

Standard diagnostic tests to assess MMR-deficiency

DOI: http://dx.doi.org/10.7554/eLife.02725.003

Tumor	Histopathology	Grade	Stage	Coverage		IHC			MSI	MLH1 hyper-methylation
Tumor	Histopathology	Grade	Stage	Tumor	Germ-line	MLH1	MSH2	MSH6	MSI	MLH1 hyper-methylation
MMR− 1	Endometrioid	3	IIIc	87.1	81.1	+	+	−(*)	+	−
MMR− 2	Serous/clear cell	3	Ib	24.8	21.9	+	−	−	−	−
MMR− 3	Endometrioid	2	Ib	28.5	30.0	−	+	+	+	+
MMR+ 1	Endometrioid	3	I	119.4	73.1	+	+	+	−	+
MMR+ 2	Serous	3	Ia	79.2	77.0	+	+	+	−	−

Tumors and matched germ-line were whole-genome sequenced using either Complete Genomics or Illumina sequencing technology. For each tumor, microsatellite instability (MSI) using the extended Bethesda panel, standard immunohistochemistry of MMR proteins (MLH1, MSH2, and MSH6), and methylation status of the MLH1 promoter are shown.

a weak positive nuclear staining in the minority of the tumor cells.

elife-02725-v2.xml

Table 1.

Validation rate of somatic indels detected upon whole-genome sequencing. These additional validation experiments for indels have been included in the revised manuscript

Tumor	Somatic Indels
Tumor	Confirmed	Not confirmed	Validation rate
MMR- 1	187	20	90.3%
MMR- 2	103	21	83.1%
MMR- 3	54	6	90.0%
MMR+ 1	0	9	0.0%
MMR+ 2	2	7	22.2%

elife-02798-v1.xml

10.7554/eLife.02798.016

Table 1.

Results of Kolmogrov-Smirnov tests for cumulative frequency distributions

DOI: http://dx.doi.org/10.7554/eLife.02798.016

Groups compared	Non-deprived	Non-deprived	Non-deprived	Non-deprived	LTMD	LTMD	LTMD	Home cage	Home cage	noise + run
Groups compared	LTMD	Home cage	noise+run	grating+run	Home cage	noise+run	grating+run	noise+run	grating+run	grating+run
Broad-spiking cells
Spontaneous firing	<0.00001	<0.0001	<0.001	<0.05	<0.01	<0.01	<0.001	<0.01	<0.05	<0.01
Grating response: closed	<0.00001	<0.00001	<0.01	n.s.	n.s.	<0.0001	<0.05	<0.05	<0.0001	<0.01
Grating response: open	<0.01	<0.05	<0.05	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.
Grating response: ODI	<0.00001	<0.00001	<0.0001	n.s.	<0.01	<0.001	<0.00001	<0.01	<0.00001	<0.001
\|dO\|	<0.00001	<0.00001	<0.00001	<0.01	n.s.	n.s.	<0.001	n.s.	<0.001	<0.001
OSI: closed	<0.00001	<0.00001	<0.00001	<0.00001	n.s.	<0.05	<0.001	<0.001	<0.001	<0.01
OSI: open	<0.01	<0.01	<0.05	<0.05	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.
Orientation tuning width: closed	<0.0001	<0.05	<0.05	<0.05	n.s.	n.s.	<0.05	n.s.	n.s.	n.s.
Orientation tuning width: open	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.
Preferred SF: closed	<0.001	<0.00001	<0.001	n.s.	n.s.	n.s.	<0.05	<0.05	0.001	<0.05
Preferred SF: open	<0.00001	<0.001	<0.001	<0.001	<0.01	<0.01	<0.01	n.s.	n.s.	n.s.
Noise response (F1): closed	<0.00001	<0.0001	<0.01	<0.001	<0.05	<0.00001	<0.001	<0.00001	<0.05	<0.0001
Noise response (F1): open	<0.0001	<0.0001	<0.0001	<0.00001	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.
Noise response: ODI	<0.00001	<0.00001	n.s.	<0.0001	<0.0001	<0.00001	<0.0001	<0.00001	<0.001	<0.001
Narrow-spiking cells
Spontaneous firing	<0.00001	<0.00001	<0.00001	<0.00001	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.
Grating response: closed	<0.00001	<0.0001	<0.0001	<0.001	n.s.	n.s.	<0.01	n.s.	<0.05	<0.05
Grating response: open	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.
Grating response: ODI	<0.00001	<0.001	<0.0001	<0.05	<0.01	n.s.	<0.001	n.s.	n.s.	<0.05
OSI: closed	<0.001	<0.0001	n.s.	n.s.	n.s.	n.s.	n.s.	<0.01	<0.01	n.s.
OSI: open	<0.01	<0.01	<0.01	<0.01	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.
Noise response (F1): closed	<0.001	<0.001	<0.01	<0.01	<0.05	<0.01	<0.05	<0.01	n.s.	n.s.
Noise response (F1): open	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.	n.s.
Noise response: ODI	<0.00001	<0.00001	<0.001	<0.01	<0.001	<0.0001	<0.0001	<0.001	<0.001	<0.05

Statistical significance levels are indicated after adjusting p-values using Bonferroni correction for multiple comparisons. n.s.:p>0.05. closed: measures through deprived eye, open: measures through open eye. ODI: ocular dominance index. |dO|: absolute difference in preferred orientation between left and right eyes. OSI: orientation selectivity index.

elife-02869-v2.xml

10.7554/eLife.02869.018

Table 2.

Clinical features at presentation of the CLL cohorts*

DOI: http://dx.doi.org/10.7554/eLife.02869.018

	TEDG analysis			SA analysis
	N	Total	%	N	Total	%
IGHV homology >98%	37	69	53.6	532	1380	38.6
del13q14	35	70	50.0	682	1403	48.6
+12	19	70	27.1	205	1403	14.6
del11q22-q23	8	70	11.4	136	1403	9.7
del17p13	20	70	28.6	114	1403	8.1
TP53 mutation	22	70	31.4	114	1401	8.1
NOTCH1 mutation	22	70	31.4	150	1403	10.7
SF3B1 mutation	17	70	24.3	100	1403	7.1
MYD88 mutation	6	70	8.6	52	1403	3.7
BIRC3 mutation	10	70	14.3	41	1403	2.9
BIRC3 deletion	6	70	8.6	79	1403	5.6

TEDG analysis, Tumor Evolutionary Directed Graphs analysis; SA analysis, Statistical Association analysis; IGHV, immunoglobulin heavy variable gene; FISH, fluorescence in situ hybridization.

elife-02917-v1.xml

10.7554/eLife.02917.003

Table 1.

Basic characteristics of patients with autism and ADHD

DOI: http://dx.doi.org/10.7554/eLife.02917.003

Characteristic		Autism		ADHD
Characteristic		No.	%	No.	%
Sex	Male	16808	69.6	33491	67.9
Sex	Female	7349	30.4	15857	32.1
Age (years)	<10	5995	24.8	8129	16.5
	10–19	9671	40.0	22854	46.3
	20–29	4215	17.4	7727	15.7
	30+	4276	17.7	10638	21.6
Time period	1987–1990	425	1.8	207	0.4
	1991–1995	656	2.7	381	0.8
	1996–2000	1199	5.0	1307	2.6
	2001–2005	6457	26.7	9953	20.2
	2006–2010	15420	63.8	37500	76.0
All		24157	100.0	49348	100.0

elife-02917-v1.xml

10.7554/eLife.02917.004

Table 2.

Risk of autism and ADHD in offspring when their parents were diagnosed with alcohol use disorder (AUD)

DOI: http://dx.doi.org/10.7554/eLife.02917.004

AUD in parent	No. of offspring at risk	Person-years of follow-up	Autism				ADHD
AUD in parent	No. of offspring at risk	Person-years of follow-up	O	SIR	95% CI		O	SIR	95% CI
Risk in sons
Father	235696	4485707	1793	1.39	1.33	1.45	5548	2.17	2.11	2.22
Mother	69214	1344766	567	1.55	1.43	1.69	1952	2.73	2.61	2.85
Parents	289763	5540362	2203	1.41	1.35	1.47	6800	2.20	2.15	2.25
Risk in daughters
Father	225317	4306194	753	1.31	1.22	1.4	2609	2.12	2.04	2.21
Mother	65,479	1275507	245	1.50	1.32	1.7	970	2.77	2.60	2.95
Parents	276439	5305285	933	1.34	1.25	1.43	3247	2.18	2.10	2.25
Risk in offspring
Father	461013	8791901	2546	1.36	1.31	1.42	8157	2.15	2.11	2.20
Mother	134693	2620273	812	1.54	1.43	1.65	2922	2.74	2.64	2.84
Parents	566202	10845647	3136	1.39	1.34	1.44	10,047	2.19	2.15	2.23
PAF			3.6%				11%

O, observed number of cases; SIR, standardized incidence ratio; CI, confidence interval.

Bold type, 95% CI does not include 1.00.

PAF, population attributable fraction.

elife-02917-v1.xml

10.7554/eLife.02917.005

Table 3.

Risk of autism and ADHD in offspring when their parents were diagnosed with alcohol use disorder (AUD) before the birth of the offspring

DOI: http://dx.doi.org/10.7554/eLife.02917.005

AUD in parent	No. of offspring at risk	Person-years of follow-up	Autism				ADHD
AUD in parent	No. of offspring at risk	Person-years of follow-up	O	SIR	95% CI		O	SIR	95% CI
Risk in sons
Father	41832	410327	442	1.44	1.31	1.59	1555	2.60	2.48	2.74
Mother	8776	80,689	99	1.67	1.35	2.03	347	3.14	2.82	3.49
Parents	48704	472596	514	1.46	1.34	1.59	1778	2.61	2.49	2.73
Risk in daughters
Father	39684	390429	145	1.40	1.18	1.64	565	3.05	2.80	3.31
Mother	8457	77259	36	1.79	1.25	2.48	119	3.44	2.85	4.12
Parents	46299	450022	175	1.47	1.26	1.70	634	3.00	2.77	3.24
Risk in offspring
Father	81516	800756	587	1.43	1.32	1.55	2120	2.71	2.59	2.83
Mother	17233	157948	135	1.70	1.42	2.01	466	3.22	2.93	3.52
Parents	95003	922618	689	1.46	1.36	1.58	2412	2.70	2.59	2.81

O, observed number of cases; SIR, standardized incidence ratio; CI, confidence interval.

Bold type, 95% CI does not include 1.00.

elife-02917-v1.xml

10.7554/eLife.02917.006

Table 4.

Risk of autism and ADHD in adoptees when their biological or adoptive parents were diagnosed with alcohol use disorder (AUD)

DOI: http://dx.doi.org/10.7554/eLife.02917.006

	No. of offspring at risk	Person-years of follow-up	Autism				ADHD
	No. of offspring at risk	Person-years of follow-up	O	SIR	95% CI		O	SIR	95% CI
Biological parents with AUD
Father	2175	51746	16	2.15	1.23	3.50	53	2.63	1.97	3.44
Mother	1381	32745	10	1.81	0.86	3.35	18	1.21	0.72	1.92
Parents	3251	77310	19	1.75	1.05	2.74	58	1.91	1.45	2.47
Adoptive parents with AUD
Father	457	10,839	1	0.75	0.00	4.28	7	1.78	0.70	3.68
Mother	229	5443	0				4	1.93	0.50	4.98
Parents	654	15546	1	0.51	0.00	2.93	9	1.59	0.72	3.04

O, observed number of cases; SIR, standardized incidence ratio; CI, confidence interval.

Bold type, 95% CI does not include 1.00.

elife-02923-v2.xml

10.7554/eLife.02923.005

Table 2.

Number of Z line streaming sites within 100 μm² grid in 2-month old wild-type and RyR1^AG/+ soleus muscle

DOI: http://dx.doi.org/10.7554/eLife.02923.005

Genotype	12-month old	2-month old
Genotype	12-month old	0.6% Diet	5.2% Diet	Enalapril	Glibenclamide
Ryr1^+/+	0.48 ± 0.21	0.04 ± 0.01	0.03 ± 0.01	0.05 ± 0.03	0.09 ± 0.08
Ryr1^AG/+	10.67 ± 0.82**	3.75 ± 0.05**	0.34 ± 0.16*	1.13 ± 0.14**	1.12 ± 0.02**

Average values from five grids per mice and three mice per group. Asterisks indicate significant value *<0.05, **<0.005.

elife-02923-v2.xml

10.7554/eLife.02923.011

Table 3.

Quantitative RT-PCR of muscles from 2-month old wild-type and heterozygous Ryr1^AG/+ mice fed for 4 weeks on the indicated diets

DOI: http://dx.doi.org/10.7554/eLife.02923.011

Gene	0.6% K Diet		5.2% K Diet
Gene	Ryr1^+/+	Ryr1^AG/+	Ryr1^+/+	Ryr1^AG/+
Abcc8 (SUR1)
Vastus lateralis	1.00 ± 0.07	1.30 ± 0.21**	1.05 ± 0.30	1.51 ± 0.33*
Tibialis anterior	1.00 ± 0.04	1.20 ± 0.17***	1.09 ± 0.23	1.31 ± 0.27*
Adductor magnus	1.00 ± 0.12	1.28 ± 0.22*	0.98 ± 0.23	1.61 ± 0.42*
Abcc9 (SUR2)
Vastus lateralis	1.00 ± 0.19	0.81 ± 0.24	1.03 ± 0.20	1.09 ± 0.18
Tibialis anterior	1.00 ± 0.23	0.86 ± 0.21	0.99 ± 0.13	1.18 ± 0.20
Adductor magnus	1.00 ± 0.18	0.88 ± 0.19	1.01 ± 0.19	1.11 ± 0.11
Atpa1 (NKAα1)
Vastus lateralis	1.00 ± 0.15	1.23 ± 0.21*	0.94 ± 0.32	0.18 ± 0.06***
Tibialis anterior	1.00 ± 0.21	1.22 ± 0.13*	0.75 ± 0.39	0.23 ± 0.06***
Adductor magnus	1.00 ± 0.26	1.25 ± 0.17*	0.93 ± 0.29	0.24 ± 0.07***
Clc1 (CLC1)
Vastus lateralis	1.00 ± 0.09	1.05 ± 0.19	0.90 ± 0.21	0.84 ± 0.25
Tibialis anterior	1.00 ± 0.10	1.10 ± 0.16	0.93 ± 0.11	0.82 ± 0.27
Adductor magnus	1.00 ± 0.12	1.03 ± 0.21	0.89 ± 0.15	0.88 ± 0.17
Kcnj2 (K_IR2.1)
Vastus lateralis	1.00 ± 0.09	0.77 ± 0.12***	1.75 ± 0.17***	1.62 ± 0.13***
Tibialis anterior	1.00 ± 0.17	0.68 ± 0.17***	1.70 ± 0.26***	1.55 ± 0.15***
Adductor magnus	1.00 ± 0.18	0.59 ± 0.13***	1.67 ± 0.33**	1.52 ± 0.18***
Kcnj8 (K_ATP6.1)
Vastus lateralis	1.00 ± 0.20	0.56 ± 0.12***	0.97 ± 0.20	0.97 ± 0.23
Tibialis anterior	1.00 ± 0.13	0.74 ± 0.19***	0.87 ± 0.11	0.91 ± 0.12
Adductor magnus	1.00 ± 0.24	0.69 ± 0.16**	1.16 ± 0.20	1.08 ± 0.17
Kcnj11 (K_ATP6.2)
Vastus lateralis	1.00 ± 0.15	0.96 ± 0.17	1.10 ± 0.13	1.42 ± 0.14***
Tibialis anterior	1.00 ± 0.18	1.01 ± 0.16	1.05 ± 0.08	1.34 ± 0.09***
Adductor magnus	1.00 ± 0.17	0.94 ± 0.09	1.0 9± 0.06	1.38 ± 0.21***
Prkaa1 (AMPK)
Vastus lateralis	1.00 ± 0.14	1.23 ± 0.15**	1.11 ± 0.10	1.07 ± 0.14
Tibialis anterior	1.00 ± 0.04	1.11 ± 0.06**	1.08 ± 0.05	1.07 ± 0.10
Adductor magnus	1.00 ± 0.11	1.20 ± 0.11***	1.01 ± 0.11	1.10 ± 0.06

Values normalized to GAPDH before normalization to Ryr1^+/+ control on 0.6% diet. Asterisks indicates significant value * = 0.05, ** = 0.001, *** = 0.005.

elife-02923-v3.xml

10.7554/eLife.02923.005

Table 2.

Number of Z line streaming sites within 100 μm² grid in 2-month old wild-type and RyR1^AG/+ soleus muscle

DOI: http://dx.doi.org/10.7554/eLife.02923.005

Genotype	12-month old	2-month old
Genotype	12-month old	0.6% Diet	5.2% Diet	Enalapril	Glibenclamide
Ryr1^+/+	0.48 ± 0.21	0.04 ± 0.01	0.03 ± 0.01	0.05 ± 0.03	0.09 ± 0.08
Ryr1^AG/+	10.67 ± 0.82**	3.75 ± 0.05**	0.34 ± 0.16*	1.13 ± 0.14**	1.12 ± 0.02**

Average values from five grids per mice and three mice per group. Asterisks indicate significant value *<0.05, **<0.005.

elife-02923-v3.xml

10.7554/eLife.02923.011

Table 3.

Quantitative RT-PCR of muscles from 2-month old wild-type and heterozygous Ryr1^AG/+ mice fed for 4 weeks on the indicated diets

DOI: http://dx.doi.org/10.7554/eLife.02923.011

Gene	0.6% K Diet		5.2% K Diet
Gene	Ryr1^+/+	Ryr1^AG/+	Ryr1^+/+	Ryr1^AG/+
Abcc8 (SUR1)
Vastus lateralis	1.00 ± 0.07	1.30 ± 0.21**	1.05 ± 0.30	1.51 ± 0.33*
Tibialis anterior	1.00 ± 0.04	1.20 ± 0.17***	1.09 ± 0.23	1.31 ± 0.27*
Adductor magnus	1.00 ± 0.12	1.28 ± 0.22*	0.98 ± 0.23	1.61 ± 0.42*
Abcc9 (SUR2)
Vastus lateralis	1.00 ± 0.19	0.81 ± 0.24	1.03 ± 0.20	1.09 ± 0.18
Tibialis anterior	1.00 ± 0.23	0.86 ± 0.21	0.99 ± 0.13	1.18 ± 0.20
Adductor magnus	1.00 ± 0.18	0.88 ± 0.19	1.01 ± 0.19	1.11 ± 0.11
Atpa1 (NKAα1)
Vastus lateralis	1.00 ± 0.15	1.23 ± 0.21*	0.94 ± 0.32	0.18 ± 0.06***
Tibialis anterior	1.00 ± 0.21	1.22 ± 0.13*	0.75 ± 0.39	0.23 ± 0.06***
Adductor magnus	1.00 ± 0.26	1.25 ± 0.17*	0.93 ± 0.29	0.24 ± 0.07***
Clc1 (CLC1)
Vastus lateralis	1.00 ± 0.09	1.05 ± 0.19	0.90 ± 0.21	0.84 ± 0.25
Tibialis anterior	1.00 ± 0.10	1.10 ± 0.16	0.93 ± 0.11	0.82 ± 0.27
Adductor magnus	1.00 ± 0.12	1.03 ± 0.21	0.89 ± 0.15	0.88 ± 0.17
Kcnj2 (K_IR2.1)
Vastus lateralis	1.00 ± 0.09	0.77 ± 0.12***	1.75 ± 0.17***	1.62 ± 0.13***
Tibialis anterior	1.00 ± 0.17	0.68 ± 0.17***	1.70 ± 0.26***	1.55 ± 0.15***
Adductor magnus	1.00 ± 0.18	0.59 ± 0.13***	1.67 ± 0.33**	1.52 ± 0.18***
Kcnj8 (K_ATP6.1)
Vastus lateralis	1.00 ± 0.20	0.56 ± 0.12***	0.97 ± 0.20	0.97 ± 0.23
Tibialis anterior	1.00 ± 0.13	0.74 ± 0.19***	0.87 ± 0.11	0.91 ± 0.12
Adductor magnus	1.00 ± 0.24	0.69 ± 0.16**	1.16 ± 0.20	1.08 ± 0.17
Kcnj11 (K_ATP6.2)
Vastus lateralis	1.00 ± 0.15	0.96 ± 0.17	1.10 ± 0.13	1.42 ± 0.14***
Tibialis anterior	1.00 ± 0.18	1.01 ± 0.16	1.05 ± 0.08	1.34 ± 0.09***
Adductor magnus	1.00 ± 0.17	0.94 ± 0.09	1.0 9± 0.06	1.38 ± 0.21***
Prkaa1 (AMPK)
Vastus lateralis	1.00 ± 0.14	1.23 ± 0.15**	1.11 ± 0.10	1.07 ± 0.14
Tibialis anterior	1.00 ± 0.04	1.11 ± 0.06**	1.08 ± 0.05	1.07 ± 0.10
Adductor magnus	1.00 ± 0.11	1.20 ± 0.11***	1.01 ± 0.11	1.10 ± 0.06

Values normalized to GAPDH before normalization to Ryr1^+/+ control on 0.6% diet. Asterisks indicates significant value * = 0.05, ** = 0.001, *** = 0.005.

elife-02999-v1.xml

Ref. No.	Sirt3 Localization	Evidence	Fig. No. in Ref.	Cell Type	Antibody	Methods
Ref. No.	Sirt3 Localization	Evidence	Fig. No. in Ref.	Cell Type	Antibody	IB	IF	GFP	Others
1	Mitochondria	Overexpressed Sirt3-FLAG was found in mitochondrial extraction.	2b	HEK293T	anti-FLAG	✔
	Mitochondria	Endogenous Sirt3 was detected in mitochondrial fraction with rabbit sirt3 antiserum (anti-sirt3 C term 15 AAs).	2c	HEK293T	anti-Sirt3 C-term	✔
	Mitochondria	Overexpressed Sirt3-GFP localized in mitochondria	2a	HeLa				✔
2	Mitochondria	Overexpressed Sirt3-EGFP was detected in mitochondria by immunoelectron microscopy.	6	Cervical carcinoma					Immunoelectron
2	Mitochondria	Overexpressed full length Sirt3-EGFP was present in mitochondria	3, 4, 5	COS7				✔
3	Mitochondria	Overexpressed Sirt3-GFP was detected in mitochondria.	1a	NHF				✔
	Mitochondria	There was no detectable signal of overexpressed Sirt3 with N-term-HA tag by immunofluorescence.	−	NHF	anti-HA,		✔
	Mitochondria	Overexpressed of Sirt3-V5-His with C-term-tag was detected in mitochondria by immunofluorescence.	3a, b	NHF HeLa	anti-V5		✔
	Mitochondria	Sirt3-V5-His was detected in mitochondrial extraction using anti-V5 antibody.	3c	HEK293T	anti-V5	✔
4	Mitochondria	Overexpressed mSirt3-FLAG was detected in mitochondria by immunofluorescence.	2a	NIH3T3 (mouse)	anti-FLAG		✔
5	Mitochondria	Co-expression of AceCS1/2 with Sirt3-FLAG down-regulated acetylation level on AceCS2 (in mitochondria), but not AceCS1 (in nucleus).	1e, 3c	COS7	anti-FLAG				✔
6	Mitochondria	Endogenous Sirt3 was detected in mitochondrial extraction using anti-sirt3 C-term serum.	1b-d	HEK293	anti-sirt3 C-term	✔
	Mitochondria	AceCS2-FLAG localized in mitochondria. Endogenous Sirt3 was co-precipitated from cell stably expressing AceCS2-FLAG using anti-FLAG antibody.	1a, 3e	HeLa HEK293	anti-FLAG anti-sirt3 C-term				✔
	Mitochondria	Overexpression of Sirt3-FLAG down-regulated acetylation level on AceCS2.	3d	COS-1					✔
7	Mitochondria	Overexpressed Sirt3-myc was detected in mitochondria by immunofluorescence.	1a	COS7	anti-Myc tag		✔
	Mitochondria	Overexpressed Sir3-Myc was detected in mitochondrial extraction using anti-Myc antibody.	1b	COS7	anti-Myc tag	✔
	Nucleus	Co-expression of Sirt5-FLAG with Sirt3-Myc promoted translocation of Sirt3 into nucleus.	2a	COS7	anti-Myc tag		✔
	Nucleus	Overexpressed Sirt3-Myc could be detected in total lysate but not in post-nuclear supernatant after co-expression with Sirt5-FLAG.	2b, c	COS7	anti-Myc tag	✔
	MTS	Sirt3-Myc with mitochondria targeting signal (72-75) mutant to 4 Ala was found in in both nucleus and cytoplasm.	3	COS7	anti-Myc tag		✔
	NTS	Sirt3-Myc with nuclear targeting signal (214-216) mutant to 3 Ala was detected in nucleus and cytoplasm when co-expressed with Sirt5.	4b, c	COS7	anti-Myc tag		✔
8	Mitochondria	Endogenous Sirt3 was detected in mitochondria isolation using anti-Sirt3 C-term antibody.	1b-d	mouse	anti-Sirt3 C-term	✔
9	Mitochondria	Overexpressed Sirt3-FLAG or Sirt3-Myc was detected in mitochondria by immunofluorescence.	1A	HeLa HEK293T U2OS	anti-FLAG, anti-Myc		✔
	Mitochondria	LMB treatment did not result in nuclear translocation of Sirt3-FLAG but did for HDAC7.	1B, C	HeLa U2OS	anti-FLAG, anti-Myc		✔
	Mitochondria	Overexpressed POLG2-HA, a positive control for mitochondrial localized proteins, was detected in mitochondria isolation, by not for Sirt3-FLAG.	2A	HEK293	anti -Sirt3 SC49744	✔
10	Nucleus	Full length Sirt3 was detected in all subcellular fractionation parts.	5	Cardiomyocytes	anti-sirt3 Ab56214,	✔
	Nucleus	Endogenous Sirt3 was detected in nucleus by microscopy.	6a-e	Cardiomyocytes	anti-sirt3 SC49744				✔
	Nucleus	Overexpressed Sirt3 was detected in nucleus by immunofluorescence.	6f 7a, b	Cardiomyocytes	anti -Sirt3 SC49744		✔
	Nucleus	Full length Sirt3 was detected in nuclear extraction using anti-Sirt3 antibody.	7d, g	Cardiomyocytes	anti-sirt3 SC49744	✔
	Nucleus	Ku70, a nuclear protein, could be co-precipitated by anti-Sirt3 antibody.	8a	Cardiomyocytes	anti-Sirt3 AP6242a				✔
	Nucleus	Ku70 was co-precipitated with FLAG antibody from Sirt3-FLAG expressing cells but not from cells expressing the FLAG tag alone.	8b	COS7	anti-FLAG,				✔
	Nucleus	Sirt3 was pulled down with Ku70 using anti-Ku70 antibody.	8c	Cardiomyocytes	anti-sirt3 PAB11098				✔
	Nucleus	Precipitation of recombinant Ku70 by recombinant Sirt3 verified their direct interaction in vitro.	8d						✔
	Nucleus	Acetylation level on Ku70 was reduced by overexpressed Sirt3 and enhanced by Sirt3 knockdown via RNAi.	9d10c, d	HeLa					✔
	Nucleus	Sirt3 was capable of deacetylation on Ku70 to enhance Ku70/Bax bindig to prevent cell death.	11, 12	HeLa					✔
11	Nucleus	Endogenous full-length Sirt3 was detected in nucleus by immunofluorescence using anti-Sirt3 N-term antibody.	1b	HeLa & HEK293T	anti-sirt3 N-term		✔
	Nucleus	Co-transfection of Gal4-Sirt3 and luciferase reporter plasmid showed the nucleus localization of Gal4-Sirt3.	3b	HEK293T	anti-Gal-DBD	✔
	Nucleus	Full length Sirt3 resided in the nucleus and expelled from nucleus upon cellular stress.	5	HeLa S3	anti-sirt3 N-term		✔
	Nucleus	The synthesis of tetracycline-inducible Sirt3 harboring a C-term HA-tag is processed in the nucleus.	6a	HEK293T	anti-HA		✔
	Nucleus	Overexpressed Sirt3-HA was detected in nuclear extraction.	6b	HEK293T	anti-HA	✔
12	Nucleus	Stress-induced the degradation of full-length Sirt3 in nuclei.	5b, c	HeLa, U2OS, HEK293T	anti-HA anti-Sirt3 sc-49744	✔
	Nucleus	SIRT3 localizes to defined chromatin regions and regulates gene expression.	6, 7, 8	U2OS					✔
	Nucleus	Interaction of endogenous Sirt3 and SKP2, a protein found outside mitochondria, was validated by immunoprecipitation.	4	HEK293T	anti-HA anti-FLAG anti-Sirt3 C73E3				✔

elife-03061-v1.xml

10.7554/eLife.03061.008

Table 1.

Results for individual mice

DOI: http://dx.doi.org/10.7554/eLife.03061.008

	Retrieval			Encoding
	Baseline	Peak	Trough	Baseline	Peak	Trough
Mouse 1	0.55	0.49	0.71	0.58	0.48	0.43
Mouse 1		p=0.09	P=0.02		p=0.07	P=0.02
Mouse 2	0.52	0.57	0.64	0.60	0.75	0.66
Mouse 2		p=0.09	P=0.02		P=0.01	p=0.06
Mouse 3	0.50	0.53	0.67	0.62	0.73	0.64
Mouse 3		p=0.10	P=0.01		P=0.03	p=0.11
Mouse 4	0.72	0.73	0.82	0.56	0.82	0.62
Mouse 4		p=0.12	P=0.04		P=0.0001	p=0.08

Probability of a correct response for four mice under six conditions: baseline (no stimulation), peak-triggered stimulation, and trough-triggered stimulation in both the retrieval and encoding segments. p-values computed from the p.d.f. of the binomial distribution with chance levels equal to the baseline performance for that mouse. Significant changes (p<0.05) are highlighted in bold.

elife-03185-v1.xml

10.7554/eLife.03185.006

Table 1.

Properties of USV categories emitted during social interactions.

DOI: http://dx.doi.org/10.7554/eLife.03185.006

Call type	n	Frequency (kHz)			Band width (kHz)			Duration (ms)
Call type	n	Mean	± SEM	20th, 80th quantiles	Mean	± SEM	20th, 80th quantiles	Mean	± SEM	20th, 80th quantiles
Trill	16,549	63.1	0.2	51.7, 76.9	10.3	0.1	5.1, 12.6	50.9	0.2	30.2, 67.1
Complex	13,662	54.8	0.1	48.1, 62.9	7.8	0.1	3.9, 8.7	39.0	0.2	23.8, 49.9
Flat	13,656	49.0	0.1	38.6, 56.0	5.2	0.1	2.7, 5.3	44.1	0.3	21.7, 56.4
Upward ramp	1280	51.6	0.4	45.7, 59.8	6.5	0.2	3.5, 8.4	26.8	0.3	15.9, 36.5
Downward ramp	258	48.0	1.0	31.7, 59.7	5.5	0.4	3.2, 6.8	19.9	0.8	11.6, 25.6
Inverted u	501	55.5	0.7	45.0, 67.4	5.7	0.2	3.2, 7.2	16.4	0.5	11.0, 18.4
Short	26	49.6	3.1	36.1, 65.1	4.1	0.3	3.1, 5.4	13.7	0.9	10.9, 15.6
Split	1072	45.2	0.5	34.0, 57.2	7.4	0.5	3.1, 7.3	68.1	1.4	38.9, 87.8
Fear call	299	28.0	0.5	22.9, 31.0	2.4	0.5	1.1, 2.3	206.5	16.6	30.2, 353.7

elife-03348-v2.xml

10.7554/eLife.03348.019

Table 1.

Average equilibrium force, extension change, folding energy, and folding energy barrier and position associated with C-terminal domain and linker domain transitions of the four different SNARE complexes

DOI: http://dx.doi.org/10.7554/eLife.03348.019

SNARE complex	C-terminal domain					Linker domain
SNARE complex	Force (pN)	Extension change (nm)	Folding energy (k_BT)	Transition state energy* (k_BT)	Transition state position† (a.a.)	Force (pN)	Extension change (nm)	Folding energy (k_BT)	Transition state energy* (k_BT)	Transition state position† (a.a.)
Neuron	16.2 (0.9)	7.2 (1.2)	−27 (4.7)	−5.5 (1.5)	17 (3)	8 (1)	4.7 (0.5)	−9.7 (1.6)	5.5 (1.5)	31 (1)
GLUT4	18.5 (1.8)	6.0 (0.9)	−23 (4.1)	−0.8 (1.0)	11 (2)	8.6 (0.9)	5.6 (1.1)	−12 (2.7)	2 (1.0)	30 (1)
Endosome	11.9 (0.9)	6.9 (0.4)	−16 (1.5)	2.1 (1.4)	12 (2)	6.3 (1.2)	5.1 (1.8)	−6.1 (2.4)	4.9 (1.5)	32 (2)
Yeast	10.1 (1.4)	5.8 (0.8)	−13 (2.5)	3.2 (1.5)	13 (2)	6.0 (1.6)	5.1 (1.2)	−5.7 (2.0)	3.6 (2.0)	32 (2)

Here, negative energy indicates downhill protein folding (Yang and Gruebele, 2003).

†

The number of the amino acids in the R SNARE C-terminal to the ionic layer (chosen as 0).

The equilibrium force and extension change were determined at an unfolding probability of 0.5 for the two-state processes. The standard deviations of the averages are shown in parenthesis. The equilibrium force distribution, the number of transitions, and the number of single molecules scored for C-terminal domain (CTD) transitions are shown in Figure 3. For parameters related to linker domain (LD) transitions, a total of 18, 35, 11, and 24 LD transitions in single neuronal, GLUT4, endosomal, and yeast SNARE complexes were scored, respectively.

elife-03372-v1.xml

10.7554/eLife.03372.006

Table 1.

Yeast strains

DOI: http://dx.doi.org/10.7554/eLife.03372.006

Strain	Genotype	Figure(s)
Strain	Genotype	Reference
RPY753	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-GFP-3xHA-GST-DYN1_331kDa-gs-DHA, pac1Ä::URA3, ndl1Ä::cgLEU2	Figure 2, Figure 2—figure supplement 1,2, Figure 5—figure supplement 1
RPY753		Huang et al., 2012
RPY816	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-PAC1, dyn1Ä::cgLEU2, ndl1Ä::Hygro^R	Figures 1–5, Figure 2—figure supplement 1,2, Figure 1—figure supplement 1, Figure 4—figure supplement 1, Figure 5—figure supplement 1
RPY816		Julie Huang, Harvard Medical School
RPY842	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-PAC1-g-1xFLAG-ga-SNAP-Kan^R, dyn1Ä::cgLEU2, ndl1Ä::Hygro^R	Figures 3,5, Figure 3—figure supplement 1, Figure 5—figure supplement 1
RPY842		Huang et al., 2012
RPY844	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-GFP-3xHA-DYN1_331kDa, pac1Ä::Hygro^R	Figures 1,4, Figure 1—figure supplement 1, Figure 3—figure supplement 1
RPY844		Huang et al., 2012
RPY1198	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-GFP-3xHA-DYN1_331kDa-gs-DHA-Kan^R, pac1Ä::Hygro^R	Figure 5, Figure 5—figure supplement 1
RPY1198		Huang et al., 2012
RPY1245	MATa, ura3-52, lys2-801, leu2-Ä1, his3-Ä200, trp1-Ä63, SPC110-GFP::TRP1, HXT1-tdTomato::HIS3	Figure 2
RPY1245		Jeff Moore, University of Colorado
RPY1248	MATa, ura3-52, lys2-801, leu2-Ä1, his3-Ä200, trp1-Ä63, SPC110-GFP::TRP1, HXT1-tdTomato::HIS3, dyn1Ä::URA3	Figure 2
RPY1248		This work
RPY1302	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-DYN1_331kDa, pac1Ä::Hygro^R	Figures 1,3
RPY1302		This work
RPY1400	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-GFP-3xHA-DYN1_331kDa-L2441ybbR, pac1Ä::Hygro^R	Figure 3, Figure 3—figure supplement 1
RPY1400		This work
RPY1422	MATa, his3-11,15, ura3-52, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-GFP-3xHA-DYN1_314kDa-gs-DHA, pac1Ä::Hygro^R	Figures 4,5, Figure 4—figure supplement 1, Figure 5—figure supplement 1
RPY1422		This work
RPY1436	MATa, his3-11,15, ura3-52, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev- DYN1_314kDa, pac1Ä::Hygro^R	Figure 5
RPY1436		This work
RPY1439	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-GFP-3xHA-GST-DYN1₃₁₄ _kDa-gs-DHA-Kan^R, pac1Ä:URA3, ndl1Ä::cgLEU2	Figure 5—figure supplement 1
RPY1439		This work
RPY1509	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-DYN1_331kDa-gs-DHA-Kan^R, pac1Ä::Hygro^R	Figure 5—figure supplement 1
RPY1509		This work
RPY1510	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-DYN1_314kDa-gs-DHA-Kan^R, pac1Ä::Hygro^R	Figure 5—figure supplement 1
RPY1510		This work
RPY1523	MATa, ura3-52, lys2-801, leu2-Ä1, his3-Ä200, trp1-Ä3, SPC110-GFP::TRP1, HXT1-tdTomato::HIS3, pac1Ä::URA3	Figure 2
RPY1523		This work
RPY1524	MATa, ura3-52, lys2-801, leu2-Ä1, his3-Ä200, trp1-Ä63, SPC110-GFP::TRP1, HXT1-tdTomato::HIS3, PAC1^R378A	Figure 2
RPY1524		This work
RPY1525	MATa, ura3-52, lys2-801, leu2-Ä1, his3-Ä200, trp1-Ä63, SPC110-GFP::TRP1, HXT1-tdTomato::HIS3, PAC1^{R275A,R301A,R378A,W419A,K437A}	Figure 2
RPY1525		This work
RPY1543	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-PAC1^R275A, dyn1Ä::cgLEU2, ndl1Ä::Hygro^R	Figure 2—figure supplement 1
RPY1543		This work
RPY1544	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-PAC1^R378A, dyn1Ä::cgLEU2, ndl1Ä::Hygro^R	Figure 2, Figure 2—figure supplement 1,2
RPY1544		This work
RPY1545	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-PAC1^W419A, dyn1Ä::cgLEU2, ndl1Ä::Hygro^R	Figure 2—figure supplement 1
RPY1545		This work
RPY1546	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-PAC1^K437A, dyn1Ä::cgLEU2, ndl1Ä::Hygro^R	Figure 2—figure supplement 1
RPY1546		This work
RPY1547	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-PAC1 ^{R275A,R301A,R378A,W419A,K437A}, dyn1Ä::cgLEU2, ndl1Ä::Hygro^R	Figure 2, Figure 2—figure supplement 1,2
RPY1547		This work
RPY1548	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-PAC1^R301A, dyn1Ä::cgLEU2, ndl1Ä::Hygro^R	Figure 2—figure supplement 1
RPY1548		This work
RPY1553	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-GFP-3xHA-DYN1_331kDa^E1849Q, pac1Ä::Hygro^R	Figure 4, Figure 4—figure supplement 1
RPY1553		This work
RPY1554	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-GFP-3xHA-DYN1_331kDa^E2819Q, pac1Ä::Hygro^R	Figure 4, Figure 4—figure supplement 1
RPY1554		This work
RPY1555	MATa, his3-11,15, ura3-52, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-GFP-3xHA-DYN1_314kDa^{K3438E,R3445E,F3446D}-gs-DHA, pac1Ä::Hygro^R	Figure 4—figure supplement 1, Figure 5—figure supplement 1
RPY1555		This work
RPY1557	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, PAC11-13xMYC-TRP1, P_GAL1-ZZ-Tev-GFP-3xHA-DYN1_331kDa^{K3438E,R3445E,F3446D}-gs-DHA-Kan^R, pac1Ä::Hygro^R	Figure 4, Figure 4—figure supplement 1
RPY1557		This work
RPY1623	MATa, his3-11,15, ura3-1, leu2-3,112, ade2-1, trp1-1, pep4Ä::HIS5, prb1Ä, P_GAL1-ZZ-Tev-GFP-3xHA-GST- DYN1_331kDa^{R2857A,N2858A,K2859A,R2861A,S2862A}-gs-DHA, pac1Ä::URA3, ndl1Ä::cgLEU2	Figure 1—figure supplement 2
RPY1623		This work

DYN1, PAC11, PAC1, and NDL1 encode the dynein heavy chain, dynein intermediate chain, Lis1 and Nudel orthologs, respectively. DHA, SNAP, and ybbR refer to the HaloTag (Promega), SNAP-tag (NEB), and ybbR tag (Yin et al., 2005), respectively. TEV indicates a Tev protease cleavage site. P_GAL1 denotes the galactose promoter, which was used for inducing strong expression of Lis1 and dynein motor domain constructs. Genes encoding proteases Pep4 and Prb1 were deleted as noted. Amino acid spacers are indicated by g (glycine), ga (glycine-alanine), and gs (glycine-serine).

elife-03564-v2.xml

10.7554/eLife.03564.010

Table 1.

Statistical analysis (two-way ANOVA) of ABR threshold and P1 amplitude changes between control and neurotrophin overexpressing (Plp1/CreER^T) mice after acoustic trauma

DOI: http://dx.doi.org/10.7554/eLife.03564.010

		Ntf3 overexpressor vs control		Bdnf overexpressor vs control
		p Value	F Statistic	p Value	F Statistic
ABR threshold	AT + 1 day	0.0051	8.469	0.6801	0.1716
	AT + 3 days	<0.0001	19.00	0.6752	0.1774
	AT + 10 days	<0.0001	17.34	0.9862	0.0003
ABR P1 amplitude	AT + 1 day	0.0342	4.695	0.1899	1.7580
	AT + 3 days	<0.0001	18.08	0.5692	0.3276
	AT + 10 days	<0.0001	18.13	0.0421	4.3160

elife-03722-v2.xml

10.7554/eLife.03722.023

Table 1.

Permutation tests for null model 1a: shuffled coordinate labels

DOI: http://dx.doi.org/10.7554/eLife.03722.023

Measures of overlap	Image analysis		Observed overlap	Shuffled overlap Values				Significance
Measures of overlap	Image analysis		Observed overlap	Mean	std	min	max	Significance
Range/Sensitivity σ→NI⋅s→PP	N = 2	R = 32	0.999	0.859	0.9 × 10⁻¹	0.704	0.983	<0.04
		R = 48	0.993	0.832	1.1 × 10⁻¹	0.651	0.978	<0.04
		R = 64	0.987	0.809	1.1 × 10⁻¹	0.614	0.974	<0.04
	N = 4	R = 32	0.998	0.825	1.1 × 10⁻¹	0.638	0.969	<0.04
		R = 48	0.994	0.812	1.1 × 10⁻¹	0.646	0.990	<0.04
		R = 64	0.991	0.794	1.1 × 10⁻¹	0.617	0.985	<0.04
Inverse Range/Threshold 〈ω→NI⋅ω→PP〉	N = 2	R = 32	0.971	0.709	1.5 × 10⁻¹	0.508	0.924	<0.04
		R = 48	0.969	0.692	1.6 × 10⁻¹	0.469	0.924	<0.04
		R = 64	0.953	0.685	1.7 × 10⁻¹	0.450	0.913	<0.04
	N = 4	R = 32	0.967	0.679	1.7 × 10⁻¹	0.447	0.908	<0.04
		R = 48	0.975	0.632	1.5 × 10⁻¹	0.400	0.880	<0.04
		R = 64	0.977	0.648	1.6 × 10⁻¹	0.411	0.894	<0.04
Fractional Principal Components f→NI⋅f→PP	N = 2	R = 32	0.994	0.382	1.5 × 10⁻¹	0.160	0.657	<0.04
		R = 48	0.995	0.485	1.2 × 10⁻¹	0.287	0.727	<0.04
		R = 64	0.991	0.487	0.7 × 10⁻¹	0.372	0.632	<0.04
	N = 4	R = 32	0.995	0.459	1.4 × 10⁻¹	0.238	0.732	<0.04
		R = 48	0.996	0.444	1.0 × 10⁻¹	0.277	0.601	<0.04
		R = 64	0.996	0.450	1.1 × 10⁻¹	0.279	0.614	<0.04
Full Principal Components 〈F→NI⋅F→PP〉	N = 2	R = 32	0.917	0.316	1.3 × 10⁻¹	0.123	0.578	<0.04
		R = 48	0.828	0.401	1.0 × 10⁻¹	0.228	0.611	<0.04
		R = 64	0.911	0.363	0.7 × 10⁻¹	0.282	0.532	<0.04
	N = 4	R = 32	0.882	0.376	1.2 × 10⁻¹	0.180	0.618	<0.04
		R = 48	0.917	0.362	1.0 × 10⁻¹	0.201	0.520	<0.04
		R = 64	0.919	0.357	1.0 × 10⁻¹	0.196	0.522	<0.04

We separately permute the sets of coordinate labels {β|−,β\/,θ,α}. We apply these permutations to the psychophysical data, therein examining all 23 non-identity permutations of the four labels. This shuffling significantly decreases the overlap between image analyses and psychophysical data. Results are significant across all six analyses considered in Figures 1 and 3 (N = 2, 4 and R = 32, 48, 64). p-values, estimated as the fraction of permutations for which the shuffled overlap exceeds the true overlap, are less than 0.04 (the minimum value given 23 permutations) for each image analysis.

elife-03722-v2.xml

10.7554/eLife.03722.024

Table 2.

Permutation Tests for null model 1b: shuffled coordinate labels

DOI: http://dx.doi.org/10.7554/eLife.03722.024

Measures of overlap	Image analysis		Observed overlap	Shuffled overlap Values				Significance
Measures of overlap	Image analysis		Observed overlap	Mean	std	min	max	Significance
Range/Sensitivity σ→NI⋅s→PP	N = 2	R = 32	0.999	0.806	6.8 × 10⁻²	0.659	0.999	0.0003
		R = 48	0.993	0.775	7.7 × 10⁻²	0.610	0.993	<0.0001
		R = 64	0.987	0.762	8.0 × 10⁻²	0.579	0.987	<0.0001
	N = 4	R = 32	0.998	0.828	6.0 × 10⁻²	0.707	0.998	<0.0001
		R = 48	0.994	0.798	7.1 × 10⁻²	0.660	0.994	0.0002
		R = 64	0.991	0.780	7.6 × 10⁻²	0.630	0.991	<0.0001
Inverse Range/Threshold 〈ω→NI⋅ω→PP〉	N = 2	R = 32	0.971	0.693	8.1 × 10⁻²	0.499	0.972	0.0002
		R = 48	0.969	0.682	8.4 × 10⁻²	0.476	0.969	0.0003
		R = 64	0.953	0.671	8.5 × 10⁻²	0.446	0.954	0.0002
	N = 4	R = 32	0.967	0.696	7.6 × 10⁻²	0.521	0.964	<0.0001
		R = 48	0.975	0.692	8.0 × 10⁻²	0.509	0.976	0.0002
		R = 64	0.977	0.689	8.2 × 10⁻²	0.493	0.978	0.0003
Fractional Principal Components 〈f→NI⋅f→PP〉	N = 2	R = 32	0.994	0.592	1.2 × 10⁻¹	0.271	0.995	0.0003
		R = 48	0.995	0.604	1.3 × 10⁻¹	0.281	0.995	0.0004
		R = 64	0.991	0.591	1.2 × 10⁻¹	0.278	0.991	0.0003
	N = 4	R = 32	0.995	0.590	1.2 × 10⁻¹	0.218	0.995	0.0001
		R = 48	0.996	0.577	1.2 × 10⁻¹	0.251	0.996	0.0002
		R = 64	0.996	0.581	1.2 × 10⁻¹	0.266	0.996	0.0004
Full Principal Components 〈F→NI⋅F→PP〉	N = 2	R = 32	0.917	0.391	1.2 × 10⁻¹	0.100	0.927	0.0002
		R = 48	0.828	0.391	1.2 × 10⁻¹	0.086	0.856	0.0008
		R = 64	0.911	0.396	1.2 × 10⁻¹	0.120	0.953	0.0003
	N = 4	R = 32	0.882	0.381	1.2 × 10⁻¹	0.066	0.989	0.0003
		R = 48	0.917	0.380	1.2 × 10⁻¹	0.090	0.902	<0.0001
		R = 64	0.919	0.387	1.2 × 10⁻¹	0.095	0.937	0.0004

We separately permute all nine coordinate labels {β|,β−,β\, β/,θ⌜,θ⌝,θ⌟,θ⌞,α}. This shuffling, applied to the psychophysical data, significantly decreases the overlap between image analyses and psychophysical data. Results are significant across all six analyses considered in Figures 1 and 3 (N = 2, 4 and R = 32, 48, 64). p-values, estimated as the fraction of permutations for which the shuffled overlap exceeds the true overlap, are less than 0.0005 for all image analyses.

elife-03722-v2.xml

10.7554/eLife.03722.025

Table 3.

Permutation tests for null model 2: shuffled patch labels

DOI: http://dx.doi.org/10.7554/eLife.03722.025

Comparisons	Image analysis		Observed overlap	Shuffled overlap Values				Significance
Comparisons	Image analysis		Observed overlap	Mean	std	min	max	Significance
Inverse Range/Threshold 〈ω→NI⋅ω→PP〉	N = 2	R = 32	0.971	0.924	0.70 × 10⁻³	0.921	0.926	<0.0001
		R = 48	0.969	0.921	1.1 × 10⁻³	0.917	0.925	<0.0001
		R = 64	0.953	0.912	1.3 × 10⁻³	0.908	0.917	<0.0001
	N = 4	R = 32	0.967	0.919	1.7 × 10⁻³	0.914	0.926	<0.0001
		R = 48	0.975	0.922	1.9 × 10⁻³	0.916	0.930	<0.0001
		R = 64	0.977	0.924	2.8 × 10⁻³	0.916	0.935	<0.0001
Fractional Principal Components 〈f→NI⋅f→PP〉	N = 2	R = 32	0.994	0.806	9.1 × 10⁻⁶	0.806	0.806	<0.0001
		R = 48	0.995	0.806	8.3 × 10⁻⁶	0.806	0.806	<0.0001
		R = 64	0.991	0.806	3.7 × 10⁻⁶	0.806	0.806	<0.0001
	N = 4	R = 32	0.995	0.807	2.5 × 10⁻⁴	0.806	0.809	<0.0001
		R = 48	0.996	0.807	4.1 × 10⁻⁴	0.806	0.810	<0.0001
		R = 64	0.996	0.807	3.5 × 10⁻⁴	0.806	0.810	<0.0001
Full Principal Components 〈F→NI⋅F→PP〉	N = 2	R = 32	0.917	0.448	5.8 × 10⁻²	0.406	0.596	<0.0001
		R = 48	0.828	0.502	5.9 × 10⁻²	0.408	0.675	<0.0001
		R = 64	0.911	0.458	4.8 × 10⁻²	0.407	0.591	<0.0001
	N = 4	R = 32	0.881	0.489	4.9 × 10⁻²	0.409	0.638	<0.0001
		R = 48	0.917	0.454	3.0 × 10⁻²	0.408	0.637	<0.0001
		R = 64	0.919	0.492	4.2 × 10⁻²	0.411	0.648	<0.0001

Within each image analyses, we separately permute image patch labels along individual coordinate axes. This shuffling does not alter the range of variation observed along individual coordinates; as a result, this test only applies to ω→ ,f→ and F→. We find that this shuffling significantly decreases the overlap between image analyses and psychophysical data. Results are significant across all six analyses considered in Figures 1 and 3 (N = 2, 4 and R = 32, 48, 64). p-values, estimated as the fraction of permutations for which the shuffled overlap exceeds the true overlap, are less than 0.0001 for each image analysis.

elife-03925-v1.xml

10.7554/eLife.03925.004

Table 1.

Baseline characteristics of 8390 children tested for malaria using blood film, by survey location

DOI: http://dx.doi.org/10.7554/eLife.03925.004

Characteristic	Location of survey				Overall (n=8390)
Characteristic	Burkina Faso (n=2821)	Mozambique (n=2266)	Rwanda (n=2085)	Senegal (n=1218)	Overall (n=8390)
Communities surveyed, n	537	607	490	371	2005
(a) Children tested for malaria, n (%)
Parasitemia	2821 (99)	2266 (100)	2085 (99)	1218 (99)	8390 (99)
Positive result among children tested for parasitemia	1696 (60)	578 (25)	16 (0.8)	22 (1.8)	2312 (28)
Pƒ-HRP-2	2821 (100)	na	2060 (99)	1217 (99)	6098 (99)*
Positive results among children tested for Pƒ-HRP-2	2051 (73)	na	35 (1.7)	27 (2.2)	2113 (35)
(b) Type of immunization received, n (%)
Bacille Calmette Guerin (BCG)	2799 (99)	2004 (96)	2050 (100)	1160 (98)	8013 (98)
Diphtheria–tetanus–pertussis (DTP)	2721 (97)	2107 (97)	2055 (98)	1161 (98)	8044 (98)
Measles	2225 (80)	1668 (78)	1727 (86)	830 (73)	6450 (80)
Poliomyelitis	2810 (100)	2156 (99)	2061 (100)	1204 (100)	8231 (99)
Vitamin A	87 (9.3)	1554 (87)	351 (72)	190 (59)	2182 (62)
(c) Children's characteristics
Age in months, median (IQR)	22 (13–32)	20 (13–31)	24 (14–36)	19 (12–29)	22 (13–32)
Girls, n (%)	1347 (48)	1151 (51)	1020 (49)	551 (45)	4069 (48)
Primigravidae, n (%)	443 (16)	477 (21)	432 (21)	251 (21)	1603 (19)
Low birth weight, n (%)	867 (31)	1003 (44)	672 (32)	536 (44)	3078 (37)
(d) Malaria-based interventions, n (%)
Child's family owns bed net	2160 (77)	1528 (67)	1983 (95)	1040 (85)	6711 (80)
Child received antimalarial during past week	314 (11)	117 (5.2)	50 (2.4)	24 (2.0)	505 (6.0)
Child's house had indoor insecticide spraying	22 (0.8)	541 (24)	na	148 (12)	711 (8.5)†
Mother took antimalarial during child's gestational period	2616 (93)	1109 (50)	337 (16)	1110 (91)	5162 (62)
(e) Genetic mechanisms of malaria protection, median (IQR)
Mean predicted HbS allele frequency	0.06 (0.05–0.06)	0.03 (0.01–0.03)	0.03 (0.03–0.03)	0.07 (0.06–0.07)	0.04 (0.03–0.06)
Median predicted G6PDd allele frequency	0.06 (0.05–0.09)	0.15 (0.15–0.17)	0.04 (0.04–0.05)	0.10 (0.09–0.13)	0.08 (0.05–0.14)
(f) Climate of communities surveyed, median (IQR)
Annual range of enhanced vegetation index (EVI)	0.29 (0.24–0.32)	0.33 (0.22–0.40)	0.25 (0.20–0.29)	0.28 (0.18–0.34)	0.28 (0.22–0.33)
Annual mean of EVI for the year	0.22 (0.18–0.25)	0.40 (0.32–0.47)	0.39 (0.36–0.42)	0.18 (0.16–0.20)	0.29 (0.20–0.40)
No. of days which EVI above annual mean	136 (120–160)	88 (56–128)	320 (168–384)	208 (184–264)	152 (120–200)
No. of days for rainy season (corresponding to first and last day EVI above annual mean)	136 (120–152)	128 (72–344)	344 (296–352)	216 (152–352)	168 (120–344)

Pƒ-HRP-2 testing not conducted as part of DHS survey protocol for Mozambique.

†

Information on insecticide spraying not collected as part of survey.

elife-03925-v1.xml

10.7554/eLife.03925.005

Table 2.

Relative risk of malaria infection after standard vaccination and vitamin A supplementation among children 6–59 months of age

DOI: http://dx.doi.org/10.7554/eLife.03925.005

Type of immunization	No. of children vaccinated/total tested (%)	No. of children with positive blood test (%)		Unadjusted RR	Adjusted RR (95% CI)‡,§
Type of immunization	No. of children vaccinated/total tested (%)	No vaccine	Vaccine	Unadjusted RR	Unweighted	Weighted (IPW)
(a) Plasmodium species (parasitemia)*
Bacille Calmette Guerin (BCG)	8013/8140 (98)	41 (32)	2227 (28)	0.81	1.25 (0.81–1.91)	1.24 (0.76–2.05)
Diphtheria–tetanus–pertussis (DTP)	8044/8235 (98)	83 (44)	2202 (27)	0.49	0.88 (0.64–1.20)	0.06 (0.01–0.47)
Measles	6450/8069 (80)	473 (29)	1784 (28)	0.93	1.11 (0.96–1.29)	1.01 (0.20–5.19)
Poliomyelitis	8231/8272 (99)	14 (34)	2278 (28)	0.74	0.80 (0.37–1.73)	0.74 (0.27–2.01)
Vitamin A supplement	2182/3523 (62)	596 (44)	438 (20)	0.31	0.46 (0.39–0.54)	0.43 (0.36–0.52)
(b) Plasmodium falciparum (antigenemia)
Bacille Calmette Guerin (BCG)	6006/6047 (99)	9 (22)	2102 (35)	1.91	4.06 (2.00–8.28)	3.52 (1.66–7.48)
Diphtheria–tetanus–pertussis (DTP)	5933/6054 (98)	59 (49)	2049 (35)	0.55	1.34 (0.88–2.02)	0.06 (0.01–0.38)
Measles	4776/5937 (80)	410 (35)	1679 (35)	0.99	1.15 (0.97–1.38)	0.68 (0.15–3.12)
Poliomyelitis	6.072/6084 (99)	5 (42)	2111 (35)	0.75	1.39 (0.55–3.49)	0.93 (0.37–2.35)
Vitamin A supplement	629/1749 (36)	621 (56)	75 (12)	0.10	0.23 (0.17–0.29)	0.22 (0.16–0.29)

HRP-2: histidine rich protein-2; RR: relative risk; CI: confidence interval; IPW: inverse probability weighted model.

Tested in four countries: Burkina Faso, Mozambique, Rwanda and Senegal.

†

Tested in three countries: Burkina Faso, Rwanda and Senegal.

‡

Adjusted for the following factors: age, gender, wealth index score, mother's highest level of education, malaria treatment during previous week, ownership of bed net, proportion of household members under 5 years using bed net during previous night, indoor household insecticide spraying, mother's access to antenatal care during last pregnancy, mother's knowledge regarding vertical HIV transmission, malaria transmission season, and type of community setting (urban vs rural).

Inverse probability weighting (IPW) based on propensity score model with following factors: age, gender, low birth weight, presence of radio or television, urban versus rural setting, breastfeeding status, wealth index score, mother's age, mother's highest education level, antenatal care during last pregnancy, and mother's tetanus status during last pregnancy.

elife-03925-v1.xml

10.7554/eLife.03925.007

Table 3.

Modifiers of the association between vitamin A supplementation and malaria infection among children 6–59 months of age

DOI: http://dx.doi.org/10.7554/eLife.03925.007

Characteristics at blood testing	Level in the model	Plasmodium species (parasitemia)*					Plasmodium falciparum (antigenemia)†
		No. of children with positive blood film (%)		Unadjusted RR	Adjusted model³		Plasmodium falciparum (antigenemia)†
		No vitamin A	Vitamin A	Unadjusted RR	RR (95% CI)	p Value (interaction term)	Adjusted RR‡ (95%CI)	p Value (interaction term)
(a) Individual level
Children's characteristics
Age at malaria screening	6–35 Months	484 (43)	344 (20)	0.33	0.46 (0.38–0.55)	<0.01#	0.26 (0.20–0.34)	<0.01#
Age at malaria screening	36–59 Months	112 (54)	94 (21)	0.23	0.34 (0.25–0.47)		0.09 (0.05–0.14)
Gender	Girl	274 (44)	226 (21)	0.34	0.54 (0.44–0.67)	0.29	0.23 (0.16–0.32)	0.99
Gender	Boy	322 (45)	212 (19)	0.29	0.40 (0.32–0.49)		0.23 (0.17–0.30)
Pregnancy order of child	Primigravidae	522 (47)	366 (21)	0.30	0.45 (0.38–0.53)	0.27	0.20 (0.15–0.27)	0.04
Pregnancy order of child	Multigravidae	74 (31)	72 (15)	0.41	0.51 (0.39–0.66)		0.33 (0.22–0.48)
Birth weight	2500 mg or greater	332 (42)	204 (15)	0.24	0.39 (0.32–0.48)	0.01	0.27 (0.20–0.36)	0.02
Birth weight	Less than 2500 mg	264 (48)	234 (28)	0.43	0.53 (0.43–0.66)		0.13 (0.09–0.18)
Treatment for intestinal worms during past 6 months	Not received	554 (46)	212 (25)	0.39	0.50 (0.40–0.61)	0.08	0.38 (0.28–0.52)	0.07
Treatment for intestinal worms during past 6 months	Received	37 (30)	221 (17)	0.46	0.66 (0.52–0.86)		0.15 (0.11–0.21)
Malaria-based interventions
Malaria treatment during previous week	Not received	550 (44)	404 (19)	0.31	0.44 (0.37–0.52)	0.24	0.20 (0.16–0.27)	0.02
Malaria treatment during previous week	Received	46 (49)	34 (33)	0.51	0.88 (0.62–1.26)		1.01 (0.60–1.68)
Mother took antimalarial during child's gestational period	No	102 (28)	226 (22)	0.69	0.78 (0.59–1.03)	<0.001	0.38 (0.19–0.74)	0.05
Mother took antimalarial during child's gestational period	Yes	491 (50)	210 (19)	0.23	0.36 (0.30–0.45)		0.20 (0.16–0.27)
Family owns bed net	Does not own bed net	141 (47)	123 (22)	0.32	0.43 (0.34–0.56)	0.42	0.20 (0.15–0.26)	0.70
Family owns bed net	Owns bed net	455 (44)	315 (41)	0.31	0.48 (0.40–0.58)		0.24 (0.18–0.32)
(B) Community level (primary sampling unit)
Type of setting	Rural	518 (50)	370 (25)	0.35	0.46 (0.39–0.56)	0.95	0.22 (0.17–0.30)	0.91
Type of setting	Urban	78 (26)	68 (9.4)	0.29	0.34 (0.22–0.51)		0.22 (0.12–0.40)
Genetic mechanisms of malaria protection
Mean predicted HbS allele frequency§	Less than 2.5%	14 (20)	104 (14)	0.78	0.78 (0.32–1.91)	<0.01#	-	0.26#
	2.5–4.9%	181 (41)	269 (25)	1.49	0.95 (0.64–1.42)		0.96 (0.24–3.91)
	5% or greater	401 (48)	65 (18)	0.21	0.31 (0.17–0.56)		0.17 (0.08–0.39)
Median predicted G6PDd allele frequency§	Less than 7.5%	336 (47)	47 (11)	0.04	5.42 (2.01–14.6)	<0.001#	1.43 (0.28–7.21)	0.02#
	7.5–14.9%	194 (43)	128 (18)	0.80	0.89 (0.52–1.50)		0.41 (0.12–1.34)
	15% or greater	66 (40)	263 (25)	0.65	0.74 (0.46–1.19)		-
Climate of communities surveyed
Season of malaria transmission	Dry season	198 (42)	220 (19)	0.32	0.40 (0.31–0.52)	0.45	0.06 (0.03–0.13)	<0.001
Season of malaria transmission	Wet season	398 (46)	218 (22)	0.32	0.53 (0.42–0.66)		0.39 (0.28–0.53)
Length of rainy season	Less than 120 days	168 (49)	151 (21)	0.27	0.43 (0.31–0.61)	<0.001#	0.28 (0.15–0.50)	0.03#
	120–179 Days	334 (56)	105 (26)	0.27	0.45 (0.33–0.62)		0.22 (0.15–0.31)
	180 Days or more	94 (23)	182 (17)	0.70	0.77 (0.56–1.05)		0.21 (0.10–0.43)
Length of time enhanced vegetation index above annual mean	Less than 120 days	105 (42)	220 (21)	0.38	0.50 (0.37–0.69)	0.18#	0.37 (0.09–1.60)	0.84#
	120–179 Days	486 (52)	206 (27)	0.34	0.52 (0.42–0.66)		0.33 (0.24–0.45)
	180 Days or more	5 (3.3)	12 (3.2)	0.97	0.43 (0.12–1.62)		0.66 (0.16–2.85)
Range of enhanced vegetation index per year	Less than 0.20	46 (25)	41 (7.9)	0.26	0.38 (0.22–0.63)	0.18#	0.24 (0.13–0.47)	0.13#
	0.20–0.29	247 (44)	105 (17)	0.25	0.48 (0.36–0.64)		0.36 (0.25–0.53)
	0.30 or greater	303 (51)	292 (28)	0.38	0.48 (0.39–0.61)		0.19 (0.13–0.29)
Annual mean for enhanced vegetation index	Less than 0.20	150 (37)	21 (7.2)	0.13	0.17 (0.11–0.28)	<0.01#	0.16 (0.10–0.25)	0.01#
	0.20–0.29	309 (59)	89 (24)	0.22	0.51 (0.37–0.70)		0.34 (0.23–0.51)
	0.30 or greater	137 (33)	328 (22)	0.56	0.61 (0.46–0.81)		0.56 (0.20–1.53)

HRP-2: histidine rich protein 2; RR: relative risk; CI: confidence interval; na: not applicable: ref: reference category; HbS: hemoglobin S; G6PD: glucose 6-phosphate dehydrogenase deficiency.

Tested in four countries: Burkina Faso, Mozambique, Rwanda and Senegal.

†

Tested in three countries: Burkina Faso, Rwanda and Senegal.

‡

Geographical waypoints were not recorded for 40 communities. Subjects from these PSUs were excluded from analysis.

Covariate treated as continuous term when testing for effect modification in the model.

elife-03925-v1.xml

Type of Vaccine	Adjusted RR (95%CI)
	Plasmodium spp. Parasitemia (Microscopic Examination of Blood Film)		Plasmodium falciparum Antigenemia (Rapid Detection of HRP2) (i.e., excl. Mozambique)
	All Children (i.e., incl. Mozambique)	Children from countries using both film & RDT (i.e., excl. Mozambique)
BCG	1.24 (0.76-2.05)	2.71 (1.36-5.39)	3.52 (1.66-7.48)
DTP	0.06 (0.01-0.47)	0.38 (0.01-10.1)	0.06 (0.01-0.38)
Measles	1.01 (0.20-5.19)	1.00 (0.18-5.45)	0.68 (0.15-3.12)
Polio	0.74 (0.27-2.01)	0.60 (0.22-1.62)	0.93 (0.37-2.35)
Vitamin A	0.43 (0.36-0.52)	0.24 (0.18-0.34)	0.22 (0.16-0.29)
Countries included in analysis	Burkina Faso, Rwanda, Senegal & Mozambique	Burkina Faso, Rwanda, Senegal

elife-03925-v1.xml

Type of Vaccine	Adjusted RR (95%CI)
	Plasmodium spp. Parasitemia (Microscopic Examination of Blood Film)		Plasmodium falciparum Antigenemia (Rapid Detection of HRP2)
	Not adjusting for mother’s HIV status	Adjusting for mother’s HIV status	Not adjusting for mother’s HIV status	Adjusting for mother’s HIV status
BCG	2.71 (1.36-5.39)	2.20 (0.68-7.10)	3.23 (1.58-6.61)	2.17 (0.66-7.10)
DTP	0.38 (0.01-10.1)	0.93 (0.23-3.82)	0.07 (0.01-0.48)	1.34 (0.51-3.54)
Measles	1.00 (0.18-5.45)	0.66 (0.30-1.45)	0.73 (0.15-3.61)	0.86 (0.43-1.72)
Polio	0.60 (0.22-1.62)	1.75 (0.56-5.49)	0.81 (0.28-2.31)	3.27 (1.17-9.15)
Vitamin A	0.24 (0.18-0.34)	0.09 (0.04-0.19)	0.23 (0.17-0.31)	0.13 (0.06-0.27)

elife-03925-v1.xml

Type of Vaccination/Supplementation	Country
Type of Vaccination/Supplementation	Burkina Faso	Mozambique	Rwanda	Senegal
BCG	Birth	Birth	Birth	Birth
DTP	8,12,16 weeks* (DTP)	6,10,14 weeks (DTPHep)	6,10,14 weeks (DTPHibHep)	6,10,14 weeks (DTPHibHep)
Measles	9 months	9 months	9 months	9 months
Polio	Birth,8,12,16 weeks*	6,10,14 weeks	Birth, 6,10,14 weeks	Birth, 6,10,14 weeks
Vitamin A	Every 6 months from ages 6-59 months Main Distribution Mechanism:Integrated Child Health campaign	Every 6 months from ages 6-59 months Main Distribution Mechanism:Integrated Child Health campaign	Every 6 months from ages 6-59 months Main Distribution Mechanism:Integrated Child Health campaign	Every 6 months from ages 6-59 months Main Distribution Mechanism:Integrated Child Health campaign

elife-04006-v2.xml

10.7554/eLife.04006.004

Table 1.

List of all n = 27 in vivo juxtacellularly filled PV interneurons and their identification based on immunocytochemistry and electron microscopy (EM)

DOI: http://dx.doi.org/10.7554/eLife.04006.004

Cell ID#	Cell type	Parvalbumin	Somatostatin	mGluR1a	SATB1	Bouton targets
Cell ID#	Cell type	Parvalbumin	Somatostatin	mGluR1a	SATB1	AnkyrinG verification	EM verification
123011c3	C-BC	+	n.t.	n.t.	n.t.	n.t.	Soma/proximal dendrite
cvi30	C-BC	+	n.t.	n.t.	n.t.	n.t.	Soma/proximal dendrite
cvi33	C-BC	+	n.t.	n.t.	n.t.	n.t.	n.t.
cvi35	C-BC	+	n.t.	n.t.	n.t.	n.t.	n.t.
cvi55	C-BC	n.t.	n.t.	n.t.	n.t.	n.t.	Soma/proximal dendrite
cvi65	C-BC	+	n.t.	n.t.	n.t.	n.t.	n.t.
cvi75	C-BC	+	n.t.	n.t.	n.t.	n.t.	n.t.
cvi151	C-BC	n.t.	n.t.	n.t.	n.t.	n.t.	n.t.
cvi251	C-BC	n.t.	n.t.	n.t.	n.t.	n.t.	n.t.
cvi240b	H-BC	+	n.t.	n.t.	n.t.	n.t.	Soma/proximal dendrite
042911c5	H-BC	+	n.t.	n.t.	n.t.	n.t.	n.t.
gs0920	H-BC	+	n.t.	n.t.	n.t.	n.t.	n.t.
gs012913	O-Bistrat	+	+	n.t.	n.t.	n.t.	n.t.
gs022713	O-Bistrat	+	+	n.t.	n.t.	n.t.	n.t.
cvi017	O-Bistrat	n.t.	+	n.t.	n.t.	n.t.	n.t.
cvi255	O-Bistrat	−	+	n.t.	n.t.	n.t.	n.t.
cvi312	O-Bistrat	n.t.	+	−	n.t.	n.t.	n.t.
cvi270	C-Bistrat	+	+	n.t.	n.t.	n.t.	n.t.
imi069	C-Bistrat	n.t.	+	n.t.	n.t.	n.t.	n.t.
cvi190	C-Bistrat	−	+	n.t.	n.t.	n.t.	n.t.
090311c3	E-AAC	+	n.t.	n.t.	n.t.	n.t.	AIS
cvi059	E-AAC	n.t.	n.t.	n.t.	n.t.	n.t.	AIS
cvi153	C-AAC	n.t.	n.t.	n.t.	n.t.	n.t.	AIS
cvi258	C-AAC	+	n.t.	n.t.	n.t.	n.t.	AIS
cvi315	C-AAC	n.t.	n.t.	n.t.	−	n.t.	n.t.
imi075	C-AAC	+	n.t.	n.t.	n.t.	AIS	n.t
07082014cs6	C-AAC	n.t.	n.t.	n.t.	n.t.	AIS	AIS

Abbreviations: n.t.: not tested; AIS: axon initial segment.

elife-04059-v3.xml

10.7554/eLife.04059.006

Table 1.

Descriptive statistics of the 16 electrophysiological parameters measured on substantia nigra pars compacta dopaminergic neurons across postnatal development

DOI: http://dx.doi.org/10.7554/eLife.04059.006

Age	ISI_avg (s)			CV_ISI (%)			τ_m (ms)			R_in (MOhm)			C_m (pF)			Sag (mV)			Rebound (ms)			AP threshold (mV)
Age	Mean	SD	N	CV_ISI (%)			τ_m (ms)			R_in (MOhm)			C_m (pF)			Sag (mV)			Rebound (ms)			AP threshold (mV)
P2–P3	1.06	0.84	9	130.5	40.1	9	200.3	8.0	5	1642	420	5	129	34	5	28.2	4.0	9	465	134	6	−43.9	3.3	9
P5	1.36	1.60	15	57.6	22.6	15	86.9	13.7	11	642	163	11	146	52	11	29.4	5.7	14	339	188	12	−40.3	4.5	15
P6	0.78	0.56	18	51.5	43.0	18	70.3	23.9	18	612	170	18	118	32	18	30.2	7.2	18	316	127	18	−43.1	4.3	19
P7	0.97	0.93	36	38.4	28.0	36	89.3	24.4	25	650	174	26	143	38	25	31.2	5.2	25	249	89	19	−39.8	4.0	35
P8–P9	1.67	1.95	18	38.0	23.2	18	90.9	38.4	21	576	268	21	200	141	21	29.6	6.2	17	401	212	15	−42.8	4.3	20
P10–P11	0.68	0.41	12	21.1	8.6	12	80.6	28.6	10	327	210	10	281	109	10	33.3	4.2	10	330	165	10	−41.7	4.2	11
P12–P13	1.04	0.67	15	19.6	15.1	15	87.9	32.7	17	369	166	17	297	226	17	32.4	3.7	16	378	341	16	−45.4	3.7	18
P14	0.64	0.48	16	12.8	8.3	16	92.3	44.0	14	460	192	14	205	68	14	35.6	2.9	10	489	448	9	−44.2	2.3	16
P15–P16	0.88	0.38	22	13.3	6.6	22	77.8	28.5	19	325	117	19	245	67	19	27.9	6.5	33	340	207	30	−44.4	3.4	30
P17	0.82	0.40	16	9.9	5.6	16	83.5	25.7	20	323	109	22	283	160	20	28.1	7.4	35	375	270	26	−44.6	3.5	28
P18	0.63	0.30	18	7.6	4.0	18	89.0	24.2	18	340	118	18	280	86	18	29.5	4.2	22	433	222	20	−41.6	3.0	21
P19	0.71	0.32	24	9.6	6.1	24	89.9	28.1	30	352	103	30	270	106	30	28.6	6.2	38	456	278	32	−44.2	4.1	33
P20	0.77	0.42	21	9.3	4.8	21	88.5	41.8	22	375	116	23	231	66	22	28.5	8.3	24	572	493	22	−44.3	4.4	24
P21–P23	0.72	0.32	19	7.5	4.5	19	93.1	48.2	21	319	115	23	293	128	21	27.5	6.6	23	388	254	22	−43.9	4.0	24
P28–P29	0.92	0.54	12	12.1	4.7	12	148.3	42.6	10	472	88	10	316	83	10	34.1	4.5	13	736	375	10	−42.8	3.0	12

Age	AP amplitude (mV)			AP half-width (ms)			AP rise slope (mV/ms)			AP decay slope (mV/ms)			AHP (mV)			Gain start (Hz/100pA)			Gain end (Hz/100pA)			SFA index
P2–P3	59.5	9.6	9	2.38	0.62	9	47.6	21.7	9	−19.6	5.2	9	14.1	4.9	9	32.1	5.9	6	20	7.8	6	1.76	0.53	6
P5	47.1	7.4	15	2.99	0.95	15	24.5	10.8	15	−16.9	4.6	15	20.1	4.5	15	17.7	5	7	8.8	2.1	7	2.07	0.71	7
P6	49.0	9.2	19	2.99	0.71	19	25.1	19.2	19	−18.0	6.6	19	21.0	3.7	19	22.7	6.5	10	11.7	3.7	10	1.97	0.27	10
P7	46.3	7.8	35	2.92	0.64	35	23.8	8.6	35	−17.6	4.1	35	22.6	3.7	35	17.5	4.7	13	8.83	2.4	13	2.08	0.71	13
P8–P9	54.4	7.4	20	2.74	0.82	20	32.8	14.8	20	−20.2	5.9	20	20.9	4.2	20	18.1	4.3	13	10.4	3.3	13	1.80	0.31	13
P10–P11	50.6	11.6	11	2.51	0.83	11	36.3	21.2	11	−21.4	7.5	11	20.7	4.9	11	11	4.5	10	11.5	5.3	10	1.01	0.30	10
P12–P13	62.1	6.3	18	1.86	0.27	18	54.2	14.5	18	−29.7	4.2	18	23.0	6.0	18	13.2	5	15	11.6	4.5	15	1.29	0.80	15
P14	61.0	7.1	16	1.91	0.54	16	54.9	18.4	16	−30.9	8.5	16	24.1	5.5	16	12.2	4	10	9.8	2.6	10	1.30	0.50	10
P15–P16	60.1	6.5	30	1.63	0.49	30	56.2	18.3	30	−39.7	11.5	30	26.1	4.0	30	9.28	3.2	26	9.28	4.2	26	1.11	0.44	26
P17	62.1	8.6	28	1.61	0.37	28	58.2	16.2	28	−38.8	8.8	28	28.1	5.0	28	7.13	2.1	14	8.28	2.9	14	0.92	0.31	14
P18	55.5	4.7	21	1.45	0.21	21	50.6	15.6	21	−41.1	7.3	21	28.4	3.2	21	6.97	2	12	7.59	2.9	12	0.99	0.35	12
P19	58.2	8.8	33	1.55	0.38	33	54.3	21.1	33	−41.4	11.4	33	27.4	4.6	33	8.32	2.6	19	9.3	2.6	19	0.93	0.31	19
P20	61.6	8.8	24	1.47	0.31	24	59.3	21.2	24	−42.6	8.8	24	28.0	5.0	24	8.15	2.4	16	9.21	3	16	0.95	0.33	16
P21–P23	62.6	8.2	24	1.50	0.37	24	61.5	21.0	24	−44.1	11.4	24	29.1	4.3	24	6.79	2.1	24	7	1.8	24	1.01	0.32	24
P28–P29	62.4	5.3	12	1.49	0.29	12	63.0	14.3	12	−43.2	8.7	12	28.6	6.2	12	6.99	2.3	10	6.82	1.4	10	1.07	0.43	10

Abbreviations: ISI_avg, averaged interspike interval; CV_ISI, coefficient of variation of the interspike interval; τ_m, membrane time constant; R_in, input resistance; C_m, membrane capacitance; Rebound, rebound delay; AP, action potential; AHP, after hyperpolarization; SFA, spike frequency adaptation.

elife-04070-v3.xml

10.7554/eLife.04070.005

Table 1.

Classification of mutant phenotypes

DOI: http://dx.doi.org/10.7554/eLife.04070.005

	Mutagen used	Observed rosette induction*		Other phenotypes
	Mutagen used	ACM	Live bacteria	Swimming†	Chain morphology
Wild type	N/A	86%	88%	Wild type	Primarily linear
Mutant class A
Rosetteless	EMS	0	0	Wild type	Primarily linear
Mutant class B
Insensate	X-rays	0	5	Wild type	Primarily linear
Mutant class C
Slacker	X-rays	20	42	Wild type	Primarily linear
Mutant class D
Uptight	X-rays	33	56	Wild type	Branched
Mutant class E
Jumble	EMS	0	0	Wild type	Branched
Branched	X-rays	0	0	Wild type	Branched
Mutant class F
Seafoam	X-rays	0	0	Wild type	Large clusters
Soapsuds	X-rays	0	0	Wild type	Large clusters
Mutant class G
Solo	X-rays	0	0	Slow, shaking	Primarily solitary

The percentage of cells in rosettes following induction.

†

Swimming phenotypes of single cells.

elife-04114-v2.xml

10.7554/eLife.04114.018

Table 1.

Cytoplasmic and nuclear subviral complexes in MDM

DOI: http://dx.doi.org/10.7554/eLife.04114.018

	Cytoplasm			Nucleus			Proportion of nuclear complexes [%]	Number of cells imaged
	RTC/PIC (n)	CA-positive RTC/PIC (n)	CA-positive RTC/PIC [%]	PIC (n)	CA-positive PIC (n)	CA-positive PIC [%]	Proportion of nuclear complexes [%]	Number of cells imaged
24 hr	90	46	51	9	9	100	9	367
48 hr	45	13	29	61	59	97	58	200
Total	135	59	44	70	68	97	34	567

The table summarizes data from primary MDM infected with NL4-3-R5(IN.eGFP) or NL4-3-4059(IN.eGFP) for 24 hr or 48 hr, respectively. Infected MDM were immunostained with antibodies against nuclear pore complexes and CA. Data were obtained as outlined in Figure 7 in cells from eight different donors in five independent experiments (cells from three donors were infected for both 24 hr and 48 hr).

elife-04251-v1.xml

10.7554/eLife.04251.010

Table 1.

Key descriptors of FG particle constitution

DOI: http://dx.doi.org/10.7554/eLife.04251.010

	Molecular weight*	Number of residues*	Number of FG motifs*	Estimated critical concentration†			Estimated intra-particle concentration‡	NQ-content*	Relative Thioflavin-T signal§
	Molecular weight*	Number of residues*	Number of FG motifs*	FG domain		FG motifs	Estimated intra-particle concentration‡	NQ-content*	Relative Thioflavin-T signal§
Homo sapiens HsNup98	≈49 kDa	500	39	≈25 nM	≈1 µg/ml	≈1 µM	≈175 mg/ml	11%	11%
Branchiostoma floridae BfNup98	≈46 kDa	479	40	≈20 nM	≈1 µg/ml	≈1 µM	≈200 mg/ml	8%	8%
Branchiostoma floridae BfNup98 + GlcNAc	≈55 kDa	479	40	≈150 nM	≈10 µg/ml	≈6 µM	ND	8%	ND#
Drosophila melongaster DmNup98	≈56 kDa	581	46	≈200 nM	≈10 µg/ml	≈9 µM	≈300 mg/ml	10%	3%
Caenorhabditis elegans CeNup98	≈48 kDa	494	36	≈700 nM	≈40 µg/ml	≈25 µM	≈300 mg/ml	18%	52%
Saccharomyces cerevisiae ScNup100	≈58 kDa	578	43	≈175 nM	≈10 µg/ml	≈7.5 µM	≈275 mg/ml	28%	100%
Saccharomyces cerevisiae ScNup116	≈65 kDa	737	47	≈700 nM	≈50 µg/ml	≈33 µM	≈350 mg/ml	26%	78%
Dictyostelium discoideum DdNup220	≈68 kDa	719	56	≈125 nM	≈10 µg/ml	≈7 µM	≈300 mg/ml	12%	4%
Arabidopsis thaliana AtNup98B	≈66 kDa	668	52	≈25 nM	≈1 µg/ml	≈1.5 µM	≈200 mg/ml	13%	1%
Tetrahymena thermophila TtMacNup98A	≈61 kDa	666	42	≈25 nM	≈1 µg/ml	≈1 µM	≈175 mg/ml	18%	2%
Trypanosoma brucei TbNup158	≈50 kDa	565	58	≈300 nM	≈15 µg/ml	≈17.5 µM	≈250 mg/ml	12%	2%

All values are given for full-length FG domains (including GLEBS domains). The molecular weight of glycosylated BfNup98 was estimated by SDS-PAGE.

†

The critical concentrations for phase separation were estimated as described in Figure 1C and the methods section.

‡

Intra-particle FG domain concentrations were estimated as described in Figure 1F and the methods section.

Thioflavin-T signals are normalised to the ScNup100 Thioflavin-T signal; also see Figure 6.

Experiments with macroscopic hydrogels suggest that the Thioflavin-T signal of glycosylated BfNup98 FG particles is even lower than the observed signal for the non-glycosylated BfNup98 FG particles.

elife-04390-v2.xml

10.7554/eLife.04390.006

Table 1.

Quantification of dendritic spine density in the hippocampus of Thy1-eGFP WT, Sema5 and Plxna mice

DOI: http://dx.doi.org/10.7554/eLife.04390.006

Genotype	Age	Dentate GC dendrite				CA1 primary dendrite				CA1 secondary dendrite
Genotype	Age	N	p Value (vs wt)	Spine density (mean ± SEM)	Distance from soma	n	p Value (vs wt)	Spine density (mean ± SEM)	Distance from soma	n	p Value (vs wt)	Spine density (mean ± SEM)	Distance from soma
WT	P30–33	4 animals (74 neurons)		1.67 ± 0.01	50–100 μm	3 animals (26 neurons)		2.76 ± 0.07	50–100 μm	3 animals (15 neurons)		2.93 ± 0.02	50–100 μm
Sema5A^+/−; Sema5B^+/−	P30–33	3 animals (41 neurons)	0.8795	1.68 ± 0.05	50–100 μm	3 animals (24 neurons)	0.6549	2.79 ± 0.019	50–100 μm	3 animals (24 neurons)	0.6333	2.99 ± 0.09	50–100 μm
Sema5A^−/−; Sema5B^+/−	P30–33	4 animals (65 neurons)	0.0012	2.05 ± 0.05	50–100 μm	3 animals (27 neurons)	0.5122	2.81 ± 0.03	50–100 μm	3 animals (21 neurons)	0.618	2.99 ± 0.09	50–100 μm
Sema5A^+/−; Sema5B^−/−	P30–33	3 animals (46 neurons)	0.8844	1.66 ± 0.05	50–100 μm	3 animals (26 neurons)	0.9797	2.76 ± 0.15	50–100 μm	3 animals (21 neurons)	0.9661	2.94 ± 0.02	50–100 μm
Sema5A^−/−; Sema5B^−/−	P30–33	3 animals (30 neurons)	0.0066	2.06 ± 0.08	50–100 μm	3 animals (27 neurons)	0.5389	2.81 ± 0.02	50–100 μm	3 animals (23 neurons)	0.4006	2.98 ± 0.03	50–100 μm
Plxna1^−/−	P30–33	3 animals (56 neurons)	0.154	1.79 ± 0.05	50–100 μm
Plxna2^−/−	P30–33	3 animals (54 neurons)	<0.0001	2.24 ± 0.07	50–100 μm
Plxna2^+/−	P30–33	4 animals (74 neurons)	0.0359	1.86 ± 0.05	50–100 μm
Sema5A^+/−; Plxna2^+/−	P30–33	4 animals (72 neurons)	<0.0001	2.39 ± 0.05	50–100 μm

elife-04490-v1.xml

10.7554/eLife.04490.029

Appendix Table 1.

Volatiles (percent IS plant⁻¹, mean ± SEM) trapped in the headspace around single plants in experimental season one (June 8th–9th).

DOI: http://dx.doi.org/10.7554/eLife.04490.029

			GLVs (percent IS plant^-1)								TPS10 products (percent IS plant^-1)																	Non-target volatiles (percent IS plant^-1)
			(Z)-Hexen-3-ol								TAB										TBF							α-Duprezianene						Germacrene A
Genotype	Day n	Night n	Day			Night					Day				Night						Day				Night			Day			Night			Day			Night
WT	8	8	0.99%	±	0.99%	7.96%	±	4.25%	}	a_lox	0.37%	±	0.29%	a	—				}	a_TPS	—			a	—			2.13%	±	0.85%	0.96%	±	0.42%	1.68%	±	0.98%	—
TPS10	7	7	2.37%	±	1.55%	2.84%	±	0.63%	}	a_lox	18.97%	±	6.03%	b	0.94%	±	0.53%	}		a_TPS	9.34%	±	3.44%	b	0.20%	±	0.20%	9.47%	±	5.26%	0.94%	±	0.26%	2.78%	±	1.52%	—
lox2/3	7	8	0.13%	±	0.13%	1.06%	±	0.64%	}	b_lox	—			a	0.15%	±	0.15%			b_TPS	—			a	—			2.75%	±	1.12%	0.60%	±	0.19%	1.68%	±	1.49%	—
lox2/3xTPS10	7	7	0.07%	±	0.07%	1.24%	±	0.84%	}	b_lox	7.39%	±	2.56%	b	2.08%	±	0.84%			b_TPS	4.47%	±	1.70%	b	0.40%	±	0.40%	3.02%	±	1.42%	0.73%	±	0.31%	0.66%	±	0.37%	—

a, b Different letters indicate significant differences between lines for a vertical category (corrected P<0.05) in Wilcoxon rank sum tests following significant Kruskal-Wallis tests across all genotypes (see Results text); P-values were corrected for multiple testing using the Holm-Bonferroni method. Community type was also tested and found not significant. Where there are no letters, there are no significant pairwise differences within a category.

} a_lox, } b_lox / } a_TPS, } b_TPS Indicate significant differences (corrected P<0.05) between lines with and without either the lox construct (WT and TPS v. lox and loxTPS) or the TPS construct (WT and lox v. TPS and loxTPS) in Wilcoxon rank sum tests for a category; P-values were corrected for multiple testing using the Holm-Bonferroni method. There are no significant pairwise differences in these categories.

IS, internal standard; GLVs, green leaf volatiles; TAB, (E)-α-bergamotene; TBF, (E)-β-farnesene; —, not detected.

elife-04490-v2.xml

10.7554/eLife.04490.029

Appendix 2—Table 1.

Volatiles (percent IS plant⁻¹, mean ± SEM) trapped in the headspace around single plants in experimental season one (June 8th–9th).

DOI: http://dx.doi.org/10.7554/eLife.04490.029

			GLVs (percent IS plant^-1)								TPS10 products (percent IS plant^-1)																	Non-target volatiles (percent IS plant^-1)
			(Z)-Hexen-3-ol								TAB										TBF							α-Duprezianene						Germacrene A
Genotype	Day n	Night n	Day			Night					Day				Night						Day				Night			Day			Night			Day			Night
WT	8	8	0.99%	±	0.99%	7.96%	±	4.25%	}	a_lox	0.37%	±	0.29%	a	—				}	a_TPS	—			a	—			2.13%	±	0.85%	0.96%	±	0.42%	1.68%	±	0.98%	—
TPS10	7	7	2.37%	±	1.55%	2.84%	±	0.63%	}	a_lox	18.97%	±	6.03%	b	0.94%	±	0.53%	}		a_TPS	9.34%	±	3.44%	b	0.20%	±	0.20%	9.47%	±	5.26%	0.94%	±	0.26%	2.78%	±	1.52%	—
lox2/3	7	8	0.13%	±	0.13%	1.06%	±	0.64%	}	b_lox	—			a	0.15%	±	0.15%			b_TPS	—			a	—			2.75%	±	1.12%	0.60%	±	0.19%	1.68%	±	1.49%	—
lox2/3xTPS10	7	7	0.07%	±	0.07%	1.24%	±	0.84%	}	b_lox	7.39%	±	2.56%	b	2.08%	±	0.84%			b_TPS	4.47%	±	1.70%	b	0.40%	±	0.40%	3.02%	±	1.42%	0.73%	±	0.31%	0.66%	±	0.37%	—

}a_lox, }b_lox / }a_TPS, }b_TPS Indicate significant differences (corrected P<0.05) between lines with and without either the lox construct (WT and TPS v. lox and loxTPS) or the TPS construct (WT and lox v. TPS and loxTPS) in Wilcoxon rank sum tests for a category; P-values were corrected for multiple testing using the Holm-Bonferroni method. There are no significant pairwise differences in these categories.

IS, internal standard; GLVs, green leaf volatiles; TAB, (E)-α-bergamotene; TBF, (E)-β-farnesene; —, not detected.

elife-04531-v2.xml

10.7554/eLife.04531.010

Table 2.

Composition and codon usage of E7 wt and mutant insert sequences

DOI: http://dx.doi.org/10.7554/eLife.04531.010

Region	Sequence (Symbol)	G+C content	CpG Total*	O/E ratio†,‡	UpA Total*	O/E ratio†,‡	Codon Usage
Region	Sequence (Symbol)	G+C content	CpG Total*	O/E ratio†,‡	UpA Total*	O/E ratio†,‡	CAI¶	ENc	CP Bias
1	Native (WT)	47.6%	51 (−)	0.730	62 (−)	0.742	0.685	56.5	−0.043
	Permuted (P)	47.6%	51 (0)	0.730	2 (0)	0.742	0.694	55.8	−0.025
	CpG/UpAL (cu)	47.5%	0 (−51)	0	19 (−43)	0.227	0.686	43.5	0.087
	Max-U	50.1%	47 (−4)	0.610	43 (−19)	0.573	0.708	49.6	0.328
	Min_E	47.5%	51 (0)	0.736	62 (0)	0.735	0.748	54.3	−0.131
	Min_U	47.5%	69 (+18)	0.992	76 (+14)	0.939	0.709	58.3	−0.134
	Min_H	49.8%	106 (+55)	1.400	79 (+17)	0.981	0.696	49.2	−0.130
2	Native (WT)	47.1%	18 (−)	0.320	48 (−)	0.695	0.743	53.2	0.015
	Permuted (P)	47.6%	18 (0)	0.320	48 (0)	0.695	0.739	49.0	0.013
	CpG/UpAL (cu)	48.5%	0 (−18)	0	48 (0)	0.214	0.739	47.2	0.118
	Max-U	46.3%	24 (+6)	0.440	43 (−3)	0.601	0.750	46.1	0.311
	Min-E	45.7%	18 (0)	0.343	48 (0)	0.657	0.785	53.3	−0.091
	Min-U	47.4%	37 (+19)	0.649	50 (+2)	0.738	0.767	57.6	−0.083
	Min-H	47.8%	68 (+50)	1.172	65 (+15)	0.970	0.715	49.7	−0.085

Total number of CpG and UpA dinucleotides in sequence. Changes in numbers between mutated and original WT sequence are indicated in parentheses.

†

Ratio of observed dinucleotide frequency (O) to that expected based on mononucleotide composition (E) that is, f(CpG)/f(C) × f(G).

‡

Values deliberately changed are shown in red (maximised) and blue (minimised).

Calculated from http://genomes.urv.es/CAIcal/ (Puigbo et al., 2008).

elife-04539-v2.xml

10.7554/eLife.04539.005

Table 1.

Direct repeat recombinant frequencies

DOI: http://dx.doi.org/10.7554/eLife.04539.005

Genotype	RTS1 orientation	Position of direct repeat	Colonies analysed	Ade⁺ His⁺ recombinant frequency (× 10⁻⁴)*		Ade⁺ His⁻ recombinant frequency (× 10⁻⁴)*
Genotype	RTS1 orientation	Position of direct repeat	Colonies analysed	Mean	p value†	Mean	p value†
wild type	IO	Flanking RTS1	77	1.36 (+/− 0.51)	–	3.48 (+/− 0.89)	–
wild type	AO	Flanking RTS1	77	134.03 (+/− 38.50)	–	113.41 (+/− 49.72)	–
rad52∆	IO	Flanking RTS1	15	0.03 (+/− 0.04)	<0.001‡	1.20 (+/− 0.21)	<0.001‡
rad52∆	AO	Flanking RTS1	15	0.13 (+/− 0.11)	<0.001§	4.07 (+/− 1.16)	<0.001§
ori-1253∆	IO	Flanking RTS1	15	2.33 (+/− 1.86)	0.060‡	4.80 (+/− 1.58)	0.007‡
ori-1253∆	AO	Flanking RTS1	16	339.88 (+/− 83.61)	<0.001§	221.02 (+/− 57.21)	<0.001§
wild type	IO	Site A	18	1.44 (+/− 0.86)	0.698‡	4.61 (+/− 1.66)	0.011‡
wild type	AO	Site A	21	128.66 (+/− 43.85)	0.746§	680.48 (+/− 305.44)	<0.001§
wild type	IO	Site B	18	0.88 (+/− 0.51)	0.023#	2.45 (+/− 1.88)	0.001#
wild type	AO	Site B	15	5.12 (+/− 2.41)	<0.001¶	85.02 (+/− 33.72)	<0.001¶
ori-1253∆	IO	Site B	15	1.58 (+/− 0.50)	<0.001**	4.86 (+/− 2.56)	0.006**
ori-1253∆	AO	Site B	15	86.03 (+/− 33.63)	<0.001††	1094.46 (+/− 443.32)	<0.001††

The values in parentheses are the standard deviations about the mean.

†

p values are derived from independent-sample t-tests comparing the mean values as indicated.

‡

Compared to the equivalent mean recombinant frequency in wild type with RTS1-IO flanked by ade6^- direct repeats.

Compared to the equivalent mean recombinant frequency in wild type with RTS1-AO flanked by ade6^- direct repeats.

Compared to the equivalent mean recombinant frequency in wild type with RTS1-IO and site A ade6^- direct repeats.

Compared to the equivalent mean recombinant frequency in wild type with RTS1-IO and site B ade6^- direct repeats.

††

Compared to the equivalent mean recombinant frequency in wild type with RTS1-AO and site B ade6^- direct repeats.

elife-04550-v2.xml

10.7554/eLife.04550.003

Table 1.

Virulence of the A. candida races on different plant host accessions

DOI: http://dx.doi.org/10.7554/eLife.04550.003

A. candida race	Arabidopsis thaliana		Brassica rapa		Brassica junceae		Brassica oleraceae
A. candida race	+	−	+	−	+	−	+	−
AcNc2	137	219	0	1	0	1	0	18
AcBoT	1*	34	0	1	0	2	15	0
Ac2V	1*,†	107	1‡	4‡	6‡	0‡	0	2

+ Host-pathogen compatible interactions (number of susceptible accessions).

− Host-pathogen incompatible interactions (number of resistant accessions).

A. thaliana Ws-eds1 (enhanced disease susceptibility) mutants were susceptible to all tested A. candida races.

†

In the laboratory conditions, the cotyledons of the A. thaliana accession Ws-3 were found to be susceptible to the Ac2V (Cooper et al., 2008).

‡

Data from (Rimmer et al., 2000) incorporated; in this study, one cultivar B. rapa (CrGC1-18, rapid-cycling accession) was infected by Ac2V race and four other tested cultivars (‘Torch’, ‘Colt’, ‘Horizon’, ‘Reward’) were incompatible with Ac2V race. All analysed cultivars of B. juncea (CrGC4-1S, ‘Burgonde’, ‘Domo’, ‘Cutlass’) were susceptible to Ac2V.

elife-04585-v2.xml

10.7554/eLife.04585.011

Table 2.

Summary of results from hypothesis-driven analyses conducted on 8 ms-IPI Experiment 1 and control Experiment 2 (IPI of 500 ms)

DOI: http://dx.doi.org/10.7554/eLife.04585.011

		Expt 1 (IPI 8 ms)				Expt 2 (IPI 500 ms)				Expt 1 vs Expt 2
		PMv-M1	AIP-PMv	pSPL-PMd	PMd-M1	PMv-M1	AIP-PMv	pSPL-PMd	PMd-M1	PMv-M1	AIP-PMv	pSPL-PMd	PMd-M1
Functional connectivity (fc)	grasp	t(13) = −2.59; p = 0.023*				t(13) = 0.94; p = 0.36				F(1,26) = 4.64; p = 0.041*
Functional connectivity (fc)	rest	t(14) = −0.07; p = 0.94				t(14) = 0.07; p = 0.95				n.a.
partial correlation fc	grasp	t(13) = −3.72; p = 0.003*	n.s.	n.s.	n.s.	t(13) = 1.00; p = 0.34	n.s.	n.s.	n.s.	F(1,26) = 7.76; p = 0.011*	n.s.	n.s.	n.s.
partial correlation fc	rest	t(14) = −0.07; p = 0.95	t(14) = −2.50; p = 0.025*	t(14) = 2.22; p = 0.04*	t(14) = 2.84; p = 0.013*	t(14) = −0.39; p = 0.70	t(14) = 1.08; p = 0.30	t(14) = −1.24; p = 0.24	t(14) = 0.47; p = 0.65	n.a.	F(1,28) = 7.15; p = 0.012*	F(1,28) = 5.29; p = 0.029*	F(1,28) = 5.92; p = 0.08
Psycho-physiological interaction (PPI)	grasp	t(13) = −4.78; p = 0.0004*				t(13) = 0.98; p = 0.35				F(1,26) = 6.92; p = 0.014*
Psycho-physiological interaction (PPI)	rest	t(14) = 0.08; p = 0.93				t(14) = 0.20; p = 0.85				n.a.
multiple regression PPI	grasp	t(13) = −2.53; p = 0.0064*	n.s.	n.s.	n.s.	t(13) = 1.18; p = 0.26	n.s.	n.s.	n.s.	F(1,26) = 7.47; p = 0.011*	n.s.	n.s.	n.s.
multiple regression PPI	rest	n.a.	t(14) = −2.55; p = 0.023*	t(14) = 1.78; p = 0.097	t(14) = 2.84; p = 0.013*	n.a.	t(14) = 0.41; p = 0.96	t(14) = −1.18; p = 0.26	t(14) = 0.01; p = 0.99	n.a.	F(1,28) = 5.74; p = 0.024*	F(1,28) = 3.66; p = 0.066	F(1,28) = 4.44; p = 0.044*

Analyses were conducted on rest and task data. Moreover in order to show that specific effects relate to plasticity induction (8 ms IPI) several higher-level analyses contrasting Experiment 1 and 2 are presented. T-tests were conducted as two-tailed paired t-tests (within subjects). Mixed-model ANOVAs were conducted between experiments (across subjects). Detailed information on all analyses is provided in the ‘Materials and methods’ section. Asterisks indicate significant results, p < 0.05. Abbreviations: n.s. = non-significant.

elife-04677-v1.xml

10.7554/eLife.04677.018

Table 2.

Decoding using PMd and M1 separately, all trials

DOI: http://dx.doi.org/10.7554/eLife.04677.018

	Forced-choice decoder performance (leave-one-out)			Decoder agreement
	Combined	PMd	M1	PMd-combined	M1-combined	PMd-M1
J1-T	0.99	0.99	0.90	0.92	0.85	0.80
J1-S	1.00	1.00	0.80	0.93	0.86	0.81
J2-T	0.98	0.97	0.80	0.96	0.87	0.86
J2-S	1.00	1.00	0.85	0.98	0.84	0.83
N1-S	0.90	0.84	0.95	0.93	0.72	0.67

Statistics for decoding choice from PMd and M1 data separately. Decoder performance refers to the fraction of trials for which the final decoded point agreed with the target that the animal reached to. This was assessed on forced-choice trials with delays of at least 300 ms, using leave-one-out cross-validation. Decoder agreement refers to the mean fraction of time points per trial for which the decoded choice was the same using the two datasets indicated. For this statistic, all successful trials with delay periods of at least 300 ms were included. ‘Combined’ refers to the decoder trained using both PMd and M1 data.

elife-04677-v1.xml

10.7554/eLife.04677.019

Table 3.

Decoding using PMd and M1 separately, free choice trials

DOI: http://dx.doi.org/10.7554/eLife.04677.019

	Free-choice decoder performance			Decoder agreement
	Combined	PMd	M1	PMd-combined	M1-combined	PMd-M1
J1-T	0.94	0.86	0.77	0.90	0.83	0.77
J1-S	0.96	0.94	0.89	0.86	0.82	0.73
J2-T	0.97	0.96	0.82	0.96	0.82	0.80
J2-S	0.95	0.95	0.86	0.98	0.78	0.78
N1-S	0.88	0.82	0.79	0.91	0.72	0.67

Same as Table 2, but only considering free-choice trials with delay periods of at least 300 ms. The decoders were trained using forced-choice trials.

elife-04970-v2.xml

10.7554/eLife.04970.011

Table 1.

Pause sites and their responses to H-NS and transcription factors

DOI: http://dx.doi.org/10.7554/eLife.04970.011

Pause position	Pausing				Termination			Sequence
Pause position	H-NS	RfaH	GreB	GreA	Rho	Rho + H-NS	Rho + NusG	Pause↓
C134	↑	?	?	?	?	?	?	CGCUGAUAACUCAAGC	UUUCUUCCUG
G162	↑	↓	↓	?	–	–	–	AAUUAAGGCUGAACUG	AAAUUUUAUU
U169	↑	–	↓	↓	–	–	↑	GCUGAACUGAAAUUUU	AUUAAUUGCA
C213	↑	–	↓	↓	–	–	–	GCGUGACACCUGCAAC	AUCCUCCAUA
C220	↑	↓	–	↓	–	–	–	ACCUGCAACAUCCUCC	AUAUUUCCGC
U226	↑	↓	–	↓	–	–	–	AACAUCCUCCAUAUUU	CCGCUCAUUU
C346	↑↑↑	–	↓	–	–	↑	–	UAGCUGGAACUCUUUC	GGGUAAAGCC
C370	–	↓	–	↓	↑	–	–	CCGCUGGAUAUCCCAC	AGCAACGGGU
C393, G394	↑	↓	↓	↓	–	↑	↑	GGUUGGGCAGCAACAC	GUUUUGCUGA
U588, U589	↑↑↑	–	↓	↓	↑	–	–	UCAAGGCAUACUCUUU	UUCUAUUCCA
A593	–	–	–	–	–	–	–	GCAUACUCUUUUUCUA	UUCCACUUGA
G624	↑	↓	↓	↓	–	–	–	UUCUUUCGCCAGCGCG	UUUUUGAAAG
G643	↑	–	↓	↓	–	–	–	UUGAAAGCCAAUUCCG	CGCCCCAUGA
A746, U747	–	–	↓	–	↑	–	↑	GCAAGGACCUUUUUUA	UAAACAAAAA
G926	↑	–	–	–	–	?	?	AAUAUGACCAUGCUCG	CAGUUAUUAA
U996	↑	–	↓	↓	–	?	?	CCAAUAAUUAAGUUAU	UGGGAUUUGU
U1011	↑	↓	↓	↓	–	?	?	UUGGGAUUUGUCUGGU	GAAUUAUUUG
U1022, U1024	↑	↓	↓	↓	–	?	?	GUCUGGUGAAUUAUUU	GUCGCUAUCU
U1079 (ops)	–	–	↓	↓	↑	?	?	CUAGUGGCGGUAGCGU	GCUUUUUUCA

Pause positions are given as 3′ RNA nucleotide identity and distance from the transcription start site as mapped by high-resolution PAGE (Figure 2—figure supplement 1). ↑, increased pause or termination. ↓, decreased pause or termination. In the sequences shown, pause 3′ ends are bold (under arrow) and the position corresponding to the incoming NTP is underlined.

elife-05005-v1.xml

10.7554/eLife.05005.014

Table 1.

The 26 features considered in the models, highlighting the 14 robustly selected through stepwise regression (bold)

DOI: http://dx.doi.org/10.7554/eLife.05005.014

Feature	Abbreviation	Description	Frequency chosen
Feature	Abbreviation	Description	8mer	7mer-m8	7mer-A1	6mer
miRNA
3′-UTR target-site abundance	TA_3UTR	Number of sites in all annotated 3′ UTRs (Arvey et al., 2010; Garcia et al., 2011)	100%	100%	100%	100%
ORF target-site abundance	TA_ORF	Number of sites in all annotated ORFs (Garcia et al., 2011)	9.4%	0.7%	68.1%	93.4%
Predicted seed-pairing stability	SPS	Predicted thermodynamic stability of seed pairing (Garcia et al., 2011)	100%	100%	100%	100%
sRNA position 1	sRNA1	Identity of nucleotide at position 1 of the sRNA	68%	100%	99.7%	97.7%
sRNA position 8	sRNA8	Identity of nucleotide at position 8 of the sRNA	0%	0.8%	100%	100%
Site
Site position 1	site1	Identity of nucleotide at position 1 of the site	N/A	57.1%	N/A	2%
Site position 8	site8	Identity of nucleotide at position 8 of the site	0.8%	95.1%	99.4%	100%
Site position 9	site9	Identity of nucleotide at position 9 of the site (Lewis et al., 2005; Nielsen et al., 2007)	15.4%	7.1%	0.9%	93.7%
Site position 10	site10	Identity of nucleotide at position 10 of the site (Nielsen et al., 2007)	0.1%	100%	8.5%	26.3%
Local AU content	local_AU	AU content near the site (Grimson et al., 2007; Nielsen et al., 2007)	100%	100%	100%	100%
3′ supplementary pairing	3P_score	Supplementary pairing at the miRNA 3′ end (Grimson et al., 2007)	42.5%	100%	100%	100%
Distance from stop codon	dist_stop	log₁₀(Distance of site from stop codon)	62.4%	10.8%	8.7%	25.7%
Predicted structural accessibility	SA	log₁₀(Probability that a 14 nt segment centered on the match to sRNA positions 7 and 8 is unpaired)	100%	100%	100%	100%
Minimum distance	min_dist	log₁₀(Minimum distance of site from stop codon or polyadenylation site) (Gaidatzis et al., 2007; Grimson et al., 2007; Majoros and Ohler, 2007)	99.9%	100%	87.4%	100%
Probability of conserved targeting	P_CT	Probability of site conservation, controlling for dinucleotide evolution and site context (Friedman et al., 2009)	100%	100%	100%	20.8%
mRNA
5′-UTR length	len_5UTR	log₁₀(Length of the 5′ UTR)	98.2%	8.2%	4.6%	17.2%
ORF length	len_ORF	log₁₀(Length of the ORF)	100%	100%	100%	100%
3′-UTR length	len_3UTR	log₁₀(Length of the 3′ UTR) (Hausser et al., 2009)	100%	100%	100%	100%
5′-UTR AU content	AU_5UTR	Fraction of AU nucleotides in the 5′ UTR	13%	38.9%	91.1%	31.3%
ORF AU content	AU_ORF	Fraction of AU nucleotides in the ORF	1.2%	72.4%	28.4%	35.8%
3′-UTR AU content	AU_3UTR	Fraction of AU nucleotides in the 3′ UTR (Robins and Press, 2005; Hausser et al., 2009)	5.4%	73.3%	65.3%	80.6%
3′-UTR offset-6mer sites	off6m	Number of offset-6mer sites in the 3′ UTR (Friedman et al., 2009)	65.9%	89.6%	99.8%	100%
ORF 8mer sites	ORF8m	Number of 8mer sites in the ORF (Lewis et al., 2005; Reczko et al., 2012)	99.5%	99.1%	100%	100%
ORF 7mer-m8 sites	ORF7m8	Number of 7mer-m8 sites in the ORF (Reczko et al., 2012)	4.7%	4.3%	85.3%	100%
ORF 7mer-A1 sites	ORF7A1	Number of 7mer-A1 sites in the ORF (Reczko et al., 2012)	68.4%	34.2%	97.8%	98.4%
ORF 6mer sites	ORF6m	Number of 6mer sites in the ORF (Reczko et al., 2012)	91%	13.3%	0.7%	36.7%

The feature description does not include the scaling performed (Table 3) to generate more comparable regression coefficients.

elife-05005-v1.xml

10.7554/eLife.05005.023

Table 3.

Scaling parameters used to normalize data to the (0, 1) interval

DOI: http://dx.doi.org/10.7554/eLife.05005.023

Feature	8mer		7mer-m8		7mer-A1		6mer
Feature	5th %	95th %	5th %	95th %	5th %	95th %	5th %	95th %
3P_score	1.000	3.500	1.000	3.500	1.000	3.500	1.000	3.500
SPS	−11.130	−5.520	−11.130	−5.490	−8.410	−3.330	−8.570	−3.330
TA_3UTR	3.113	3.865	3.067	3.887	3.145	3.887	3.113	3.887
Len_3UTR	2.392	3.637	2.409	3.615	2.413	3.630	2.405	3.620
Len_ORF	2.788	3.753	2.773	3.729	2.773	3.730	2.775	3.731
Min_dist	1.415	3.113	1.491	3.096	1.431	3.117	1.477	3.106
Local_AU	0.308	0.814	0.277	0.782	0.342	0.801	0.295	0.772
SA	−4.356	−0.661	−5.218	−0.725	−4.230	−0.588	−5.082	−0.666
P_CT	0.000	0.816	0.000	0.364	0.000	0.449	0.000	0.193

Provided are the 5th and 95th percentile values for continuous features that were scaled, after the values of the feature were appropriately transformed as indicated (Table 1).

elife-05075-v1.xml

10.7554/eLife.05075.002

Table 1.

Frequency of inclusion of species in titles and abstracts of published papers

DOI: http://dx.doi.org/10.7554/eLife.05075.002

10.7554/eLife.05075.003Table 1—source data 1.Is the species name mentioned in the title, impact statement, abstract and digest of eLife papers (July–Sept 2014)?

DOI: http://dx.doi.org/10.7554/eLife.05075.003

Journal	Issues	# of articles*	Is the species included in the title?			If not included in the title, is the species included in the abstract?			Species not included in title or abstract%
Journal	Issues	# of articles*	Yes	No	% No	Yes	No	% No	Species not included in title or abstract%
Nature Genetics	Jan–Apr 2012	52	19	33	65	24	9	27	17
	June–Sept 2014	60	20	40	67	32	8	20	13
Cell	Feb–May 2012	96	13	83	90	46	37	45	39
	July–Sept 2014	82	18	64	78	29	35	55	43
Science	Mar–May 2012	54	22	32	59	21	11	34	20
	July–Sept 2014	59	29	30	51	20	10	33	17
PNAS	Mar–May 2012	252	111	141	56	72	69	49	27
	July 2014	119	49	70	59	36	34	49	29
PLOS Genetics	Apr–May 2012	107	56	51	48	46	5	10	5
	Aug–Sept 2014	82	44	38	46	31	7	18	9
Hum Mol Genetics	Apr–June 2012	67	26	41	61	35	6	15	9
eLife	Mar–June 2014	105	23	82	78	34	44	54	42
	July–Sept 2014	93	27	66	71	32	34	52	37

Only biological articles are included.

elife-05166-v1.xml

10.7554/eLife.05166.004

Table 1.

Characteristics of patients included in the analysis and distribution of lineages

DOI: http://dx.doi.org/10.7554/eLife.05166.004

	Lineage				Overall	p*
	1	2	3	4	Overall	p*
Overall	269 (16.0)	74 (4.4)	205 (12.2)	1139 (67.5)	1687
Age
<20	9 (12.3)	7 (9.6)	9 (12.3)	48 (65.7)	73
20–29	46 (10.3)	26 (5.8)	48 (10.7)	327 (73.2)	447
30–39	109 (18.4)	17 (2.9)	81 (13.7)	386 (65.1)	593
40–49	61 (19.8)	18 (5.8)	39 (12.7)	190 (61.7)	308
50+	44 (16.5)	6 (2.3)	28 (10.5)	188 (70.7)	266	0.001
Sex
Female	130 (14.6)	47 (5.3)	94 (10.6)	617 (69.5)	888
Male	139 (17.4)	27 (3.4)	111 (13.9)	522 (65.3)	799	0.02
Year
1995–1998	55 (15.5)	8 (2.3)	29 (8.2)	263 (74.1)	355
1999–2001	43 (11.5)	23 (6.1)	43 (11.5)	266 (70.9)	375
2002–2004	80 (19.4)	22 (5.3)	54 (13.1)	257 (62.2)	413
2005–2007	54 (17.4)	11 (3.5)	44 (14.2)	202 (65.0)	311
2008–2010	37 (15.9)	10 (4.3)	35 (15.0)	151 (64.8)	233	0.004
TB type
Smear+	212 (17.3)	52 (4.3)	156 (12.8)	804 (65.7)	1224
Smear−	46 (12.1)	19 (5.0)	38 (10.0)	276 (72.8)	379
Extrapulmonary	11 (13.1)	3 (3.6)	11 (13.1)	59 (70.2)	84	0.1
HIV status
Negative	47 (10.8)	23 (5.3)	57 (13.0)	310 (70.9)	437
Positive	148 (19.3)	28 (3.6)	107 (13.9)	486 (63.2)	769	0.001
Previous TB
No	251 (16.7)	66 (4.4)	171 (11.4)	1019 (67.6)	1507
Yes	18 (10.0)	8 (4.4)	34 (18.9)	120 (66.7)	180	0.007
Isoniazid resistance
Resistant	20 (17.2)	0 (0.0)	21 (18.1)	75 (64.7)	116
Sensitive	244 (15.9)	74 (4.8)	181 (11.8)	1033 (67.4)	1532	0.03
Residence
Karonga	198 (16.4)	53 (4.4)	148 (12.3)	806 (66.9)	1205
Malawi	48 (16.6)	13 (4.5)	32 (11.1)	196 (67.8)	289
Other country	11 (11.5)	7 (7.3)	17 (17.7)	61 (63.5)	96	0.4
Birth place
Karonga	174 (17.0)	46 (4.5)	135 (13.2)	667 (65.3)	1022
Malawi	55 (16.3)	14 (4.1)	31 (9.2)	238 (70.4)	338
Other country	34 (11.7)	14 (4.8)	37 (12.7)	206 (70.8)	291	0.2

From Χ² comparison between lineages.

elife-05166-v1.xml

10.7554/eLife.05166.012

Table 2.

Characteristics associated with disease due to recent infection

DOI: http://dx.doi.org/10.7554/eLife.05166.012

Characteristic	Linked/Total		Association with links (unadjusted)	p (lrtest)	Adjusted for age, sex, year, lineage	Adjusted for other variables included in model*	p (lrtest)
Characteristic	n/N	%	OR (95% CI)	p (lrtest)	OR (95% CI)	OR (95% CI)	p (lrtest)
Overall	409/1074	38.1
Lineage
1	56/183	30.6	0.76 (0.53–1.1)		0.81 (0.57–1.2)	0.81 (0.57–1.2)
2	34/52	65.4	3.2 (1.8–5.9)		3.0 (1.6–5.4)	3.2 (1.7–5.8)
3	58/129	45.0	1.4 (0.96–2.1)		1.5 (1.0–2.2)	1.5 (1.0–2.2)
4	261/710	36.8	1	<0.001	1	1	<0.001
Age
<20	19/36	65.8	2.9 (1.4–6.0)		2.5 (1.2–5.4)	2.6 (1.2–5.6)
20–29	113/276	45.8	1.8 (1.2–2.7)		1.6 (1.1–2.5)	1.8 (1.2–2.8)
30–39	152/404	39.6	1.5 (1.0–2.3)		1.5 (0.99–2.2)	1.6 (1.0–2.3)
40–49	81/201	44.2	1.7 (1.1–2.7)		1.0 (1.0–2.6)	1.7 (1.1–2.6)
50+	44/157	33.5	1	0.007†	1	1	0.03†
Sex
Female	229/575	39.8	1
Male	180/499	36.1	0.85 (0.67–1.1)	0.05	0.93 (0.72–1.2)	0.94 (0.72–1.2)	0.4
Year
1999–2001	141/311	45.3	1		1	1	<0.001†
2002–2004	117/322	36.3	0.69 (0.50–0.95)		0.73 (0.52–1.0)	0.69 (0.50–0.97)
2005–2007	92/244	37.7	0.73 (0.52–1.0)		0.78 (0.55–1.1)	0.70 (0.49–1.0)
2008–2010	59/197	30.0	0.52 (0.35–0.75)	0.001†	0.53 (0.36–0.77)	0.48 (0.32–0.70)
TB type
Smear-positive pulmonary	312/821	38.0	1		1
Smear-negative pulmonary	97/253	38.3	1.0 (0.76–1.4)	0.9	0.95 (0.71–1.3)
HIV status
HIV−	102/283	36.0	1
HIV+ no ART	173/436	39.7	1.2 (0.85–1.6)		1.1 (0.75–1.5)
HIV+ on ART	27/77	35.1	0.96 (0.56–1.6)	0.5	1.0 (0.56–1.8)
INH resistance
No	375/979	38.3	1		1
Yes	28/64	43.8	1.3 (0.75–2.1)	0.4	1.4 (0.81–2.3)
Unknown
Recent residence
Karonga	328/816	40.2	1			1	0.005
Other Malawi	56/176	31.8	0.69 (0.49–0.98)		0.58 (0.41–0.84)	0.58 (0.40–0.84)
Other country	16/54	29.6	0.63 (0.34–1.1)	0.04	0.48 (0.26–0.91)	0.48 (0.26–0.91)
Birth place
Karonga	267/659	40.5	1		1
Other Malawi	81/227	35.7	0.81 (0.60–1.1)		0.79 (0.57–1.1)
Other country	59/180	32.8	0.72 (0.51–1.0)	0.1	0.67 (0.47–0.97)

In this analysis individuals are defined as linked (‘backwards links’) using the cut-offs described in the text and if the closest link was with a patient within the previous 5 years. Extrapulmonary, recurrent cases, and cases before 1999 were excluded. Odds ratios (OR) calculated using logistic regression.

In this model a dummy variable was used for the 32 individuals with missing data on recent residence.

†

Test for trend.

elife-05166-v1.xml

10.7554/eLife.05166.013

Table 3.

Characteristics associated with transmissibility

DOI: http://dx.doi.org/10.7554/eLife.05166.013

Characteristic	Any Linked/Total		Association with links	p	Adjusted for age, sex, year, lineage, smear status	p (lrtest)
Characteristic	n/N	%	OR (95% CI)	p	OR (95% CI)	p (lrtest)
Overall	431/1346	32.0
Lineage
1	59/217	27.2	0.87 (0.63–1.2)		0.94 (0.66–1.3)
2	27/61	44.3	1.7 (1.0–2.7)		1.9 (1.1–3.2)
3	65/154	42.2	1.6 (1.2–2.3)		1.9 (1.4–2.7)
4	280/914	30.6	1	0.006	1	<0.001
Age
<20	20/50	40.0	2.3 (1.2–4.4)		1.9 (0.98–3.7)
20–29	134/349	38.4	2.3 (1.5–3.3)		2.2 (1.5–3.3)
30–39	159/490	32.5	1.7 (1.2–2.5)		2.0 (1.3–2.9)
40–49	71/238	29.8	1.6 (1.0–2.4)		1.7 (1.1–2.7)
50+	47/219	21.5	1	<0.001	1	0.002
Sex
Female	239/718	33.3	1		1
Male	192/628	30.6	0.87 (0.69–1.1)	0.2	0.93 (0.73–1.2)	0.5
Year
1995–1998	159/314	50.6	1		1
1999–2001	119/345	34.5	0.49 (0.36–0.66)		0.42 (0.31–0.58)
2002–2004	95/389	24.4	0.30 (0.22–0.41)		0.27 (0.19–0.37)
2005–2007	58/298	19.5	0.22 (0.16–0.32)	<0.001	0.20 (0.14–0.29)	<0.001
TB type
Smear pos pulm	338/1003	33.7	1		1
Smear neg pulm	93/343	27.1	0.72 (0.55–0.94)	0.01	0.73 (0.55–0.96)	<0.001
HIV status
HIV−	91/318	28.6	1		1
HIV+ no ART	170/540	31.5	1.1 (0.83–1.5)		1.1 (0.81–1.6)
HIV+ on ART	11/48	22.9	0.70 (0.35–1.4)	0.3	1.4 (0.62–3.1)	0.6
Previous TB
No	391/1200	32.6	1		1
Yes	40/146	27.4	0.77 (0.53–1.1)	0.2	0.85 (0.58–1.3)	0.4
INH resistance
No	402/1237	32.5	1		1
Yes	29/100	29.0	0.86 (0.55–1.3)	0.5	0.86 (0.54–1.4)	0.5
Recent residence
Karonga	284/942	30.2	1		1
Other Malawi	80/234	34.2	1.2 (0.89–1.6)		1.0 (0.74–1.4)
Other country	20/74	27.0	0.88(0.52–1.5)	0.4	0.57 (0.33–0.98)	0.09
Birth place
Karonga	276/811	34.0	1		1
Other Malawi	80/272	29.4	0.83 (0.62–1.1)		0.82 (0.60–1.1)
Other country	64/234	27.4	0.77 (0.56–1.1)	0.2	0.71 (0.51–0.99)	0.08

The numbers of likely transmissions (‘forward links’) were compared by individual characteristics using ordered logistic regression. Extrapulmonary cases and cases occurring after 2007 were excluded.

elife-05255-v1.xml

10.7554/eLife.05255.013

Table 2.

Correlation between methylation levels and environment-of-origin variables (Hancock et al., 2011)

DOI: http://dx.doi.org/10.7554/eLife.05255.013

Environmental variable	Growing temp.	CG			CHG			CHH
Environmental variable	Growing temp.	r	rho	p-value	r	rho	p-value	r	rho	p-value
Latitude	10	0.69	0.52	7.8E-11	−0.24	−0.19	2.7E-02	0.10	0.14	1.1E-01
Latitude	16	0.62	0.47	3.2E-07	−0.21	−0.20	4.2E-02	0.04	−0.11	2.5E-01
Longitude	10	0.59	0.54	1.2E-11	−0.14	−0.09	3.1E-01	0.23	0.28	7.5E-04
Longitude	16	0.55	0.53	4.4E-09	−0.12	−0.03	7.4E-01	0.14	0.15	1.2E-01
Temperature seasonality	10	0.68	0.49	1.6E-09	−0.27	−0.24	4.8E-03	0.09	0.09	2.8E-01
Temperature seasonality	16	0.62	0.42	1.1E-05	−0.23	−0.26	6.6E-03	0.04	−0.12	2.1E-01
Max. temp. (warmest month)	10	−0.14	0.06	4.6E-01	−0.07	−0.13	1.3E-01	0.14	0.20	2.0E-02
Max. temp. (warmest month)	16	−0.03	0.10	2.9E-01	−0.10	−0.20	3.8E-02	0.05	0.03	7.3E-01
Min. temp. (coldest month)	10	−0.70	−0.56	9.1E-13	0.27	0.21	1.2E-02	−0.07	−0.06	4.7E-01
Min. temp. (coldest month)	16	−0.63	−0.48	2.7E-07	0.24	0.24	1.4E-02	0.00	0.19	5.6E-02
Precipitation (wettest month)	10	0.45	0.52	1.2E-10	−0.25	−0.27	1.2E-03	−0.20	−0.12	1.7E-01
Precipitation (wettest month)	16	0.29	0.43	4.0E-06	−0.26	−0.24	1.2E-02	−0.22	−0.19	5.8E-02
Precipitation (driest month)	10	0.31	0.40	1.5E-06	−0.33	−0.29	6.5E-04	−0.24	−0.21	1.6E-02
Precipitation (driest month)	16	0.21	0.32	7.4E-04	−0.26	−0.24	1.4E-02	−0.15	−0.18	6.0E-02
Precipitation seasonality	10	0.42	0.44	7.1E-08	−0.07	−0.16	5.4E-02	0.05	0.01	9.0E-01
Precipitation seasonality	16	0.36	0.37	1.2E-04	−0.13	−0.16	1.1E-01	0.01	−0.01	9.1E-01
PAR (spring)	10	0.04	0.22	8.9E-03	0.20	0.18	3.7E-02	0.24	0.23	7.3E-03
PAR (spring)	16	0.03	0.18	6.6E-02	0.27	0.21	3.5E-02	0.38	0.35	2.8E-04
Length of growing season	10	−0.59	−0.57	5.5E-13	0.24	0.23	7.3E-03	−0.16	−0.18	3.3E-02
Length of growing season	16	−0.58	−0.54	4.0E-09	0.23	0.21	3.0E-02	−0.04	0.01	8.9E-01
No. consecutive cold days	10	0.60	0.53	4.0E-11	−0.19	−0.13	1.2E-01	0.17	0.28	1.1E-03
No. consecutive cold days	16	0.57	0.53	4.2E-09	−0.17	−0.09	3.7E-01	0.10	0.08	4.1E-01
No. consecutive frost-free days	10	−0.59	−0.49	1.2E-09	0.29	0.27	1.5E-03	0.02	0.03	7.1E-01
No. consecutive frost-free days	16	−0.51	−0.39	4.9E-05	0.30	0.30	1.6E-03	0.07	0.13	1.9E-01
Relative humidity (spring)	10	0.62	0.47	5.6E-09	−0.23	−0.18	3.9E-02	0.09	0.06	4.5E-01
Relative humidity (spring)	16	0.53	0.37	1.2E-04	−0.20	−0.26	7.6E-03	0.04	−0.08	4.3E-01
Daylength (spring)	10	0.69	0.50	7.2E-10	−0.27	−0.21	1.4E-02	0.08	0.05	5.7E-01
Daylength (spring)	16	0.63	0.41	1.5E-05	−0.23	−0.29	2.7E-03	0.04	−0.17	8.7E-02
Aridity	10	0.53	0.49	8.4E-10	−0.35	−0.31	1.9E-04	−0.18	−0.21	1.3E-02
Aridity	16	0.43	0.42	8.4E-06	−0.28	−0.24	1.3E-02	−0.13	−0.20	3.8E-02

r = Pearson's correlation, rho = Spearman's rank correlation, p-value = significance of rho.

PAR = photosynthetically active radiation.

elife-05423-v2.xml

10.7554/eLife.05423.007

Table 2.

Mapping of me69 on chromosome I

DOI: http://dx.doi.org/10.7554/eLife.05423.007

No. F2s*	WBVar 00240 394†	WBVar 00240 397	WBVar 00240 399	WBVar 00155 231	WBVar 00240 416	WBVar 00240 407	WBVar 00159 097	WBVar 00240 414	WBVar 00161 629
No. F2s*	825026	5482531	6351803	8646304	10614690	11472093	12433167	13066381	14154889
16	B/B				B/B				B/B
6	H/B				B/B				B/B
2	H/B	B/B	B/B	B/B	B/B	B/B	B/B	H/B	H/B
3	B/B	B/B	B/B	B/B	B/B	B/B	B/B	H/B	H/B
1	H/B	H/B	H/B	B/B	B/B	B/B	B/B	B/B	B/B

F2 males from the cross described in Table 1 were scored for SNPs across chromosome I. Animals were either homozygous Bristol (B/B) or heterozygous for the Hawaiian allele (H/B) at each SNP.

Number of F2 males showing each pattern.

†

SNP designation and genomic position on chromosome I. Wicks et al. (2001); WormBase.

elife-05604-v1.xml

10.7554/eLife.05604.031

Table 4.

PCA comparison of GSL profiles produced by GSL genotypes from synthetic laboratory population grown in the chamber and all three environments

DOI: http://dx.doi.org/10.7554/eLife.05604.031

Environment	PCA1 = 48.5%		PCA2 = 29%		PCA3 = 16%		PCA4 = 6%
Environment	R	p value	R	p value	R	p value	R	p value
Chamber	1.00		1.00		1.00		1.00
UCD2012	0.97	<0.001	0.97	<0.001	0.82	<0.001	0.96	<0.001
UWY2011	0.91	<0.001	0.95	<0.001	0.74	<0.001	0.97	<0.001
UWY2012	0.90	<0.001	0.91	<0.001	0.85	<0.001	0.86	<0.001

Glucosinolate analysis was conducted on the 17 genotypes within a Long-day growth chamber (16 hr light) set to match the median light regime for the three environmments. Principal component analysis was conducted on the mean glucosinolate accumulation for the aliphatic glucosinoles within the chamber environment. This creates a set of mathematical descriptors of the chemotype variation across the 17 genotypes. The first three eigenvectors were used to generate scores from the lsmeans of the glucosinolates across the 17 glucosinolate genotypes independently for the chamber and three different field environments values. These scores were then correlated to test if the GSL profiles were similar or not across the environments. The R of the correlation to the Chamber scores for the 17 genotypes for each of the three PCA vectors are shown in conjunction with the p value as determined by Pearson correlation. To the right of each PCA vector label is shown the fraction of total variance approximated by the given vector. In total, the four vectors describe >99% of the GSL profile variance.

elife-05607-v2.xml

10.7554/eLife.05607.011

Table 5.

Correlation between human GWAS candidate gene expression in mouse liver and adipose tissue with hepatic TG level

DOI: http://dx.doi.org/10.7554/eLife.05607.011

	Liver		Adipose
	r	p	r	p
Pnpla3	0.07	0.423	−0.04	0.645
Gckr	0.19	0.044*	0.14	0.156
Ncan	−0.10	0.316	0.37	6.1 × 10-5*
Tm6sf2	0.15	0.123	−0.23	0.012*
Lyplal1	0.27	0.003*	−0.12	0.228
Trib1	−0.10	0.313	0.24	0.012*

Denotes p < 0.05.

elife-05660-v2.xml

10.7554/eLife.05660.005

Table 1.

Summary of data from electrophysiological recordings and locomotion analyses

DOI: http://dx.doi.org/10.7554/eLife.05660.005

		Evoked EPSC Amp. (nA)	Endogenous EPSC		Locomotion speed (µm/s)
		Evoked EPSC Amp. (nA)	Frequency (Hz)	Amp. (pA)	Locomotion speed (µm/s)
Wild type (N2)		3.2 ± 0.2 (n = 23)	49.8 ± 2.5 (n = 30)	22.4 ± 1.0	140 ± 8 (n = 65)
unc-26 (s1710)	–	0.9 ± 0.1 (n = 15)†	12.0 ± 1.5 (n = 16)†	20.7 ± 0.6	28 ± 3 (n = 65)†
	Si[Prab-3::unc-26::gfp]	3.1 ± 0.2 (n = 16)#	50.8 ± 5.4 (n = 16)#	23.2 ± 1.4	139 ± 8 (n = 60)#
	Si[Prab-3::unc-26∆PRD::gfp]	3.4 ± 0.3 (n = 16)#	47.4 ± 5.0 (n = 17)#	24.8 ± 1.3	141 ± 10 (n = 60)#
	Ex[Psnb-1::mSYJ1∆PRD]	3.1 ± 0.3 (n = 7)#	49.6 ± 6.1 (n = 11)#	21.5 ± 0.6	143 ± 10 (n = 37)#
	Ex[Prab-3::gfp::unc-26(C378S,D380N)]	3.5 ± 0.2 (n = 10)#	53.1 ± 6.6 (n = 10)	23.8 ± 1.3	135 ± 9 (n = 60)#
	Ex[Prab-3::gfp::unc-26∆PRD(C378S,D380N)]	3.2 ± 0.3 (n = 10)#	50.7 ± 5.7 (n = 10)	24.2 ± 0.9	130 ± 9 (n = 60)#
	Ex[Prab-3::gfp::unc-26(D716A)]	0.8 ± 0.1 (n = 14)	10.0 ± 1.8 (N = 15)	20.9 ± 0.8	28 ± 3 (n = 60)
	Ex[Prab-3::gfp::unc-26∆Sac1]	1.2 ± 0.2 (n = 10)	7.2 ± 1.9 (N = 10)	21.3 ± 1.2	31 ± 3 (n = 60)
	Ex[Prab-3::unc-26Sac1 + Prab-3::unc-26∆Sac1]	1.0 ± 0.2 (n = 10)	16.1 ± 1.8 (n = 10)	20.4 ± 0.5	32 ± 3 (n = 60)
	Ex[Prab-3::unc-26Sac1::IntN + Prab-3::IntC::unc-26∆Sac1]	3.2 ± 0.4 (n = 10)#	53.1 ± 7.1 (n = 10)#	24.8 ± 1.2	100 ± 7 (n = 60)#
	Ex[Prab-3::unc26∆Sac1::rab-3]	1.0 ± 0.2 (n = 10)	13.2 ± 2.3 (n = 10)	20.4 ± 0.9
	Ex[Prab-3::unc-26∆Sac1::snb-1]	1.4 ± 0.2 (n = 11)	17.9 ± 2.6 (n = 11)	21.1 ± 0.8
	Ex[Prab-3::bem1PX::unc-26∆Sac1]	0.8 ± 0.1 (n = 7)	6.3 ± 0.6 (n = 7)	18.8 ± 1.2
	Ex[Prab-3::plc∂PH::unc-26∆Sac1]	1.0 ± 0.2 (n = 7)	8.5 ± 1.8 (n = 7)	18.7 ± 1.1
	Ex[Prab-3::btkPH::unc-26∆Sac1]	1.2 ± 0.2 (n = 11)	11.4 ± 1.2 (n = 11)	18.4 ± 0.8
	Ex[Prab-3::apa-2::unc-26∆Sac1]	1.1 ± 0.1 (n = 11)	12.8 ± 1.8 (n = 11)	19.4 ± 0.8
	Ex[Prab-3::apb-1::unc-26∆Sac1]	0.9 ± 0.1 (n = 11)	13.2 ± 2.5 (n = 11)	18.2 ± 1.5
	Ex[Prab-3::apm-2::unc-26∆Sac1]	1.1 ± 0.1 (n = 10)	15.3 ± 2.7 (n = 10)	21.0 ± 0.9
	Ex[Prab-3::aps-2::unc-26∆Sac1]	1.3 ± 0.2 (n = 9)	12.7 ± 1.4 (n = 9)	20.1 ± 0.9
	Ex[Prab-3::unc-57::unc-26∆Sac1]	2.5 ± 0.3 (n = 11)#	28.0 ± 4.1 (n = 11)§	23.0 ± 1.4
	Ex[Prab-3::dyn-1::unc-26∆Sac1]	1.3 ± 0.3 (n = 10)	14.4 ± 2.9 (n = 10)	19.4 ± 0.9
	Ex[Prab-3::itsn-1::unc-26∆Sac1]	0.9 ± 0.1 (n = 9)	13.9 ± 1.4 (n = 9)	21.5 ± 1.4
	Ex[Prab-3::unc-57::unc-26∆Sac1∆PRD]	3.0 ± 0.3 (n = 11)#	36.7 ± 5.4 (n = 11)§	21.7 ± 1.3
	Ex[Prab-3::unc-57::unc-26∆Sac1(D716A)]	0.8 ± 0.2 (n = 9)	13.0 ± 2.3 (n = 9)	21.0 ± 0.7
	Ex[Prab-3::unc-57BAR::unc-26∆Sac1]	2.9 ± 0.2 (n = 12)#	23.9 ± 2.5 (n = 12)#	21.3 ± 0.8
	Ex[Prab-3::rEndoBAR::unc-26∆Sac1]	3.1 ± 0.4 (n = 13)#	28.5 ± 4.6 (n = 13)#	24.1 ± 1.4
	Ex[Prab-3::mAmphBAR::unc-26∆Sac1]	1.4 ± 0.2 (n = 10)	19.2 ± 2.3 (n = 10)	20.8 ± 0.8
	Ex[Prab-3::mNadrin2BAR::unc-26∆Sac1]	1.7 ± 0.2 (n = 11)‡	16.1 ± 3.1 (n = 11)	23.8 ± 1.9
	Ex[Prab-3::rEndoBAR∆N::unc-26∆Sac1]	1.3 ± 0.2 (n = 12)	9.1 ± 0.9 (n = 12)	18.9 ± 0.4
	Ex[Prab-3::rEndoBAR(K76E,K78E)::unc-26∆Sac1]	1.5 ± 0.2 (n = 10)	13.5 ± 1.3 (n = 10)	19.3 ± 0.7
N2	Prab-3::unc-26∆PRD(D716A) overexpression	1.5 ± 0.3 (n = 9)*	24.6 ± 3.8 (n = 10)*	25.7 ± 0.9
	Prab-3::unc-26∆PRD overexpression	2.9 ± 0.3 (n = 9)	53.5 ± 4.6 (n = 9)	25.4 ± 1.3
	Prab-3::unc-26∆Sac1∆PRD(D716A) overexpression	3.5 ± 0.3 (n = 10)	49.0 ± 7.5 (n = 10)	25.9 ± 1.9
unc-57(e406); unc-26(s1710)	–	0.8 ± 0.2 (n = 9)†	8.6 ± 0.8 (n = 10)†	21.9 ± 1.1	27 ± 3 (n = 60)†
	Si[Psnb-1::unc-57∆SH3::mCherry]; Si[Prab-3::unc-26∆PRD::gfp]	3.2 ± 0.2 (n = 9)¶	50.3 ± 4.1 (n = 9)¶	23.1 ± 1.0	142 ± 9 (n = 62)¶
	Si[Psnb-1::rEndoBAR::unc-26∆Sac1∆PRD]	3.0 ± 0.3 (n = 10)¶	50.9 ± 4.1 (n = 10)¶	26.5 ± 1.1	109 ± 4 (n = 68)¶

p < 0.001 when compared with N2.

†

p < 0.0001 when compared with N2.

‡

p < 0.05 when compared with unc-26 mutant.

p < 0.001 when compared with unc-26 mutant.

p < 0.0001 when compared with unc-26 mutant.

p < 0.0001 when compared with unc-57; unc-26 double mutants.

Si: single-copy transgene (MosSci insertion).

Ex: extrachromosomal array.

‘Amp.’ indicates amplitude.

elife-05914-v1.xml

10.7554/eLife.05914.011

Table 1.

Analysis and stereological parameters of tibia proximal region in WT and gal-8 Tg mice

DOI: http://dx.doi.org/10.7554/eLife.05914.011

	In vivo CT		In vitro CT
	WT (n = 7)	Tg (n = 7)	WT (n = 5)	Tg (n = 5)
BV/TV	0.40 ± 0.02	0.25 ± 0.03**	0.12 ± 0.01	0.04 ± 0.01**
Tb.N (1/mm)	3.19 ± 0.02	1.86 ± 0.25**	3.86 ± 0.51	1.68 ± 0.34**
Tb.Sp (mm)	0.19 ± 0.01	0.48 ± 0.08**	0.24 ± 0.03	0.68 ± 0.18*
BMD (%)	100% ± 15%	52% ± 5%**	100% ± 8%	68% ± 6%**

14-week-old WT and Tg mice (n = 7 each group) were scanned using a small animal in vivo μCT scanner. Tibial bones were removed from 16-week-old WT and Tg mice (n = 5 each group) and scanned using an in vitro CT scanner. Analysis was performed on the proximal region of the tibia. The parameters calculated are Tb.N (trabecular number), Tb.Sp (trabecular separation), BV/TV (bone volume/tissue volume), and BMD (bone mineral density). Results shown are mean values ± SEM. BMD is given as relative to the average BMD of WT mice (**p < 0.01 vs WT mice).

elife-06303-v2.xml

10.7554/eLife.06303.005

Table 1.

Atypical cells: quantitation of denticle polarities in relation to neighbouring cells showing the effect of the Ds/Ft system

DOI: http://dx.doi.org/10.7554/eLife.06303.005

Wild type				ds⁻ ft⁻
Anterior neighbour	Denticle polarity of atypical Row 2 cells†		Posterior neighbour	Anterior neighbour	Denticle polarity of atypical Row 2 cells§		Posterior neighbour
Anterior neighbour	Anteriorly	Posteriorly	Posterior neighbour	Anterior neighbour	Anteriorly	Posteriorly	Posterior neighbour
T1 cell	0	52	Row 3 cell	T1 cell	16	21	Row 3 cell
Row 2 cell	0	35	Row 3 cell	Row 2 cell	14	13	Row 3 cell

Anterior neighbour	Denticle polarity of atypical Row 4 cells‡		Posterior neighbour	Anterior neighbour	Denticle polarity of atypical Row 4 cells¶		Posterior neighbour
Anterior neighbour	Anteriorly	Posteriorly	Posterior neighbour	Anterior neighbour	Anteriorly	Posteriorly	Posterior neighbour
Row 3 cell	110	8*	T2 cell	Row 3 cell	54*	37	T2 cell
Row 3 cell	8**	41	Row 4 cell	Row 3 cell	24	20**	Row 4 cell

†

Denticles of 29 atypical cells.

‡

Denticles of 27 atypical cells. 8 of 8* (and 6 of 8**) were predenticles located in ambiguous positions and their denticles were arbitrarily allocated to those classes favouring the null hypothesis. Fisher exact test p-value: <2.2⁻¹⁶.

Denticles of 23 atypical cells. Fisher exact test p-value: 0.6135.

Denticles of 24 atypical cells. 1 of 54* (and 1 of 20**) were predenticles located in ambiguous positions and their denticles were arbitrarily allocated to those classes disfavouring the null hypothesis. Fisher exact test p-value: 0.7104.

Numbers in bold emphasise the main result of the table that is, the effect of neighbours on denticle polarities in the wildtype. This effect does not exist in the mutant larvae.

elife-06322-v1.xml

10.7554/eLife.06322.012

Table 1.

Clinical characteristics and genetic causes of 134 index patients with PK

DOI: http://dx.doi.org/10.7554/eLife.06322.012

	Genetic causes of 134 index patients with PK
	MVK (39*)	PMVK (9)	MVD (62*)	FDPS (4)	Unknown (21)
Sex
Male	27	9	38	1	17
Female	12	0	24	3	4
Number of lesions
0–10	4	4	0	0	6
10–100	20	5	13	0	5
100–500	5	0	39	0	5
>500†	10	0	10	4	5
Diameter of lesions
Minimum	2 mm	5 mm	1 mm	1 mm	1 mm
Maximum	20 cm	5 cm	2 cm	1 cm	2 cm
Age of onset
At birth	0	0	0	0	3
0–20	23	4	20	1	0
20–40	12	3	28	1	9
40–60	3	1	12	2	5
>60	1	1	2	0	4
Variants of PK
DSAP/DSP	26	0	56	4	10
SFP	0	0	6	0	0
PM	23	9	0	0	6
HPM	13	3	1	0	0
Giant plaque of PPt	19	0	0	0	0
Genital PK (localized)	0	4	0	0	0
Porokeratoma	0	5	0	0	0
LP	1	1	3	0	5
Comorbidity
Psoriasis vulgaris	4	0	2	0	0

One PK patient (proband of family-28, female), who has both the mutation c. 235G>A (MVK) and the mutation c. 746T>C (MVD), was included in both MVK and MVD groups.

†

The number of lesions is more than 500.

DSAP, disseminated superficial actinic porokeratosis; DSP, disseminated superficial porokeratosis; HPM, hyperkeratotic porokeratosis, LP, linear porokeratosis, PK, porokeratosis; PM, porokeratosis of Mibelli, PPt, porokeratosis ptychotropica; SFP, solar facial porokeratosis.

elife-06328-v2.xml

10.7554/eLife.06328.012

Table 1.

Acyl-chain composition of PC species with changed levels in LPCAT3-deficient mice

DOI: http://dx.doi.org/10.7554/eLife.06328.012

PC subclass	Acyl-chain composition	LPCAT3+/+ peak area		LPCAT3−/− peak area		KO/WT (%)	p value
PC subclass	Acyl-chain composition	Mean	SEM	Mean	SEM	KO/WT (%)	p value
34:4	14:0–20:4	32,607	1253	11,609	835	36	<0.0001
34:4	16:1–18:3	42,145	2574	41,340	4555	98	0.8816
36:4	16:0–20:4	1,037,887	21,426	917,642	8844	88	0.0008
	18:1–18:3	122,575	8421	61,410	1726	50	0.0001
	18:2–18:2	366,675	17,961	250,350	26,185	68	0.0064
36:5	16:0–20:5	147,054	8925	3872	1095	3	<0.0001
	16:1–20:4	104,768	7773	79,851	4883	76	0.0265
	18:2–18:3	36,381	3669	16,762	1790	46	0.0013
38:4	16:0–22:4	81,093	6150	169,849	9408	209	<0.0001
	18:0–20:4	670,488	23,121	624,853	18,289	93	0.1602
	18:1–20:3	230,517	10,302	108,788	8009	47	<0.0001
	18:2–20:2	29,789	1587	14,567	701	49	<0.0001
40:4	16:0–24:4	10,392	1617	20,865	3072	201	0.0167
	18:0–22:4	176,325	4788	293,832	6785	167	<0.0001
	18:1–22:3	22,450	2704	62,145	3805	277	<0.0001
	20:0–20:4	12,131	1265	6590	899	54	0.0073
	20:1–20:3	32,191	2591	4991	1740	16	<0.0001
40:5	16:0–24:5	1535	1258	5381	1162	350	0.0549
	18:0–22:5	110,752	7361	163,723	14,186	148	0.0106
	18:1–22:4	39,603	2862	117,362	5425	296	<0.0001
	20:1–20:4	58,465	3767	32,595	2075	56	0.0003
42:4	18:0–24:4	1907	403	12,412	1762	651	0.0004
	18:1–24:3	1663	777	9584	639	576	<0.0001
	18:2–24:2	4497	950	1587	605	35	0.0736
	22:0–20:4	11,180	930	5039	1154	45	0.0032
42:5	18:0–24:5	3092	629	14,907	882	482	<0.0001
	18:1–24:4	1258	405	11,476	858	912	<0.0001
	22:1–20:4	25,450	2790	11,728	1853	46	0.0035

SRM analyses for discrimination of fatty acids were performed for the indicated PC species (n = 5). Anions of the fatty acids indicated at the second position (e.g., 20:4 for 14:0–20:4 PC) were used for selection at Q3. Sample concentration was adjusted based on tissue weight.

elife-06328-v2.xml

10.7554/eLife.06328.014

Table 2.

Acyl-chain composition of PE species with changed levels in LPCAT3-deficient mice

DOI: http://dx.doi.org/10.7554/eLife.06328.014

PE subclass	Acyl-chain composition	LPCAT3+/+ peak area		LPCAT3−/− peak area		KO/WT (%)	p value
PE subclass	Acyl-chain composition	Mean	SEM	Mean	SEM	KO/WT (%)	p value
38:4	16:0–22:4	373,458	20,239	1,073,902	50,565	288	<0.0001
	18:0–20:4	8,394,810	381,499	4,349,617	102,271	52	<0.0001
	18:1–20:3	1,503,041	38,884	689,131	14,846	46	0.0002
40:4	18:0–22:4	1,831,032	80,319	3,803,421	98,424	208	<0.0001
	18:1–22:3	124,638	4846	236,224	23,357	190	0.0016
	20:0–20:4	187,358	8687	45,797	4286	24	<0.0001
	20:1–20:3	35,837	3019	11,721	2388	33	0.0002
40:5	18:0–22:5	523,416	4657	2,056,845	111,780	393	<0.0001
	18:1–22:4	731,947	43,088	1,934,984	35,746	264	<0.0001
	20:1–20:4	224,759	3572	64,708	3066	29	<0.0001

SRM analyses for discrimination of fatty acids were performed for the indicated PE species (n = 5). Anions of the fatty acids indicated at the second position (e.g., 22:4 for 16:0–22:4 PE) were used for selection at Q3. Sample concentration was adjusted based on tissue weight.

elife-06356-v1.xml

10.7554/eLife.06356.004

Table 1.

Identification of all active brain regions in adults and infants following acute noxious stimulation at all stimulus intensities (applied force: adults 32–512 mN; infants 32–128 mN)

DOI: http://dx.doi.org/10.7554/eLife.06356.004

				Adults							Infants
		Anatomical area	Region	Peak Z within cluster	MNI coords			Rank	Slope of regression (*E-03)	P val*	Peak Z within cluster	Neonate template coords			Rank	Slope of regression (*E-03)	P val*
		Anatomical area	Region	Peak Z within cluster	x	y	z	Rank	Slope of regression (*E-03)	P val*	Peak Z within cluster	x	y	z	Rank	Slope of regression (*E-03)	P val*
Active regions in both adults and infants	Intensity encoding regions (in adults)	Temporal gyrus	Contra	3.92	64	−34	20	1	1.01	0.0002	3.05	32	−32	12	1	2.46	0.0083
		Cingulate gyrus	Anterior	4.11	6	4	40	2	0.65	0.0005	2.58	−1	1	26	11	1.01	0.3971
		Opercular cortex	Contra	5.60	40	6	10	3	0.63	0.0001	3.38	32	−13	19	2	2.23	0.0391
		Insula	Contra	4.18	34	14	6	4	0.61	0.0001	3.04	19	−22	23	3	2.15	0.0207
		Supramarginal gyrus	Contra	4.33	64	−38	20	5	0.60	0.0008	3.29	25	−23	39	9	1.08	0.1749
		Postcentral gyrus	Contra	4.28	58	−18	22	6	0.60	0.0012	3.85	15	−22	52	10	1.01	0.2667
		Visual cortex	Contra	3.62	44	−62	4	7	0.59	0.0004	3.25	21	−52	34	6	1.41	0.0814
		Putamen	Contra	3.68	22	6	6	8	0.55	0.0001	3.30	17	−17	18	8	1.20	0.1656
		Thalamus	Contra	3.51	14	−14	0	9	0.50	0.0010	3.58	6	−16	15	4	1.91	0.0592
		Insula	Ipsi	4.67	−38	−18	14	10	0.49	0.0001	2.59	−26	−14	14	5	1.69	0.1015
		Supplementary motor area	Contra	3.91	8	4	46	11	0.39	0.0008	3.50	6	−18	48	7	1.23	0.2315
	Non intensity encoding regions (in adults)	Cerebellum	Ipsi	3.88	−20	−66	−44		0.35	0.0029	3.53	−3	−46	−6		3.57	0.0164
		Temporal gyrus	Ipsi	3.72	−52	−56	10		0.18	0.5487	3.41	−32	−22	14		2.90	0.0196
		Supramarginal gyrus	Ipsi	4.59	−64	−28	20		0.51	0.0035	3.13	−31	−24	30		2.79	0.0055
		Cerebellum	Contra	3.36	20	−70	−50		0.31	0.0246	3.16	2	−44	−6		2.72	0.1634
		Opercular cortex	Ipsi	5.23	−50	−28	26		0.50	0.0018	2.69	−27	−12	13		2.23	0.0710
		Postcentral gyrus	Ipsi	4.71	−62	−18	24		0.44	0.0375	3.52	−31	−15	41		2.12	0.0845
		Thalamus	Ipsi	3.52	−12	−14	10		0.42	0.0018	3.48	−1	−20	13		1.67	0.1009
		Angular gyrus	Ipsi	3.59	−58	−50	18		0.53	0.0107	2.98	−23	−39	33		1.56	0.0528
		Precentral gyrus	Ipsi	4.01	−58	0	10		0.43	0.0578	3.46	−23	−17	48		1.53	0.1247
		Frontal gyrus	Contra	3.88	58	12	0		0.56	0.0212	3.11	11	−12	48		1.42	0.0646
		Cingulate gyrus	Posterior	3.71	−14	−28	38		0.08	0.2480	3.18	−9	−23	35		1.42	0.1101
		Angular gyrus	Contra	3.71	60	−46	18		0.54	0.0080	3.12	22	−51	35		1.42	0.0407
		Precuneous cortex	Contra	3.60	16	−68	40		0.38	0.0714	3.70	5	−30	52		1.19	0.1623
		Visual cortex	Ipsi	3.82	−52	−70	10		−0.09	0.3758	2.59	−7	−40	11		1.17	0.1657
		Brainstem		3.86	10	−26	−8		0.33	0.1710	2.99	−3	−27	−10		1.11	0.4350
		Parietal lobule	Contra	3.10	20	−44	68		0.61	0.1097	3.10	27	−24	46		1.09	0.1271
		Putamen	Ipsi	3.63	−16	10	−2		0.45	0.0023	3.13	−14	−14	19		0.92	0.2813
		Supplementary motor area	Ipsi	3.55	−6	4	44		0.40	0.0219	3.16	−4	−10	46		0.91	0.3903
		Precentral Gyrus	Contra	4.05	58	4	8		0.44	0.0276	3.76	6	−20	53		0.88	0.2672
		Frontal gyrus	Ipsi	3.57	−8	22	32		−0.24	0.1954	2.79	−13	−9	50		0.70	0.4820
		Pallidum	Contra	3.40	16	−4	−4		0.49	0.0071	2.84	13	−13	13		0.64	0.4863
Active regions in adults only		Amygdala	Contra	3.49	20	−2	−14		0.69	0.0160
		Amygdala	Ipsi	4.28	−20	−2	−12		0.43	0.0860
		Orbitofrontal cortex	Ipsi	3.40	−18	4	−16		0.42	0.0157	no activity
		Orbitofrontal cortex	Contra	3.57	34	30	−2		0.44	0.0460
Active regions in infants only		Precuneous cortex	Ipsi								3.80	−1	−26	52		1.26	0.1699
		Pallidum	Ipsi								3.16	−8	−5	14		0.59	0.4787
		Parietal lobule	Ipsi								3.31	−28	−23	33		0.99	0.2711
		Auditory cortex	Contra								2.89	26	−14	18		3.07	0.0119
		Auditory cortex	Ipsi								3.34	−17	−29	19		2.56	0.0304
		Caudate	Contra	no activity							3.61	13	−17	22		0.59	0.5822
		Caudate	Ipsi								3.47	−7	−8	18		1.05	0.3415
		Hippocampus	Contra								2.61	21	−25	9		1.84	0.1288
		Hippocampus	Ipsi								2.77	−15	−31	9		1.00	0.3326
		Parahippocampus	Contra								3.02	11	−23	0		1.53	0.3740
		Parahippocampus	Ipsi								2.99	−7	−24	−8		0.19	0.9013

elife-06426-v1.xml

10.7554/eLife.06426.005

Table 1.

Univariate group-results for seed-to-voxel connectivity of PRC and PHC seeds with the EC

DOI: http://dx.doi.org/10.7554/eLife.06426.005

	Cluster	Cluster	Cluster	Peak	Peak coordinate (template)			Side
	P_FWE-corr	P_FDR-corr	Size	Z-score	x	y	z	Side
Experiment 1
PRC seed	<0.001	<0.001	517	5.05	153	149	8	R
PRC seed	<0.001	<0.001	273	4.82	108	146	12	L
PHC seed	<0.001	<0.001	380	5.29	150	129	9	R
PHC seed	<0.001	<0.001	510	5.05	106	138	12	L
PRC > PHC	0.038	0.022	42	4.31	151	150	8	R
PRC > PHC	0.001	0.001	91	4.04	101	146	9	L
PHC > PRC	0.008	0.005	61	4.15	150	131	10	R
PHC > PRC	0.001	0.002	87	3.53	108	136	11	L
Experiment 2
PRC seed	<0.001	<0.001	777	4.82	109	152	20	L
PRC seed	<0.001	<0.001	849	4.73	149	145	10	R
PHC seed	<0.001	<0.001	669	5.31	147	137	13	R
PHC seed	<0.001	<0.001	637	4.91	107	139	14	L
PRC > PHC	<0.001	<0.001	167	4.70	105	153	15	L
PHC > PRC	0.022	0.024	66	4.09	153	130	9	R
PHC > PRC	0.047	0.026	53	3.74	108	136	18	L

Entorhinal subregions showing significant functional connectivity (one-sample t-test) or differential connectivity (paired t-test) with bilateral PRC or PHC seeds (Z > 2.3, p_cluster <0.05, N_{Exp. 1} = 15, N_{Exp. 2} = 14). Single-subject beta maps were normalized on the group-specific T1-template and masked with a manually defined EC ROI. The EC covered 26 coronal slices on the template (y = 154: most anterior slice, y = 129: most posterior slice), with coronal slices being oriented orthogonal to the hippocampal long-axis. See also Figure 1 and Figure 1—figure supplement 1.

elife-06434-v1.xml

Figure 1B
	Mean	Assumed variance				Assumed N
		2%	15%	28%	40%	Assumed N
Let-7b levels in LAPC4 CD44⁺ cells	30%	0.6	4.5	8.4	12	3
miR-34 levels in LAPC4 CD44⁺ cells	3%	0.06	0.45	0.84	1.2	3

elife-06487-v2.xml

10.7554/eLife.06487.006

Table 1.

Summary of the characteristics of cheetah-prey pursuits with prey nominally ranked in order of mass (top smallest to bottom largest)

DOI: http://dx.doi.org/10.7554/eLife.06487.006

Prey	Chase parameters
	No. hunts	Success	Total duration (s)		No. of turns		Turn rate (Hz)
	N	%	Mean	SD	Mean	SD	Mean	SD
Hare	2	100	10.8	–	5		0.5	0.26
Steenbok	19	53	28.7	11.9	5.47	2.97	0.32	0.19
Duiker	1	100	–	–	–	–	–	–
Springbok	7	57	28.3	7	6.17	3.06	0.32	0.17
Ostrich	1	100	–	–	–	–	–	–
Wildebeest	2	50	35	3.2	6.5	0.71	0.22	0.09
Gemsbok	4	75	18.6	10.6	2.33	1.53	0.15	0.05

Two species were pursued where no corresponding acceleration data were available.

elife-06576-v1.xml

10.7554/eLife.06576.006

Table 1.

SS-induced changes in amplitude of low-frequency fluctuations (ALFF); SS group vs Saline group; p < 0.001 corrected for multiple comparisons

DOI: http://dx.doi.org/10.7554/eLife.06576.006

Brain region	Left		Right
Brain region	Cluster size	t-value	Cluster size	t-value
ALFF increased
ACx	167	3.812	178	3.746
IC	72	3.383	68	3.473
MGB	52	3.432	48	3.339
SSCx	37	3.383	40	3.402
VCx	32	3.342	39	3.312
SC	40	4.123	43	4.094
AMY	61	4.192	60	3.923
RN/PnO	35	3.249	28	3.290
PnO/PMr	12	3.498	10	3.313
PFL	38	3.349	37	3.292
CB4	38	3.349	37	3.292
ALFF decreased
HIP	108	−4.087	92	−4.002
CPu	72	−3.772	71	−3.741

Abbreviations: auditory cortex (ACx), inferior colliculus (IC), medial geniculate body (MGB), somatosensory cortex (SSCx), visual cortex (VCx), superior colliculi (SC), amygdala (AMY), gigantocellular reticular nucleus (RN), pontine reticular nucleus oral (PnO), paramedian raphe nucleus (PMr), parafloccular lobe of cerebellum (PFL), cerebellum lobule 4 (CB4), hippocampus (HIP), caudate-putamen (CPu), sodium salicylate (SS).

elife-06576-v1.xml

10.7554/eLife.06576.009

Table 2.

SS-induced increases in functional connectivity (FC); p < 0.001 corrected for multiple comparisons

DOI: http://dx.doi.org/10.7554/eLife.06576.009

Seed region	Brain region	Left		Right
Seed region	Brain region	Cluster size	t-value	Cluster size	t-value
ACx	MGB	62	3.900	70	3.859
	IC	82	3.912	88	3.632
	AMY	67	3.897	68	3.839
	RN	52	3.983	48	3.902
	PFL	39	3.992	35	3.954
	CB4	51	4.066	53	4.070
MGB	ACx	195	4.074	210	4.084
MGB	HIP	162	4.032	178	4.109
IC	MGB	72	4.098	60	4.013
IC	HIP	140	4.064	131	3.904

Abbreviations: medial geniculate body (MGB), inferior colliculus (IC), amygdala (AMY), reticular nucleus (RN), parafloccular lobe of cerebellum (PFL), cerebellum lobule 4 (CB4), auditory cortex (ACx), hippocampus (HIP), sodium salicylate (SS).

elife-06638-v1.xml

10.7554/eLife.06638.007

Table 1.

Protein intact mass MS analysis

DOI: http://dx.doi.org/10.7554/eLife.06638.007

Protein	Vector	Molecular mass (Da)
Protein	Vector	Calculated	Observed	Δ
SfbI-A40-TED	pOPIN-F*	24,156.9	24,139.6	−17.3
SfbI-A40-TED:Cys109Ala	pOPIN-F*	24,124.9	24,124.7	−0.2
SfbI-A346-TED	pDEST†	24,835.8	24,818.2	−17.6
SfbI-A346-TED:Cys103Ala	pOPIN-E‡	25,626.6	25,626.3	−0.3
SfbI-A20-TED	pOPIN-E‡	25,996.1	25,978.5	−17.6
SfbI-A20-TED:Cys97Ala	pOPIN-E‡	25,964.1	25,963.6	−0.5
GfbA-TED	pDEST†	24,382.4	24,364.7	−17.7
FbaB-TED	pOPIN-F*	21,683.0	21,665.6	−17.4
FbaB-TED:Cys94Ala	pOPIN-E§	22,447.7	22,447.5	−0.2
Cpa-TED2	pOPIN-F*	22,377.8	22,360.5	−17.3
CpTIE-TED	pOPIN-F*	21,261.0	21,243.7	−17.3
CpTIE-TED:Cys138Ala	pOPIN-F*	21,228.9	21,227.8	−1.1
CodTIE-TED	pOPIN-F*	25,011.6	24,994.3	−17.3
CodTIE-TED:Cys157Ala	pOPIN-F*	24,979.5	24,979.1	−0.4
PnTIE-TED	pDEST†	25,779.0	25,761.7	−17.3
PnTIE-TED:Cys94Ala	pHisTEV†	25,746.9	25,746.5	−0.4
BaTIE-TED	pHisTEV†	28,541.1	28,523.7	−17.4
SaTIE-TED	pHisTEV†	33,167.9	33,151.3	−16.6
CdTEP-TED	pHisTEV#	46,363.7	46,345.7	−18.0

Non-native residues remaining after 3C cleavage: N-terminal GP.

†

Non-native residues remaining after TEV cleavage: N-terminal GAM.

‡

Non-native residues remaining: N-terminal M, C-terminal KHHHHHH.

Non-native residues remaining: C-terminal KHHHHH only. N-terminal M removed.

Non-native residue remaining after TEV cleavage: N-terminal M.

elife-06638-v1.xml

10.7554/eLife.06638.010

Table 2.

X-ray data collection and refinement statistics

DOI: http://dx.doi.org/10.7554/eLife.06638.010

(A) CpTIE-TED and CpTIE-TED:Cys138Ala
	CpTIE-TED	CpTIE-TED:Cys138Ala	Iodide
	Native	Native	Iodide
Data collection
Space group	P1	P2₁2₁2	P2
Cell dimensions
a, b, c (Å)	70.82, 74.36, 82.81	98.42, 110.72, 68.77	97.91, 110.63, 68.45
α, β, γ (°)	107.32, 104.32, 98.63	90, 90, 90	90, 90, 90
Resolution (Å)*	44.88–2.62 (2.69–2.62)	44.97–1.60 (1.64–1.60)	58.21–2.83 (2.90–2.83)
R_merge	13.3 (76.4)	5.4 (74.4)	19.5 (101.8)
I/σI	7.5 (1.8)	31.6 (4.3)	22.7 (4.4)
Completeness (%)
Overall	98.0 (97.3)	100 (99.9)	98.2 (97.3)
Anomalous			98.1 (96.2)
Redundancy
Overall	4.7 (4.9)	18.1 (18.1)	33.3 (33.0)
Anomalous			17.5 (16.8)
CC(1/2) (%)	99.3 (58.9)	100 (90.9)	99.8 (86.0)
Refinement
Resolution (Å)	44.8–2.62 (2.69–2.62)	44.97–1.60 (1.64–1.60)
No. reflections	42,485 (3115)	94,622 (6864)
R_work/R_free	19.6/22.6 (35.1/33.7)	17.7/21.0 (20.5/22.0)
No. atoms
Protein	8260	6310
Ligand/ion/water	36	403
B-factors
Protein	50.9	24.5
Ligand/ion/water	37.8	28.5
R.m.s deviations
Bond lengths (Å)	0.014	0.013
Bond angles (°)	1.60	1.57
MolProbity Score	1.11 (100th percentile)	1.13 (99th percentile)

(B) SfbI-A40-TED and PnTIE-TED
	SfbI-A40-TED	PnTIE-TED
	Native/Zinc	Native	Iodide
Data collection
Space group	I4₁	P4₁2₁2	P4₁2₁2
Cell dimensions
a, b, c (Å)	165.12, 165.12, 42.52	59.86, 59.86, 121.70	59.37, 59.37, 122.4
α, β, γ (°)	90, 90, 90	90, 90, 90	90, 90, 90
Resolution (Å)†	52.22–1.35 (1.39–1.35)	42.67–1.30 (1.32–1.30)	31.22–2.80 (2.95–2.80)
R_merge	5.3 (75.4)	5.4 (30.4)	13.3 (35.7)
I/σI	18.7 (2.7)	33.8 (7.4)	24.9 (13.0)
Completeness (%)
Overall	99.9 (99.1)	93.6 (62.7)	100 (100)
Anomalous	99.6 (97.5)		100 (100)
Redundancy
Overall	9.2 (9.1)	23.9 (11.9)	32.8 (31.9)
Anomalous	4.6 (4.6)		18.1 (16.6)
CC(1/2) (%)	99.9 (85.2)	100 (96.2)	99.6 (99.2)
Refinement
Resolution (Å)	52.22–1.35 (1.39–1.35)	53.71–1.30 (1.33–1.30)
No. reflections	119869 (8679)	48,978 (2374)
R_work/R_free	13.1/15.3 (22.6/22.9)	11.9/15.1 (12.6/15.9)
No. atoms
Protein	3389	1848
Ligand/ion/water	470	252
B-factors
Protein	23.0	12.5
Ligand/ion/water	39.4	26.9
R.m.s deviations
Bond lengths (Å)	0.012	0.012
Bond angles (°)	1.53	1.50
MolProbity Score	1.06 (99th percentile)	1.11 (98th percentile)

The highest resolution shell is shown in parenthesis.

†

The highest resolution shell is shown in parenthesis.

elife-06738-v1.xml

10.7554/eLife.06738.003

Table 1.Selection of regions associated with the posterior-medial (PM) and the anterior-temporal (AT) system (<xref ref-type="bibr" rid="bib34">Libby et al., 2012</xref>).

The coordinates of the PM system reflect peak voxel coordinates of a seed-based connectivity contrast of right parahippocampal cortex > right perirhinal cortex connectivity reported by Libby et al. (Libby et al., 2012). The coordinates of the AT system reflect peak voxel coordinates of a seed-based connectivity contrast of right perirhinal cortex > right parahippocampal cortex connectivity. Coordinates are in MNI space.

DOI: http://dx.doi.org/10.7554/eLife.06738.003

	Left hemisphere			Left hemisphere
	x	y	z	x	y	z
PM System
Medial posterior occipital cortex (BA 18)	–	–	–	14	−72	8
Occipital pole (BA 17)	−16	−96	22	–	–	–
Parahippocampal cortex	−12	−42	−8	22	−32	−8
Posterior cingulate cortex (BA 29)	−4	−46	4	10	−44	10
Posterior hippocampus	−20	−30	−2	18	−36	0
Posterior thalamus	−20	−34	0	22	−30	6
Retrosplenial cortex (BA 30)	−16	−52	−4	22	−46	0
AT System
Dorsolateral prefrontal cortex (BA 9)	−24	60	24	18	58	24
Dorsomedial prefrontal cortex (BA 8)	−2	−60	34	–	–	–
Frontal polar cortex (BA 10)	–	–	–	40	60	−2
Lateral precentral gyrus (BA 6)	–	–	–	54	4	10
Medial prefrontal cortex (BA 8)	−2	−60	34	–	–	–
Orbitofrontal cortex (BA 11/47)	−6	16	−22	8	22	−20
Postcentral gyrus (BA 4)	–	–	–	62	−10	16
Posterior superior temporal gyrus (BA 22)	−62	−34	14	–	–	–
Rostrolateral prefrontal cortex (BA 10)	–	–	–	38	60	−12
Temporal polar cortex (BA 38)	–	–	–	34	22	−36
Ventrolateral prefrontal cortex (BA 44/45)	−56	6	18	–	–	–

elife-06808-v2.xml

10.7554/eLife.06808.007

Table 1.

Parameter values for the models shown in Figures 3, 6, 7

DOI: http://dx.doi.org/10.7554/eLife.06808.007

	Model wild-type	Model shi2-1	Model SHI ox-5	Model CKX2oe	Model IPT1oe
	(Figure 3F)	(Figure 6A)	(Figure 6B)	(Figure 7A)	(Figure 7B)
H_apex	µ = 80, σ = 20	µ = 48, σ = 12	µ = 240, σ = 60
H	µ = 20, σ = 4.5	µ = 12, σ = 2.7	µ = 60, σ = 13.5
T	µ = 3.0, σ = 0.8			µ = 0.45, σ = 0.2	µ = 5.4, σ = 0.8
ν	0.01
K_A	0.05
K_B	0.05

Parameter µ represents the mean and σ the variance of the normally distributed stochastic variables H and T. Parameter values left blank are identical to the wild-type model.

elife-06808-v2.xml

10.7554/eLife.06808.008

Table 2.

Refitted parameter values for the models shown in Figure 9

DOI: http://dx.doi.org/10.7554/eLife.06808.008

	Model wild-type	Model 10 µM DDG	Model 25 µM DDG
	(Figure 9A)	(Figure 9B)	(Figure 9C)
H_apex	μ = 30, σ = 10
H	μ = 5, σ = 1.5
T	μ = 0.7, σ = 0.2
ν	0.002
K_A	0.025	0.045	0.07
K_B	0.025	0.045	0.07

elife-07166-v2.xml

10.7554/eLife.07166.010

Table 1.

Electrophysiological parameters of SPs and LPs listed in the order they appear in the main text

DOI: http://dx.doi.org/10.7554/eLife.07166.010

Parameter	Patch clamp		Suction electrode
Parameter	SPs	LPs	SPs
V_dark (mV)	−43.2 ± 0.7 (n = 30)	−45.9 ± 1.1 (n = 10)	–
IR_membrane (MΩ)	518 ± 41 (n = 8)	442 ± 68 (n = 9)	–
τ_membrane (ms)	31.9 ± 4.9 (n = 8)[]_a	12.9 ± 1.3 (n = 9) [***]_a	–
Max response (mv)	30	32	–
i_1/2 (520 nm ph·µm⁻²); control	149 ± 25 (n = 10) []_b	1.9 × 10⁵ ± 1.1 × 10⁵ (n = 7) []_c	–
i_1/2 (520 nm ph·µm⁻²); regenerated	63 ± 11 (n = 12) [**]_b	2385 ± 513 (n = 7) [*]_c	–
Sensitivity 520/590; control	4.4 ± 0.9 (n = 5) []_d	1.1 ± 0.04 (n = 6) []_e	–
Sensitivity 520/590; regenerated	5.6 ± 1.0 (n = 5) [n.s.]_d	1.8 ± 0.1 (n = 7) [**]_e	–
Integration time, dim flash (s); control	0.32 ± 0.05 (n = 13) []_f	–	–
Integration time, dim flash (s); regenerated	0.81 ± 0.14 (n = 9) [***]_f	–	1.45 ± 0.10 (n = 10)
TTP at i_1/2 (s); regenerated	0.29 ± 0.04 (n = 11) []_g	0.11 ± 0.007 (n = 10) [***]_g	–
τ_rec at i_1/2 (s); regenerated	1.05 ± 0.27 (n = 11) []_h	0.12 ± 0.02 (n = 10) [***]_h	–
i_1/2 (λ_max ph·µm⁻²); regenerated	63 ± 11 (n = 12) []_i	777 ± 167 (n = 7) [***]_i	–
Dim-flash sensitivity (mV·ph⁻¹·µm²); regenerated	0.61 ± 0.17 (n = 8)	–	–
Dim-flash sensitivity (%·ph⁻¹·µm²); regenerated	3.0 ± 0.6 (n = 8)	–	–
a (pA); regenerated	–	–	0.41 ± 0.04 (n = 10)
a_% (%·R^{* −1}); regenerated	2.6 ± 0.5 (n = 8)	–	2.6 ± 0.3 (n = 10)
SNR; regenerated	–	–	1.5 ± 0.1 (n = 10)
I_dark (pA); regenerated	13 ± 3 (n = 4)	–	16 ± 1 (n = 10)
Collecting area (µm²·R^*·ph⁻¹); regenerated	–	–	0.83 ± 0.17 (n = 10)
Amplification constant (s⁻²); regenerated	–	–	0.59 ± 0.09 (n = 10)

Values are given as ‘mean ± SEM (sample size) [statistical significance]_{identifier letter}’; n.s.: not significant; *p < 0.05; **p < 0.01; ***p < 0.001; V_dark: dark membrane potential; IR_membrane: input resistance; τ_membrane: membrane time constant; i_1/2: half-maximal response flash strength; TTP: time-to-peak; τ_rec: decay time constant; a: absolute single photon response; a_%: fractional single photon response; SNR: signal-to-noise ratio; I_dark: dark current; SPs: short photoreceptors; LPs: long photoreceptors.

elife-07432-v2.xml

10.7554/eLife.07432.012

Table 2.

Localization of the cross-links identified in Mot1:TBP:DNA:NC2 complex

DOI: http://dx.doi.org/10.7554/eLife.07432.012

10.7554/eLife.07432.013Table 2—source data 1.

Full list of the detected cross-links.

DOI: http://dx.doi.org/10.7554/eLife.07432.013

Experiment	Crystal structure	Within Mot1^CTD		Latch-crystal structure	Latch– Mot1^CTD	Crystal structure– Mot1^CTD	Total	Decoy§	Estimated FDR [%]
Experiment	Crystal structure	Intralobe*	Interlobe^†	Latch-crystal structure	Latch– Mot1^CTD	Crystal structure– Mot1^CTD	Total	Decoy§	Estimated FDR [%]
ADP·BeF_x	46 (42)	21 (17)	15 (12)	8 (8)	5 (5)	37 (31) + 1 (1)‡	133 (116)	2	0.8
ATPγS	51 (44)	17 (14)	10 (9)	11 (11)	3 (3)	37 (28)	129 (109)	1	1.5
ADP	40 (36)	14 (11)	7 (7)	11 (10)	4 (3)	21 (15)	97 (82)	2	2.0

Within RecA1 or RecA2 subdomain.

†

Between RecA1 and RecA2 subdomain.

‡

Between Mot1^CTD and the linker joining N- and C-terminal domains (could not be mapped).

Detected from a reverse database, estimating false-discovery rate.

Numbers refer to the total number of cross links, including cross-linked sites which were detected more than once (i.e., from miss-cleaved peptides). Numbers in brackets refer to non-redundant linkages only.

elife-07432-v2.xml

10.7554/eLife.07432.017

Table 3.

Distances of the cross-links detected between RecA1 and RecA2 subdomains of Mot1^CTD mapped on different structural models

DOI: http://dx.doi.org/10.7554/eLife.07432.017

	Detected linkages		Euclidean C_α–C_α distance [Å]			Total number of detected cross links
	Residue 1	Residue 2	SsoRad54-like (‘open’)	DrRad54 (‘closed’)	ScChd1 (‘semi-closed’)	ADP·BeF_x	ATPγS	ADP
A	796	1013	16	22	20	1	1	1
	796	1200	25	17	16	1	1	0
	842	1055	58	52	52	0	1	0
	864	1039	39	49	50	1	1	1
	1003	1013	12	11	10	1	0	1
	1003	1200	15	18	16	2	1	1
	1008	1200	12	14	12	2	0	1
B	864	1200	34	24	24	1	1	1
B	919	1086	25	42	47	1	1	1
C	865	1200	31	20	21	1	1	0
	919	1051	63	22	43	1	0	0
	919	1055	57	19	36	2	2	0
	919	1060	51	25	36	1	0	0

Part A shows the cross links, which do not distinguish between the conformations. Part B and C list cross-links, for which the mapped distances were significantly different depending on the model used (i.e., <30 Å for one model and >30 Å for another). Eight of these cross-links (shown also in Figure 6C) were detected only in the presence of ADP·BeF_x and ATPγS and are listed in part C.

elife-07433-v2.xml

10.7554/eLife.07433.017

Table 2.

Amino acid changes between PSI-LHCI structures

DOI: http://dx.doi.org/10.7554/eLife.07433.017

Subunit	Number of amino acids	Modeled amino acids		Number of changes
Subunit	Number of amino acids	4Y28	2WSC	Number of changes
PsaA	758	741	729	1
PsaB	734	732	732	1
PsaC	81	80	81	1
PsaD*	156	140	135	5
PsaE*	92	68	65	9
PsaF*	154	150	154	18
PsaG*	98	95	95	15
PsaH*	95	84	69	11
PsaJ*	42	41	42	5
PsaK*	134	79	85	10
PsaL*	168	160	161	21
Lhca1*	204	193	165	12
Lhca2	256	206	176	3
Lhca3	242	210	162	16
Lhca4	252	197	166	3

The number of modeled amino acids in each subunit is shown and compared to the most recent PSI-LHCI structure (2WSC). Insertions, deletions and extensions are counted as a single change. Since the genome sequence of Pisum Sativum is not completely known (genes with no DNA data are marked with an *) we relied on high-throughput mRNA sequence data for verification (Franssen et al., 2011).

elife-07460-v1.xml

10.7554/eLife.07460.002

Table 1.

Number of variants and derived puzzles used in Fraxinus version 1

DOI: http://dx.doi.org/10.7554/eLife.07460.002

Fungal sample	SNP		INDEL
Fungal sample	Variants	Puzzles	Variants	Puzzles
Ashwellthorpe1	250	2937	53	521
Ashwellthorpe2	353	1121	51	170
Upton broad and marshes1	397	4964	56	374
Total	1000	9022	160	1065

SNP, single nucleotide polymorphisms; INDEL, insertion–deletion polymorphism.

elife-07600-v2.xml

10.7554/eLife.07600.017

Table 1.

Benchmark of MCM on RNAs with crystal structures

DOI: http://dx.doi.org/10.7554/eLife.07600.017

RNA	Length	M²/Rosetta (no MOHCA, control)		MCM
RNA	Length	RMSD to crystal (Å) (accuracy)	p-value§	RMSD to crystal (Å) (accuracy)	p-value§
Tetrahymena ribozyme P4–P6 domain	158	38.3	>0.9	8.6	<1.0 × 10⁻¹⁶
V. cholerae cyclic-di-GMP riboswitch aptamer, ligand-bound*	89	11.3	2.6 × 10⁻³	7.6	6.3 × 10⁻⁷
F. nucleatum double glycine riboswitch ligand-binding domain, ligand-bound*	159	30.5	>0.9	7.9	<1.0 × 10⁻¹⁶
S. thermophilum adenosylcobalamin riboswitch aptamer, ligand-bound*	168	17.1†	5.3 × 10⁻⁷	11.9	4.0 × 10⁻¹⁵
Class I ligase	127	26.3	>0.9	14.5	6.8 × 10⁻⁵
Class I ligase, core domain‡	87	14.0	0.13	11.1	3.1 × 10⁻³
D. iridis lariat-capping ribozyme	188	9.6†	<1.0 × 10⁻¹⁶	8.2	<1.0 × 10⁻¹⁶
D. iridis lariat-capping ribozyme, MCM refined regions‡	69	17.0†	n.a.§	11.2	n.a.§

MCM modeling was performed with MOHCA-seq constraints from data sets collected on the ligand-bound state; ligands were not included during Rosetta modeling.

†

M²/Rosetta statistics are reported for RNA-puzzle submission rank 1 models, which included subdomains built by homology modeling.

‡

Calculated over core domain residues or refined regions after alignment using MAMMOTH; (Ortiz et al., 2002) see ‘Materials and methods’.

p-value computed using analytical formula for secondary-structure-constrained 3D modeling in ref. (Hajdin et al., 2010); it is not applicable to peripheral domains. Values above 0.9 are not well-determined and are presented as > 0.9.

MCM: multidimensional chemical mapping; RMSD: root-mean-squared-deviation.

elife-07616-v1.xml

10.7554/eLife.07616.003

Table 1.

Description of environments defined by principal components analysis (PCA) of physico-chemical parameters

DOI: http://dx.doi.org/10.7554/eLife.07616.003

	Akonolinga				Bankim
	PC1	PC2	PC3	PC4	PC1	PC2	PC3	PC4
Variance explained	0.47	0.31	0.14	0.09	0.59	0.22	0.13	0.07
Loadings
pH	−0.33	0.7	−0.47	0.41	−0.51	0.51	−0.43	0.55
Dissolved oxygen	−0.6	0.31	0.31	−0.67	−0.57	0.33	0.11	−0.75
Water flow	−0.59	−0.32	0.46	0.59	−0.51	−0.29	0.72	0.36
Temperature	0.43	0.55	0.69	0.19	0.4	0.74	0.53	0.1

Separate PCA was performed for Akonolinga and Bankim, and only the most potentially relevant parameters were included.

elife-07616-v1.xml

10.7554/eLife.07616.011

Appendix table 1.

Results of multivariate analyses for Akonolinga (12 months of sampling) and Bankim (4 months of sampling)

DOI: http://dx.doi.org/10.7554/eLife.07616.011

Variable	Akonolinga (n = 183)			Bankim (n = 61)
Variable	Effect	Std. error	p-value	Effect	Std. error	p-value
Model AIC	400.7	–	–	182.7	–	–
Variance of random effect	0.20	–	–	1.77	–	–
(Intercept)	−12.56	4.40	<0.001	−7.40	1.97	<0.001
Seasonality
Sine(2pi*Month/12)	0.34	0.14	0.02	–	–	–
Sine(2pi*Month/4)	–	–	–	–	–	–
Cos(2pi*Month/12)	–	–	–	–	–	–
Cos(2pi*Month/4)	–	–	–	–	–	–
Physico-chemical parameters
Temperature	–	–	–	–	–	–
pH	8.63	2.44	<0.001	–	–	–
Dissolved oxygen	–	–	–	–	–	–
Conductivity	–	–	–	–	–	–
Iron	–	–	–	–	–	–
Water flow (Lentic)	–	–	–	−2.10	0.47	<0.001
Water flow (Lotic)	–	–	–	−3.18	0.69	<0.001
Physico-chemical parameters (PCA)
PC1	–	–	–	–	–	–
PC2	–	–	–	–	–	–
PC3	–	–	–	–	–	–
Community
Abundance	−0.64	0.17	<0.001	–	–	–
Shannon	–	–	–	4.16	0.97	<0.001
Orders (%)
Fish	–	–	–	−1.62	0.35	<0.001
Anura	−0.34	0.14	0.02	−0.84	0.32	0.01
Gastropoda	−0.64	0.16	<0.001	–	–	–
Decapoda (presence)	−1.37	0.37	<0.001	–	–	–
Odonata	–	–	–	–	–	–
Ephemeroptera	–	–	–	−0.94	0.21	<0.001
Hemiptera	−0.47	0.20	0.02	–	–	–
Tricoptera	–	–	–	–	–	–
Oligochaeta (presence)	–	–	–	–	–	–
Hirudinea (presence)	0.59	0.23	0.01	–	–	–
Coleoptera	–	–	–	–	–	–
Diptera	–	–	–	1.08	0.36	<0.001
Hydracarine	–	–	–	−1.58	0.49	<0.001

The models used are Binomial regressions with random effect site, selected with forward–backwards procedure (see section 1 for details).

elife-07646-v2.xml

10.7554/eLife.07646.007

Table 2.

Ago2-target affinities

DOI: http://dx.doi.org/10.7554/eLife.07646.007

t1 nucleotide	K_D (nM)
t1 nucleotide	WT Ago2	A481T-Ago2
A	0.75 ± 0.04	1.5 ± 0.13
G	1.9 ± 0.09	1.8 ± 0.11
U	1.9 ± 0.10	–
C	1.8 ± 0.12	–
DAP	0.45 ± 0.03	–
I	1.7 ± 0.09	–
m6A	1.8 ± 0.12	–

Dissociation constants for wild-type (WT) and mutant Ago2 binding short target RNAs with different t1 nucleotides.

elife-07750-v2.xml

10.7554/eLife.07750.005

Table 1.

Average Yʹ telomere length in sirΔ cells containing TLC1, tlc1Δ48, or TLC1(Ku)₃

DOI: http://dx.doi.org/10.7554/eLife.07750.005

SIR Genotype	TLC1 Genotype
SIR Genotype	TLC1	tlc1Δ48	TLC1(Ku)₃
SIR	0	−86 ± 23†	Dysregulated*
sir4Δ	−53 ± 13†	−71 ± 26†	−148 ± 36‡
sir2Δ§	−41 ± 16	−50 ± 74	−71 ± 26
sir3Δ§	−51 ± 20	−84 ± 14	−123 ± 2

The weighted-average mobility of the Yʹ telomeric restriction fragments was calculated as described in the ‘Materials and methods’. The numbers shown are averages of multiple biological-replicate samples ± standard deviation.

Yʹ telomere length was not quantified in this condition because signal from Yʹ telomere restriction fragments overlapped with that from the non-telomeric control fragment.

†

n = 6.

‡

n = 4.

n = 2.

elife-07902-v2.xml

10.7554/eLife.07902.005

Table 1.

Descriptive statistics for the three behavioural conditions

DOI: http://dx.doi.org/10.7554/eLife.07902.005

10.7554/eLife.07902.006Table 1—source data 1.

Raw behavioural data from the oddity task.

DOI: http://dx.doi.org/10.7554/eLife.07902.006

	Accuracy		RT
	Mean	SD	Mean	SD
Face	0.87	0.07	2932.40	479.68
Scene	0.85	0.06	3147.86	557.49
Size	0.84	0.12	2464.10	668.31

Mean and standard deviation (SD) are reported for both accuracy (proportion correct) and reaction time (RT). Raw behavioural data for the three oddity categories are available in Table 1—source data 1.

elife-07902-v2.xml

10.7554/eLife.07902.007

Table 2.

Descriptive statistics for the fornix (left) and inferior longitudinal fasciculus (ILF, right)

DOI: http://dx.doi.org/10.7554/eLife.07902.007

10.7554/eLife.07902.008Table 2—source data 1.

Raw values for the DTI metrics.

DOI: http://dx.doi.org/10.7554/eLife.07902.008

	Fornix		ILF
	Mean	SD	Mean	SD
FA	0.373	0.031	0.429	0.023
MD	1.058	0.054	0.758	0.017

Mean and standard deviations are reported for fractional anisotropy (FA) and mean diffusivity (MD × 10⁻³ mm² s⁻¹). Individual FA and MD values for each participant (and tract) are available in Table 2—source data 1.

elife-07902-v2.xml

10.7554/eLife.07902.009

Table 3.

Summary table for the DTI-behaviour correlations

DOI: http://dx.doi.org/10.7554/eLife.07902.009

	Fornix				ILF
	MD		FA		MD		FA
	r	p	r	p	r	p	r	p
Face	−0.14	0.23	0.15	0.22	−0.57	0.00	0.30	0.06
Scene	−0.46	0.01	0.36	0.03	0.12	0.27	0.04	0.43
Size	−0.29	0.06	0.18	0.18	−0.26	0.09	0.09	0.32

Correlation coefficients (and one-tailed p values) are reported for each metric (fractional anisotropy [FA], mean diffusivity [MD]) of fornix and inferior longitudinal fasciculus (ILF) microstructure and each task condition (face, scene, size).

DTI, diffusion tensor imaging.

elife-07903-v2.xml

10.7554/eLife.07903.011

Table 1.

Reaction times (mean ± SEM) for the test phase.

DOI: http://dx.doi.org/10.7554/eLife.07903.011

		HR			LR
		Direct	Inference 1	Inference 2	Direct	Inference 1	Inference 2
Sleep	Mean	939.83 ± 19.16	1144.29 ± 21.51	1167.24 ± 22.35	1207.46 ± 21.36	1434.43 ± 22.69	1318.69 ± 22.61
Sleep	Median	752.07 ± 18.59	1006.20 ± 21.39	1024.83 ± 21.86	1066.83 ± 20.12	1385.43 ± 23.82	1132.13 ± 22.21
Wake	Mean	1164.14 ± 19.18	1353 ± 27.81	1405.74 ± 21.91	1220.55 ± 20.87	1305.55 ± 21.74	1290.21 ± 26.50
Wake	Median	994.17 ± 20.83	1226.83 ± 29.18	1261.27 ± 22.99	1067.90 ± 21.86	1197.50 ± 23.13	1231.40 ± 27.78

elife-07903-v2.xml

10.7554/eLife.07903.014

Table 4.

Reaction times (mean ± SEM) for the certain answers of the test phase.

DOI: http://dx.doi.org/10.7554/eLife.07903.014

		HR			LR
		Direct	Inference 1	Inference 2	Direct	Inference 1	Inference 2
Sleep	Mean	727.98 ± 18.52	876.96 ± 19.29	882.20 ± 20.68	609.91 ± 21.69	952.90 ± 21.21	721.28 ± 23.30
Sleep	Median	665.43 ± 17.20	792.3 ± 18.77	770.67 ± 19.71	553.5 ± 21.06	861.167 ± 21.05	682.93 ± 22.71
Wake	Mean	844.88 ± 18.21	1064.95 ± 24.45	1095.13 ± 27.81	686.73 ± 24.63	881.59 ± 21.59	767.54 ± 22.88
Wake	Median	743.23 ± 18.11	1086.60 ± 28.67	1068.27 ± 27.28	637.33 ± 23.90	712.17 ± 20.62	651.80 ± 22.05

elife-07916-v2.xml

10.7554/eLife.07916.008

Table 1.

Donors included in the study.

DOI: http://dx.doi.org/10.7554/eLife.07916.008

All donors	cHCV	SVR	HD
All donors	n=29	n=37	n=25
Male, n (%)	16 (55)	21 (57)	12 (48)
Age, years, median (IQR1-3)	48 (42-55)	48 (44-58)	38 (31-46)
IgG anti-CMV positive, n (%)	14 (48)	24 (51)	11 (44)
Cirrhosis, n (%)	5 (17)	8 (22)	na
Treatment experienced, n (%)	18 (62)	37 (100)	na
Treatment (n per type: 0/1/2/3)	11/12/6/0	0/26/10/1	na
Delay post-treatment, years, median (IQR1-3)	3.8 (3.4-4.2)	1.7 (0.9-3.2)	na

elife-07919-v2.xml

10.7554/eLife.07919.009

Table 1.

Synapse properties of pair recordings

DOI: http://dx.doi.org/10.7554/eLife.07919.009

	Amplitude (pA)			Success rate	Neurolucida analysis	Distance from soma (µm)
	mean	sd	max	Success rate	Neurolucida analysis	Distance from soma (µm)
IPSC
CS4	−5.7	5.1	−19.5	0.6
CS8	−8.6	4.0	−17.6	0.5	yes	48.8
CS20	−10.9	5.3	−27.4	0.9	yes	51.8
CS21*	−7.6	3.2	−17.8	0.6
CS22*	−8.0	3.4	−14.5	0.6
CS28	−76.9	20.9	−107.3	1.0	yes	48.8
CS36*	−6.5	2.6	−12.5	0.4
CS41	−8.6	4.3	−20.8	0.7	yes	41.3
CS44	−6.2	2.1	−12.6	0.5	yes	66.6
CS45*	−7.1	4.1	−21.2	0.7	yes	53.2
CS55	−91.3	11.2	−111.0	1.0	yes	35.8
CS56	−17.3	3.0	−24.9	1.0	yes	20.6
CS61	−9.6	4.6	−22.2	0.8
CS62	−36.4	14.0	−69.5	1.0
EPSC
CS10	67.5	22.2	109.3	1.0	yes	26.5
CS21*	18.6	8.7	44.5	0.9
CS22*	70.9	38.3	201.6	1.0
CS23	45.3	14.2	83.4	1.0	yes	51.2
CS36*	4.4	1.0	6.5	0.5
CS45*	43.1	19.0	86.1	1.0	yes	53.2

Reciprocal connection between FS and pyramidal cell was observed.

elife-07919-v2.xml

10.7554/eLife.07919.023

Table 5.

IPSC properties of pair CS56 and CS55

DOI: http://dx.doi.org/10.7554/eLife.07919.023

	CS56		CS55
	Electric	peak	Electric	peak
	Charge (fC)	(pA)	Charge (fC)	(pA)
Average	193.1	−17.3	895.2	−91.3
SD	56.2	3.0	96.2	11.2
Max	326.1	−24.9	1057.8	−111.0
Min	89.9	−11.8	766.0	−74.0
n	60	60	10	10
Average Trace	217.5	−14.2	994.6	−89.4

elife-08105-v1.xml

10.7554/eLife.08105.011

Table 2.

Replay statistics

DOI: http://dx.doi.org/10.7554/eLife.08105.011

	Correct trials
	Candidate-start		Candidate-stem
Number	1893			810
Replay type	Path-start	Episodic-start	Path-stem	Episodic-center	Episodic-junction
Number	345	71	190	17	17
Percent confirmed	18.2%	20.6%	23.5%	21.5%	15.3%
Percent SWR coincident	100%	100%	99.5%	98.7%	100%

	Erroneous trials
	Candidate-start		Candidate-stem
Number	59		58
Replay type	Path-start	Episodic-start	Path-stem	Episodic-center	Episodic-junction
Number	9	1	8	0	2
Percent confirmed	15.3%	12.5%	13.8%	0%	25.0%
Percent SWR coincident	100%	100%	100%	–	100%

SWR, sharp wave/ripple.

elife-08401-v2.xml

10.7554/eLife.08401.005

Table 1.

The list of identified mutp53-interaction protein candidates

DOI: http://dx.doi.org/10.7554/eLife.08401.005

Gene names	Average counts
Gene names	Normal thymus	Thymic lymphoma
Ctsb	0	19
Tfrc	0	15.5
Bag2	0	15
Stip1	0	14.5
Hyou1	0	14.5
Cad	0	14.5
Rps19	0	14.5
Pfn1	0	14
Cand1	0	11.5
Hspa2	0	11
Lcp1	0	11
Sar1a	0	10.5
Fam49b	0	10.5
Khsrp	0	10
Ifi47	0	9.5
Cse1l	0	9.5
Ipo5	0	9.5
Hsp90b1	0	9
Hspbp1	0	8.5
Rfc5	0	8.5
Tkt	0	8.5
myosin	0	8
Hadhb	0	8
Hsp70	1	66
Phgdh	1	20
Myh9	5	81.5
Hspd1	2	32.5
Rpl9-ps4	1	16
Ubr5	1	13.5
Dars	1	13.5
Iqgap1	1	12
Slc25a3	1	11.5
Rars	1	11.5
Ruvbl2	1	11
Ddb1	1	10
Hsph1	4	38.5
Dnajb4	1	9
Aldoa	1	8.5
Pcna	2	16.5
Eprs	1	8
Hsp90	2	15.5
Gm9755	2	12.5
Dnaja1	3	18
Atp5b	3	18
Cltc	7	41
Gm5506	5	26
Dnaja2	3	15
Bag5	7	31.5
Rps7	5	22.5
Ywhae	2	9
Eef2	10	38.5
Adsl	2	7.5
Hsp90ab1	20	74.5
Gnb2l1	6	22
Copg	2	7
Rpl23	2	7
Psmc6	2	7
Pcbp2	2	7
Pcbp1	3	10
Pabpc4	5	15.5
Hspa8	77	237.5
Fcgr4	13	38.5
Mcm7	4	11.5
Hadha	3	8.5
Kpnb1	5	14
Atp5a1	9	25
Pontin	4	11
Bat3	3	8
Pdia6	3	7.5
Dnajc7	38	86
Rps15a	6	13.5
Aldh2	4	9
Trim28	5	11
Eef1a1	16	35
St13	6	13
Cct8	36	54
Psmd11	6	9

elife-08490-v3.xml

10.7554/eLife.08490.021

Table 1.

Accuracy of host prediction based on distance (d) between tetranucleotide frequencies of viral and microbial genomes

DOI: http://dx.doi.org/10.7554/eLife.08490.021

	Predicted	Host order		Host family		Host genus
	Predicted	Correct	Ratio (%)	Correct	Ratio (%)	Correct	Ratio (%)
All reference sequences
d < 4 × 10⁻⁰⁴	98	97	98.98	97	98.98	97	98.98
4 × 10⁻⁰⁴ ≤ d < 1 × 10⁻⁰³	10,173	9361	92.02	8971	88.18	5261	51.72
1 × 10⁻⁰³ ≤ d	2508	1872	74.64	1757	70.06	917	36.56
Host species excluded
d < 4 × 10⁻⁰⁴	21	20	95.24	20	95.24	20	95.24
4 × 10⁻⁰⁴ ≤ d < 1 × 10⁻⁰³	10,003	9067	90.64	8372	83.69	2992	29.91
1 × 10⁻⁰³ ≤ d	2755	1981	71.91	1840	66.79	818	29.69
Host genus excluded
d < 4 × 10⁻⁰⁴	1	0	0.00	0	0.00	0	0.00
4 × 10⁻⁰⁴ ≤ d < 1 × 10⁻⁰³	9085	7303	80.39	6181	68.04	0	0.00
1 × 10⁻⁰³ ≤ d	3693	1768	47.87	1388	37.58	0	0.00

For each viral genome, the order, family, and genus of its host were predicted from the taxonomy of the closest microbial genome (based on the mean absolute difference between tetranucleotide frequency vectors) and compared to the order, family, and genus of the actual host (i.e., the taxonomy of the genome with which the virus was identified). These predictions were computed with (i) all microbial genomes, (ii) excluding specifically all genomes from the host species, and (iii) excluding all genomes from the host genus. Cases with over 75% of prediction accuracy are highlighted in gray.

elife-08586-v1.xml

10.7554/eLife.08586.011

Table 1.

Probability distribution fit parameters from Figure 3

DOI: http://dx.doi.org/10.7554/eLife.08586.011

Sample	Query				Spc42-reference
Sample	x	y	FWHM_x	FWHM_y	x	FWHM_x	FWHM_y
YFP-Spc42	−96.4 (2.2)	−15.6 (0.6)	141.1 (2.7)	108.1 (1.4)	−104.9 (1.3)	140.2 (3.0)	104.6 (1.2)
YFP-Spc42	80.4 (2.8)	−15.6 (0.6)	148.4 (5.0)	108.1 (1.4)	104.9 (1.3)	136.4 (5.5)	104.6 (1.2)
Kar1-YFP	−12.4 (2.8)	44.2 (0.6)	178.8 (3.3)	118.8 (1.1)	−106.0 (1.6)	136.8 (4.6)	112.9 (1.4)
Kar1-YFP	−12.4 (2.8)	44.2 (0.6)	178.8 (3.3)	118.8 (1.1)	106.0 (1.6)	129.8 (8.0)	112.9 (1.4)
Mps3-YFP	10.9 (2.3)	−58.5 (0.5)	318.1 (17.8)	158.1 (1.2)	−109.2 (1.3)	158.0 (3.7)	114.7 (1.3)
Mps3-YFP	10.9 (2.3)	−58.5 (0.5)	318.1 (17.8)	158.1 (1.2)	109.2 (1.3)	133.7 (6.5)	114.7 (1.3)
GFP-Sfi1	−100.3 (7.5)	12.1 (0.8)	153.6 (3.8)	110.3 (2.2)	−108.4 (1.5)	139.5 (3.2)	131.3 (1.3)
GFP-Sfi1	106.4 (8.3)	12.1 (0.8)	194.9 (14.5)	110.3 (2.2)	108.4 (1.5)	131.4 (6.1)	131.3 (1.3)
Sfi1-GFP	−25.9 (3.2)	29.4 (1.5)	214.3 (6.6)	153.9 (5.1)	−110.8 (2.0)	147.0 (3.4)	123.8 (1.3)
Sfi1-GFP	−25.9 (3.2)	29.4 (1.5)	214.3 (6.6)	153.9 (5.1)	110.8 (2.0)	140.1 (8.7)	123.8 (1.3)
YFP-Cdc31	−152.4 (15.4)	50.4 (2.3)	247.9 (29.4)	180.7 (7.6)	−118.9 (1.4)	195.7 (3.7)	158.2 (1.1)
YFP-Cdc31	49.2 (6.9)	50.4 (2.3)	143.8 (14.1)	180.7 (7.6)	118.9 (1.4)	156.7 (4.8)	158.2 (1.1)

Notes: All values are in nm. In all cases ‘x’ refers to the mother-satellite axis and ‘y’ refers to the pole axis. The zero x and y axis value is defined as midway between the C-terminal Spc42 reference peaks in our realignment scheme. The full-width half-maximum (FWHM) is 2.35 times the standard deviation of the Gaussian fit, and this can be converted into 95% integral values by multiplying each by 1.7. In all cases the mother spindle pole body (SPB) peak is shown on the first line and the satellite peak, if applicable, is shown on the second line. FWHM_y in cells containing two foci was determined by the averages over the two peaks. Errors are in parentheses and are standard deviations from Monte Carlo random fits as described in ‘Materials and methods’.

elife-08586-v1.xml

10.7554/eLife.08586.016

Table 2.

Probability distribution fit parameters from Figure 8

DOI: http://dx.doi.org/10.7554/eLife.08586.016

Sample	Query				Spc110-reference
Sample	x	y	FWHM_x	FWHM_y	FWHM_x	FWHM_y
Spc42-mT	−60.3 (0.9)	0.0	73.0 (1.1)	111.2 (1.5)	109.4 (1.2)	144.6 (1.4)
Spc42-mT	60.3 (1.2)	0.0	71.2 (1.8)	111.2 (1.5)	109.4 (1.2)	144.6 (1.4)
Spc29-mT	−60.0 (0.9)	−25.8 (1.0)	70.9 (1.1)	111.4 (0.9)	101.5 (1.2)	157.7 (1.4)
Spc29-mT	49.5 (1.3)	−25.8 (1.0)	69.7 (1.8)	111.4 (0.9)	101.5 (1.2)	157.7 (1.4)
Nud1-mT	−65.3 (1.2)	−11.6 (1.7)	78.0 (2.1)	112.3 (3.8)	101.8 (1.7)	148.2 (1.0)
Nud1-mT	61.6 (1.8)	−11.6 (1.7)	73.5 (2.6)	112.3 (3.8)	101.8 (1.7)	148.2 (1.0)
Cnm67-mT	−60.1 (1.1)	−19.0 (1.6)	79.9 (1.9)	91.0 (2.8)	97.0 (1.3)	140.1 (1.6)
Cnm67-mT	74.4 (2.6)	−19.0 (1.6)	61.6 (4.1)	91.0 (2.8)	97.0 (1.3)	140.1 (1.6)
Ndc1-mT	−62.7 (2.3)	−34.2 (1.1)	97.0 (5.6)	130.9 (1.3)	106.9 (1.3)	137.4 (1.4)
Ndc1-mT	56.0 (3.3)	−34.2 (1.1)	56.2 (5.4)	130.9 (1.3)	106.9 (1.3)	137.4 (1.4)
Nbp1-mT	−66.5 (1.2)	−48.8 (1.0)	77.7 (4.3)	106.8 (1.1)	102.1 (1.0)	119.1 (1.0)
Nbp1-mT	3.0 (1.8)	−48.8 (1.0)	50.6 (2.3)	106.8 (1.1)	102.1 (1.0)	119.1 (1.0)
Mps2-mT	−63.1 (1.9)	−37.2 (1.4)	60.0 (6.4)	96.4 (2.1)	146.6 (3.3)	132.8 (2.0)
Mps2-mT	42.8 (3.0)	−37.2 (1.4)	47.2 (6.2)	96.4 (2.1)	146.6 (3.3)	132.8 (2.0)
Bbp1-mT	−53.8 (1.5)	−35.8 (1.5)	87.5 (3.2)	108.2 (2.2)	113.0 (2.3)	137.6 (2.6)
Bbp1-mT	62.9 (2.2)	−35.8 (1.5)	65.3 (2.8)	108.2 (2.2)	113.0 (2.3)	137.6 (2.6)

Notes: All values are in nm. In all cases ‘x’ refers to the mother-satellite axis and ‘y’ refers to the pole axis. The origin is at the center point between the C-terminal Spc42 peaks as in Figure 3. The Spc110 distributions are all centered at −44.2 (1.3) in x and −61.1 (0.8) in y. For Nbp1, Ndc1, and Mps2 a third Gaussian centered on the half-bridge with a broad width was added to allow for proper Gaussian fitting of the visible peaks. As in Table 1, the FWHM is 2.35 times the standard deviation of the Gaussian fit, and this can be converted into 95% integral values by multiplying each by 1.7. In all cases the mother SPB peak is shown on the first line and the satellite peak, if applicable, is shown on the second line. FWHM_y in cells containing two foci was determined by the averages over the two peaks. Errors are in parentheses and are standard deviations from Monte Carlo random fits as described in ‘Materials and methods’.

elife-08648-v1.xml

10.7554/eLife.08648.013

Table 1.

GenTAC human data

DOI: http://dx.doi.org/10.7554/eLife.08648.013

	Aortic dissection		Aortic surgery
	Marfan	Other	Marfan	Other
	n = 531	n = 1819	n = 531	n = 1819
Odds in CCB	5.1%	0.57%	28.1%	10.70%
Odds in non-CCB	0.41%	0.12%	5.1%	4.4%
Odds ratio	12.5	4.7	5.5	2.4
p-value	0.032	NS	<0.001	<0.01
Odds ratio (BP)*	12.7	5.6	5.4	2.2
p-value	0.06	NS	<0.001	0.016
Odds ratio (Aortic Size)*	11.2	4.1	5.0	2.2
p-value	0.08	NS	<0.01	0.017
Odds ratio (β-blocker)*	15.9	3.7	5.7	2.0
p-value	0.045	NS	<0.01	0.026

Odds of ‘aortic dissection’ and ‘aortic surgery’ in patients with Marfan syndrome (‘Marfan’) and other forms of inherited thoracic aortic aneurysm (‘Other’). Odds (written as %) = number of people who incurred an event (i.e., dissection or surgery) divided by the number who did not. Odds of aortic dissection or surgery were calculated separately for patients who had used CCBs (‘Odds in CCB’) compared to those who had not (i.e., ‘Odds in non-CCB’). Odds Ratio = Odds of aortic dissection or surgery in patients who had taken CCBs divided by the odds in patients who had not taken CCBs.

The Odds Ratio was then adjusted for blood pressure (‘BP’), aortic size (‘Aortic Size’), and β-blocker use (‘β-blocker’) at enrollment, with corresponding p-values.

elife-08648-v2.xml

10.7554/eLife.08648.013

Table 1.

GenTAC human data

DOI: http://dx.doi.org/10.7554/eLife.08648.013

	Aortic dissection		Aortic surgery
	Marfan	Other	Marfan	Other
	n = 531	n = 1819	n = 531	n = 1819
Odds in CCB	5.1%	0.57%	28.1%	10.70%
Odds in non-CCB	0.41%	0.12%	5.1%	4.4%
Odds ratio	12.5	4.7	5.5	2.4
p-value	0.032	NS	<0.001	<0.01
Odds ratio (BP)*	12.7	5.6	5.4	2.2
p-value	0.06	NS	<0.001	0.016
Odds ratio (Aortic Size)*	11.2	4.1	5.0	2.2
p-value	0.08	NS	<0.01	0.017
Odds ratio (β-blocker)*	15.9	3.7	5.7	2.0
p-value	0.045	NS	<0.01	0.026

The Odds Ratio was then adjusted for blood pressure (‘BP’), aortic size (‘Aortic Size’), and β-blocker use (‘β-blocker’) at enrollment, with corresponding p-values.

elife-08709-v1.xml

10.7554/eLife.08709.010

Table 2.

Intact masses for proteins expressed and purified in this study

DOI: http://dx.doi.org/10.7554/eLife.08709.010

Protein	Vector	Molecular Mass (Da)
Protein	Vector	Calculated	Observed	Δ
Pikp-HMA	pOPINS3C*	7805.23	7804.97	−0.26
AVR-PikD	pOPINS3C*	10,835.31	10,832.95	−2.36§
AVR-PikD	pOPINA†	10,812.33	10,809.99	−2.34
AVR-PikD	pOPINE‡	11,786.33	11,784.16	−2.17
AVR-PikE	pOPINS3C*	10,812.27	10,809.91	−2.36
AVR-PikE	pOPINE‡	11,763.29	11,760.96	−2.33
AVR-PikA	pOPINS3C*	10,844.27	10,841.80	−2.47
AVR-PikA	pOPINE‡	11,795.29	11,793.01	−2.28
AVR-PikC	pOPINS3C*	10,856.28	10,853.72	−2.56
AVR-PikC	pOPINE‡	11,807.30	11,804.97	−2.33
AVR-PikD^His46Glu	pOPINE‡	11,778.30	11,776.07	−2.23
AVR-PikD^Ile49Glu	pOPINE‡	11,802.28	11,800.04	−2.24
AVR-PikD^Arg64Ala	pOPINE‡	11,701.22	11,698.94	−2.28
AVR-PikD^Asp66Arg	pOPINE‡	11,827.43	11,825.31	−2.12
AVR-PikD^Ala67Asp	pOPINE‡	11,830.34	11,828.20	−2.14
AVR-PikD^{Pro47Ala, Gly48Asp}	pOPINE‡	11,818.32	11,816.20	−2.12

Non-native residues remaining after 3C cleavage: N-terminal Gly–Pro.

†

Non-native residues remaining: N-terminal Met.

‡

Non-native residues remaining after 3C cleavage: N-terminal Gly–Pro; C-terminal Lys-His-His-His-His-His-His.

The measured mass of each AVR-Pik protein should be 2.0156 Da (2 × 1.0078) less than its calculated mass due to formation of the di-sulphide bond.

elife-08716-v2.xml

10.7554/eLife.08716.019

Table 2.

DNA constructs used in this study

DOI: http://dx.doi.org/10.7554/eLife.08716.019

Substrate	Oligonucleotide components	Junction sequence
Substrate	Oligonucleotide components	−2	−1	1	IC
Substrate 1	1a, 1b, 1c	A	G	A	T
Substrate 1-FAM	1a, 1b-3′-FAM, 1c	A	G	A	T
SacI substrate	SacI-a, SacI-b, 1c	A	G	C	T
Substrate 2	2a, 2b, 1c	A	G	G	T
Substrate 3	2a, 3b, 1c	A	G	G	A
3′-phos substrate	2a, 3b, 1c-3′P	A	G	G	A
Substrate 4	2a, 4b, 1c	A	G	G	C
Substrate 5	2a, 5b, 1c	A	G	G	G
Substrate 6	6a, 6b, 1c	A	G	C	A
Substrate 7	7a, 7b, 1c	A	G	T	A
Substrate 8	1a, 8b, 1c	A	G	A	A
Substrate 9	9a, 3b, 9c	A	T	G	A
Substrate 10	10a, 3b, 10c	A	A	G	A
Substrate 11	11a, 3b, 11c	A	C	G	A
Substrate 12	12a, 3b, 12c	G	A	G	A
Substrate 13	13a, 3b, 13c	C	A	G	A
Substrate 14	14a, 3b, 14c	T	A	G	A
Substrate 15	2a, 4b, 1c	A	G	G	C
Substrate 16	11a, 4b, 11c	A	C	G	C
Substrate 17	10a, 4b, 10c	A	A	G	C
Substrate 18	9a, 4b, 9c	A	T	G	C
Substrate 19	19a, 19b, 19c	C	G	G	A
Gap10	19a, 19b, 19c, 20d-10	C	G	G	A
Gap5	19a, 19b, 19c, 20d-5	C	G	G	A
Nick	19a, 19b, 19c, 20d	C	G	G	A
Y-junction	19a, 19b, 20c-d	C	G	G	A
Spacer 3-1 substrate	Sp3-1a, Sp3-1b, Sp3-1c	G	A	G	A
Spacer 3-2 substrate	Sp3-2a, Sp3-2b, Sp3-2c	A	C	G	C

The sequence of the central portion of the junction (positions −2, −1, 1 and the incoming nucleotide (IC)) for each substrate is shown. The oligonucleotides used to assemble the complete substrate are indicated.

elife-08843-v1.xml

Protein	Molar ratio of lipid: protein in RPL reactions*	Molar ratio of lipid: protein on vacuoles		Ratio (RPLs/vacuoles) of molar protein: lipid ratios in std. reactions†
Protein	Molar ratio of lipid: protein in RPL reactions*	BJ3505	DKY6218
Vam7p	2 × 10³	30 × 10⁴	6.5 × 10⁴	7 × 10¹
Vam3p	2 × 10³	11 × 10⁴	22 × 10⁴	7 × 10¹
Vti1p	2 × 10³	10 × 10⁴	13 × 10⁴	5 × 10¹
Nyv1p	2 × 10³	4.3 × 10⁴	8.1 × 10⁴	3 × 10¹
Ypt7p	4 × 10³	1.9 × 10⁴	1.8 × 10⁴	0.5 × 10¹
Sec17p	7 × 10³	41 × 10⁴	13 × 10⁴	3 × 10¹
Sec18p	1 × 10³	10 × 10⁴	13 × 10⁴	10 × 10¹
Vps33p	6 × 10³	17 × 10⁴	31 × 10⁴	3 × 10¹

elife-08843-v1.xml

Protein	Molar ratio of lipid: protein in RPL reactions*	Molar ratio of lipid: protein on vacuoles		Ratio (RPLs/vacuoles) of molar protein: lipid ratios in std. reactions†
Protein	Molar ratio of lipid: protein in RPL reactions*	BJ3505	DKY6218
Vam7p	2 × 10³	30 × 10⁵	6.5 × 10⁵	7 × 10¹
Vam3p	2 × 10³	11 × 10⁵	22 × 10⁵	7 × 10¹
Vti1p	2 × 10³	10 × 10⁵	13 × 10⁵	5 × 10¹
Nyv1p	2 × 10³	4.3 × 10⁵	8.1 × 10⁵	3 × 10¹
Ypt7p	4 × 10³	1.9 × 10⁵	1.8 × 10⁵	0.5 × 10¹
Sec17p	7 × 10³	41 × 10⁵	13 × 10⁵	3 × 10¹
Sec18p	1 × 10³	10 × 10⁵	13 × 10⁵	10 × 10¹
Vps33p	6 × 10³	17 × 10⁵	31 × 10⁵	3 × 10¹

elife-08935-v2.xml

10.7554/eLife.08935.004

Table 1.

Number of cleaned fascicles for the three pathways of interest in patients and control participants

DOI: http://dx.doi.org/10.7554/eLife.08935.004

Subject	LGN ↔ hMT+		Crossing hMT+		SC ↔ hMT+
Subject	Ipsi-lesional	Contra-lesional	Left → right	Right → left	Ipsi-lesional	Contra-lesional
Blindsight positive patients
PB1	75	115	9	no	12	12
PB2	19	196	6	no	no	18
PB3	50	67	24	24	17	17
PB4	19	315	no	no	no	15
PB5	93	83	7	19	14	14
PB6	12	64	13	15	no	17
PB7	397	17	no	no	16	8
PB8	87	37	12	16	20	17
PB9	635	53	no	no	16	no
PB10	32	29	no	no	no	no
PB11	291	47	9	18	12	no
PB12	194	17	17	13	15	no
Blindsight negative patients
PN1	157	19	no	no	15	8
PN2	17	226	13	15	7	21
PN3	351	89	no	no	19	16
PN4	no	101	no	no	no	19
PN5	15	122	no	no	no	13
Controls
C1	308	339	19	14	14	18
C2	619	269	no	no	39	17
C3	57	59	8	16	18	no
C4	176	114	8	6	18	16
C5	84	30	5	8	17	16
C6	57	19	no	no	15	16
C7	78	46	no	no	9	no
C8	498	182	19	14	35	14
C9	653	62	57	52	31	9

(1) Ipsilateral pathway between LGN and hMT+ (2) Pathway between hMT+ bilaterally via the corpus callosum (3) Ipsilateral pathway between SC and hMT+. Results are shown separately for the intact and damaged ‘ipsi-lesion’ hemispheres (right and left for control participants). ‘no’ = zero fascicles survived the cleaning process.

elife-09083-v2.xml

10.7554/eLife.09083.029

Table 7.

Top 10 highly recurring CDR3 sequences (peptide and V(D)J recombination) detected in listed splenic B-1a samples from age-matched SPF and GF mice.

DOI: http://dx.doi.org/10.7554/eLife.09083.029

sB-1a samples (4 months)	Top 10 IgH CDR3 sequences
sB-1a samples (4 months)		Peptide	V(D)J
germ-free #1	1	MRYGSSYWYFDV	V11-2 D1-1 J1
	2	ARGAY	V1-80 J2
	3	ARNPDGYYTYYYAMDY	V2-2 D2-9 J4
	4	ARDPFYYYGSSYWYFDV	V5-16 D1-1J1
	5	MRYSNYWYFDV	V11-2 D2-6 J1
	6	AITRAY	V1-55 J3
	7	ARRYYGSSYWYFDV	V1-55 D1-1 J1
	8	ARSDYYGSSSLSY	V1-26 D1-1 J2
	9	ASGGNYFDY	V1-75 J2
	10	ARSLYN	V1-9 J2
germ-free #2	1	ARNYGSSYDY	V1-53 D1-1 J2
	2	TRPSYYGSDY	V14-4 D1-1 J2
	3	TRESYDGYYVWYAMDY	V5-9-1 D2-9 J4
	4	ARGDY	V14-3 J2
	5	ASNWAY	V1-53 D4-1 J2
	6	MRYSNYWYFDV	V11-2 D2-6 J1
	7	AKGDYYGSSYYFDY	V1-9 D1-1 J2
	8	VRHGPRAFDY	V10-1 D3-2 J2
	9	ARLNGDY	V1-69 J2
	10	MRYGNYWYFDV	V11-2 D2-8 J1
specific pathogen free #1 (from Caltech)	1	ASYSNSDV	V3-6 D2-6 J1
	2	ARVSYSRAMDY	V14-3 D2-6 J4
	3	ARSGNYGAMDY	V1-7 D2-8 J4
	4	ASRLRSTFAY	V2-6-8 D1-1 J3
	5	ARVTTVHAMDY	V1-55 D1-1 J4
	6	ARNYGSSYWYFDV	V1-53 D1-1 J1
	7	ARTPNWEARDY	V1-55 D4-1 J4
	8	ARRYYGSSYWYFDV	V1-55 D1-1 J1
	9	ARPLLYRYYFDY	V1-75 D2-6 J2
	10	ARNYGSSYDWYFDV	V1-9 D1-1 J1
specific pathogen free #2 (from Caltech)	1	ARGGIYYDYDEVYYYAMDY	V1-55 D2-4 J4
	2	MRYSNYWYFDV	V11-2 D2-6 J1
	3	ARDYYGSSWYFDV	V1-26 D1-1 J1
	4	MRYGNYWYFDV	V11-2 D2-8 J1
	5	MRYGSSYWYFDV	V11-2 D1-1 J1
	6	ARYYDGYYGYYAMDY	V1-26 D2-4 J4
	7	ALITTWYFDV	V1-78 D1-2 J1
	8	ARHYYGSSWGY	V1-53 D1-1 J2
	9	ARSFSPYYFDY	V1-26 J2
	10	ARSHGYYPFDY	V1-54 D2-9 J2
specific pathogen free #1 (from Stanford)	1	ARSADYGGYFDV	V1-64 D2-4 J1
	2	ARGAY	V1-80 J2
	3	ARSYYDYPWFAY	V1-76 D2-4 J3
	4	ARRWLLNAMDY	V1-9 D2-9 J4
	5	ARPYYYGSSPWFAY	V1-69 D1-1 J3
	6	ARNDYPYWYFDV	V1-4 D2-4 J1
	7	ARSGDY	V1-64 J2
	8	ARVIGDY	V1-53 D2-14 J4
	9	ARANY	V1-55 J3
	10	AVNWDYAMDY	V1-84 D4-1 J4
specific pathogen free #2 (from Stanford)	1	ARGNY	V1-80 J2
	2	ARWVYYGSSSYWYFDV	V1-54 D1-1 J1
	3	ARSSNYAMDY	V1-78 D2-11 J4
	4	ARYYYGSNYAMDY	V7-3 D1-1 J4
	5	ARGAY	V1-80 J2
	6	ARRYYGSSYWYFDV	V1-55 D1-1 J1
	7	ARSPYYSNYEGYFDV	V1-72 D2-6 J1
	8	ARKNYGSSYWYFDV	V1-55 D1-1 J1
	9	ARLEIYYGNYGRVFDV	V1-80 D2-8 J2
	10	ARRDYYGSSYVLAY	V1-9 D1-1 J3

Table lists the top 10 highly recurring CDR3 sequences (peptide and V(D)J recombination) shown in each of CDR3 tree-map plot (Figure 9A).

elife-09083-v3.xml

10.7554/eLife.09083.029

Table 7.

Top 10 highly recurring CDR3 sequences (peptide and V(D)J recombination) detected in listed splenic B-1a samples from age-matched SPF and GF mice.

DOI: http://dx.doi.org/10.7554/eLife.09083.029

sB-1a samples (4 months)	Top 10 IgH CDR3 sequences
sB-1a samples (4 months)		Peptide	V(D)J
germ-free #1	1	MRYGSSYWYFDV	V11-2 D1-1 J1
	2	ARGAY	V1-80 J2
	3	ARNPDGYYTYYYAMDY	V2-2 D2-9 J4
	4	ARDPFYYYGSSYWYFDV	V5-16 D1-1J1
	5	MRYSNYWYFDV	V11-2 D2-6 J1
	6	AITRAY	V1-55 J3
	7	ARRYYGSSYWYFDV	V1-55 D1-1 J1
	8	ARSDYYGSSSLSY	V1-26 D1-1 J2
	9	ASGGNYFDY	V1-75 J2
	10	ARSLYN	V1-9 J2
germ-free #2	1	ARNYGSSYDY	V1-53 D1-1 J2
	2	TRPSYYGSDY	V14-4 D1-1 J2
	3	TRESYDGYYVWYAMDY	V5-9-1 D2-9 J4
	4	ARGDY	V14-3 J2
	5	ASNWAY	V1-53 D4-1 J2
	6	MRYSNYWYFDV	V11-2 D2-6 J1
	7	AKGDYYGSSYYFDY	V1-9 D1-1 J2
	8	VRHGPRAFDY	V10-1 D3-2 J2
	9	ARLNGDY	V1-69 J2
	10	MRYGNYWYFDV	V11-2 D2-8 J1
specific pathogen free #1 (from Caltech)	1	ASYSNSDV	V3-6 D2-6 J1
	2	ARVSYSRAMDY	V14-3 D2-6 J4
	3	ARSGNYGAMDY	V1-7 D2-8 J4
	4	ASRLRSTFAY	V2-6-8 D1-1 J3
	5	ARVTTVHAMDY	V1-55 D1-1 J4
	6	ARNYGSSYWYFDV	V1-53 D1-1 J1
	7	ARTPNWEARDY	V1-55 D4-1 J4
	8	ARRYYGSSYWYFDV	V1-55 D1-1 J1
	9	ARPLLYRYYFDY	V1-75 D2-6 J2
	10	ARNYGSSYDWYFDV	V1-9 D1-1 J1
specific pathogen free #2 (from Caltech)	1	ARGGIYYDYDEVYYYAMDY	V1-55 D2-4 J4
	2	MRYSNYWYFDV	V11-2 D2-6 J1
	3	ARDYYGSSWYFDV	V1-26 D1-1 J1
	4	MRYGNYWYFDV	V11-2 D2-8 J1
	5	MRYGSSYWYFDV	V11-2 D1-1 J1
	6	ARYYDGYYGYYAMDY	V1-26 D2-4 J4
	7	ALITTWYFDV	V1-78 D1-2 J1
	8	ARHYYGSSWGY	V1-53 D1-1 J2
	9	ARSFSPYYFDY	V1-26 J2
	10	ARSHGYYPFDY	V1-54 D2-9 J2
specific pathogen free #1 (from Stanford)	1	ARSADYGGYFDV	V1-64 D2-4 J1
	2	ARGAY	V1-80 J2
	3	ARSYYDYPWFAY	V1-76 D2-4 J3
	4	ARRWLLNAMDY	V1-9 D2-9 J4
	5	ARPYYYGSSPWFAY	V1-69 D1-1 J3
	6	ARNDYPYWYFDV	V1-4 D2-4 J1
	7	ARSGDY	V1-64 J2
	8	ARVIGDY	V1-53 D2-14 J4
	9	ARANY	V1-55 J3
	10	AVNWDYAMDY	V1-84 D4-1 J4
specific pathogen free #2 (from Stanford)	1	ARGNY	V1-80 J2
	2	ARWVYYGSSSYWYFDV	V1-54 D1-1 J1
	3	ARSSNYAMDY	V1-78 D2-11 J4
	4	ARYYYGSNYAMDY	V7-3 D1-1 J4
	5	ARGAY	V1-80 J2
	6	ARRYYGSSYWYFDV	V1-55 D1-1 J1
	7	ARSPYYSNYEGYFDV	V1-72 D2-6 J1
	8	ARKNYGSSYWYFDV	V1-55 D1-1 J1
	9	ARLEIYYGNYGRVFDV	V1-80 D2-8 J2
	10	ARRDYYGSSYVLAY	V1-9 D1-1 J3

Table lists the top 10 highly recurring CDR3 sequences (peptide and V(D)J recombination) shown in each of CDR3 tree-map plot (Figure 9A).

elife-09186-v2.xml

10.7554/eLife.09186.004

Table 1.

Overview of modeling publications on the 2013-present EVD epidemic.

DOI: http://dx.doi.org/10.7554/eLife.09186.004

Ref.	Date of latest EVD data	Date published	EVD data was pre-existing and public	Uncertainties addressed
Ref.	Date of latest EVD data	Date published	EVD data was pre-existing and public	R	Interventions	Forecast	Spread	Phylogenetics	Clinical trials
Baize et al., 2014	3/20/14	4/16/14	No					*
Dudas and Rambaut, 2014	3/20/14	5/2/14	Yes					*
Alizon et al., 2014	6/18/14	12/13/14	Yes	*		*
Gire et al., 2014	6/18/14	8/28/14	No				*	*
Stadler et al., 2014	6/18/14	10/6/14	Yes	*
Volz and Pond, 2014	6/18/14	10/24/14	Yes	*
Pandey et al., 2014	8/7/14	10/30/14	Yes	*	*	*
Gomes et al., 2014	8/9/14	9/2/14	Yes	*		*	*
Valdez et al., 2015	8/15/14	7/20/15	Yes	*	*	*	*
Merler et al., 2015	8/16/14	1/7/15	Yes	*	*	*	*
Rainisch et al., 2015	8/16/14	2/18/15	Yes				*
Althaus, 2014	8/20/14	9/2/14	Yes	*
Fisman et al., 2014	8/22/14	9/8/14	Yes	*		*
Nishiura and Chowell, 2014	8/26/14	9/11/14	Yes	*		*
Poletto et al., 2014	8/27/14	10/23/14	Yes		*		*
Meltzer et al., 2014	8/28/14	9/26/14	Yes	*	*	*
Agusto et al., 2015	8/29/14	4/23/15	Yes	*	*
Althaus, 2015	8/31/14	4/19/15	Yes	*
Scarpino et al., 2014	8/31/14	12/15/14	Yes	*
Weitz and Dushoff, 2015	8/31/14	3/4/15	Yes	*	*
Drake et al., 2015	9/2/14	10/30/14	Yes	*	*	*
Towers et al., 2014	9/8/14	9/18/14	Yes	*		*
Bellan et al., 2014	9/14/14	10/14/14	Yes			*
Chowell et al., 2015	9/14/14	1/19/15	Yes		*
Cooper et al., 2015	9/14/14	4/14/15	Yes						*
Read et al., 2015	9/14/14	11/12/14	Yes		*		*
WHO Ebola Response Team, 2014	9/14/14	9/23/14	No	*		*	*
Faye et al., 2015	9/16/14	1/23/15	No	*	*
Bogoch et al., 2015	9/21/14	10/21/14	Yes		*		*
Yamin et al., 2014	9/22/14	10/28/14	No	*	*
Lewnard et al., 2014	9/23/14	10/24/14	Yes	*	*	*
Webb et al., 2015	9/23/14	1/30/15	Yes	*	*	*
Shaman et al., 2014	9/28/14	10/27/14	Yes	*		*
Chowell et al., 2014	10/1/14	11/20/14	Yes	*		*
Fasina et al., 2014	10/1/14	10/9/14	Yes		*
Khan et al., 2015	10/1/14	2/24/15	Yes	*
Rivers et al., 2014	10/5/14	10/16/14	Yes	*	*	*
Xia et al., 2015	10/7/14	9/8/15	Yes	*	*
Majumder et al., 2014	10/11/14	4/28/15	Yes	*	*
Kiskowski, 2014	10/15/14	11/13/14	Yes	*		*
Fisman and Tuite, 2014	10/18/14	11/21/14	Yes	*	*	*
Althaus et al., 2015	10/20/14	1/15/15	Yes	*	*	*
Simon-Loriere et al., 2015	10/25/14	6/24/15	No					*
Rainisch et al., 2015	10/31/14	6/16/15	Yes				*
Fast et al., 2015	11/1/14	5/15/15	Yes		*
Kucharski et al., 2015	11/1/14	2/18/15	Yes	*	*	*
Tong et al., 2015	11/11/14	5/13/15	No				*	*
Hoenen et al., 2015	11/21/14	3/26/15	No					*
Cope et al., 2014	12/3/14	12/10/14	Yes		*		*
White et al., 2014	12/3/14	1/30/15	Yes	*	*	*
WHO Ebola Response Team, 2015	12/14/14	12/24/14	No	*		*
Chowell et al., 2014	12/17/14	1/21/15	Yes	*
Siettos et al., 2014	12/21/14	3/9/15	Yes	*		*
Park et al., 2015	12/26/14	6/18/15	No					*
Nadhem and Nejib, 2015	12/30/14	6/14/15	Yes			*
Camacho et al., 2015	1/18/15	2/10/15	Yes	*		*
Carroll et al., 2015	1/31/15	6/17/15	No				*	*
Bellan et al., 2015	2/9/15	4/15/15	Yes			*			*
Barbarossa et al., 2015	2/13/15	7/21/15	Yes	*	*	*
Kugelman et al., 2015	2/14/15	6/12/15	No					*
Cleaton et al., 2015	2/28/15	9/3/15	Yes	*
Wang and Zhong, 2015	3/18/15	3/24/15	Yes	*
Toth et al., 2015	3/31/15	7/14/15	Yes		*		*
Dong et al., 2015	4/3/15	9/5/15	Yes		*	*
Browne et al., 2015	4/12/15	5/14/15	Yes	*	*
Zinszer et al., 2015	5/13/15	9/1/15	Yes				*

elife-09215-v1.xml

10.7554/eLife.09215.016

Table 1.

Electrophysiology results from sensory cortex single-unit recordings. See also Table 1—source data 1.

DOI: http://dx.doi.org/10.7554/eLife.09215.016

10.7554/eLife.09215.017Table 1—source data 1.Firing rates before, during, and after repeated 20 s stimulation periods for each of the 11 neurons recorded in somatosensory cortex.

Exact p values comparing the somatosensory cortex firing rate before and during stimulation are provided. The 20 s stimulation period was divided into four consecutive 5 s blocks to evaluate the change in firing rate over time.

DOI: http://dx.doi.org/10.7554/eLife.09215.017

Stimulation frequency	Effect on sensory cortex firing rate	Percentage of neurons with significant change in firing rate (n = 11)
Stimulation frequency	Effect on sensory cortex firing rate	0–5 s after stim. onset	5–10 s after stim. onset	10–15 s after stim. onset	15–20 s after stim. onset
10 Hz	Increase	0%	0%	0%	0%
10 Hz	Decrease	0%	91%	82%	9%
40 Hz	Increase	100%	91%	36%	55%
40 Hz	Decrease	0%	0%	0%	0%
100 Hz	Increase	100%	82%	82%	82%
100 Hz	Decrease	0%	0%	0%	0%

elife-09248-v2.xml

10.7554/eLife.09248.006

Table 1.

Transmembrane protein benchmark

DOI: http://dx.doi.org/10.7554/eLife.09248.006

PDB	Name	Seq/len	Full protein		Converged		Aligned
PDB	Name	Seq/len	rmsd	Length	rmsd	Length	rmsd	Length
4HE8_H (3.3)	NADH-quinone oxidoreductase subunit 8	17.3	4.9	269	2.1	183	2.2	234
1SOR_A (N/A)	Aquaporin-0	26.2	2.7	221	2.1	188	2.0	200
4Q2E_A (3.4)	Phosphatidate cytidylyltransferase	18.6	5.4	262	3.5	176	2.8	178
4HTT_A (6.8)	Sec-independent protein translocase protein	14.6	3.9	225	1.8	124	2.4	181
4P6V_E (3.5)	Na(+)-translocating NADH-quinone reductase subunit D	14.3	5.0	194	1.4	49	2.8	155
4J72_A (3.3)	Phospho-N-acetylmuramoyl-pentapeptide-transferase	19.9	6.6	323	3.1	251	2.4	237
3V5U_A (1.9)	Sodium/Calcium exchanger	10.2	3.9	297	3.7	284	2.3	245
4PGS_A (2.5)	Uncharacterized protein YetJ	15.4	3.5	207	2.7	175	2.2	183
4QTN_A (2.8)	Vitamin B3 transporter PnuC	9.0	4.2	202	3.0	155	2.8	178
4OD4_A (3.3)	4-hydroxybenzoate octaprenyltransferase	22.8	3.9	275	3.4	242	2.8	231
4O6M_A (1.9)	CDP-alcohol phosphotransferase	13.3	4.1	188	4.0	165	2.3	159
4WD8_A (2.3)	Bestrophin domain protein	5.94	N/A	268	Not converged
4F35_A (3.2)	Transporter, NadC family	14.5	N/A	434	Not converged

Column 1, PDB code (resolution of the crystal structure); column 2, protein name; column 3, sequences per length, after filtering to reduce the redundancy to 90%; column 4, RMSD of predicted structure to native structure; column 5, length of native structure modeled; column 6, RMSD over converged and constrained region; column 7, length of converged and constrained region; column 8, RMSD over TM-align structural alignment; column 9, length of structurally aligned region.

elife-09376-v1.xml

10.7554/eLife.09376.006

Table 1.

Effective diffusion coefficients (K; µm²/s) and anomalous diffusion exponents (α) for macromolecules in each condition.

DOI: http://dx.doi.org/10.7554/eLife.09376.006

Condition	POA1 Locus		pLacO Plasmid		URA3 Locus		GFA1 mRNP		FBA1 mRNP
Condition	K	α	K	α	K	α	K	α	K	α
(+) Glucose	0.0057	0.69	0.0067	0.78	0.0076	0.65	0.0420	0.83	0.0501	0.85
(-) Glucose	0.0023	0.64	0.0021	0.80	0.0022	0.73	0.0131	0.77	0.0139	0.77
(-) Glucose pH 7.4	0.0015	0.65	--	--	--	--	0.0120	0.75	--	--
DMSO	0.0059	0.56	0.0046	0.70	0.0060	0.61	0.0491	0.83	0.0541	0.83
Nocodazole	0.0040	0.48	0.0025	0.57	0.0046	0.51	0.0364	0.85	0.0397	0.85
Latrunculin A	0.0038	0.50	0.0024	0.63	0.0038	0.55	0.0476	0.82	0.0550	0.81
Nocodazole + LatA	0.0028	0.48	0.0014	0.49	0.0026	0.52	0.0303	0.81	0.0367	0.82
2 mM K⁺Sorbate	0.0056	0.73	0.0051	0.80	0.0059	0.68	0.0402	0.82	0.0296	0.80
4 mM K⁺Sorbate	0.0050	0.75	0.0044	0.72	0.0048	0.71	0.0406	0.78	0.0242	0.79
6 mM K⁺Sorbate	0.0039	0.70	0.0018	0.66	0.0027	0.66	0.0378	0.76	0.0270	0.78
8 mM K⁺Sorbate	0.0023	0.64	0.0012	0.61	0.0014	0.61	0.0340	0.76	0.0164	0.77
0.4 M NaCl	0.0030	0.69	0.0026	0.75	--	--	0.0129	0.83	0.0146	0.85
0.6 M NaCl	0.0012	0.60	0.0011	0.58	--	--	0.0047	0.83	0.0057	0.84
0.8 M NaCl	0.0009	0.63	0.0011	0.63	--	--	0.0013	0.67	0.0016	0.77
Quiescence	--	--	--	--	--	--	0.0004	0.29	0.0015	0.68
0.02% Azide (Wash)	0.0037	0.74	--	--	--	--	0.0293	0.82	--	--
0.02% Azide (Spike)	0.0012	0.67	--	--	--	--	0.0155	0.81	--	--

elife-09376-v2.xml

10.7554/eLife.09376.006

Table 1.

Effective diffusion coefficients (K; µm²/s) and anomalous diffusion exponents (α) for macromolecules in each condition.

DOI: http://dx.doi.org/10.7554/eLife.09376.006

Condition	POA1 Locus		pLacO Plasmid		URA3 Locus		GFA1 mRNP		FBA1 mRNP
Condition	K	α	K	α	K	α	K	α	K	α
(+) Glucose	0.0057	0.69	0.0067	0.78	0.0076	0.65	0.0420	0.83	0.0501	0.85
(-) Glucose	0.0023	0.64	0.0021	0.80	0.0022	0.73	0.0131	0.77	0.0139	0.77
(-) Glucose pH 7.4	0.0015	0.65	--	--	--	--	0.0120	0.75	--	--
DMSO	0.0059	0.56	0.0046	0.70	0.0060	0.61	0.0491	0.83	0.0541	0.83
Nocodazole	0.0040	0.48	0.0025	0.57	0.0046	0.51	0.0364	0.85	0.0397	0.85
Latrunculin A	0.0038	0.50	0.0024	0.63	0.0038	0.55	0.0476	0.82	0.0550	0.81
Nocodazole + LatA	0.0028	0.48	0.0014	0.49	0.0026	0.52	0.0303	0.81	0.0367	0.82
2 mM K⁺Sorbate	0.0056	0.73	0.0051	0.80	0.0059	0.68	0.0402	0.82	0.0296	0.80
4 mM K⁺Sorbate	0.0050	0.75	0.0044	0.72	0.0048	0.71	0.0406	0.78	0.0242	0.79
6 mM K⁺Sorbate	0.0039	0.70	0.0018	0.66	0.0027	0.66	0.0378	0.76	0.0270	0.78
8 mM K⁺Sorbate	0.0023	0.64	0.0012	0.61	0.0014	0.61	0.0340	0.76	0.0164	0.77
0.4 M NaCl	0.0030	0.69	0.0026	0.75	--	--	0.0129	0.83	0.0146	0.85
0.6 M NaCl	0.0012	0.60	0.0011	0.58	--	--	0.0047	0.83	0.0057	0.84
0.8 M NaCl	0.0009	0.63	0.0011	0.63	--	--	0.0013	0.67	0.0016	0.77
Quiescence	--	--	--	--	--	--	0.0004	0.29	0.0015	0.68
0.02% Azide (Wash)	0.0037	0.74	--	--	--	--	0.0293	0.82	--	--
0.02% Azide (Spike)	0.0012	0.67	--	--	--	--	0.0155	0.81	--	--

elife-09418-v2.xml

10.7554/eLife.09418.017

Table 2.

The onset times in time-direction maps. The first main column shows the onset time calculated from trials aligned on target onset and the second main column shows the onset time calculated from trials aligned on saccade onset. Within each main column, the first minor column shows the time when the neural activity was significantly different from background activity (-20 to 0 before target onset). The second minor column shows the time when the neural activity represented the choice. In no-choice trials, this corresponds to the time when the activity of neurons with a preferred direction within ± 30° of the target was significantly different from the activity of neurons where no target was presented (the neurons with preferred direction within 240–300°). For choice trial, it corresponds to the time when the activity for the chosen target was significant different form the activity for the non-chosen target (in both cases the neurons with preferred direction within ± 30° of their respective target). A permutation test with multiple comparison correction was used to calculate the onset times.

DOI: http://dx.doi.org/10.7554/eLife.09418.017

	Time from target onset		Time from saccade onset
	Activity vs background	Chosen vs non-chosen	Activity vs background	Chosen vs non-chosen
No-choice	44 ms		-141 ms
Choice	40 ms	105 ms	-185 ms	-70 ms
Choice (dV>=0.4)	44 ms	92 ms	-129 ms	-68 ms
Choice (dV<0.4)	41 ms	139 ms	-169 ms	-42 ms

elife-09419-v2.xml

10.7554/eLife.09419.006

Table 1.

Baseline demographic characteristics of the 201 patients who underwent CXCL13 analyses.

DOI: http://dx.doi.org/10.7554/eLife.09419.006

Characteristics	Total			Highly polluted region (HPR)			Control region (CR)			p values (HPR vs CR)
Characteristics	Case, n	CXCL13 high, n (%)	p values	Case, n	CXCL13 high, n (%)	p values	Case, n	CXCL13 high, n (%)	p values	p values (HPR vs CR)
Total	201	134 (66.7)		70	63 (90)		131	71 (54.2)		0.0000003
G: Male	134	88 (65.7)	0.67	47	41 (87.2)	0.27	87	47 (54)	0.95	0.0001
Female	67	46 (68.7)		23	22 (95.7)		44	24 (54.5)		0.0006
A: <65 y	140	98 (70)	0.21	56	51 (91.1)	0.55	84	47 (56)	0.7	0.000009
≥65 y	56	34 (60.7)		14	12 (85.7)		42	22 (52.4)		0.03
Unknown	5	2 (40)					5	2 (40)
S: Smoker	107	75 (70.1)	0.18	36	31 (86.1)	0.17	71	44 (62)	0.04	0.01
Non-smoker	87	53 (60.9)		27	26 (96.3)		60	27 (45)		0.000006
Unknown	7	6 (85.7)		7	6 (85.7)
H: Adenocarcinoma (AD)	131	91 (69.5)	0.45	48	44 (91.7)	0.37	83	47 (56.6)	0.84	0.00003
Squamous cell carcinoma (SCC)	61	39 (63.9)		19	16 (84.2)		42	23 (54.8)		0.03
Others	9	4 (44.4)		3	3 (100)		6	1 (16.7)
Tumor node metastasis (TNM): I	88	51 (58)	0.007	29	23 (79.3)	0.02	59	28 (47.5)	0.05	0.004
II	27	17 (63)		9	8 (88.9)		18	9 (50)		0.005
III	58	43 (74.1)		17	17 (100)		41	26 (63.4)		0.004
IV	22	19 (86.4)		11	11 (100)		11	8 (72.7)		0.06
Unknown	6	4 (66.7)		4	4 (100)		2	0 (0)

G, gender; A, age; S, smoke; H, histology.

elife-09651-v2.xml

10.7554/eLife.09651.008

Table 2.

R² values quantifying goodness of fit for ideal observer (σ_d = 0) and three alternative decisional noise magnitudes (σ_d >0) which cause increasing degrees of Performance without Awareness. Decisional noise greater than 0 – i.e., increased level of Performance without Awareness – causes a drop in goodness of fit between model and human data. See Methods and Appendix 4 for more details.

DOI: http://dx.doi.org/10.7554/eLife.09651.008

Expt	Subject	Decisional noise σ_d
Expt	Subject	0 (Ideal observer)	0.1	0.2	0.3
1	1	0.465	0.459	0.456	0.447
	2	0.580	0.578	0.565	0.544
	3	0.470	0.464	0.448	0.428
	4	0.396	0.392	0.381	0.363
	5	0.649	0.655	0.645	0.628
	6	0.480	0.473	0.458	0.434
	7	0.453	0.452	0.444	0.427
	8	0.602	0.595	0.583	0.563
	9	0.503	0.509	0.512	0.504
2	1	0.624	0.624	0.622	0.612
	2	0.783	0.780	0.775	0.766
	3	0.777	0.778	0.767	0.753
Mean R² (σ)		0.565 (0.126)	0.563(0.128)	0.555(0.129)	0.539 (0.131)

elife-09651-v3.xml

10.7554/eLife.09651.008

Table 2.

DOI: http://dx.doi.org/10.7554/eLife.09651.008

Expt	Subject	Decisional noise σ_d
Expt	Subject	0 (Ideal observer)	0.1	0.2	0.3
1	1	0.465	0.459	0.456	0.447
	2	0.580	0.578	0.565	0.544
	3	0.470	0.464	0.448	0.428
	4	0.396	0.392	0.381	0.363
	5	0.649	0.655	0.645	0.628
	6	0.480	0.473	0.458	0.434
	7	0.453	0.452	0.444	0.427
	8	0.602	0.595	0.583	0.563
	9	0.503	0.509	0.512	0.504
2	1	0.624	0.624	0.622	0.612
	2	0.783	0.780	0.775	0.766
	3	0.777	0.778	0.767	0.753
Mean R² (σ)		0.565 (0.126)	0.563 (0.128)	0.555 (0.129)	0.539 (0.131)

elife-09656-v1.xml

10.7554/eLife.09656.007

Table 1.

Urine output (A), fluid intake (B), Urine osmolality (C) and urine sodium concentration (D) in rats injected into the SON and PVN with either, control, scrambled shRNA or Caprin-2 shRNA, in euhydrated (water: W1–3) and salt-loading (SL 1–7) conditions

DOI: http://dx.doi.org/10.7554/eLife.09656.007

	Scrambled shRNA			Caprin 2 shRNA
	Mean	SEM	N	Mean	SEM	N
A. Urine output (ml/100 g b.m.)
W1	4.661	0.344	9	3.954	0.222	5
W2	4.784	0.339	9	4.048	0.423	5
W3	4.803	0.413	9	4.230	0.461	5
SL1	11.649	1.590	9	10.600	1.155	5
SL2	14.482	2.005	9	9.488	1.062	5
SL3	17.790	2.294	9	10.814	1.776	5
SL4	20.884	3.086	9	11.860	1.485	5
SL5	22.046	3.564	9	11.982	2.223	5
SL6	22.473	3.367	9	13.598	2.666	5
SL7	22.833	3.828	9	12.194	2.135	5
B. Fluid intake (ml/100 g b.m.)
W1	9.353	0.668	9	9.674	0.421	5
W2	9.752	0.607	9	8.832	0.251	5
W3	9.684	0.542	9	9.203	0.425	5
SL1	14.127	1.665	9	13.806	1.224	5
SL2	18.270	2.145	9	14.483	1.156	5
SL3	22.002	2.325	9	15.707	1.460	5
SL4	25.351	3.211	9	16.680	1.886	5
SL5	26.842	3.580	9	16.818	2.437	5
SL6	27.166	3.912	9	18.209	3.124	5
SL7	28.952	3.805	9	16.554	2.108	5
C. Urine osmolality (mOsmol/kg)
W1	1943.333	154.937	9	1994.000	175.516	5
W2	1986.667	190.343	9	2090.000	65.651	5
W3	2105.556	204.702	9	1860.000	176.437	5
SL1	1532.222	108.189	9	1362.000	87.772	5
SL2	1390.000	85.261	9	1690.000	120.831	5
SL3	1280.000	80.035	9	1606.000	178.342	5
SL4	1181.111	83.773	9	1520.000	149.767	5
SL5	1188.889	115.548	9	1620.000	195.090	5
SL6	1121.111	75.064	9	1438.000	152.918	5
SL7	1093.333	79.861	9	1474.000	156.831	5
D. Urine sodium (mM)
W1-3	295.929	15.179	25	321.306	13.196	15
SL1-3	726.221	7.102	27	746.221	14.048	15
SL2-4	721.850	6.852	27	761.959	11.233	15
SL3-5	713.653	7.925	27	759.992	13.389	15
SL4-6	703.270	7.888	27	758.025	14.093	15
SL5-7	701.085	8.319	27	763.926	15.838	15

elife-10034-v2.xml

10.7554/eLife.10034.005

Table 1.

Data collection and refinement statistics

DOI: http://dx.doi.org/10.7554/eLife.10034.005

	^ScXPO1-RanGppNHp-Yrb1p bound to NES of:
	Selenomethione-hRio2	CPEB4	Selenomethione-hRio2-R	CPEB4-R	PKI-Flip3
Data collection
Space group	P4₃2₁2
Cell dimensions
a, b, c (Å)	106.48, 106.48, 303.73	105.96, 105.96, 304.00	106.69, 106.69, 304.50	106.48, 106.48, 303.73	105.96, 105.96, 304.00
a, b, g (°)	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90
Resolution (Å)	50.00–2.28 (2.32–2.28)*	50.00–2.10 (2.14–2.10)	50.00–2.28 (2.32–2.28)	50.00–2.94 (3.00–2.94)	50.00–2.55 (2.59–2.55)
R_pim	2.9 (37.7)	3.5 (43.4)	3.5 (38.6)	4.9 (40.6)	4.1 (46.5)
I/sI	24.3 (2.17)	19.5 (1.70)	22.5 (2.72)	13.3 (1.87)	19.0 (1.92)
Completeness (%)	98.6 (99.8)	99.5(100)	98.0 (99.2)	94.6 (96.0)	99.6 (100)
Redundancy	7.0 (5.9)	6.0 (6.1)	7.0 (7.0)	6.2 (5.7)	5.5 (5.5)
Refinement
Resolution (Å)	45.7–2.28 (2.32–2.28)	40.2–2.09 (2.12–2.09)	37.7–2.28 (2.31–2.28)	47.5–2.94 (3.02–2.94)	47.5–2.54 (2.60–2.54)
No. reflections	77,245 (2833)	98,659 (1793)	79,492 (3267)	34,265 (2013)	56862 (3361)
R_work/R_free	17.8 (25.8)/21.9 (27.3)	17.0 (23.8)/20.8 (27.0)	16.8 (24.7)/21.2 (27.6)	18.1 (25.2)/24.0 (31.3)	18.6 (25.0)/22.6 (30.6)
No. atoms
Protein	10,859	11,114	10,823	10,708	10797
Ligand/ion	60	76	59	51	51
Water	271	660	358	8	253
NES Peptide/Φ	111/46	122/43	130/46	112/43	105/43
B-factors
Protein	42.0	39.3	43.9	53.8	46.5
Ligand/ion	44.3	51.7	46.9	41.8	41.6
Water	33.4	34.8	35.4	23.3	35.3
NES peptide/Φ	80.5/77.3	77.6/70.4	67.5/61.7	81.2/80.5	98.6/96.0
R.m.s deviations
Bond lengths (Å)	0.003	0.003	0.006	0.003	0.004
Bond angles (°)	0.617	0.689	0.835	0.578	0.673
PDB code	5DHF	5DIF	5DI9	5DHA	5DH9

Highest resolution shell is shown in parenthesis.

One crystal was used for each structure.

elife-10095-v1.xml

RNA	Length	M²/Rosetta (no MOHCA, control)		MCM
RNA	Length	RMSD to crystal (Å) (accuracy)	p-value§	RMSD to crystal (Å) (accuracy)	p-value§
Tetrahymena ribozyme P4–P6 domain	158	38.3	>0.9	8.6	<1.0 × 10⁻¹⁶
V. cholerae cyclic-di-GMP riboswitch aptamer, ligand-bound*	89	11.3	2.6 × 10⁻³	7.6	6.3 × 10⁻⁷
F. nucleatum double glycine riboswitch ligand-binding domain, ligand-bound*	159	30.5	>0.9	7.9	<1.0 × 10⁻¹⁶
S. thermophilum adenosylcobalamin riboswitch aptamer, ligand-bound*	168	17.1†	5.3 × 10⁻⁷	11.9	4.0 × 10⁻¹⁵
Class I ligase	127	26.3	>0.9	14.5	6.8 × 10⁻⁵
Class I ligase, core domain‡	87	14.0	0.13	11.1	3.1 × 10⁻³
D. iridis lariat-capping ribozyme	188	9.6†	<1.0 × 10⁻¹⁶	8.2	<1.0 × 10⁻¹⁶
D. iridis lariat-capping ribozyme, MCM refined regions‡	69	17.0†	n.a.§	11.2	n.a.§

elife-10095-v1.xml

RNA	Length	M²/Rosetta		MCM
RNA	Length	RMSD to crystal (Å) (accuracy)	p-value§	RMSD to crystal (Å) (accuracy)	p-value§
Tetrahymena ribozyme P4–P6 domain	158	38.3	1.0	8.6	5.1 × 10⁻¹²
V. cholerae cyclic-di-GMP riboswitch aptamer, ligand-bound*	89	11.3	0.28	7.6	4.3 × 10⁻³
F. nucleatum double glycine riboswitch ligand-binding domain, ligand-bound*	159	30.5	1.0	7.9	2.1 × 10⁻¹³
S. thermophilum adenosylcobalamin riboswitch aptamer, ligand-bound*	168	17.1†	3.9 × 10⁻³	11.9	1.5 × 10⁻⁸
Class I ligase	127	26.3	1.0	14.5	5.6 × 10⁻²
Class I ligase, core domain‡	87	14.0	0.86	11.1	0.30
D. iridis lariat-capping ribozyme	188	9.6†	1.2 × 10⁻¹⁵	8.2	<1.0 × 10⁻¹⁶
D. iridis lariat-capping ribozyme, MCM refined regions‡	69	17.0†	n.a.§	11.2	n.a.§

elife-10565-v2.xml

10.7554/eLife.10565.018

Table 3.

Analysis of transposon integration sequences in human genomes induced by PGBD5

DOI: http://dx.doi.org/10.7554/eLife.10565.018

	Intact transposon		Mutant transposon
	TTAA ITR	Non-ITR	TTAA ITR	Non-ITR
Transposase
GFP-PGBD5	82% (65)^†	18% (14)	11% (4)^‡	89% (33)
GFP Control	17% (2)	83% (10)	40% (27)	60% (40)

Cells expressing GFP-PGBD5 and intact transposons exhibit significantly higher frequency of genomic integration as compared to either GFP control, or GFP-PGBD5 with mutant transposons, with 82% (65 out of 79) of sequences demonstrating DNA transposition of ITR transposons into TTAA sites (†p = 1.8 × 10-5). Mutation of the transposon ITR significantly reduces ITR-mediated integration, with only 11% (4 out of 37) of sequences (‡p = 0.0016). Numbers in parentheses denote absolute numbers of identified insertion sites.

GFP, green fluorescent protein; ITR, inverted terminal repeat.

elife-10860-v1.xml

1	Sense	5’-GCUUGAAUCUCCCAAGAUATT-3’
1	Antisense	5’-UAUCUU GGGAGAUUCAAGCTT-3’
2	Sense	5’-CAAAGUAUCUUGGAUCAAATT-3’
2	Antisense	5’-UUUGAUCCAAGAUACUUUGCC-3’
3	Sense	5’-GAGGAGUU UCGGGAGUUCAACAAAU-3’
3	Antisense	5’-AUUUGUUGAACUCCCGAA ACUCCUC-3’

elife-11290-v3.xml

10.7554/eLife.11290.008

Table 1.

Optomotry-measured contrast sensitivity improvements after MD

DOI: http://dx.doi.org/10.7554/eLife.11290.008

	Contrast sensitivity
	Day 0
Spatial frequency (cyc/deg)	Control	GM6001	Control+MD	GM6001+MD
0.031	3.6 ± 0.04	3.5 ± 0.02	3.5 ± 0.01	3.5 ± 0.01
0.064	12.7 ± 0.52	11.8 ± 0.16	11.6 ± 0.23	12.0 ± 0.15
0.092	11.7 ± 0.51	10.9 ± 0.18	10.7 ± 0.22	11.3 ± 0.17
0.103	10.3 ± 0.54	10.2 ± 0.10	10.0 ± 0.16	10.6 ± 0.12
0.192	6.9 ± 0.07	6.9 ± 0.12	7.0 ± 0.11	6.8 ± 0.05
0.272	3.5 ± 0.04	3.5 ± 0.02	3.5 ± 0.01	3.5 ± 0.01
	Day 7
0.031	3.6 ± 0.04	3.5 ± 0.02	5.1 ± 0.17	3.6 ± 0.02
0.064	12.7 ± 0.47	11.8 ± 0.18	26.9 ± 2.35	12.6 ± 0.29
0.092	11.7 ± 0.44	11.0 ± 0.15	23.3 ± 2.17	12.0 ± 0.22
0.103	10.5 ± 0.49	10.3 ± 0.10	21.8 ± 1.83	11.3 ± 0.17
0.192	7.0 ± 0.08	7.0 ± 0.10	13.5 ± 1.08	7.5 ± 0.21
0.272	3.5 ± 0.04	3.5 ± 0.01	4.9 ± 0.17	3.8 ± 0.25

elife-11290-v3.xml

10.7554/eLife.11290.014

Table 2.

Optomotry-measured contrast sensitivity improvements after MD

DOI: http://dx.doi.org/10.7554/eLife.11290.014

	Contrast sensitivity
	Day 0
Spatial frequency (cyc/deg)	PT+vehicle	PT+GM6001	PT+MDvehicle	PT+MDGM6001
0.031	3.5 ± 0.02	3.5 ± 0.04	3.5 ± 0.02	3.5 ± 0.02
0.064	11.4 ± 0.35	11.4 ± 0.32	11.8 ± 0.57	11.8 ± 0.15
0.092	10.5 ± 0.36	10.5 ± 0.34	10.7 ± 0.39	11.0 ± 0.16
0.103	9.8 ± 0.26	9.9 ± 0.28	10.0 ± 0.37	10.0 ± 0.32
0.192	6.9 ± 0.12	6.7 ± 0.09	6.7 ± 0.13	6.5 ± 0.26
0.272	3.5 ± 0.03	3.5 ± 0.04	3.4 ± 0.01	3.5 ± 0.02
	Day 7
0.031	3.5 ± 0.02	3.5 ± 0.04	3.5 ± 0.01	5.0 ± 0.11
0.064	11.4 ± 0.39	11.5 ± 0.32	12.1 ± 0.42	25.2 ± 1.53
0.092	10.5 ± 0.36	10.5 ± 0.34	11.4 ± 0.28	21.9. ± 1.14
0.103	9.9 ± 0.24	9.9 ± 0.28	10.6 ± 0.26	19.7 ± 1.25
0.192	6.9 ± 0.11	6.8 ± 0.07	7.0 ± 0.02	12.8 ± 0.91
0.272	3.5 ± 0.02	3.5 ± 0.04	3.5 ± 0.02	4.9 ± 0.12

elife-11466-v4.xml

	Analysis of CRM1 binders (all species)	Analysis of nucleocytoplasmic partitioning
	Analysis of CRM1 binders (all species)	Replicate 1	Replicate 2	Replicate 3
Sample preparation	SDS-PAGE, digestion with trypsin	SDS-PAGE, digestion with trypsin	SDS-PAGE, digestion with trypsin	Digestion with Lys-C and trypsin, reverse phase HPLC at pH 10
LC-MS instrumentation	Dionex Ultimate 3000 HPLC Q-Exactive HF	EASY nLC-1000 Q-Exactive	Dionex Ultimate 3000 HPLC Q-Exactive HF	Dionex Ultimate 3000 HPLC Orbitrap Fusion

elife-11479-v2.xml

10.7554/eLife.11479.005

Table 1.

Dissociation constants K_D of mant-nucleotides for mGBP2 WT and C586S mutant determined by fluorescence titrations and GTPase activity parameters obtained by protein concentration-dependent hydrolysis.

DOI: http://dx.doi.org/10.7554/eLife.11479.005

	Nucleotide binding			GTP-hydrolysis
	mant-GTPγS	mant-GDP	mant-GMP	GTP-hydrolysis
	K_D (µM)	K_D (µM)	K_D (µM)	K_max (min^-1)	Dimer K_D (µM)	GMP (%)
WT	0.45	0.54	14.4	102	0.029	74
C586S	0.50	0.45	15.5	133	0.026	72

The % GMP indicates the relative amount of the two products, GDP and GMP

elife-11571-v2.xml

10.7554/eLife.11571.009

Table 1.

List of the streotaxic coordinates for the functional networks nodes in rat brain.

DOI: http://dx.doi.org/10.7554/eLife.11571.009

	Abbreviation	Paxinos atlas (mm)
	Abbreviation	ML	DV	AP
IC1
Left Hippocampus	Hp_L	-2.6	3.2	-3.2
Right Hippocampus	Hp_R	2.6	3.2	-3.2
Medial Prefrontal Cotex	MedF	0.0	3.8	4
IC5
Retrosplenial Cortex	Rsp	0.0	1.8	-6.4
IC8
Left motor cortex	Mot_L	-2.2	2.2	2.2
Right motor cortex	Mot_R	2.2	2.2	2.2
IC9
Left somatosensory cortex	SS_L	-5.0	3.8	0.6
Right somatosensory cortex	SS_R	5.0	3.8	0.6

ML: medial-lateral; AP: anterior-posterior; DV: dorsal-ventral; IC: independent component.

elife-11614-v2.xml

10.7554/eLife.11614.006

Table 2.

Cardiovascular abnormalities in E14.5 embryos. Table shows the numbers of different cardiac defects found in embryos from the indicated duplication strains and in Wt littermate controls.

DOI: http://dx.doi.org/10.7554/eLife.11614.006

Types of defects			Dp1Tyb		Dp9Tyb		Dp2Tyb		Dp3Tyb		Ts1Rhr		Dp4Tyb		Dp5Tyb		Dp6Tyb
Types of defects			Wt	Dp 1Tyb	Wt	Dp 9Tyb	Wt	Dp 2Tyb	Wt	Dp 3Tyb	Wt	Ts 1Rhr	Wt	Dp 4Tyb	Wt	Dp 5Tyb	Wt	Dp 6Tyb
Single defects	Septal defects	ASD	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
		pVSD	3	9	0	1	2	5	2	0	4	1	0	4	1	1	4	1
		mVSD	0	0	1	0	0	2	0	4	0	0	0	0	0	0	2	1
	OFT defects	OA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	OFT defects	DORV	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	AVSD		0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Multiple defects	OFT + VSD		1	2	0	0	0	1	0	0	0	0	0	0	2	0	0	0
	pVSD+ mVSD		1	3	0	0	0	1	0	0	0	2	0	0	0	0	0	0
	VSD + AVSD		1	3	0	0	0	0	0	6	1	2	0	0	0	2	0	0
	OFT + VSD + AVSD		0	5	0	0	0	0	0	1	0	0	0	0	0	0	0	0
Total number of CHD			7	24	1	1	2	9	3	11	5	5	0	4	3	3	6	2
Embryos analyzed			26	39	22	17	16	26	26	25	20	21	15	19	11	20	28	19
% of CHD			26.9	61.5	4.5	5.9	12.5	34.6	12	44	25	24	0	21	27	15	21	11

elife-11614-v3.xml

Table 2.Cardiovascular abnormalities in E14.5 embryos.

Table shows the numbers of different cardiac defects found in embryos from the indicated duplication strains and in Wt littermate controls.


Types of defects			Dp1Tyb		Dp9Tyb		Dp2Tyb		Dp3Tyb		Ts1Rhr		Dp4Tyb		Dp5Tyb		Dp6Tyb
Types of defects			Wt	Dp1Tyb	Wt	Dp9Tyb	Wt	Dp2Tyb	Wt	Dp3Tyb	Wt	Ts1Rhr	Wt	Dp4Tyb	Wt	Dp5Tyb	Wt	Dp6Tyb
Single defects	Septal defects	ASD	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
		pVSD	3	9	0	1	2	5	2	0	4	1	0	4	1	1	4	1
		mVSD	0	0	1	0	0	2	0	4	0	0	0	0	0	0	2	1
	OFT defects	OA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	OFT defects	DORV	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	AVSD		0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Multiple defects	OFT + VSD		1	2	0	0	0	1	0	0	0	0	0	0	2	0	0	0
	pVSD + mVSD		1	3	0	0	0	1	0	0	0	2	0	0	0	0	0	0
	VSD + AVSD		1	4	0	0	0	0	0	6	1	2	0	0	0	1	0	0
	OFT + VSD + AVSD		0	5	0	0	0	0	0	1	0	0	0	0	0	1	0	0
Total number of CHD			7	24	1	1	2	9	3	11	5	5	0	4	3	3	6	2
Embryos analyzed			26	39	22	17	16	26	26	25	20	21	15	19	11	20	28	19
% of CHD			26.9	61.5	4.5	5.9	12.5	34.6	11.5	44.0	25.0	23.8	0	21.0	27.2	15.0	21.4	10.5

elife-12089-v2.xml

10.7554/eLife.12089.006

Table 1.

Characteristics of disease associated variants at sixteen SLE risk loci.

DOI: http://dx.doi.org/10.7554/eLife.12089.006

Risk locus	Signal	Peak SNP	Minor allele	Odds ratio (Minor allele)	Allele Freq. (Cases)	Allele Freq. (Controls)	SLE association P-value	SLE associated Annotated variants	Variants in LD with peak SNP (D' >0.8)
Risk locus	Signal	Peak SNP	Minor allele	Odds ratio (Minor allele)	Allele Freq. (Cases)	Allele Freq. (Controls)	SLE association P-value	SLE associated Annotated variants	Total variants	Total potentially functional variants	Total coding variants
STAT4	1	rs12612769	C	1.7	0.29	0.19	5E-10	52	49	9	0
HLA-D	1	rs9271593 (XL9)	C	1.7	0.55	0.42	7E-10	835	530	398	0
	2	rs9274678 (DQB1)	G	2.1	0.24	0.13	6E-09	736	216	69	0
	3	rs36101847 (DRB1)	T	0.5	0.13	0.23	8E-09	760	296	126	0
ITGAM-ITGAX	1	rs41476751	C	1.9	0.25	0.15	8E-09	153	121	62	3
IRF5_TNPO3	1	rs34350562	G	1.8	0.23	0.14	3E-09	245	189	124	0
UBE2L3	1	rs181366	T	1.5	0.27	0.20	2E-07	82	79	55	1
BANK1	1	rs4699260	T	0.7	0.20	0.28	9E-06	267	143	29	2
TNIP1	1	rs62382335	A	1.4	0.14	0.10	6E-05	46	22	16	0
TNFAIP3	1	rs57087937	T	1.9	0.10	0.06	2E-06	69	63	40	1
CCL22-CX3CL1	1	rs223889	T	1.5	0.34	0.27	5E-07	32	25	20	0
RAVER1-ZGLP1	1	rs35186095	T	1.3	0.21	0.17	2E-04	43	24	19	0
ICA1	1	rs74787882	A	0.7	0.06	0.09	2E-03	34	10	6	0
TNFSF4	1	rs1819717	G	0.7	0.29	0.36	2E-05	73	30	14	0
TNFSF4	2	rs4916313	C	1.3	0.39	0.32	2E-04	73	30	21	0
BLK	1	rs7822109	C	0.8	0.46	0.52	9E-05	97	61	38	0
XKR6	1	rs4840545	A	2.0	0.13	0.07	1E-07	335	51	23	0
XKR6	2	rs7000132	C	0.9	0.42	0.46	5E-04	335	178	118	0
NMNAT2-SMG7	1	rs41272536	G	2.9	0.11	0.05	2E-08	33	8	8	0
NMNAT2-SMG7	2	rs111487113	A	0.6	0.13	0.18	5E-04	33	17	5	0
ETS1	1	rs34516251	A	0.8	0.18	0.21	7E-03	18	10	6	0

elife-12115-v1.xml

10.7554/eLife.12115.005

Table 1.

Summary of foot feathering QTL.

DOI: http://dx.doi.org/10.7554/eLife.12115.005

Trait	LG	Loc (cM)	Scaffold	Position	LOD	PVE	Mean ± S.D.
Trait	LG	Loc (cM)	Scaffold	Position	LOD	PVE	SS	SF	FF
Proportion tarsus feathered	11	117	79	9,205,286	7.69	28.4	0.46 ± 0.04	0.58 ± 0.03**	0.80 ± 0.04***
Number of toe feathers	11	124	79	12,325,977	6.73	21.3	43.6 ± 8.9	67.3 ± 6.5*	105.3 ± 8.1***
Number of toe feathers	20	15	95	1,451,127	5.36	16.5	45.3 ± 8.1	78.2 ± 6.5**	100.3 ± 9.9***
Toe feather length (mm)	20	0	70	136,746	20.89	52.2	5.2 ± 2.3	19.9 ± 2.0***	37.3 ± 2.5***
Toe feather length (mm)	11	124	79	12,325,977	8.51	15.8	11.4 ± 3.3	18.7 ± 2.4*	28.5 ± 3.0**

LG, linkage group; Loc, genetic location of peak LOD score in centimorgans; S, allele from scaled parent; PVE, percent variance explained; F, allele from feathered parent; LOD, log10 odds ratio. (Welch two sample t-test of means compared to SS homozygote; *p≤ 0.05, **p≤0.005, ***p≤0.0005.)

elife-12115-v1.xml

10.7554/eLife.12115.006

Table 2.

Summary of QTL for numbers of feathers on individual toes.

DOI: http://dx.doi.org/10.7554/eLife.12115.006

Digit	LG	Loc (cM)	Scaffold	Position	LOD	PVE	Mean ± S.D.
Digit	LG	Loc (cM)	Scaffold	Position	LOD	PVE	SS	SF	FF
Digit 2, left foot	11	148	79	11,624,701	5.20	20.24	3.75 ± 1.13	6.95 ± 1.12*	12.19 ± 1.16***
Digit 3, right foot	20	0	70	136,746	7.71	24.1	9.06 ± 1.70	17.35 ± 1.48**	19.86 ± 1.83***
Digit 3, right foot	11	148	79	11,624,701	6.47	19.5	9.98 ± 1.60	15.60 ± 1.62*	21.02 ± 1.65***
Digit 3, left foot	20	0	70	136,746	10.79	29.84	8.66 ± 1.59	17.06 ± 1.41**	21.09 ± 1.86***
Digit 3, left foot	11	148	79	11,624,701	9.48	25.52	9.37 ± 1.52	16.26 ± 1.52**	21.30 ± 1.57***
Digit 4, right foot	20	32	95	2,464,788	7.33	21.36	2.44 ± 0.90	7.24 ± 0.75**	10.14 ± 1.10***
Digit 4, right foot	11	118	79	5,475,474	6.78	19.5	3.17 ± 0.89	6.91 ± 0.92*	9.95 ± 1.00***
Digit 4, left foot	20	30	95	2,464,788	9.37	26.83	2.44 ± 0.79	6.63 ± 0.66**	9.65 ± 0.96***
Digit 4, left foot	11	148	79	11,624,701	7.58	20.83	3.75 ± 1.14	6.95 ± 1.13*	12.19 ± 1.17***

elife-12192-v2.xml

10.7554/eLife.12192.012

Table 2.

Pattern of changes of mind for each subject. Total trials performed with percentage of trials for different types of changes of mind. The average additional points earned is the difference in the points earned on change of minds trials compared to those that would have been earned had the subject not changed their mind, divided by the total number of change of mind trials.

DOI: http://dx.doi.org/10.7554/eLife.12192.012

Subject	Total trials	%Trials				Average additional points earned per trial with a change
Subject	Total trials	Δconfidence only	Δdecision only	Δconfidence & Δdecision	All changes	Average additional points earned per trial with a change
1	9022	4.97	2.57	1.30	8.83	1.12
2	9023	2.78	1.31	0.40	4.49	0.90
3	9018	1.38	0.49	0.17	2.03	0.72
4	5000	4.26	2.40	1.62	8.28	0.90

elife-12215-v1.xml

10.7554/eLife.12215.010

Table 1.

Maximum likelihood parameters of the model (see Materials and methods for details) with the best BIC score (see Table 2).

DOI: http://dx.doi.org/10.7554/eLife.12215.010

Participant	Perception noise, σ_p	Prior bias, Δ	Decision noise
Participant	Perception noise, σ_p	Prior bias, Δ	Stimulus-dependent, β	Stimulus-independent, κ
1	0.5	0.58°	1.4	0.044
2	0.5	0.61°	1.9	0.12
3	0.3	0.54°	1.5	0.10

elife-12215-v1.xml

10.7554/eLife.12215.011

Table 2.

Model comparison results using Bayesian information criterion (BIC, lower is better). Each row is a different model using a different combination of included (+) and excluded (–) parameters (columns, see Materials and methods for details). Last column shows BIC score relative to the BIC of the best model (number 4).

DOI: http://dx.doi.org/10.7554/eLife.12215.011

Model	Perception noise, σ_p	Prior bias		Decision noise		BIC
Model	Perception noise, σ_p	Scale, α	Offset, Δ	Stimulus-dependent, β	Stimulus-independent, κ	BIC
1	+	–	–	+	–	160
2	+	–	–	+	+	139
3	+	–	+	+	–	58
4	+	–	+	+	+	0
5	+	+	–	+	–	105
6	+	+	–	+	+	102

elife-12215-v2.xml

10.7554/eLife.12215.010

Table 1.

Maximum likelihood parameters of the model (see Materials and methods for details) with the best BIC score (see Table 2).

DOI: http://dx.doi.org/10.7554/eLife.12215.010

Participant	Perception noise, σ_p	Prior bias, Δ	Decision noise
Participant	Perception noise, σ_p	Prior bias, Δ	Stimulus-dependent, β	Stimulus-independent, κ
1	0.5	0.58°	1.4	0.044
2	0.5	0.61°	1.9	0.12
3	0.3	0.54°	1.5	0.10

elife-12215-v2.xml

10.7554/eLife.12215.011

Table 2.

DOI: http://dx.doi.org/10.7554/eLife.12215.011

Model	Perception noise, σ_p	Prior bias		Decision noise		BIC
Model	Perception noise, σ_p	Scale, α	Offset, Δ	Stimulus-dependent, β	Stimulus-independent, κ	BIC
1	+	–	–	+	–	160
2	+	–	–	+	+	139
3	+	–	+	+	–	58
4	+	–	+	+	+	0
5	+	+	–	+	–	105
6	+	+	–	+	+	102

elife-12215-v3.xml

10.7554/eLife.12215.010

Table 1.

Maximum likelihood parameters of the model (see Materials and methods for details) with the best BIC score (see Table 2).

DOI: http://dx.doi.org/10.7554/eLife.12215.010

Participant	Perception noise, σ_p	Prior bias, Δ	Decision noise
Participant	Perception noise, σ_p	Prior bias, Δ	Stimulus-dependent, β	Stimulus-independent, κ
1	0.5	0.58°	1.4	0.044
2	0.5	0.61°	1.9	0.12
3	0.3	0.54°	1.5	0.10

elife-12215-v3.xml

10.7554/eLife.12215.011

Table 2.

DOI: http://dx.doi.org/10.7554/eLife.12215.011

Model	Perception noise, σ_p	Prior bias		Decision noise		BIC
Model	Perception noise, σ_p	Scale, α	Offset, Δ	Stimulus-dependent, β	Stimulus-independent, κ	BIC
1	+	–	–	+	–	160
2	+	–	–	+	+	139
3	+	–	+	+	–	58
4	+	–	+	+	+	0
5	+	+	–	+	–	105
6	+	+	–	+	+	102

elife-12572-v2.xml

10.7554/eLife.12572.014

Table 1.

Maximum likelihood fits of transition rates in wild type C. elegans. Each cohort was fitted separately; values are expressed as mean ± sem (n = 5 cohorts). Data from wild type cohorts were obtained on the same days as the experimental cohorts for which they served as controls (Tables 3 and 4), but experimental cohorts in this study were separated by weeks to months. All transition rates were constrained to be ≥0. Transition rates that were calculated using the synaptic constraints (Equation 35) are shaded orange; other constrained values are shaded grey. Mean dwell times and state probabilities were calculated from the transition rates. Column A shows fits using the standard model, which has 8 rate constants with two synaptic constraints, resulting in 6 free parameters that determine the 6 synaptic weights (Figure 2C,D; Materials and methods Equations 31–35). Column B shows fits to a model that has only one pause state (X); this model was derived from the standard model by imposing two more constraints: aFY=aRY≅0, yielding 4 free parameters. To allow comparison of models A and B by the likelihood ratio test, which requires that model B be a special case of model A, aRY and aFY were set slightly >0 (10^-10 s^-1), thereby avoiding infinite values for aYF and aYR when applying the synaptic constraints, while maintaining a vanishingly small probability of being in state Y (pY< 10^-18). The log_e likelihood (summed over the 5 cohorts) for model B was 1854 less than for model A, with 30 degrees of freedom for model A (6 per cohort × 5 cohorts) and 20 degrees of freedom for model B (4 per cohort × 5 cohorts). Applying the likelihood ratio test, the difference was highly significant (p<10^-100; p=Chi-squared(2L, df), where L = 1854 and df = 30–20 =10. Model C is the most general 3-state (F, R, P) model, which allows all six transitions between the three states. The fitted transition rates for model C were nearly identical to model B. Likelihood values are relative to model A.

DOI: http://dx.doi.org/10.7554/eLife.12572.014

	A	B	C
	2 pause states6 free parameters	1 pause state4 free parameters	1 pause state6 free parameters
Δ log_e likelihood	0	-1854	-1836
Degrees of freedom	30	20	30
	mean ± sem (n = 5)	mean ± sem (n = 5)	mean ± sem (n = 5)
aXR (s^-1)	1.201 ± 0.099	1.019 ± 0.085	1.008 ± 0.090
aXF (s^-1)	1.115 ± 0.087	1.915 ± 0.152	1.914 ± 0.152
aRX (s^-1)	0.025 ± 0.008	0.507 ± 0.013	0.507 ± 0.013
aRY (s^-1)	0.490 ± 0.015	10^-10
aFX (s^-1)	0.182 ± 0.007	0.198 ± 0.009	0.196 ± 0.008
aFY (s^-1)	0.007 ± 0.002	10^-10
aYR (s^-1)	0.411 ± 0.019	>10⁹
aYF (s^-1)	4.575 ± 0.533	>10⁹
aFR (s^-1)			0.001 ± 0.001
aRF (s^-1)			0.000 ± 0.000
dF (s)	5.329 ± 0.245	5.096 ± 0.235	5.135 ± 0.227
dR (s)	1.945 ± 0.043	1.975 ± 0.049	1.976 ± 0.049
dX (s)	0.441 ± 0.032	0.349 ± 0.026	0.351 ± 0.027
dY (s)	0.208 ± 0.019	<10^-9
pF	0.762 ± 0.015	0.7641 ± 0.015	0.764 ± 0.014
pR	0.158 ± 0.007	0.158 ± 0.007	0.155 ± 0.007
pX	0.063 ± 0.006	0.081 ± 0.008	0.080 ± 0.008
pY	0.017 ± 0.002	<10^-18

elife-12572-v2.xml

10.7554/eLife.12572.024

Table 6.

Effects of mutations on model parameters. Significance was determined using the likelihood ratio test as described in Table 4. The sign of the change (Δ) caused by the mutation is shown as “+” if the value moved away from 0, “–” if the value moved towards 0. All p-values are shown without correction for multiple comparisons. Blue denotes significance at p<0.05. Red denotes significance at p<0.05 after Bonferroni correction for 27 comparisons.

DOI: http://dx.doi.org/10.7554/eLife.12572.024

	HYP												DEP
	HYP A: eat-4(ad572)				HYP B: eat-4(ky5)				HYP C: glr-1(n2461)				DEP A: glr-1::glr-1(A/T)				DEP B: nmr-1::glr-1(A/T)
	Control	Mutant	∆	p <	Control	Mutant	∆	p<	Control	Mutant	∆	p<	Control	Mutant	∆	p<	Control	Mutant	∆	p<
dF (s)	4.771	9.564	+	10^-87	4.956	8.643	+	10^-64	5.181	7.871	+	10^-33	4.771	0.940	–	10^-99	5.181	0.742	–	10^-99
dR (s)	2.043	2.821	+	10^-7	1.910	2.769	+	10^-12	2.018	3.004	+	10^-16	2.045	0.875	–	10^-99	2.018	0.709	–	10^-9 ⁹
dX (s)	0.481	1.040	+	0.005	0.529	0.844	+	10^-43	0.459	0.727	+	10^-39	0.482	0.328	–	10^-49	0.460	0.235	–	10^-99
dY (s)	0.247	0.382	+	10^-5	0.238	0.290	+	0.005	0.221	0.164	–	10^-5	0.247	0.097	–	10^-93	0.221	0.079	–	10^-99
dP (s)	0.428	0.982	+	10^-99	0.466	0.793	+	10^-52	0.409	0.677	+	10^-43	0.428	0.286	–	10^-61	0.409	0.204	–	10^-99
pF	0.729	0.839	+	10^-27	0.734	0.832	+	10^-26	0.755	0.785	+	0.003	0.728	0.410	–	10^-99	0.755	0.407	–	10^-99
pR	0.177	0.062	–	10^-37	0.167	0.079	–	10^-29	0.161	0.135	–	10^-4	0.177	0.389	+	10^-99	0.161	0.404	+	10^-99
pX	0.073	0.090	+	10^-5	0.077	0.081	+	0.3	0.067	0.073	+	0.03	0.073	0.164	+	10^-99	0.067	0.151	+	10^-99
pY	0.022	0.009	–	10^-13	0.021	0.008	–	10^-25	0.018	0.007	–	10^-27	0.022	0.037	+	10^-21	0.018	0.037	+	10^-41

elife-12572-v3.xml

10.7554/eLife.12572.014

Table 1.Maximum likelihood fits of transition rates in wild type <italic>C. elegans</italic>.

Each cohort was fitted separately; values are expressed as mean ± sem (n = 5 cohorts). Data from wild type cohorts were obtained on the same days as the experimental cohorts for which they served as controls (Tables 3 and 4), but experimental cohorts in this study were separated by weeks to months. All transition rates were constrained to be ≥0. Transition rates that were calculated using the synaptic constraints (Equation 35) are shaded orange; other constrained values are shaded grey. Mean dwell times and state probabilities were calculated from the transition rates. Column A shows fits using the standard model, which has 8 rate constants with two synaptic constraints, resulting in 6 free parameters that determine the 6 synaptic weights (Figure 2C,D; Materials and methods Equations 31–35). Column B shows fits to a model that has only one pause state (X); this model was derived from the standard model by imposing two more constraints: aFY=aRY≅0, yielding 4 free parameters. To allow comparison of models A and B by the likelihood ratio test, which requires tht model B be a special case of model A, aRY and aFY were set slightly >0 (10^-10 s^-1), thereby avoiding infinite values for aYF and aYR when applying the synaptic constraints, while maintaining a vanishingly small probability of being in state Y (pY< 10^-18). The log_e likelihood (summed over the 5 cohorts) for model B was 1854 less than for model A, with 30 degrees of freedom for model A (6 per cohort × 5 cohorts) and 20 degrees of freedom for model B (4 per cohort × 5 cohorts). Applying the likelihood ratio test, the difference was highly significant (p<10^-100; p=Chi-squared(2L, df), where L = 1854 and df = 30–20 =10. Model C is the most general 3-state (F, R, P) model, which allows all six transitions between the three states. The fitted transition rates for model C were nearly identical to model B. Likelihood values are relative to model A.

	A	B	C
	2 pause states6 free parameters	1 pause state4 free parameters	1 pause state6 free parameters
Δ log_e likelihood	0	-1854	-1836
Degrees of freedom	30	20	30
	mean ± sem (n = 5)	mean ± sem (n = 5)	mean ± sem (n = 5)
aXR (s^-1)	1.201 ± 0.099	1.019 ± 0.085	1.008 ± 0.090
aXF (s^-1)	1.115 ± 0.087	1.915 ± 0.152	1.914 ± 0.152
aRX (s^-1)	0.025 ± 0.008	0.507 ± 0.013	0.507 ± 0.013
aRY (s^-1)	0.490 ± 0.015	10^-10
aFX (s^-1)	0.182 ± 0.007	0.198 ± 0.009	0.196 ± 0.008
aFY (s^-1)	0.007 ± 0.002	10^-10
aYR (s^-1)	0.411 ± 0.019	>10⁹
aYF (s^-1)	4.575 ± 0.533	>10⁹
aFR (s^-1)			0.001 ± 0.001
aRF (s^-1)			0.000 ± 0.000
dF (s)	5.329 ± 0.245	5.096 ± 0.235	5.135 ± 0.227
dR (s)	1.945 ± 0.043	1.975 ± 0.049	1.976 ± 0.049
dX (s)	0.441 ± 0.032	0.349 ± 0.026	0.351 ± 0.027
dY (s)	0.208 ± 0.019	<10^-9
pF	0.762 ± 0.015	0.7641 ± 0.015	0.764 ± 0.014
pR	0.158 ± 0.007	0.158 ± 0.007	0.155 ± 0.007
pX	0.063 ± 0.006	0.081 ± 0.008	0.080 ± 0.008
pY	0.017 ± 0.002	<10^-18

elife-12572-v3.xml

10.7554/eLife.12572.024

Table 6.Effects of mutations on model parameters.

Significance was determined using the likelihood ratio test as described in Table 4. The sign of the change (Δ) caused by the mutation is shown as “+” if the value moved away from 0, “–” if the value moved towards 0. All p-values are shown without correction for multiple comparisons. Blue denotes significance at p<0.05. Red denotes significance at p<0.05 after Bonferroni correction for 27 comparisons.

	HYP												DEP
	HYP A: eat-4(ad572)				HYP B: eat-4(ky5)				HYP C: glr-1(n2461)				DEP A: glr-1::glr-1(A/T)				DEP B: nmr-1::glr-1(A/T)
	Control	Mutant	∆	p <	Control	Mutant	∆	p<	Control	Mutant	∆	p<	Control	Mutant	∆	p<	Control	Mutant	∆	p<
dF (s)	4.771	9.564	+	10^-87	4.956	8.643	+	10^-64	5.181	7.871	+	10^-33	4.771	0.940	–	10^-99	5.181	0.742	–	10^-99
dR (s)	2.043	2.821	+	10^-7	1.910	2.769	+	10^-12	2.018	3.004	+	10^-16	2.045	0.875	–	10^-99	2.018	0.709	–	10^-9 ⁹
dX (s)	0.481	1.040	+	0.005	0.529	0.844	+	10^-43	0.459	0.727	+	10^-39	0.482	0.328	–	10^-49	0.460	0.235	–	10^-99
dY (s)	0.247	0.382	+	10^-5	0.238	0.290	+	0.005	0.221	0.164	–	10^-5	0.247	0.097	–	10^-93	0.221	0.079	–	10^-99
dp (s)	0.428	0.982	+	10^-99	0.466	0.793	+	10^-52	0.409	0.677	+	10^-43	0.428	0.286	–	10^-61	0.409	0.204	–	10^-99
pF	0.729	0.839	+	10^-27	0.734	0.832	+	10^-26	0.755	0.785	+	0.003	0.728	0.410	–	10^-99	0.755	0.407	–	10^-99
pR	0.177	0.062	–	10^-37	0.167	0.079	–	10^-29	0.161	0.135	–	10^-4	0.177	0.389	+	10^-99	0.161	0.404	+	10^-99
pX	0.073	0.090	+	10^-5	0.077	0.081	+	0.3	0.067	0.073	+	0.03	0.073	0.164	+	10^-99	0.067	0.151	+	10^-99
pY	0.022	0.009	–	10^-13	0.021	0.008	–	10^-25	0.018	0.007	–	10^-27	0.022	0.037	+	10^-21	0.018	0.037	+	10^-41

elife-12613-v1.xml

10.7554/eLife.12613.020

Table A1.2.

The fraction of discordant true and false SNPs between COCALL and GATK population-based variant calling. COCALL had a greater proportion of true SNPs – confirmed by visual inspection of mapping reads – both in terms of the number of variant sites, and across the population of samples.

DOI: http://dx.doi.org/10.7554/eLife.12613.020

SNP caller	Sites		Mutations
SNP caller	True	False	True	False
COCALL	106	33	991	118
COCALL	76.3%	23.7%	89.4%	10.6%
GATK population caller	33	106	118	991
GATK population caller	23.7%	76.3%	10.6%	89.4%

elife-12613-v1.xml

10.7554/eLife.12613.021

Table A1.3.

The rate of SNP calling for different combinations of read libraries of samples BPK282/0cl4, BPK087/0cl11 and BPK275/0cl18. BPK282/0cl4 was the reference genome strain and so should possess only heterozygous SNPs, and so its variant discovery rate was substantially lower. COCALL identified more rare variant SNPs in mixed libraries.

DOI: http://dx.doi.org/10.7554/eLife.12613.021

Read library combinations			Unique to COCALL	Shared	Unique to GATK population caller
BPK282/0cl4	BPK275/0cl18	BPK087/0cl11	Unique to COCALL	Shared	Unique to GATK population caller
	89%	11%	14	140	6
	80%	20%	7	182	7
	70%	30%	6	191	7
	60%	40%	9	193	7
	50%	50%	7	194	7
	40%	60%	5	196	6
	30%	70%	7	191	6
	20%	80%	7	178	8
	11%	89%	9	145	6
89%		11%	10	50	5
80%		20%	11	112	5
70%		30%	5	129	4
60%		40%	7	131	5
50%		50%	7	131	6
40%		60%	6	132	6
30%		70%	5	133	6
20%		80%	4	130	6
11%		89%	4	127	6
89%	11%		15	64	3
80%	20%		14	107	4
70%	30%		4	129	3
60%	40%		4	132	3
50%	50%		3	133	4
40%	60%		3	132	5
30%	70%		4	131	4
20%	80%		3	130	5
11%	89%		3	126	6

elife-12613-v1.xml

10.7554/eLife.12613.022

Table A1.4.

The probabilities of observing alleles at a specific frequency in the core population and ISC1. We assessed whether or not the SNPs we discovered in our sample of ISC L. donovani were likely to be representative of the variation existing in the wider population of parasites circulating in the ISC. We first assessed the chance of discovering alleles at frequency f as 1-(1-f)^2n in the core population (n=191) and ISC1 (n=12) sample sets (Gutenkunst et al., 2009). As a second approach, we evaluated the chance of sampling at least one derived allele in n sampled chromosomes (as above) assuming these come from a population of size N=1000 following a hypergeometric distribution (Tennessen et al., 2012). Both approaches confirm we have good power (>99% probability) of sampling alleles with population frequencies as low as 1.2% in the core population, but are likely to miss many variants in ISC1.

DOI: http://dx.doi.org/10.7554/eLife.12613.022

Allele Frequency	P(derived allele)=1-(1-f)²ⁿ		M0 N-Mn /Nn
	P(derived allele)=1-(1-f)²ⁿ		P(derived allele)=1 –
	Core population	ISC1	Core population	ISC1
0.001	0.318	0.024	0.382	0.024
0.002	0.535	0.047	0.618	0.047
0.003	0.683	0.07	0.91	0.07
0.004	0.784	0.092	0.945	0.092
0.005	0.853	0.113	0.966	0.115
0.006	0.9	0.134	0.979	0.136
0.007	0.932	0.155	0.987	0.157
0.008	0.953	0.175	0.992	0.177
0.009	0.968	0.195	0.997	0.197
0.01	0.978	0.214	0.999	0.217
0.012	0.99	0.252	0.999	0.254
0.015	0.997	0.304	0.999	0.307
0.021	0.999	0.399	0.999	0.403
0.024	0.999	0.442	1	0.446
0.029	0.999	0.507	1	0.511
0.038	0.999	0.605	1	0.61
0.039	0.999	0.615	1	0.619
0.04	1	0.625	1	0.629
0.049	1	0.701	1	0.705
0.065	1	0.801	1	0.805
0.092	1	0.901	1	0.904
0.173	1	0.99	1	0.99
0.272	1	1	1	1

elife-12613-v1.xml

10.7554/eLife.12613.023

Table A1.5.

The percentage of SNP pairs for all pairs on the same chromosome for which both SNPs occur within a block, for different block sizes (kb) for Cortex, GATK, Samtools Mpileup and Pileup (Supplementary Table 6). Singletons may have clustered for Samtools Pileup, but not for Cortex, GATK or Samtools Mpileup. The mean distance was calculated the average distance between SNPs of the given type on the same chromosome. Non-rare SNPs were those found in three or more samples.

DOI: http://dx.doi.org/10.7554/eLife.12613.023

SNP Caller	SNP type	Block size (kb)
SNP Caller	SNP type	0.01	0.1	0.5	1	5	10	50	100	500
Cortex	Non-rare	0.0	0.3	0.9	1.1	1.7	3.4	9.6	17.0	61.5
	Doubletons	1.5	1.5	1.5	1.5	3.1	3.1	10.8	13.8	64.6
	Singletons	0.0	0.0	0.0	0.0	3.8	3.8	23.1	30.8	80.8
	All	0.0	0.3	0.9	1.1	1.7	3.3	9.6	17.0	61.5
GATK	Non-rare	0.0	0.1	0.2	0.3	1.1	2.1	9.3	17.8	64.4
	Doubletons	1.3	1.3	1.3	1.3	1.3	1.3	5.3	13.3	61.3
	Singletons	0.0	0.0	0.0	0.0	1.1	3.2	11.8	18.3	77.4
	All	0.0	0.1	0.2	0.3	1.1	2.1	9.3	17.8	64.4
Samtools Mpileup	Non-rare	0.0	0.1	0.3	0.4	1.2	2.2	9.5	17.9	64.4
	Doubletons	0.0	0.0	0.0	0.0	6.7	6.7	6.7	20.0	60.0
	Singletons	0.0	0.0	0.0	0.0	9.1	9.1	9.1	9.1	81.8
	All	0.0	0.1	0.3	0.4	1.2	2.2	9.5	17.9	64.4
Samtools Pileup	Non-rare	0.0	0.1	0.2	0.3	1.1	2.1	9.3	17.8	64.4
	Doubletons	2.6	3.3	3.3	3.3	5.3	6.6	11.8	21.1	63.2
	Singletons	0.8	4.4	5.2	5.2	5.7	6.3	13.4	24.9	71.6
	All	0.0	0.1	0.2	0.3	1.1	2.1	9.3	17.8	64.5

elife-13073-v1.xml

10.7554/eLife.13073.008

Table 1.

Peak current amplitude of Na_v1.1-F383S and Na_v1.1-F383S-S1328P expressed in human NgN2 neurons.

DOI: http://dx.doi.org/10.7554/eLife.13073.008

10.7554/eLife.13073.009Table 1—source data 1.The peak INa amplitude for each neuron described in <xref ref-type="table" rid="tbl3">Table 1</xref>.

DOI: http://dx.doi.org/10.7554/eLife.13073.009

Mean (95% CI)	Na_v1.1-F383S		Na_v1.1-F383S-S1328P
Mean (95% CI)	2 µg/ml Dox (10 cells)	0.1 µg/ml Dox (8 cells)	2 µg/ml Dox (9 cells)	0.1 µg/ml Dox (7 cells)
I_max (pA/pF)	152.4 (114.4, 190.3)	141.7 (83.04, 200.4)	109.6 (44.94, 174.2)	77.03 (17.77, 136.3)

I_max is the maximal inward current detected in a neuron and normalized to the whole cell capacitance. By two-way ANOVA using Na_v1.1 variants as factor 1 and Dox concentration as factor 2, F (1, 30) = 5.135 and p = 0.0308 for factor 1.

elife-13073-v1.xml

10.7554/eLife.13073.025

Table 3.

Cell-type specific comparisons of I_Na activation between control and Dravet iPSC-derived neurons.

DOI: http://dx.doi.org/10.7554/eLife.13073.025

10.7554/eLife.13073.026Table 3—source data 1.Parameters characterizing INa activation for each neuron described in <xref ref-type="table" rid="tbl1">Table 3</xref>.

DOI: http://dx.doi.org/10.7554/eLife.13073.026

Mean (95% CI)	Excitatory neurons		Inhibitory neurons
Mean (95% CI)	Control (3 subjects, 45 cells)	Dravet (2 subjects, 45 cells)	Control (4 subjects, 28 cells)	Dravet (2 subjects, 20 cells)
I_max (pA/pF)	63.62 (55.01, 72.23)	62.15 ^p1 (52.19, 72.11)	100.5 (74.78, 126.2)	64.27 ^p4 (46.07, 82.47)
V_R (mV)	37.34 (34.51, 40.16)	34.23 ^p2 (31.43, 37.02)	27.34 (24.32, 30.36)	28.28 ^p5 (23.74, 32.83)
V_1/2 (mV)	−29.89 (−31.58,−28.21)	−28.81 ^p3 (−30.31, −27.31)	−27.63 (− 30.06, −25.19)	−25.31 ^p6 (−28.98, −21.64)

I_max is the maximal inward current detected in a neuron and normalized to the whole cell capacitance. V_R is the reversal potential for sodium currents. V_1/2 describes the membrane potential at which 50% of the sodium channels are activated. V_R and V_1/2 were determined for each neuron by curve fitting in GraphPad Prism using the equation I = g*(V-V_R)/(1+exp(-0.03937*z*(V-V_1/2))) (see Materials and methods). 95% CI is the 95% confidence interval. p1 = 0.8225, p2 = 0.1291, p3 = 0.3505, in corresponding t-tests between Control and Dravet excitatory neurons. p4 = 0.034, p5 = 0.7259, p6 = 0.2885, in corresponding t-tests between Control and Dravet inhibitory neurons.

elife-13073-v1.xml

10.7554/eLife.13073.027

Table 4.

Cell-type specific comparisons of I_Na steady-state inactivation between control and Dravet iPSC-derived neurons.

DOI: http://dx.doi.org/10.7554/eLife.13073.027

10.7554/eLife.13073.028Table 4—source data 1.V1/2’ values for each neuron described in <xref ref-type="table" rid="tbl2">Table 4</xref>.

DOI: http://dx.doi.org/10.7554/eLife.13073.028

Mean (95% CI)	Excitatory neurons		Inhibitory neurons
Mean (95% CI)	Control (3 subjects, 37 cells)	Dravet (2 subjects, 40 cells)	Control (4 subjects, 25 cells)	Dravet (2 subjects, 19 cells)
V_1/2^’ (mV)	−44.87 (−46.13, −43.61)	−45.27 ^p1 (−46.47, -44.07)	−45.32 (−47.84, −42.79)	−43.31 ^p2 (−46.08, −40.55)

V_1/2^’ describes the membrane potential at which 50% of the sodium channels are inactivated. V_1/2^’ was determined per neuron by curve fitting in GraphPad Prism using the equation I = 1/(1+exp((V- V_1/2’)/a’)) (see Materials and methods). 95% CI is the 95% confidence interval. p1 = 0.6551 by t-test between control and Dravet excitatory neurons. p2 = 0.3035 by t-test between control and Dravet inhibitory neurons.

elife-13135-v1.xml

10.7554/eLife.13135.004

Table 2.

Summary of PASC analysis.

DOI: http://dx.doi.org/10.7554/eLife.13135.004

10.7554/eLife.13135.005Table 2—source data 1.PASC analysis.

DOI: http://dx.doi.org/10.7554/eLife.13135.005

Sample ID	Country of origin	PASC: S segment		PASC: L segment
Sample ID	Country of origin	Sequence identity (%)	Closest virus	Sequence identity (%)	Closest virus
C0617	Cambodia	88.80	Wēnzhōu virus	86.27	Wēnzhōu virus
C0649	Cambodia	88.51	Wēnzhōu virus	85.98	Wēnzhōu virus
R4937	Thailand	70.63	Wēnzhōu virus	62.71	Wēnzhōu virus
R5074	Thailand	70.29	Wēnzhōu virus	63.08	Wēnzhōu virus

elife-13135-v2.xml

10.7554/eLife.13135.004

Table 2.

Summary of PASC analysis.

DOI: http://dx.doi.org/10.7554/eLife.13135.004

10.7554/eLife.13135.005Table 2—source data 1.PASC analysis.

DOI: http://dx.doi.org/10.7554/eLife.13135.005

Sample ID	Country of origin	PASC: S segment		PASC: L segment
Sample ID	Country of origin	Sequence identity (%)	Closest virus	Sequence identity (%)	Closest virus
C0617	Cambodia	88.80	Wēnzhōu virus	86.27	Wēnzhōu virus
C0649	Cambodia	88.51	Wēnzhōu virus	85.98	Wēnzhōu virus
R4937	Thailand	70.63	Wēnzhōu virus	62.71	Wēnzhōu virus
R5074	Thailand	70.29	Wēnzhōu virus	63.08	Wēnzhōu virus

elife-13152-v2.xml

10.7554/eLife.13152.018

Table 3.

Summary of the best set 1 candidate models by interface energy.

DOI: http://dx.doi.org/10.7554/eLife.13152.018

Ligand	Set	Best model by interface energy
Ligand	Set	Interface energy score (kcal/mol)	Rosetta total energy (kcal/mol)	H-bond and Salt bridges Interactions	Distances between corresponding atom pairs (Å)
PS	1A	-6.64	-1464.65	Head - R29	2.90, 2.77
				P - R66	2.67
				Tail - R66	3.45, 2.93
	1B	-3.06	-1461.49	Head - R29	2.84, 2.90, 3.32
	1B	-3.06	-1461.49	P - R66	2.89, 3.32
	1C	-3.15	-1461.72	Head - R29	2.87, 3.43
				Head - E36	2.95
				P - R66	2.86
PE	1A	-2.90	-1465.81	Head - E63	2.92
				P - R66	3.19
				Tail - R66	2.76, 3.24
				Tail - R29	2.92
	1B	-2.92	-1464.62	Head - E63	2.95
	1B	-2.92	-1464.62	P - R66	2.88, 3.43
	1C	-2.61	-1466.02	Head - E63	2.98
	1C	-2.61	-1466.02	P - R66	2.84, 3.61

Ligand in set 1A has the longest tail construct (kept up to the α carbon). Ligand in set 1B only has head group and phosphate. Ligand in set 1C has one carbon after the ester linkage. Head is the ligand head group. P is the ligand phosphate moiety. Tail includes the ligand glycerol moiety and two fatty acid chains.

elife-13292-v1.xml

10.7554/eLife.13292.015

Table 1.

Proteins Co-Purified by PCH1 AP-MS in WT and phyB-9. Proteins co-purified with PCH1 were identified from affinity purification coupled with mass spectrometry (AP-MS) analyses using 12L:12D grown, 10-day-old PCH1ox3 plants (in either WT or phyB-9 mutant backgrounds) harvested at ZT12.

DOI: http://dx.doi.org/10.7554/eLife.13292.015

10.7554/eLife.13292.016Table 1—source data 1.The full list of proteins identified by AP-MS, listing unique peptides and the percent coverage.

The full list is generated and exported by Scaffold (Proteome Software Inc., Portland, Oregon; v.4.4.3) showing all co-purified proteins from all replicates of PCH1ox3 AP-MS and the GFP Control. The file contains reports on exclusive unique peptide counts and percent coverage for each co-purified proteins, with their names, accession numbers and molecular weight.

DOI: http://dx.doi.org/10.7554/eLife.13292.016

AGI number	Protein name	ELF3 AP-MS^b	Exclusive unique peptide count/Percent coverage^a
			PCH1ox3 in WT			PCH1ox3 in phyB-9
			rep1	rep2	rep3	rep1	rep2
At2g16365	PCH1^c	Y	30/73%	41/85%	37/79%	40/85%	32/77%
At2g18790	phyB	Y	46/69%	47/65%	41/60%	—	—
At5g35840	phyC	Y	31/44%	23/28%	25/29%	—	—
At4g16250	phyD	Y	22/47%	19/34%	20/38%	22/38%	6/11%
At4g18130	phyE	Y	41/55%	40/52%	45/60%	49/60%	31/41%
At1g09570	phyA	Y	31/46%	36/49%	35/45%	36/48%	29/39%
At2g37678	FHY1	N	2/22%	2/21%	4/28%	4/28%	2/21%
At3g42170	DAYSLEEPER	Y	5/13%	—	4/11%	3/8%	2/6%
At1g09340	CRB	Y	—^d	—^d	4/17%	6/24%	3/13%
At5g43630	TZP	Y	9/15%	6/12%	12/23%	—	—
At2g32950	COP1	Y	7/15%	8/16%	8/18%	—	—
At2g46340	SPA1	Y	8/14%	5/7%	8/12%	—	—
At2g25930	ELF3	Y	6/12%	11/25%	12/26%	—	—
At2g40080	ELF4	Y	—^d	4/60%	3/42%	—	—
At3g46640	LUX	Y	2/6%	—^d	4/15%	—	—
At3g03940	MLK2	Y	—^d	2/6%	2/6%	—	—
At1g15750	TPL	N	—^d	3/3%	4/5%	2/2%	—
At1g47128	RD21a	Y	—^d	3/8%	2/4%	—^d	—^d
Also see Table 1—source data 1

^a All listed proteins match 99% protein threshold, minimum number peptides of 2 and peptide threshold as 95%. Proteins not matching the criteria were marked with "—".

^b ELF3 AP-MS (Huang et al., 2015) was used for comparison.

^c Percent coverage for PCH1 is calculated using protein encoded by At2g16365.2.

^d Only one exclusive unique peptide was detected.

elife-13292-v1.xml

10.7554/eLife.13292.017

Table 2.

Proteins Co-Purified by PCH1 AP-MS in elf4-2 and elf3-2, compared to WT. Proteins co-purified with PCH1 were identified from affinity purification coupled with mass spectrometry (AP-MS) analyses using 12L:12D grown, 10-day-old PCH1ox3 plants in either elf4-2 or elf3-2 mutant backgrounds harvested at ZT12.

DOI: http://dx.doi.org/10.7554/eLife.13292.017

AGI number	Protein name	ELF3 AP-MS^b	Exclusive unique peptide count/Percent coverage^a
			PCH1ox3 in WT^c			PCH1ox3 in elf4-2		PCH1ox3 in elf3-2
			rep1	rep2	rep3	rep1	rep2	rep1	rep2
At2g16365	PCH1^d	Y	30/73%	41/85%	37/79%	29/77%	34/78%	42/82%	36/82%
At2g18790	phyB	Y	46/69%	47/65%	41/60%	47/70%	31/46%	42/63%	40/56%
At5g35840	phyC	Y	31/44%	23/28%	25/29%	30/43%	13/16%	20/28%	15/18%
At4g16250	phyD	Y	22/47%	19/34%	20/38%	20/42%	12/25%	20/37%	16/30%
At4g18130	phyE	Y	41/55%	40/52%	45/60%	42/57%	37/50%	43/55%	40/53%
At1g09570	phyA	Y	31/46%	36/49%	35/45%	32/47%	24/34%	34/49%	27/38%
At2g37678	FHY1	N	2/22%	2/21%	4/28%	—^e	3/21%	—^e	3/21%
At3g42170	DAYSLEEPER	Y	5/13%	—	4/11%	3/7%	5/11%	2/5%	—^e
At1g09340	CRB	Y	—^e	—^e	4/17%	2/9%	5/22%	3/13%	3/13%
At5g43630	TZP	Y	9/15%	6/12%	12/23%	4/7%	—^e	12/21%	2/3%
At2g32950	COP1	Y	7/15%	8/16%	8/18%	3/7%	—^e	12/25%	7/11%
At2g46340	SPA1	Y	8/14%	5/7%	8/12%	5/10%	2/4%	17/26%	7/11%
At2g25930	ELF3	Y	6/12%	11/25%	12/26%	4/9%	3/6%	—	—
At2g40080	ELF4	Y	—^e	4/60%	3/42%	—	—	—	—^e
At3g46640	LUX	Y	2/6%	—^e	4/15%	—^e	—	—	—
At3g03940	MLK2	Y	—^e	2/6%	2/6%	—	—	2/4%	—
At1g15750	TPL	N	—^e	3/3%	4/5%	2/3%	3/3%	4/5%	4/5%
At1g47128	RD21a	Y	—^e	3/8%	2/4%	—^e	2/8%	3/8%	—^e
Also see Table 1—source data 1

^a All listed proteins match 99% protein threshold, minimum number peptides of 2 and peptide threshold as 95%. Proteins not matching the criteria were marked with "—".

^b ELF3 AP-MS (Huang et al., 2015) was used for comparison.

^c PCH1ox3 in WT is as shown in Table 1, for comparison with PCH1ox3 in elf4-2 and elf3-2.

^d percent coverage for PCH1 is calculated using protein encoded by At2g16365.2

^e only one exclusive unique peptide was detected.

elife-13292-v2.xml

10.7554/eLife.13292.015

Table 1.

DOI: http://dx.doi.org/10.7554/eLife.13292.015

10.7554/eLife.13292.016Table 1—source data 1.The full list of proteins identified by AP-MS, listing unique peptides and the percent coverage.

DOI: http://dx.doi.org/10.7554/eLife.13292.016

AGI number	Protein name	ELF3 AP-MS^b	Exclusive unique peptide count/Percent coverage^a
			PCH1ox3 in WT			PCH1ox3 in phyB-9
			rep1	rep2	rep3	rep1	rep2
At2g16365	PCH1^c	Y	30/73%	41/85%	37/79%	40/85%	32/77%
At2g18790	phyB	Y	46/69%	47/65%	41/60%	—	—
At5g35840	phyC	Y	31/44%	23/28%	25/29%	—	—
At4g16250	phyD	Y	22/47%	19/34%	20/38%	22/38%	6/11%
At4g18130	phyE	Y	41/55%	40/52%	45/60%	49/60%	31/41%
At1g09570	phyA	Y	31/46%	36/49%	35/45%	36/48%	29/39%
At2g37678	FHY1	N	2/22%	2/21%	4/28%	4/28%	2/21%
At3g42170	DAYSLEEPER	Y	5/13%	—	4/11%	3/8%	2/6%
At1g09340	CRB	Y	—^d	—^d	4/17%	6/24%	3/13%
At5g43630	TZP	Y	9/15%	6/12%	12/23%	—	—
At2g32950	COP1	Y	7/15%	8/16%	8/18%	—	—
At2g46340	SPA1	Y	8/14%	5/7%	8/12%	—	—
At2g25930	ELF3	Y	6/12%	11/25%	12/26%	—	—
At2g40080	ELF4	Y	—^d	4/60%	3/42%	—	—
At3g46640	LUX	Y	2/6%	—^d	4/15%	—	—
At3g03940	MLK2	Y	—^d	2/6%	2/6%	—	—
At1g15750	TPL	N	—^d	3/3%	4/5%	2/2%	—
At1g47128	RD21a	Y	—^d	3/8%	2/4%	—^d	—^d
Also see Table 1—source data 1

^a All listed proteins match 99% protein threshold, minimum number peptides of 2 and peptide threshold as 95%. Proteins not matching the criteria were marked with "—".

^b ELF3 AP-MS (Huang et al., 2015) was used for comparison.

^c Percent coverage for PCH1 is calculated using protein encoded by At2g16365.2.

^d Only one exclusive unique peptide was detected.

elife-13292-v2.xml

10.7554/eLife.13292.017

Table 2.

DOI: http://dx.doi.org/10.7554/eLife.13292.017

AGI number	Protein name	ELF3 AP-MS^b	Exclusive unique peptide count/Percent coverage^a
			PCH1ox3 in WT^c			PCH1ox3 in elf4-2		PCH1ox3 in elf3-2
			rep1	rep2	rep3	rep1	rep2	rep1	rep2
At2g16365	PCH1^d	Y	30/73%	41/85%	37/79%	29/77%	34/78%	42/82%	36/82%
At2g18790	phyB	Y	46/69%	47/65%	41/60%	47/70%	31/46%	42/63%	40/56%
At5g35840	phyC	Y	31/44%	23/28%	25/29%	30/43%	13/16%	20/28%	15/18%
At4g16250	phyD	Y	22/47%	19/34%	20/38%	20/42%	12/25%	20/37%	16/30%
At4g18130	phyE	Y	41/55%	40/52%	45/60%	42/57%	37/50%	43/55%	40/53%
At1g09570	phyA	Y	31/46%	36/49%	35/45%	32/47%	24/34%	34/49%	27/38%
At2g37678	FHY1	N	2/22%	2/21%	4/28%	—^e	3/21%	—^e	3/21%
At3g42170	DAYSLEEPER	Y	5/13%	—	4/11%	3/7%	5/11%	2/5%	—^e
At1g09340	CRB	Y	—^e	—^e	4/17%	2/9%	5/22%	3/13%	3/13%
At5g43630	TZP	Y	9/15%	6/12%	12/23%	4/7%	—^e	12/21%	2/3%
At2g32950	COP1	Y	7/15%	8/16%	8/18%	3/7%	—^e	12/25%	7/11%
At2g46340	SPA1	Y	8/14%	5/7%	8/12%	5/10%	2/4%	17/26%	7/11%
At2g25930	ELF3	Y	6/12%	11/25%	12/26%	4/9%	3/6%	—	—
At2g40080	ELF4	Y	—^e	4/60%	3/42%	—	—	—	—^e
At3g46640	LUX	Y	2/6%	—^e	4/15%	—^e	—	—	—
At3g03940	MLK2	Y	—^e	2/6%	2/6%	—	—	2/4%	—
At1g15750	TPL	N	—^e	3/3%	4/5%	2/3%	3/3%	4/5%	4/5%
At1g47128	RD21a	Y	—^e	3/8%	2/4%	—^e	2/8%	3/8%	—^e
Also see Table 1—source data 1

^a All listed proteins match 99% protein threshold, minimum number peptides of 2 and peptide threshold as 95%. Proteins not matching the criteria were marked with "—".

^b ELF3 AP-MS (Huang et al., 2015) was used for comparison.

^c PCH1ox3 in WT is as shown in Table 1, for comparison with PCH1ox3 in elf4-2 and elf3-2.

^d percent coverage for PCH1 is calculated using protein encoded by At2g16365.2

^e only one exclusive unique peptide was detected.

elife-13571-v3.xml

10.7554/eLife.13571.008

Table 1.

Amino acid sequences of the synthetic multivalent R-motif containing peptides.

DOI: http://dx.doi.org/10.7554/eLife.13571.008

Peptide Name^#	Peptide amino acid sequence
Peptide Name^#	Peptide amino acid sequence	rpL5	²¹RRRREGKTDY₁₀YARKRLV³⁷
GNL2	⁶⁸²RRRAVRQQRP₁₀KKVGVRYYET₂₀HNVKNRNR⁷⁰⁹
SURF6	²⁹⁹RRAQRQRRWE₁₀KRTAGVVEKM₂₀QQRQDRRR³²⁶
rpL23a	⁴⁷RRPKTLRLRR₁₀QPKYPRKSAP₂₀RR⁶⁸
rpL5-RA	²¹RRRREGKTDY₁₀YAAKALV³⁷
rpL5-2xLinker	RRRREGKTDY₁₀YAEGKTDYYA₂₀RKRLV

^#The peptides are referred to by the same name as the protein they originate from and the residue numbers of their N- and C-termini are indicated.

elife-13571-v3.xml

10.7554/eLife.13571.013

Table 2.

Binding affinities for interactions between N122 (NPM1 residues 1–122, displaying only A1) and N130 (displaying both A1 and A2) and the multivalent R-motif-containing peptides, determined using isothermal titration calorimetry (ITC), at concentrations below the critical phase separation threshold.

DOI: http://dx.doi.org/10.7554/eLife.13571.013

Peptide	N122		N130
Peptide	N (sites)	K_D (μM)	N (sites)	K_D (μM)
rpL5	0.63 ± 0.09	19.0 ± 2.7	2.18 ± 0.19	20.5 ± 5.0
GNL2	0.66 ± 0.04	10.2 ± 1.3	n.d.^*	n.d.^*
SURF6	0.55 ± 0.06	9.2 ± 0.5	1.4 ± 0.02	19.0 ± 0.8
rpL23a	n.d.^#	n.d.^#	n.d.^*	n.d.^*
rpL5-RA	1.0 ± 0.06	50.9 ± 3.18	0.84 ± 0.07	140.1 ± 9.29

^* Not determined due to multiple, unresolved binding events

^# Heat change was too weak for accurate data analysis

Average values from a minimum of three independent experiments are reported ± SD

elife-13732-v2.xml

10.7554/eLife.13732.004

Table 1.

Behavioral performance.

DOI: http://dx.doi.org/10.7554/eLife.13732.004

Task	Placebo (n = 18)		Baclofen (n = 14)		P value of group × session interaction
Task	Pre	Post	Pre	Post	P value of group × session interaction
MMSE	29.89 ± 0.11	29.94 ± 0.06	29.93 ± 0.07	30.00 ± 0	0.86
Digit span (forward)	7.22 ± 0.22	7.72 ± 0.14	7.14 ± 0.31	7.43 ± 0.20	0.55
Digit span (backward)	6.00 ± 0.20	6.00 ± 0.29	5.57 ± 0.31	5.71 ± 0.27	0.69
Trail making test B (s)	48.32 ± 2.70	39.05 ± 2.01	57.62 ± 5.42	47.11 ± 5.67	0.85
Stanford sleepiness scale	2.44 ± 0.17	2.22 ± 0.21	1.93 ± 0.20	2.50 ± 0.33	0.041*
Sniffin’ Sticks (odor detection threshold)	7.08 ± 0.84	9.65 ± 1.06	7.82 ± 0.95	8.57 ± 1.01	0.22
UPSIT (odor identification)	36.28 ± 0.61	36.00 ± 0.56	34.57 ± 0.49	33.79 ± 0.63	0.55
α- vs. β-pinene triangle test (fine odor discrimination)	0.66 ± 0.05	0.72 ± 0.05	0.72 ± 0.05	0.73 ± 0.07	0.45
Odor intensity ratings	4.00 ± 0.32	4.13 ± 0.31	3.05 ± 0.18	2.91 ± 0.28	0.39
Odor pleasantness ratings	5.43 ± 0.16	5.63 ± 0.16	5.64 ± 0.13	5.63 ± 0.16	0.12
Odor category descriptor ratings (within – across)	7.47 ± 0.44	7.49 ± 0.36	7.44 ± 0.46	7.78 ± 0.34	0.59
Odor pairwise similarity ratings (within – across)	4.16 ± 0.60	5.14 ± 0.55	3.93 ± 0.32	4.53 ± 0.44	0.59
Odor categorization catch trial accuracy	0.87 ± 0.04	0.89 ± 0.03	0.81 ± 0.04	0.81 ± 0.04	0.80
Odor categorization catch trial RT (s)	3.29 ± 0.23	2.85 ± 0.15	3.89 ± 0.38	3.48 ± 0.34	0.93
Visual categorization catch trial accuracy	0.97 ± 0.01 (n = 14)	0.99 ± 0.004	0.97 ± 0.01 (n = 11)	0.96 ± 0.01	0.21
Visual categorization catch trial RT (s)	0.42 ± 0.02	0.40 ± 0.03	0.44 ± 0.04	0.52 ± 0.06	0.25

Data are shown for cognitive and olfactory tests, as well as for behavioral performance in fMRI experiments from placebo and baclofen groups in pre- and post-drug sessions. Scores are presented as mean ± s.e.m. P values reported are for the interaction effects between group and session, based on a 2-way ANOVA, with one between-group ‘drug’ factor (placebo/baclofen) and one within-subject ‘session’ factor (pre/post). *P < 0.05.

elife-13732-v3.xml

10.7554/eLife.13732.004

Table 1.

Behavioral performance.

DOI: http://dx.doi.org/10.7554/eLife.13732.004

Task	Placebo (n = 18)		Baclofen (n = 14)		P value of group × session interaction
Task	Pre	Post	Pre	Post	P value of group × session interaction
MMSE	29.89 ± 0.11	29.94 ± 0.06	29.93 ± 0.07	30.00 ± 0	0.86
Digit span (forward)	7.22 ± 0.22	7.72 ± 0.14	7.14 ± 0.31	7.43 ± 0.20	0.55
Digit span (backward)	6.00 ± 0.20	6.00 ± 0.29	5.57 ± 0.31	5.71 ± 0.27	0.69
Trail making test B (s)	48.32 ± 2.70	39.05 ± 2.01	57.62 ± 5.42	47.11 ± 5.67	0.85
Stanford sleepiness scale	2.44 ± 0.17	2.22 ± 0.21	1.93 ± 0.20	2.50 ± 0.33	0.041*
Sniffin’ Sticks (odor detection threshold)	7.08 ± 0.84	9.65 ± 1.06	7.82 ± 0.95	8.57 ± 1.01	0.22
UPSIT (odor identification)	36.28 ± 0.61	36.00 ± 0.56	34.57 ± 0.49	33.79 ± 0.63	0.55
α- vs. β-pinene triangle test (fine odor discrimination)	0.66 ± 0.05	0.72 ± 0.05	0.72 ± 0.05	0.73 ± 0.07	0.45
Odor intensity ratings	4.00 ± 0.32	4.13 ± 0.31	3.05 ± 0.18	2.91 ± 0.28	0.39
Odor pleasantness ratings	5.43 ± 0.16	5.63 ± 0.16	5.64 ± 0.13	5.63 ± 0.16	0.12
Odor category descriptor ratings (within – across)	7.47 ± 0.44	7.49 ± 0.36	7.44 ± 0.46	7.78 ± 0.34	0.59
Odor pairwise similarity ratings (within – across)	4.16 ± 0.60	5.14 ± 0.55	3.93 ± 0.32	4.53 ± 0.44	0.59
Odor categorization catch trial accuracy	0.87 ± 0.04	0.89 ± 0.03	0.81 ± 0.04	0.81 ± 0.04	0.80
Odor categorization catch trial RT (s)	3.29 ± 0.23	2.85 ± 0.15	3.89 ± 0.38	3.48 ± 0.34	0.93
Visual categorization catch trial accuracy	0.97 ± 0.01 (n = 14)	0.99 ± 0.004	0.97 ± 0.01 (n = 11)	0.96 ± 0.01	0.21
Visual categorization catch trial RT (s)	0.42 ± 0.02	0.40 ± 0.03	0.44 ± 0.04	0.52 ± 0.06	0.25

elife-14003-v1.xml

10.7554/eLife.14003.004

Table 1.

Comparison of antimicrobial susceptibility by Salmonella Typhi lineage.

DOI: http://dx.doi.org/10.7554/eLife.14003.004

E test	Non-H58 (N=13)			H58 (N=65)			p value*
E test	MIC50	MIC90	GM (range)	MIC50	MIC90	GM (range)
Amoxicillin	0.5	1	0.77 (0.38–38)	0.75	>256	1.43 (0.38–>256)	0.0412
Chloramphenicol	3	4	2.7 (1.5–8)	4	12	5.7 (2–>256)	0.0147
Ceftriaxone	0.06	0.06	0.06 (0.05–0.13)	0.09	0.19	0.11 (0.03–0.64)	0.0004
Gatifloxacin	0.13	0.25	0.06 (0.01–2)	0.13	2	0.21 (0.01–3)	0.1197
Nalidixic acid	>256	>256	21.6 (1–>256)	>256	>256	346.8 (1–>256)	0.0004
Ofloxacin	0.25	0.75	0.24 (0.03–>32)	0.5	>3232	1.09 (0.03–>32)	0.0240
Trimethoprim sulphate	0.02	0.05	0.03 (0.02–0.05)	0.05	0.32	0.09 (0.01–>32)	0.0016
Ciprofloxacin	0.13	0.75	0.11 (0.01–>32)	0.38	>32	0.80 (0.02–>32)	0.0051
Ciprofloxacin susceptibility group							0.0008^#
- Susceptible	6 (46.2%)			4 (6.2%)
- Intermediate	4 (30.8%)			48 (73.8%)
- Resistant	3 (23.1%)			13 (20.0%)

*Comparisons between Salmonella Typhi lineage for MICs and ciprofloxacin susceptibility groups were based on the Wilcoxon rank sum test and Fisher’s exact test. respectively.

MIC: minimum inhibitory concentration, measured in µg/ml

#p value for comparison of susceptible vs. intermediate/resistant combined between groups by Fisher’s exact test is 0.001.

GM: geometric mean, the upper range of the values was determined by multiplying the MIC by 2 if the result was >X (for example, >256 = 256*2 = 512).

elife-14022-v3.xml

10.7554/eLife.14022.008

Table 1.

From an initial number of possible networks (Step 1), RDNets progressively identifies reaction-diffusion networks that can form a pattern (Step 6).

DOI: http://dx.doi.org/10.7554/eLife.14022.008

Steps	3 nodes		4 nodes
Steps	# networks	# topologies	# networks	# topologies
1. Minimal systems	84	5376	11440	1464320
2. Strongly connected	48	3072	2284	292352
3. Non-symmetrical	25	1600	597	76416
4. Stable	24	556	324	8640
5-6. Reaction-diffusion	21	84	64	512

elife-14119-v2.xml

10.7554/eLife.14119.003

Table 1.

Properties of employed FG domain constructs. See Table 1—source data 1 for the full amino acid sequences of these constructs.

DOI: http://dx.doi.org/10.7554/eLife.14119.003

10.7554/eLife.14119.004Table 1—source data 1.Amino acid sequence of employed FG domain constructs.

FG domains are shown in black letters, His tags in blue letters, and remaining parts (i.e., TEV cleavage sites, Cys tags and spacers) in grey letters. FxFG motifs are marked in yellow, GLFG motifs in green, other FG motifs in purple. Nup98-glyco features O-GlcNAc on ~30 of the S and T residues.

DOI: http://dx.doi.org/10.7554/eLife.14119.004

FG domain	amino acids ^a	sequence	FG motifs			FG motifs/amino acids
FG domain	amino acids ^a	sequence	FxFG	GLFG	Other	FG motifs/amino acids
Nsp1	615	irregular, natural	19	0	14	0.054
Nup98-glyco	496	irregular, natural	3	8	28	0.079
reg-FSFG	315	regular, artificial	16	0	0	0.051

^a Excluding the His tags but including all other auxiliary amino acids (TEV cleavage sites, Cys tags and spacers).

elife-14170-v2.xml

10.7554/eLife.14170.046

Table 5.

pFRG/RTN slices respond to CO₂ if the EP3R is present. The average mean frequency of all cells in the network and the average mean frequency of NK1R-positive cells during the control period or during exposure to hypercapnia are shown (pCO₂ = 55 mmHg, pH = 7.5). N.S.: not significant. N: number of slices, n: number of cells. Data are presented as mean ± SD.

DOI: http://dx.doi.org/10.7554/eLife.14170.046

	Mean frequency (mHz)
	Network			NK1R+ cells
	Control	Hypercapnia		Control	Hypercapnia
pFRG/RTN - WT (N=7, n=343)	21.6 ± 3.2	54.1 ± 2.7*	p<0.05	14.4 ± 0.9	38.5 ± 5.5*	p<0.05
pFRG/RTN - Ptger3^−/− (N=5, n=448)	25.0 ± 7.9	26.0 ± 1.9	N.S.	11.4 ± 5.8	11.6 ± 3.8	N.S.
preBötC - WT (N=5, n=1737)	16.4 ± 2.5	16.5 ± 1.3	N.S.	16.6 ± 4.6	15.7 ± 5.3	N.S.
preBötC - Ptger3^−/− (N=4, n=822)	21.1 ± 8.6	17.3 ± 3.8	N.S.	22.7 ± 5.9	17.8 ± 7.7	N.S.

elife-14170-v2.xml

10.7554/eLife.14170.057

Table 6.

PGE₂ increases the frequency of pFRG/RTN neurons and decreases the frequency of preBötC neurons.The mean frequencies of NK1R-positive cells during the control period or during exposure to 10 nM PGE₂ are shown. N.S.: not significant. N: number of slices, n: number of cells. Data are presented as mean ± SD.

DOI: http://dx.doi.org/10.7554/eLife.14170.057

	Mean frequency (mHz)
	Control	PGE₂
pFRG/RTN - WT (N=5, n=343)	13.7 ± 1.1	21.5 ± 2.9*	p<0.05
pFRG/RTN - Ptger3−/− (N=4, n=448)	12.1 ± 2.0	8.5 ± 2.9	N.S.
preBötC - WT (N=7, n=1737)	20.3 ± 2.2	8.7 ± 1.4*	p<0.05
preBötC - Ptger3−/− (N=5, n=822)	22.8 ± 2.3	16.4 ± 1.1	N.S.

elife-14170-v2.xml

10.7554/eLife.14170.063

Table 7.

Silencing of Ptger3-expressing cells inhibits the response to hypercapnia.Mean frequencies of the pFRG/RTN network during the control period and during exposure to hypercapnia with and without Halo57 stimulation are shown. N.S.: not significant. N: number of slices. Data are presented as mean ± SD.

DOI: http://dx.doi.org/10.7554/eLife.14170.063

N=41	Mean frequency (mHz)
N=41	Control	Hypercapnia
Control	22.9 ± 9.0*	34.0 ± 4.3*	p<0.05
Halo57 stimulation	9.0 ± 1.7	10.3 ± 1.1	N.S.

elife-14734-v2.xml

10.7554/eLife.14734.008

Table 3.

Repartition of Δ133p53 isoforms in the Tayside breast cancer cohort (2x2 table). (A) Δ133p53α X Δ133p53β. (B) Δ133p53α X Δ133p53γ. (C) Δ133p53β X Δ133p53γ (−) not detected, (+) amplified.

DOI: http://dx.doi.org/10.7554/eLife.14734.008

A
		Δ133p53α
		−	+	Total
Δ133p53β	− +	174 2	76 21	250 23
Total		176	97	273

B
		Δ133p53α
		−	+	Total
Δ133p53γ	− +	138 3	27 53	165 56
Total		141	80	221

C
		Δ133p53γ
		−	+	Total
Δ133p53β	− +	156 9	42 14	198 23
Total		165	56	221

elife-14734-v2.xml

10.7554/eLife.14734.009

Table 4.

Univariate analysis of Δ133p53 isoforms expression in relation to clinical pathological markers. Tumor grade, cancer type (ductal or others), tumor size (>or < 20 mm) were analyzed by Fisher’s t-test. Association with the number of invaded lymph nodes were analyzed by Mann-Whitney method.

DOI: http://dx.doi.org/10.7554/eLife.14734.009

		grade			type			size			nb invaded Lymph nodes
		1-2	3	p value	ductal	others	p value	<20 mm	>20 mm	p value	nb invaded Lymph nodes
∆133p53α	− +	76 34	98 61	p<0.21	140 80	36 17	p<0.56	62 29	113 67	p<0.39	p<0.97
∆133p53β	− +	102 8	144 15	p<0.54	201 19	49 4	p<0.8	81 10	167 13	p<0.30	p<0.60
∆133p53γ	− +	75 21	87 35	p<0.25	133 46	32 10	p<0.8	59 19	105 37	p<0.79	p<0.78

elife-14734-v3.xml

10.7554/eLife.14734.008

Table 3.

DOI: http://dx.doi.org/10.7554/eLife.14734.008

A
		Δ133p53α
		−	+	Total
Δ133p53β	− +	174 2	76 21	250 23
Total		176	97	273

B
		Δ133p53α
		−	+	Total
Δ133p53γ	− +	138 3	27 53	165 56
Total		141	80	221

C
		Δ133p53γ
		−	+	Total
Δ133p53β	− +	156 9	42 14	198 23
Total		165	56	221

elife-14734-v3.xml

10.7554/eLife.14734.009

Table 4.

DOI: http://dx.doi.org/10.7554/eLife.14734.009

		grade			type			size			nb invaded Lymph nodes
		1-2	3	p value	ductal	others	p value	<20 mm	>20 mm	p value	nb invaded Lymph nodes
∆133p53α	− +	76 34	98 61	p<0.21	140 80	36 17	p<0.56	62 29	113 67	p<0.39	p<0.97
∆133p53β	− +	102 8	144 15	p<0.54	201 19	49 4	p<0.8	81 10	167 13	p<0.30	p<0.60
∆133p53γ	− +	75 21	87 35	p<0.25	133 46	32 10	p<0.8	59 19	105 37	p<0.79	p<0.78

elife-15085-v1.xml

10.7554/eLife.15085.003

Table 2.

WHO-classified G6PD deficiency alleles observed in this study. Locus refers to GRCh37, dbSNP137 and Ensembl build 84. WHO refers to grade of G6PD deficiency based on the WHO classification scheme. Allele frequency is calculated in population controls. GM Gambia; ML, Mali; BF, Burkina Faso; GH-N, Ghana (Noguchi); GH-K, Ghana (Kumasi); NG Nigeria; CM, Cameroon; KY, Kenya; TZ, Tanzania; MW, Malawi; VN, Vietnam; PNG, Papua New Guinea.

DOI: http://dx.doi.org/10.7554/eLife.15085.003

SNP	Locus	Base change	WHO	Allele frequency
SNP	Locus	Base change	WHO	GM	ML	BF	GH-N	GH-K	NG	CM	KY	TZ	MW	VN	PNG
CM973154	153760261	A/C	I	0.0004	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
rs72554665	153760484	C/A	II	0.0004	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0055	0.0000
CM920290	153760605	G/A	II	0.0002	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0014	0.0028
rs137852342	153761184	G/A	III	0.0000	0.0020	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0014	0.0000
rs76723693	153761240	968T>C	III	0.0695	0.0082	0.0009	0.0000	0.0003	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
rs137852327	153761337	C/T	II	0.0006	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0096	0.0141
CM014189	153761820	T/A	II	0.0004	0.0000	0.0000	0.0000	0.0008	0.0000	0.0000	0.0004	0.0000	0.0000	0.0000	0.0000
rs137852328	153762340	680G>T	III	0.0002	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
rs137852330	153762605	G/A	II	0.0004	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0003	0.0000
rs5030868	153762634	563G>A	II	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0003	0.0000	0.0000	0.0000	0.0085
rs5030872	153762655	542A>T	II	0.0145	0.0041	0.0009	0.0000	0.0003	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
CM970547	153763462	G/A	II	0.0008	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
rs78365220	153763485	A/G	II	0.0002	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0366
rs1050829	153763492	376T>C	IV	0.3206	0.4132	0.4186	0.4476	0.4267	0.5574	0.3429	0.4060	0.3787	0.3920	0.0000	0.0000
rs1050828	153764217	202C>T	III	0.0273	0.1616	0.1447	0.1713	0.1847	0.3167	0.1075	0.1930	0.2071	0.1988	0.0000	0.0000

elife-15085-v1.xml

10.7554/eLife.15085.012

Table 5.

Calculation of the G6PD deficiency (G6PDd) score. The G6PDd score is calculated on the basis of the haplotypes at the 15 WHO-classified SNPs. For each haplotype, the loss of normal G6PD function is determined according to the WHO severity class (0, I, II, III or IV) of the most severe mutation carried. See Materials and methods for more details. The G6PDd score for each individual is then the average loss of function across the two haplotypes, where males are treated as homozygous females. For example, the assigned loss of normal G6PD function for a haplotype where the most severe mutation is the class III mutation G6PD+202T is 65, so an individual with this haplotype and another with no deficiency mutations will average a G6PDd score of 32.5. Individuals were further categorized on the basis of their G6PDd score as normal G6PDd (G6PDd score = 0); Low G6PDd (0 < G6PDd score < 25, blue boxes); Medium G6PDd (25 ≤ G6PDd score < 50, yellow boxes); High G6PDd (50 ≤ G6PDd score < 85, orange boxes); or Very High (G6PDd ≥ 85, red box). Scores not observed in our study are shown in grey boxes.

DOI: http://dx.doi.org/10.7554/eLife.15085.012

G6PDd score			Haplotype 1
			Severity class (loss of normal G6PD function)
			0 (0)	IV (20)	III (65)	II (95)	I (100)
Haplotype 2	Severity class (Loss of normal G6PD function)	0 (0)	0	10	32.5	47.5	50
		IV (20)	10	20	42.5	57.5	60
		III (65)	32.5	42.5	65	80	82.5
		II (95)	47.5	57.5	80	95	97.5
		I (100	50	60	82.5	97.7	100

elife-15085-v1.xml

10.7554/eLife.15085.013

Table 6.

G6PD deficiency score categorical model association test results. Counts, odds ratios (ORs), 95% confidence intervals (95% CI) and P-values are presented for the effect of each category of G6PD deficiency (G6PDd) score, compared to individuals with G6PDd score = 0, for all severe malaria cases and for the two subtypes cerebral malaria and severe malarial anaemia. P-value shown in bold is for overall model fit. P-value for the overall model fit. Results are shown for all individuals combined at each site and across all sites. Results are adjusted for the sickle-cell trait, ethnicity and sex. n.c., not calculated.

DOI: http://dx.doi.org/10.7554/eLife.15085.013

Sample	G6PDd score category	Controls	Severe malaria			Cerebral malaria			Severe malarial anaemia
Sample	G6PDd score category	N (%)	N (%)	OR (95% CI)	P	N (%)	OR (95% CI)	P	N (%)	OR (95% CI)	P
Females	0	3,761 (46.4)	2,299 (42.6)	–	–	672 (42.3)	-–	-–	400 (39.8)	-–	-–
All	(0–25)	2,132 (26.3)	1,626 (30.1)	0.98 (0.9–1.08)	0.72	495 (31.2)	1.02 (0.89–1.17)	0.81	306 (30.4)	1.08 (0.9–1.29)	0.41
	(25–50)	2,001 (24.7)	1,310 (24.3)	0.88 (0.8–0.97)	8.59E-03	377 (23.7)	0.83 (0.71–0.96)	1.04E-02	252 (25.1)	1 (0.83–1.21)	0.99
All	(50–85)	210 (2.6)	156 (2.9)	1.02 (0.81–1.28)	0.85	44 (2.8)	0.93 (0.66–1.31)	0.67	45 (4.5)	1.71 (1.16–2.53)	6.86E-03
	≥85	2 (0)	8 (0.1)	7.3 (1.43–37.24)	0.02	0 (0)	n.c	n.c.	2 (0.2)	9.72 (1.01–93.12)	0.05
	Overall	8,106	5,399		3.68E-03	1,588	–	0.06	1,005	–	0.03
Males	0	5,960 (67.9)	4,216 (65.1)	-–	-–	1,212 (68.4)	–	–	707 (60)	–	–
All	(0–25)	1,572 (17.9)	1,303 (20.1)	1.08 (0.99–1.19)	0.08	342 (19.3)	1.01 (0.88–1.16)	0.86	227 (19.3)	1.05 (0.87–1.25)	0.63
	(25–50)	0 (0)	0 (0)	n.c	n.c.	0 (0)	n.c	n.c.	0 (0)	n.c	n.c.
All	(50–85)	1,196 (13.6)	923 (14.3)	1.05 (0.95–1.16)	0.35	214 (12.1)	0.79 (0.67–0.94)	6.31E-03	236 (20)	1.44 (1.2–1.74)	1.17E-04
	≥85	55 (0.6)	30 (0.5)	0.65 (0.4–1.04)	0.07	3 (0.2)	0.26 (0.08–0.85)	0.03	9 (0.8)	1.24 (0.58–2.67)	0.58
	Overall	8,783	6,472	-–	0.08	1,771	-–	1.49E-03	1,179	–	1.97E-03
All	0	9,721 (57.6)	6,515 (54.9)	–	–	1,884 (56.1)	–	–	1,107 (50.7)	–	–
All	(0–25)	3,704 (21.9)	2,929 (24.7)	1.05 (0.99–1.12)	0.12	837 (24.9)	1.03 (0.93–1.13)	0.56	533 (24.4)	1.05 (0.93–1.19)	0.45
	(25–50)	2,001 (11.8)	1,310 (11)	0.94 (0.86–1.03)	0.16	377 (11.2)	0.86 (0.75–0.99)	0.04	252 (11.5)	0.95 (0.8–1.14)	0.6
	(50–85)	1,406 (8.3)	1,079 (9.1)	1.02 (0.93–1.12)	0.71	258 (7.7)	0.8 (0.69–0.93)	2.95E-03	281 (12.9)	1.49 (1.26–1.76)	2.22E-06
	≥85	57 (0.3)	38 (0.3)	0.87 (0.55–1.36)	0.54	3 (0.1)	0.28 (0.09–0.86)	0.03	11 (0.5)	1.44 (0.66–3.17)	0.36
All	Overall	16,889	11,871	–	0.14	3,359	–	2.29E-04	2184	–	1.02E-04

elife-15085-v1.xml

10.7554/eLife.15085.016

Table 7.

Fitness arrays suggested by observed OR estimates of effect at G6PD+202 on cerebral malaria and severe malarial anaemia. A₁ represents the wild-type allele and A₂ the derived allele. In females, odds ratios (ORs) for association with cerebral malaria in derived homozygotes and heterozygotes compared to wild-type homozygotes are 0.87 and ~1, respectively, suggesting a symmetrical heterozygous advantage. In males, the OR for association with cerebral malaria in derived, compared to wild-type, hemizygotes is 0.82, suggesting a moderate fitness difference between male genotypes. For severe malarial anaemia, in females, the ORs in derived homozygotes and heterozygotes, compared to wild-type heterozygotes, are 1.84 and 1, respectively, suggesting selection against derived homozygotes; in males, the OR in derived hemizygotes, compared to wild-type, is 1.48, suggesting selection against derived male hemizygotes. The case fatality rate is estimated to be 20% (m = 0.2) for cerebral and 10% (m = 0.1) for severe malarial anaemia.

DOI: http://dx.doi.org/10.7554/eLife.15085.016

Genotype		Females			Males
Genotype		A₁A₁	A₁A₂	A₂A₂	A₁	A₂
		w₁₁	w ₁₂	w ₂₂	w ₁	w ₂
Cerebral malaria selection
	Observed OR*	1	0.87 (0.75–1)	1.02 (0.7–1.48)	1	0.82 (0.69–0.97)
	Fitness Array^†	1–s_f^CM	1	1–s_f^CM	1–s_m^CM	1
	Fitness (w)	0.974	1	0.974	0.964	1
Severe malarial anaemia selection
	Observed OR*	1	0.97 (0.8–1.17)	1.84 (1.21–2.79)	1	1.48 (1.22–1.8)
	Fitness Array^‡	1	1	1–s_f^SMA	1	1–s_m^SMA
	Fitness (w)	1	1	0.954	1	0.968

*Odds ratios are estimated from a genotypic model and are adjusted for sickle-cell trait and ethnicity.

^†s_f^CM = m(1–OR) = 0.2 (1 0.87) = 0.26. s_m^CM = 0.2(1–0.82) = 0.036.

^‡s_f^SMA = m (1–1/OR) = 0.1 (1–1/1.84) = 0.046; s_m^SMA = m(1–1/OR) = 0.1 (1 1/1.48) = 0.032.

elife-15085-v2.xml

10.7554/eLife.15085.003

Table 2.

DOI: http://dx.doi.org/10.7554/eLife.15085.003

SNP	Locus	Base change	WHO	Allele frequency
SNP	Locus	Base change	WHO	GM	ML	BF	GH-N	GH-K	NG	CM	KY	TZ	MW	VN	PNG
CM973154	153760261	A/C	I	0.0004	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
rs72554665	153760484	C/A	II	0.0004	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0055	0.0000
CM920290	153760605	G/A	II	0.0002	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0014	0.0028
rs137852342	153761184	G/A	III	0.0000	0.0020	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0014	0.0000
rs76723693	153761240	968T>C	III	0.0695	0.0082	0.0009	0.0000	0.0003	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
rs137852327	153761337	C/T	II	0.0006	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0096	0.0141
CM014189	153761820	T/A	II	0.0004	0.0000	0.0000	0.0000	0.0008	0.0000	0.0000	0.0004	0.0000	0.0000	0.0000	0.0000
rs137852328	153762340	680G>T	III	0.0002	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
rs137852330	153762605	G/A	II	0.0004	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0003	0.0000
rs5030868	153762634	563G>A	II	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0003	0.0000	0.0000	0.0000	0.0085
rs5030872	153762655	542A>T	II	0.0145	0.0041	0.0009	0.0000	0.0003	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
CM970547	153763462	G/A	II	0.0008	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
rs78365220	153763485	A/G	II	0.0002	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000	0.0366
rs1050829	153763492	376T>C	IV	0.3206	0.4132	0.4186	0.4476	0.4267	0.5574	0.3429	0.4060	0.3787	0.3920	0.0000	0.0000
rs1050828	153764217	202C>T	III	0.0273	0.1616	0.1447	0.1713	0.1847	0.3167	0.1075	0.1930	0.2071	0.1988	0.0000	0.0000

elife-15085-v2.xml

10.7554/eLife.15085.012

Table 5.

DOI: http://dx.doi.org/10.7554/eLife.15085.012

G6PDd score			Haplotype 1
			Severity class (loss of normal G6PD function)
			0 (0)	IV (20)	III (65)	II (95)	I (100)
Haplotype 2	Severity class (Loss of normal G6PD function)	0 (0)	0	10	32.5	47.5	50
		IV (20)	10	20	42.5	57.5	60
		III (65)	32.5	42.5	65	80	82.5
		II (95)	47.5	57.5	80	95	97.5
		I (100	50	60	82.5	97.7	100

elife-15085-v2.xml

10.7554/eLife.15085.013

Table 6.

DOI: http://dx.doi.org/10.7554/eLife.15085.013

Sample	G6PDd score category	Controls	Severe malaria			Cerebral malaria			Severe malarial anaemia
Sample	G6PDd score category	N (%)	N (%)	OR (95% CI)	P	N (%)	OR (95% CI)	P	N (%)	OR (95% CI)	P
Females	0	3,761 (46.4)	2,299 (42.6)	–	–	672 (42.3)	-–	-–	400 (39.8)	-–	-–
All	(0–25)	2,132 (26.3)	1,626 (30.1)	0.98 (0.9–1.08)	0.72	495 (31.2)	1.02 (0.89–1.17)	0.81	306 (30.4)	1.08 (0.9–1.29)	0.41
	(25–50)	2,001 (24.7)	1,310 (24.3)	0.88 (0.8–0.97)	8.59E-03	377 (23.7)	0.83 (0.71–0.96)	1.04E-02	252 (25.1)	1 (0.83–1.21)	0.99
All	(50–85)	210 (2.6)	156 (2.9)	1.02 (0.81–1.28)	0.85	44 (2.8)	0.93 (0.66–1.31)	0.67	45 (4.5)	1.71 (1.16–2.53)	6.86E-03
	≥85	2 (0)	8 (0.1)	7.3 (1.43–37.24)	0.02	0 (0)	n.c	n.c.	2 (0.2)	9.72 (1.01–93.12)	0.05
	Overall	8,106	5,399		3.68E-03	1,588	–	0.06	1,005	–	0.03
Males	0	5,960 (67.9)	4,216 (65.1)	-–	-–	1,212 (68.4)	–	–	707 (60)	–	–
All	(0–25)	1,572 (17.9)	1,303 (20.1)	1.08 (0.99–1.19)	0.08	342 (19.3)	1.01 (0.88–1.16)	0.86	227 (19.3)	1.05 (0.87–1.25)	0.63
	(25–50)	0 (0)	0 (0)	n.c	n.c.	0 (0)	n.c	n.c.	0 (0)	n.c	n.c.
All	(50–85)	1,196 (13.6)	923 (14.3)	1.05 (0.95–1.16)	0.35	214 (12.1)	0.79 (0.67–0.94)	6.31E-03	236 (20)	1.44 (1.2–1.74)	1.17E-04
	≥85	55 (0.6)	30 (0.5)	0.65 (0.4–1.04)	0.07	3 (0.2)	0.26 (0.08–0.85)	0.03	9 (0.8)	1.24 (0.58–2.67)	0.58
	Overall	8,783	6,472	-–	0.08	1,771	-–	1.49E-03	1,179	–	1.97E-03
All	0	9,721 (57.6)	6,515 (54.9)	–	–	1,884 (56.1)	–	–	1,107 (50.7)	–	–
All	(0–25)	3,704 (21.9)	2,929 (24.7)	1.05 (0.99–1.12)	0.12	837 (24.9)	1.03 (0.93–1.13)	0.56	533 (24.4)	1.05 (0.93–1.19)	0.45
	(25–50)	2,001 (11.8)	1,310 (11)	0.94 (0.86–1.03)	0.16	377 (11.2)	0.86 (0.75–0.99)	0.04	252 (11.5)	0.95 (0.8–1.14)	0.6
	(50–85)	1,406 (8.3)	1,079 (9.1)	1.02 (0.93–1.12)	0.71	258 (7.7)	0.8 (0.69–0.93)	2.95E-03	281 (12.9)	1.49 (1.26–1.76)	2.22E-06
	≥85	57 (0.3)	38 (0.3)	0.87 (0.55–1.36)	0.54	3 (0.1)	0.28 (0.09–0.86)	0.03	11 (0.5)	1.44 (0.66–3.17)	0.36
All	Overall	16,889	11,871	–	0.14	3,359	–	2.29E-04	2184	–	1.02E-04

elife-15085-v2.xml

10.7554/eLife.15085.016

Table 7.

DOI: http://dx.doi.org/10.7554/eLife.15085.016

Genotype		Females			Males
Genotype		A₁A₁	A₁A₂	A₂A₂	A₁	A₂
		w₁₁	w ₁₂	w ₂₂	w ₁	w ₂
Cerebral malaria selection
	Observed OR*	1	0.87 (0.75–1)	1.02 (0.7–1.48)	1	0.82 (0.69–0.97)
	Fitness Array^†	1–s_f^CM	1	1–s_f^CM	1–s_m^CM	1
	Fitness (w)	0.974	1	0.974	0.964	1
Severe malarial anaemia selection
	Observed OR*	1	0.97 (0.8–1.17)	1.84 (1.21–2.79)	1	1.48 (1.22–1.8)
	Fitness Array^‡	1	1	1–s_f^SMA	1	1–s_m^SMA
	Fitness (w)	1	1	0.954	1	0.968

*Odds ratios are estimated from a genotypic model and are adjusted for sickle-cell trait and ethnicity.

^†s_f^CM = m(1–OR) = 0.2 (1 0.87) = 0.26. s_m^CM = 0.2(1–0.82) = 0.036.

^‡s_f^SMA = m (1–1/OR) = 0.1 (1–1/1.84) = 0.046; s_m^SMA = m(1–1/OR) = 0.1 (1 1/1.48) = 0.032.

elife-15155-v1.xml

10.7554/eLife.15155.024

Table 1.

Fitting parameters for the gap-derived strand memory experiment.

DOI: http://dx.doi.org/10.7554/eLife.15155.024

	%gap [95% Confidence Interval]			%A→G repair [95% Confidence Interval]
	t_1/2 (min)	%gap at 0 min	R²	t_1/2 (min)	%repair at 0 min	R²
ΔMutS/MutL	0.60 [0.51−0.73]	100 [96.7−103.3]	0.99	1.87 [1.52−2.45]	74.8 [68.6−80.7]	0.97
ΔMutS	0.68 [0.58−0.81]	100 [96.4−103.5]	0.99	2.00 [1.76−2.31]	82.8 [79.0−86.6]	0.99
ΔMutL	0.75 [0.66−0.88]	100 [96.5−103.5]	0.99	39.6 [12.3− +∞]	72.8 [63.6−81.9]	0.80

Parameters for the one-phase exponential decay fitting of the data described in Figure 7B and D are presented. %gap: percentage of remaining gaps (100 - %closed), t_1/2: half-life, R²: coefficient of determination. n = 3. Curve fitting was carried out using the GraphPad Prism 6 software (GraphPad Software, CA, USA)

elife-15155-v1.xml

10.7554/eLife.15155.029

Table 2.

Fitting parameters for the gap-derived strand memory experiment with MutSα mutants

DOI: http://dx.doi.org/10.7554/eLife.15155.029

	%gap [95% Confidence Interval]			%A→G repair [95% Confidence Interval]
	t_1/2 (min)	%gap at 0 min	R²	t_1/2 (min)	%repair at 0 min	R²
+buffer	1.44 [0.51−0.73]	100 [95.2−104.7]	0.99	2.94 [2.32−3.98]	75.7 [69.2−82.2]	0.97
+xMutSα^WT	1.35 [0.58−0.81]	100 [95.1−104.9]	0.99	25.5 [17.6−46.1]	84.8 [80.5−89.2]	0.98
+xMutSα^PIP	1.48 [1.18−2.00]	100 [95.4−104.6]	0.99	12.5 [10.9−14.7]	81.9 [78.5−85.4]	0.99
+xMutSα^ΔN	1.43 [1.14−1.93]	100 [95.6−104.4]	0.99	12.3 [11.3−13.6]	81.9 [79.8−84.0]	1.00

Parameters for the one-phase exponential decay fitting of the data described in Figure 9B and D are presented. %gap: percentage of remaining gaps (100 - %closed), t_1/2: half-life, R²: coefficient of determination. n = 3.

elife-15691-v1.xml

10.7554/eLife.15691.003

Table 1.

Clinical and tumor characteristics of patients treated with cTACE and TILA-TACE in the nonrandomized study.

DOI: http://dx.doi.org/10.7554/eLife.15691.003

Variables	Patients
Variables	TILA-TACE	cTACE
Patient number	30	27
Median age, years	57 (Range 32–81)	54 (Range 37–81)
Gender (M/F)	27/3 (90.0%/10.0%)	27/0 (100%/0%)
Aetiology
HBV	24 (80.0%)	25 (92.6%)
HCV	0 (0%)	0 (0%)
Non B-non C	6 (20.0%)	2 (7.4%)
Cirrhosis (radiology)	30 (100%)	27 (100%)
Bilirubin, μM	16.9 ± 9.4	22.5 ± 11.6
Albumin, g/L	39.0 ± 6.9	37.4 ± 5.3
AST, U/L	74.9 ± 102.3	83.5 ± 54.1
ALT, U/L	54.1 ± 80.4	67.3 ± 43.5
AFP, >400 ng/mL	9 (30.0%)	15 (55.6%)
Child-Pugh class, A/B	27/3 (90.0%/10.0%)	25/2 (92.6%/7.4%)
The size of largest tumor (cm)	9.2 (range 5.0–13.6)	10.3 (range 5.0–14.6)
Tumor >10 cm	14 (46.7%)	15 (55.6%)
Tumor 5~10 cm	16 (53.3%)	12 (44.4%)
Multifocal tumors in 1 lobe	8 (26.7%)	12 (44.4%)
Multifocal tumors in 2 lobes	8 (26.7%)	12 (44.4%)
BCLC stage
B	19 (63.3%)	18 (66.7%)
C	11 (36.7%)	9 (33.3%)
Macrovascular invasion	5 (16.7%)	4 (14.8%)
The right branch of portal vein	4 (13.3%)	2 (7.4%)
Hepatic vein	–	1 (3.7%)
The right branch of portal + hepatic vein	1 (3.3%)	1 (3.7%)
Extra-hepatic metastasis	8 (26.7%)	8 (29.6%)
Lung	1 (3.3%)	6 (22.2%)
Lung + bone	1 (3.3%)	0 (0%)
Soft tissue	–	0 (0%)
Lymph nodes	5 (12.2%)	0 (0%)
Bone	1 (2.0%)	1 (3.7%)
Bone+lymph node	–	1 (3.7%)

HBV, hepatitis B virius;

HCV, hepatitis C virius;

AST, Aspartate transaminase;

ALT, Alanine aminotransferase;

AFP, alpha-feto-protein.

elife-15691-v1.xml

10.7554/eLife.15691.009

Table 3.

Clinical and tumor characteristics of patients in RCT.

DOI: http://dx.doi.org/10.7554/eLife.15691.009

Variables	Patients
Variables	TILA-TACE	cTACE
Patient number	10	10
Median age, years	58 (Range 40–86)	53 (43–81)
Gender (M/F)	9 /1 (90.0%/10.0%)	7 /3 (70.0%/ 30.0%)
Aetiology
HBV	9 (90.0%)	8 (80.0%)
HCV	0 (0%)	0 (0%)
Non B-non C	1 (10.0%)	2 (20.0%)
Cirrhosis (radiology)	10 (100%)	10 (100%)
Bilirubin, μM	17.2 ± 10.1	16.7 ± 7.6
Albumin, g/L	38.7 ± 3.1	38.1 ± 5.2
AST, U/L	64.8 ± 44.8	52.8 ± 19.2
ALT, U/L	60.6 ± 48.0	41.0 ± 29.9
AFP, >400 ng/mL	3 (30.0%)	4 (40.0%)
Child-Pugh class, A/B	10/0 (100%/0%)	10/0 (100%/0%)
The size of largest tumor (cm)	7.9 (range 5.0–13.5)	7.5 (range 5.0–13.0)
Tumor >10 cm	3 (30.0%)	3 (30.0%)
Tumor 5~10 cm	7 (70.0%)	7 (70.0%)
Multifocal tumors in 1 lobe	3 (30.0%)	3 (30.0%)
Multifocal tumors in 2 lobes	4 (40.0%)	2 (20.0%)
BCLC stage
B	7 (70.0%)	8 (70.0%)
C	3 (30.0%)	2 (20.0%)
Macrovascular invasion	2 (20.0%)	1 (10.0%)
The right branch of portal vein	1 (10.0%)	1 (10.0%)
The left branch of portal vein	1 (10.0%)	0 (0%)
Extra-hepatic metastasis	1 (10.0%)	2 (20.0%)
Brain	0 (0%)	1 (10.0%)
Lymph nodes	1 (10.0%)	1 (10.0%)

HBV, hepatitis B virius;

HCV, hepatitis C virius;

AST, Aspartate transaminase;

ALT, Alanine aminotransferase;

AFP, alpha-feto-protein.

elife-15691-v2.xml

Table 1.Clinical and tumor characteristics of patients treated with cTACE and TILA-TACE in the nonrandomized study.

Variables	Patients
Variables	TILA-TACE	cTACE
Patient number	30	27
Median age, years	57 (Range 32–81)	54 (Range 37–81)
Gender (M/F)	27/3 (90.0%/10.0%)	27/0 (100%/0%)
Aetiology
HBV	24 (80.0%)	25 (92.6%)
HCV	0 (0%)	0 (0%)
Non B-non C	6 (20.0%)	2 (7.4%)
Cirrhosis (radiology)	30 (100%)	27 (100%)
Bilirubin, μM	16.9 ± 9.4	22.5 ± 11.6
Albumin, g/L	39.0 ± 6.9	37.4 ± 5.3
AST, U/L	74.9 ± 102.3	83.5 ± 54.1
ALT, U/L	54.1 ± 80.4	67.3 ± 43.5
AFP, >400 ng/mL	9 (30.0%)	15 (55.6%)
Child-Pugh class, A/B	27/3 (90.0%/10.0%)	25/2 (92.6%/7.4%)
The size of largest tumor (cm)	9.2 (range 5.0–13.6)	10.3 (range 5.0–14.6)
Tumor >10 cm	14 (46.7%)	15 (55.6%)
Tumor 5~10 cm	16 (53.3%)	12 (44.4%)
Multifocal tumors in 1 lobe	8 (26.7%)	12 (44.4%)
Multifocal tumors in 2 lobes	8 (26.7%)	12 (44.4%)
BCLC stage
B	19 (63.3%)	18 (66.7%)
C	11 (36.7%)	9 (33.3%)
Macrovascular invasion	5 (16.7%)	4 (14.8%)
The right branch of portal vein	4 (13.3%)	2 (7.4%)
Hepatic vein	–	1 (3.7%)
The right branch of portal + hepatic vein	1 (3.3%)	1 (3.7%)
Extra-hepatic metastasis	8 (26.7%)	8 (29.6%)
Lung	1 (3.3%)	6 (22.2%)
Lung + bone	1 (3.3%)	0 (0%)
Soft tissue	–	0 (0%)
Lymph nodes	5 (12.2%)	0 (0%)
Bone	1 (2.0%)	1 (3.7%)
Bone+lymph node	–	1 (3.7%)

HBV, hepatitis B virius;

HCV, hepatitis C virius;

AST, Aspartate transaminase;

ALT, Alanine aminotransferase;

AFP, alpha-feto-protein.

elife-15691-v2.xml

Table 3.

Variables	Patients
Variables	TILA-TACE	cTACE
Patient number	10	10
Median age, years	58 (Range 40–86)	53 (43–81)
Gender (M/F)	9 /1 (90.0%/10.0%)	7 /3 (70.0%/ 30.0%)
Aetiology
HBV	9 (90.0%)	8 (80.0%)
HCV	0 (0%)	0 (0%)
Non B-non C	1 (10.0%)	2 (20.0%)
Cirrhosis (radiology)	10 (100%)	10 (100%)
Bilirubin, μM	17.2 ± 10.1	16.7 ± 7.6
Albumin, g/L	38.7 ± 3.1	38.1 ± 5.2
AST, U/L	64.8 ± 44.8	52.8 ± 19.2
ALT, U/L	60.6 ± 48.0	41.0 ± 29.9
AFP, >400 ng/mL	3 (30.0%)	4 (40.0%)
Child-Pugh class, A/B	10/0 (100%/0%)	10/0 (100%/0%)
The size of largest tumor (cm)	7.9 (range 5.0–13.5)	7.5 (range 5.0–13.0)
Tumor >10 cm	3 (30.0%)	3 (30.0%)
Tumor 5~10 cm	7 (70.0%)	7 (70.0%)
Multifocal tumors in 1 lobe	3 (30.0%)	3 (30.0%)
Multifocal tumors in 2 lobes	4 (40.0%)	2 (20.0%)
BCLC stage
B	7 (70.0%)	8 (70.0%)
C	3 (30.0%)	2 (20.0%)
Macrovascular invasion	2 (20.0%)	1 (10.0%)
The right branch of portal vein	1 (10.0%)	1 (10.0%)
The left branch of portal vein	1 (10.0%)	0 (0%)
Extra-hepatic metastasis	1 (10.0%)	2 (20.0%)
Brain	0 (0%)	1 (10.0%)
Lymph nodes	1 (10.0%)	1 (10.0%)

HBV, hepatitis B virius;

HCV, hepatitis C virius;

AST, Aspartate transaminase;

ALT, Alanine aminotransferase;

AFP, alpha-feto-protein.

elife-15691-v3.xml

Table 1.Clinical and tumor characteristics of patients treated with cTACE and TILA-TACE in the nonrandomized study.

Variables	Patients
Variables	TILA-TACE	cTACE
Patient number	30	27
Median age, years	57 (Range 32–81)	54 (Range 37–81)
Gender (M/F)	27/3 (90.0%/10.0%)	27/0 (100%/0%)
Aetiology
HBV	24 (80.0%)	25 (92.6%)
HCV	0 (0%)	0 (0%)
Non B-non C	6 (20.0%)	2 (7.4%)
Cirrhosis (radiology)	30 (100%)	27 (100%)
Bilirubin, μM	16.9 ± 9.4	22.5 ± 11.6
Albumin, g/L	39.0 ± 6.9	37.4 ± 5.3
AST, U/L	74.9 ± 102.3	83.5 ± 54.1
ALT, U/L	54.1 ± 80.4	67.3 ± 43.5
AFP, >400 ng/mL	9 (30.0%)	15 (55.6%)
Child-Pugh class, A/B	27/3 (90.0%/10.0%)	25/2 (92.6%/7.4%)
The size of largest tumor (cm)	9.2 (range 5.0–13.6)	10.3 (range 5.0–14.6)
Tumor >10 cm	14 (46.7%)	15 (55.6%)
Tumor 5~10 cm	16 (53.3%)	12 (44.4%)
Multifocal tumors in 1 lobe	8 (26.7%)	12 (44.4%)
Multifocal tumors in 2 lobes	8 (26.7%)	12 (44.4%)
BCLC stage
B	19 (63.3%)	18 (66.7%)
C	11 (36.7%)	9 (33.3%)
Macrovascular invasion	5 (16.7%)	4 (14.8%)
The right branch of portal vein	4 (13.3%)	2 (7.4%)
Hepatic vein	–	1 (3.7%)
The right branch of portal + hepatic vein	1 (3.3%)	1 (3.7%)
Extra-hepatic metastasis	8 (26.7%)	8 (29.6%)
Lung	1 (3.3%)	6 (22.2%)
Lung + bone	1 (3.3%)	0 (0%)
Soft tissue	–	0 (0%)
Lymph nodes	5 (12.2%)	0 (0%)
Bone	1 (2.0%)	1 (3.7%)
Bone+lymph node	–	1 (3.7%)

HBV, hepatitis B virius;

HCV, hepatitis C virius;

AST, Aspartate transaminase;

ALT, Alanine aminotransferase;

AFP, alpha-feto-protein.

elife-15691-v3.xml

Table 3.

Variables	Patients
Variables	TILA-TACE	cTACE
Patient number	10	10
Median age, years	58 (Range 40–86)	53 (43–81)
Gender (M/F)	9 /1 (90.0%/10.0%)	7 /3 (70.0%/ 30.0%)
Aetiology
HBV	9 (90.0%)	8 (80.0%)
HCV	0 (0%)	0 (0%)
Non B-non C	1 (10.0%)	2 (20.0%)
Cirrhosis (radiology)	10 (100%)	10 (100%)
Bilirubin, μM	17.2 ± 10.1	16.7 ± 7.6
Albumin, g/L	38.7 ± 3.1	38.1 ± 5.2
AST, U/L	64.8 ± 44.8	52.8 ± 19.2
ALT, U/L	60.6 ± 48.0	41.0 ± 29.9
AFP, >400 ng/mL	3 (30.0%)	4 (40.0%)
Child-Pugh class, A/B	10/0 (100%/0%)	10/0 (100%/0%)
The size of largest tumor (cm)	7.9 (range 5.0–13.5)	7.5 (range 5.0–13.0)
Tumor >10 cm	3 (30.0%)	3 (30.0%)
Tumor 5~10 cm	7 (70.0%)	7 (70.0%)
Multifocal tumors in 1 lobe	3 (30.0%)	3 (30.0%)
Multifocal tumors in 2 lobes	4 (40.0%)	2 (20.0%)
BCLC stage
B	7 (70.0%)	8 (70.0%)
C	3 (30.0%)	2 (20.0%)
Macrovascular invasion	2 (20.0%)	1 (10.0%)
The right branch of portal vein	1 (10.0%)	1 (10.0%)
The left branch of portal vein	1 (10.0%)	0 (0%)
Extra-hepatic metastasis	1 (10.0%)	2 (20.0%)
Brain	0 (0%)	1 (10.0%)
Lymph nodes	1 (10.0%)	1 (10.0%)

HBV, hepatitis B virius;

HCV, hepatitis C virius;

AST, Aspartate transaminase;

ALT, Alanine aminotransferase;

AFP, alpha-feto-protein.

elife-15784-v2.xml

10.7554/eLife.15784.017

Table 1.

The distribution of the postsynaptic targets.

DOI: http://dx.doi.org/10.7554/eLife.15784.017

Postsynaptic target	Completely traced axons		Partially traced axons		All
Postsynaptic target	count	%	count	%	count	%
Excitatory somata	60*	15.0	46^†	10.5	106	12.6
Excitatory dendritic shafts	184	45.9	225	51.4	409	48.7
Excitatory dendritic spines	119	29.7	134	30.6	253	30.2
Excitatory axons	7	1.7	8	1.8	15	1.8
All excitatory	370	92.3	413	94.3	783	93.3
Inhibitory dendritic shafts	17	4.2	20	4.6	37	4.4
Inhibitory dendritic spines	0	0	0	0	0	0
Inhibitory axons			1	0.2	1	0.1
All inhibitory	17	4.2	21	4.8	38	4.5
Uncategorized dendritic spines	14	3.5	4	0.9	18	2.1
Total	401		438		839

* Including 10 synapses onto somatic spines;

^† Including 8 synapses on somatic spines

elife-15828-v2.xml

10.7554/eLife.15828.004

Table 1.

In vitro properties of GCD-0810.

DOI: http://dx.doi.org/10.7554/eLife.15828.004

Compound	ER binding^∗		Transcription^†		Cell viability^‡		ERα degradation^§
	ERα	ERβ	3X ERE~LUC		CellTiter-Glo		In-Cell Western
	K_i [nM]		IC₅₀ [nM]	E_max [% E2]	IC₅₀ [nM]	E_max [% E2]	EC₅₀ [nM]	E_max [% Veh.]
GDC-0810	3.8 ± 1.6	3.7 ± 4.0	1.3 ± 0.8	6.1 ± 2.8	2.5 ± 2.1	24.6 ± 3.3	0.65 ± 0.50	15.3 ± 3.4
4-OH Tam	2.2 ± 1.3	3.6 ± 1.7	6.7 ± 3.6	4.7 ± 2.9	0.53 ± 0.25	48.0 ± 4.7	0.14 ± 0.04	51.9 ± 2.7^#
Fulvestrant	13.1 ± 10.8	13.2 ± 7.6	0.3 ± 0.2	4.1 ± 2.6	0.56 ± 0.70	25.4 ± 3.7	0.39 ± 0.18	6.4 ± 2.0

^∗ Binding affinities (Ki) of GDC-0810, 4-hydroxytamoxifen (4-OHT), and fulvestrant for ERα and ERβ. Shown are the mean and standard deviation of 3–4 experiments run in duplicate.

^† ERα antagonist reporter assay. Results are the mean and standard deviation of 3 experiments.

^‡ Relative cell viability after 5 d incubation with compound. Shown are the mean and standard deviation of more than 50 assays run in triplicate.

^§ Relative ERα immunofluorescence activity in MCF7 In-Cell Western.

^# The apparent reduction in ERα immunoreactivity is not reproduced in western blots.

elife-15828-v3.xml

10.7554/eLife.15828.004

Table 1.In vitro properties of GCD-0810.

Compound	ER binding^∗		Transcription^†		Cell viability^‡		ERα degradation^§
	ERα	ERβ	3X ERE~LUC		CellTiter-Glo		In-Cell Western
	K_i [nM]		IC₅₀ [nM]	E_max [% E2]	IC₅₀ [nM]	E_max [% E2]	EC₅₀ [nM]	E_max [% Veh.]
GDC-0810	3.8 ± 1.6	3.7 ± 4.0	1.3 ± 0.8	6.1 ± 2.8	2.5 ± 2.1	24.6 ± 3.3	0.65 ± 0.50	15.3 ± 3.4
4-OH Tam	2.2 ± 1.3	3.6 ± 1.7	6.7 ± 3.6	4.7 ± 2.9	0.53 ± 0.25	48.0 ± 4.7	0.14 ± 0.04	51.9 ± 2.7^#
Fulvestrant	13.1 ± 10.8	13.2 ± 7.6	0.3 ± 0.2	4.1 ± 2.6	0.56 ± 0.70	25.4 ± 3.7	0.39 ± 0.18	6.4 ± 2.0

^∗ Binding affinities (Ki) of GDC-0810, 4-hydroxytamoxifen (4-OHT), and fulvestrant for ERα and ERβ. Shown are the mean and standard deviation of 3–4 experiments run in duplicate.

^† ERα antagonist reporter assay. Results are the mean and standard deviation of 3 experiments.

^‡ Relative cell viability after 5 d incubation with compound. Shown are the mean and standard deviation of more than 50 assays run in triplicate.

^§ Relative ERα immunofluorescence activity in MCF7 In-Cell Western.

^# The apparent reduction in ERα immunoreactivity is not reproduced in western blots.

elife-16090-v2.xml

10.7554/eLife.16090.006

Table 1.

Summary of data collated in the three meta-analyses. The number of data points is subdivided according to the insecticides or LLIN tested and the predominant mosquito species in each population tested. Studies which did not determine species in the Anopheles gambiae complex are shown separately. All Published Data can be downloaded from Dryad Digital Repository whilst a list of the studies included their geographical range are given in the Material and methods.

DOI: http://dx.doi.org/10.7554/eLife.16090.006

Meta-analysis description		Details	No. Studies	Number data points
Meta-analysis description		Details	No. Studies	Anopheles gambiae s.s.	Anopheles arabiensis	Anopheles gambiae s.l.	Anopheles funestus	Total
M1	Bioassay and experimental hut trial mortality	Deltamethrin	5	2	1	10	0	13
		Permethrin	8	2	1	3	0	6
		Other	1	0	0	1	1	2
		Total	13	4	2	14	1	21
M2	Impact of PBO in pyrethroid bioassays	Deltamethrin	16	15	5	29	8	57
		Permethrin	20	22	7	30	9	68
		Other	4	2	0	4	6	12
		Total	24	39	12	63	23	137
M3	Experimental hut trials of standard and PBO LLINS	Olyset	6	6	0	10	0	16
		PermaNet	6	18	4	6	0	28
		Total	12	24	4	16	0	44

elife-16371-v2.xml

10.7554/eLife.16371.010

Table 3.

Model results for GLMMs testing the occurrence of tool use. p-values are presented only for the first model as the two other models were not significant (see Table 2). All numeric predictor variables were standardized to mean = 0 and SD = 1. For sex, ‘female’ is the reference level.

DOI: http://dx.doi.org/10.7554/eLife.16371.010

	1 week				7 weeks				13 weeks
	β	± se	z	p	β	± se	z	p	β	± se	z	p
Intercept	−3.55	0.42	−8.47	0.0000	−3.39	0.37	–	–	−3.40	0.37	–	–
Ripe fruit feeding	−0.24	0.26	−0.93	0.3525	−0.33	0.24	–	–	−0.35	0.24	–	–
Travel time	0.67	0.30	2.25	0.0242	0.30	0.27	–	–	0.32	0.26	–	–
Sex (male)	−0.07	0.58	−0.12	0.9062	0.04	0.54	–	–	0.04	0.55	–	–
Age	−0.56	0.33	−1.72	0.0855	−0.56	0.29	–	–	−0.55	0.29	–	–
Auto-correlation	0.80	0.18	4.44	0.0000	0.52	0.16	–	–	0.50	0.16	–	–

elife-16443-v2.xml

10.7554/eLife.16443.005

Table 1.

Neuronal database. N is the number of recorded neurons that passed inclusion criteria. The recording span represents the stable recording period (in seconds) for each neuron. The isolation score ranges from 0 to 1. The recording span and isolation score were averaged for each structure and state. Values are means ± standard deviation (SD). For each neuronal assembly, statistics were calculated and are presented for both monkeys.

DOI: http://dx.doi.org/10.7554/eLife.16443.005

Neuronal assembly	before MPTP			after MPTP
Neuronal assembly	N	Recording span (s)	Isolation score	N	Recording span (s)	Isolation score
striatum (MSN)	150	1096.8 ± 564.8	0.85 ± 0.10	128	950.6 ± 616.1	0.85 ± 0.12
striatum (TAN)	116	1568.8 ± 907.6	0.89 ± 0.08	81	1217.8 ± 708.8	0.89 ± 0.09
STN	103	1080.0 ± 411.1	0.77 ± 0.12	111	780.0 ± 317.7	0.80 ± 0.12
GPe	182	1760.4 ± 978.2	0.91 ± 0.08	105	877.7 ± 332.7	0.91 ± 0.09
GPi	119	1437.0 ± 607.9	0.89 ± 0.08	none
SNr	110	1205.2 ± 366.4	0.90 ± 0.08	121	874.7 ± 445.4	0.90 ± 0.09

elife-16616-v2.xml

10.7554/eLife.16616.004

Table 1.

Atoms coordinating the binding site ions in the crystal structures and from the MD simulations. O is the backbone carbonyl oxygen atom. OG and OG1 are the hydroxyl oxygen atoms in serine and threonine. OD1 and OD2 are the carboxyl oxygen atoms in asparate. OE1 and OE2 are the carboxyl oxygen atoms in glutamate. OH2 is the water oxygen.

DOI: http://dx.doi.org/10.7554/eLife.16616.004

E₁	Site I				Site II				Site III
E₁	x-ray		MD		x-ray		MD		x-ray		MD
	A323	O	T772	OG1	V322	O	E779	OE1	Y771	O	Y771	O
	E779	OE1	T772	O	V325	O	D804	OD1	T774	O	T774	O
	D808	OD1	N776	OD1	E327	OE2	D808	OD1	Q923	OE1	Q923	OE1
			D808	OD1	D804	OD1	Water	OH2			D926	OD1
			D808	OD2	Water	OH2

E₂	Site I				Site II
E₂	x-ray		MD		x-ray		MD
	T772	O	S775	OG	V322	O	A323	O
	S775	OG	N776	OD1	V325	O	V325	O
	N776	OD1	D804	OD2	E779	OE2	E779	OE1
	D804	OD2			D804	OD2	D804	OD1

elife-16620-v1.xml

10.7554/eLife.16620.005

Table 1.

Karyotypes are stable in select BubR1 mutant overexpressing MEFs. Karyotype analysis of passage 5 MEFs of indicated genotype. n ≥ 3 lines, 50 cells per line. Data are mean ± s.d. WT, wild-type. FL, full-length. (See associated Table 1— source data 1).

DOI: http://dx.doi.org/10.7554/eLife.16620.005

10.7554/eLife.16620.006Table 1—source data 1.Source file for MEF aneuploidy rate data.

DOI: http://dx.doi.org/10.7554/eLife.16620.006

Mitotic MEF genotype (n)	Mitotic figures	Aneuploid figures % (s.d)	Karyotype with indicated chromosome number
Mitotic MEF genotype (n)	Mitotic figures	Aneuploid figures % (s.d)	36	37	38	39	40	41	42	43	44
WT (5)	250	9 (6)	1	1	0	5	227	9	7	0	0
FL-Bub1b (3)	150	10 (3)	0	0	1	2	135	7	5	0	0
Bub1b^ΔI (3)	150	8 (3)	0	0	1	2	138	9	0	0	0
Bub1b^ΔN (5)	250	18 (6)*	0	0	2	15	204	23	6	0	0
Bub1b^N (3)	150	6 (2)	0	0	1	3	141	4	1	0	0

*p<0.05.

elife-16950-v2.xml

10.7554/eLife.16950.008

Table 1.

Prediction output and performance of HeLa organellar maps. The table shows the combined organellar prediction output from six replicate maps from HeLa cells. Prediction performance is judged by the proportion of correctly assigned organellar marker proteins. Please also refer to Supplementary file 1 (compact format) and 4 (complete database), which contain detailed information for all 8710 proteins covered in this study, including nuclear and cytosolic predictions. Supplementary file 2 shows the performance of each individual map.

DOI: http://dx.doi.org/10.7554/eLife.16950.008

Compartment	Number of marker proteins	Correctly predicted markers		All proteins predicted in this compartment
Compartment	Number of marker proteins	Number	%	All proteins predicted in this compartment
Endosome	85	75	88.2%	304
ER	127	127	100.0%	530
ER, high curvature	11	11	100.0%	45
ERGIC/cisGolgi	26	25	96.2%	73
Golgi	33	29	87.9%	190
Lysosome	43	41	95.3%	88
Mitochondrion	242	239	98.8%	658
Peroxisome	21	15	71.4%	25
Plasma membrane	127	123	96.9%	510
All organellar proteins	715	685	95.8%	2423
Average per organelle			92.7%
Large Protein Complexes	361	353	97.8%	2739
Total	1076	1038	96.5%	5162

elife-16950-v3.xml

10.7554/eLife.16950.008

Table 1.

DOI: http://dx.doi.org/10.7554/eLife.16950.008

Compartment	Number of marker proteins	Correctly predicted markers		All proteins predicted in this compartment
Compartment	Number of marker proteins	Number	%	All proteins predicted in this compartment
Endosome	85	75	88.2%	304
ER	127	127	100.0%	530
ER, high curvature	11	11	100.0%	45
ERGIC/cisGolgi	26	25	96.2%	73
Golgi	33	29	87.9%	190
Lysosome	43	41	95.3%	88
Mitochondrion	242	239	98.8%	658
Peroxisome	21	15	71.4%	25
Plasma membrane	127	123	96.9%	510
All organellar proteins	715	685	95.8%	2423
Average per organelle			92.7%
Large Protein Complexes	361	353	97.8%	2739
Total	1076	1038	96.5%	5162

elife-16962-v1.xml

10.7554/eLife.16962.034

Table 4.

Input to left and right dorsal and medial muscle bands from motor neuron pairs at their neuromuscular junctions.

DOI: http://dx.doi.org/10.7554/eLife.16962.034

Motor neuron pair	Left muscle band				Right muscle band				Ratios
	Dorsal		Medial		Dorsal		Medial		Left: Right
	No. syn	No. sec	No. syn	No. sec	No. syn	No. sec	No. syn	No. sec	No. syn	No. sec
MN1	192	969	47	145	230	1181	130	558	40: 60	39: 61
MN2	224	1583			258	1636			46: 54	49: 51
MN3	42	156			28	101			60: 40	61: 39
MN4	45	189			30	116			60: 40	62: 38
MN5	21	128			15	55			58: 42	70: 30

Number of synapses (No. syn) and number of synaptic profiles (No. sec) provided for each motor neuron and left:right ratios expressed as percentages of neuromuscular junction input from left and right partners for each motor neuron pair.

elife-17061-v1.xml

10.7554/eLife.17061.015

Table 1.

FGT1 interacts with chromatin remodeling proteins in vivo. FGT1-interacting proteins identified by native co-immunoprecipitation followed by mass spectrometry (nHPLC-MS/MS) from 5 d-old 35S::FGT1-YFP seedlings subjected to ACC or NHS 28 h before sampling. Col-0 and 35S::YFP were used as controls. The data represent the number of unique peptides found in the indicated experiments.

DOI: http://dx.doi.org/10.7554/eLife.17061.015

Background	Treatment	Exp	Number of peptides
Background	Treatment	Exp	FGT1	CHR11/ CHR17	Chr11	Chr17	BRM	SWI3a	SWI3b	SWI3d	SWP73b
35S::FGT1-YFP	ACC	1	58	4	1	-	-	-	-	-	-
		2	56	12	3	2	2	3	1	1	3
		3	43	11	-	-	2	-	-	-	-
	NHS	1	33	2	-	-	-	-	-	-	1
		2	52	11	4	2	1	4	-	-	3
		3	51	4	-	-	-	-	-	-	-
Col-0	ACC	1-3	-	-	-	-	-	-	-	-	-
Col-0	NHS	1-3	-	-	-	-	-	-	-	-	-
35S::YFP	NHS	1-3	-	-	-	-	-	-	-	-	-

elife-17219-v2.xml

10.7554/eLife.17219.010

Table 1.

Structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

DOI: http://dx.doi.org/10.7554/eLife.17219.010

	EMD ID	PDB ID	Reported resolution [Å]	Symmetry	Number of amino acids*	MolProbity^†				EMRinger score^†	iFSC^‡
	EMD ID	PDB ID	Reported resolution [Å]	Symmetry	Number of amino acids*	Score	Clash score	Rotamer outliers [%]	Ramachandran favored [%]	EMRinger score^†	iFSC^‡
TRPV1	5778	3j5p	3.4	C4	489 (1956)	3.81 / 1.45	86.35 / 1.96	28.78 / 0.00	95.65 / 91.93	0.65 / 2.34	0.612 / 0.607
Frh	2513	4ci0	3.4	T	893 (10,716)^§	3.98 / 1.59	120.42 / 3.22	39.11 / 0.27	96.51 / 92.18	1.06 / 2.17	0.743 / 0.708
Mitoribosome	2762	3j7y	3.4	N/A	7469^¶	2.71 / 1.50	8.38 / 3.51	8.49 / 0.08	89.86 / 94.86	2.09 / 2.40	0.692 / 0.676

*Number of protein residues in the asymmetric unit and (the total residues) modeled.

^†Scores from deposited (left) versus (/) Rosetta refined (right) model.

^‡Integrated Fourier Shell Correlation (iFSC) from 10–3.4Å resolution shells.

^§In addition to protein residues, nine residues of ligand per asymmetric unit–including a [NiFe] cluster, two metal ions (Fe and Zn), and four [4Fe4S] clusters, and an FAD–were included in the refinement.

^¶In addition to protein residues, 1529 base pairs of RNA molecule were included in the refinement.

elife-17219-v2.xml

10.7554/eLife.17219.017

Table 2.

Comparison of structure refinement results between Rosetta and phenix.real_space_refine*.

DOI: http://dx.doi.org/10.7554/eLife.17219.017

	RSCC*^,†,‡ validation map	iFSC*^,†,§ validation map	EMRinger Score*^,† validation map	MolProbity^†				Number of residues with better RSCC^†,¶
	RSCC*^,†,‡ validation map	iFSC*^,†,§ validation map	EMRinger Score*^,† validation map	Score	Clash score	Rotamer outliers [%]	Ramachandran favored [%]	Number of residues with better RSCC^†,¶
TRPV1	0.785 / 0.790	0.546 / 0.566	1.84 / 1.90	1.59 / 1.48	4.30 / 2.14	0.00 / 0.00	94.41 / 91.72	86 / 250
Frh	0.835 / 0.835	0.504 / 0.517	1.36 / 1.27	1.68 / 1.62	7.99 / 3.66	0.68 / 0.13	96.31 / 92.67	677 / 1328
Mitoribosome	0.832 / 0.832	0.476 / 0.478	2.05 / 1.98	1.88 / 1.62	6.17 / 4.08	0.38 / 0.00	90.19 / 93.49	415 / 564

*To avoid over-fitting, refinement using both methods was carried out using the half-map approach, in which the models were subject to refinement using the training maps. The results showing here were evaluated using the validation-maps. The input model information is the same as reported at Table 1.

^†Numbers (scores) from phenix.real_space_refine (left) versus (/) Rosetta refined (right) model.

^‡Real-space correlation coefficients were evaluated using UCSF Chimera.

^§Integrated Fourier shell correlation (iFSC) from 10–3.4Å resolution shells.

^¶We calculate per-residue real-space correlation coefficient and report the number of residues which show the value of ΔRSCC greater than 0.05.

elife-17243-v2.xml

10.7554/eLife.17243.003

Table 1.

Patients' demographic, clinical and experimental details.

DOI: http://dx.doi.org/10.7554/eLife.17243.003

Patient code*	Sex	Age	Seizure onset zone(s)	Voluntary blinks blocks	Black /gray gap control	Gradual / abrupt gap control	Total analyzed electrodes	Total visually responsive electrodes	Number of visually responsive electrodes in each ROI
									Retinotopic					High-level
									V1	V2	V3	V4	VO	FC	N-FC
P20	F	30	RH: Supramarginal Gyrus	✓			103	6	0	0	2	0	0	1	2
P25	M	45	RH: Inferior Frontal Gyrus, Precentral S.	✓			117	8	0	0	0	0	0	2	6
P32	M	23	RH: Superior Temporal Gyrus, Hippocampus	✓			181	10	2	2	0	1	0	1	2
P33	F	52	LH: Hippocampus, Middle Entorhinal Cortex	✓			83	8	0	0	0	0	0	4	1
P36	M	24	RH: Parahippocampal Gyrus, Temporal Pole	**	✓		58	8	0	0	1	0	1	1	4
P39	M	25	RH: Hippocampus, Amygdala	✓	✓		128	18	3	2	2	1	2	3	4
P44	M	30	RH: Anterior Temporal Lobe	✓	✓		118	10	1	1	1	0	1	1	1
P46	M	45	RH: Hippocampus, Parahippocampal Gyrus	✓	✓	✓	58	15	3	2	2	1	2	1	4
P47	F	34	LH: Anterior Temporal Lobe	✓	✓	✓	142	7	0	0	0	1	1	3	2
P50	M	27	LH: Amygdala, Hippocampus, Parahippocampal Gyrus, Anterior Fusiform Gyrus, Post Central Gyrus	✓	✓	✓	108	3	2	1	0	0	0	0	0
P54	M	21	RH: Medial Temporal, Middle Occipital Gyrus, Parieto-Occipital-Sulcus, Middle Temporal Gyrus, LH: Hippocampus	✓	✓	✓	160	23	2	3	4	2	0	2	0
P57	M	29	RH: Amygdala		✓	✓	110	6	1	0	1	0	0	0	2
P59	M	50	RH: Parieto-Occipital Sulcus		✓	✓	94	13	3	0	0	0	1	0	2
P62	F	44	LH: Hippocampus, Anterior Cingulate Gyrus, Amygdala, Parahippocampal Gyrus		✓	✓	125	8	0	1	2	1	0	0	0

LH/RH – left/right hemisphere, VO – ventral-occipital, FC – face-selective electrodes, N-FC non-face selective high-level electrodes. * Patients' identities were coded by order of admission to surgery. Since not every admitted patient performed the experiment, the codes are not consecutive. ** Failed to follow the instruction to voluntary blink due to language barrier.

elife-17328-v1.xml

10.7554/eLife.17328.004

Table 1.

Summary of task conditions.

DOI: http://dx.doi.org/10.7554/eLife.17328.004

Task	CS (% outcome)					Reward trials (%)	Free reward (%)
Task	Outcome	Odor A (Reward CS)	Odor B (Nothing CS)	Odor C (Air puff CS)	Odor D (Reward and air puff CS)	Reward trials (%)	Free reward (%)
Mixed prediction task	Water	25	0	0	25	13	2
Mixed prediction task	Air puff	0	0	75	75	13	2
Low reward probability task	Water	20	0	0		7	6
Low reward probability task	Air puff	0	0	90		7	6
High reward probability task	Water	90	0	0		30	6
High reward probability task	Air puff	0	0	90		30	6
High reward probability task 2	Water	90	0	0		30	7
High reward probability task 2	Air puff	0	0	80		30	7

elife-17556-v1.xml

10.7554/eLife.17556.008

Table 1.

Thermodynamic parameters describing the binding of Sir3 protein to nucleosomes. Data from more than 2 replicate titration experiments were pooled and the BLI data were fit with Hill equation (see Materials and methods). Uncertainties show 68% confidence intervals around fit parameters (±1 SD) reported by fitting algorithm.

DOI: http://dx.doi.org/10.7554/eLife.17556.008

Binding experiments		BLI		EMSA^*
Binding experiments		Apparent K_D (µM)	Hill coefficient	Apparent K_D (µM)
MonoN	Sir3	1.4 ± 0.06	1.3 ± 0.1	1.7 ± 0.20
	Sir3+Sir4CC	N/A	N/A	1.4 ± 0.10
	Sir3∆wH	1.2 ± 0.10	0.93 ± 0.07	1.0 ± 0.10
	Sir3∆wH+Sir4CC	N/A	N/A	0.9 ± 0.05
	Sir3BAH	1.4 ± 0.10	1.5 ± 0.2	2.1 ± 0.20
DiN	Sir3	0.12 ± 0.01	1.9 ± 0.2	0.17 ± 0.10
	Sir3+Sir4CC	N/A	N/A	0.08 ± 0.01
	Sir3∆wH	1.1 ± 0.05	1.2 ± 0.1	0.62 ± 0.10
	Sir3∆wH+Sir4CC	N/A	N/A	0.12 ± 0.01
	Sir3BAH	1.6 ± 0.10	1.4 ± 0.1	1.40 ± 0.20
Sir3	acMonoN	N/A	N/A	4.0 ± 0.20
	meMonoN	N/A	N/A	5.2 ± 0.20
	acDiN	N/A	N/A	0.7 ± 0.05
	meDiN	N/A	N/A	0.8 ± 0.05
	ac/meMonoN	N/A	N/A	>11^†
	ac/meDiN	N/A	N/A	>3^†

*Hill coefficients obtained from EMSA appeared unreliable due to assay artifacts, such as non-specific binding to DNA, and are not reported.

^† Nonspecific binding could not be measured accurately due to low affinity.

elife-17556-v2.xml

10.7554/eLife.17556.008

Table 1.

DOI: http://dx.doi.org/10.7554/eLife.17556.008

Binding experiments		BLI		EMSA^*
Binding experiments		Apparent K_D (µM)	Hill coefficient	Apparent K_D (µM)
MonoN	Sir3	1.4 ± 0.06	1.3 ± 0.1	1.7 ± 0.20
	Sir3+Sir4CC	N/A	N/A	1.4 ± 0.10
	Sir3∆wH	1.2 ± 0.10	0.93 ± 0.07	1.0 ± 0.10
	Sir3∆wH+Sir4CC	N/A	N/A	0.9 ± 0.05
	Sir3BAH	1.4 ± 0.10	1.5 ± 0.2	2.1 ± 0.20
DiN	Sir3	0.12 ± 0.01	1.9 ± 0.2	0.17 ± 0.10
	Sir3+Sir4CC	N/A	N/A	0.08 ± 0.01
	Sir3∆wH	1.1 ± 0.05	1.2 ± 0.1	0.62 ± 0.10
	Sir3∆wH+Sir4CC	N/A	N/A	0.12 ± 0.01
	Sir3BAH	1.6 ± 0.10	1.4 ± 0.1	1.40 ± 0.20
Sir3	acMonoN	N/A	N/A	4.0 ± 0.20
	meMonoN	N/A	N/A	5.2 ± 0.20
	acDiN	N/A	N/A	0.7 ± 0.05
	meDiN	N/A	N/A	0.8 ± 0.05
	ac/meMonoN	N/A	N/A	>11^†
	ac/meDiN	N/A	N/A	>3^†

*Hill coefficients obtained from EMSA appeared unreliable due to assay artifacts, such as non-specific binding to DNA, and are not reported.

^† Nonspecific binding could not be measured accurately due to low affinity.

elife-17666-v2.xml

10.7554/eLife.17666.018

Table 3.

Changes in marker gene expression in the placodes after injection of various constructs.

DOI: http://dx.doi.org/10.7554/eLife.17666.018

	Injection	Six1-MO*	Eya1-MO*	Six1-EnR	Eya1-mmMO	Six1-GR^§	Eya1-GR^§
	Phenotype	%	%	%	%	%	%
	Phenotype	(n)	(n)	(n)	(n)	(n)	(n)
Atoh1	Reduced	77**	90^‡	94	10	26	42
	Reduced	(26)	(20)	(18)	(21)	(19)	(12)
	Increased	0	0	0	0	35	42
	Increased	(26)	(20)	(18)	(21)	(17)	(12)
Gfi1a	Reduced	82^†	67^†	69	31	57	36
	Reduced	(27)	(17)	(16)	(26)	(14)	(14)
	Increased	0	0	0	0	7	43
	Increased	(27)	(17)	(16)	(26)	(14)	(14)
Hes8	Reduced	74^‡	83^‡	70	17	60	57
	Reduced	(35)	(35)	(46)	(24)	(40)	(56)
	Increased	0	0	24	0	15	29
	Increased	(35)	(35)	(46)	(24)	(40)	(56)
Hes9	Reduced	73^‡	76^‡	84	11	75	29
	Reduced	(45)	(33)	(38)	(27)	(12)	(29)
	Increased	0	0	8	0	0	0
	Increased	(45)	(33)	(38)	(27)	(12)	(29)
Isl2	Reduced	66^†	100^‡	nd	27	50	24
	Reduced	(38)	(17)	nd	(22)	(18)	(17)
	Increased	6	0	nd	0	31	41
	Increased	(38)	(17)	nd	(22)	(16)	(17)
Ngn1	Reduced	65^‡	49^†	84	17	17	36
	Reduced	(51)	(43)	(31)	(24)	(30)	(59)
	Increased	0	16	6	4	23	41
	Increased	(51)	(43)	(31)	(24)	(30)	(59)
Pou4f1.2	Reduced	67^‡	63^†	71	16	47	81
	Reduced	(48)	(30)	(35)	(19)	(15)	(37)
	Increased	0	0	0	0	13	0
	Increased	(48)	(30)	(35)	(19)	(15)	(37)
Sox2	Reduced	74^‡	78^‡	87	6	90	48
	Reduced	(19)	(18)	(30)	(16)	(21)	(33)
	Increased	0	0	23^#	0	0	12
	Increased	(19)	(18)	(30)	(16)	(21)	(33)
Sox3	Reduced	68^‡	54^†	39	9	49	40
	Reduced	(25)	(26)	(31)	(22)	(25)	(23)
	Increased	0	0	71^#	0	16	17
	Increased	(25)	(26)	(31)	(22)	(25)	(23)
Tlx1	Reduced	84^†	91^‡	100	33	40	7
	Reduced	(31)	(32)	(13)	(15)	(10)	(15)
	Increased	6	0	0	0	40	73
	Increased	(31)	(32)	(13)	(15)	(10)	(15)

* Significant differences (Fisher’s exact test);

^† p<0.05,

^‡ p<0.001) to Eya1-mmMO injections are indicated.

^§ Dexamethasone treatment from stages 16–18 on.

^# Expression ectopic in epidermis.

n: Number of embryos analysed at both neural plate (stage 14–16) and tail bud (stage 21–26) stage.

nd: Not determined.

elife-17686-v1.xml

10.7554/eLife.17686.007

Table 3.

Synaptic targets of GABA(+); UNC-47(+) neurons. Coloured box indicates that GABAergic output neuron synapses onto this target cell (<5 synapses [grey]; 5-20 synapses [orange]; >20 synapses [pink]) and genes in the boxes represent expression of ionotropic GABA_A-type receptor subunits in the target cell (Figure 4). For a complete list of GABA receptor (+) neurons, see Table 4. Blue shading indicates that the target neurons is GABA(+). Wiring data is from www.wormwiring.org and includes all synapses observed. * = RMDL/R only.

DOI: http://dx.doi.org/10.7554/eLife.17686.007

Targets		GABAergic output neurons
Targets		ALA	RIB	RIS	AVL	DVB	RME	SMD	DD/VD
muscle					exp-1, lgc-37, gab-1	exp-1, lgc-37, gab-1	unc-49, lgc-37, gab-1	unc-49, lgc-37, gab-1	unc-49, lgc-37, gab-1
sensory neuron(9 classes)	ASG
	ASJ
	BAG
	CEPD
	CEPV
	IL1
	IL2							lgc-38
	PHC
	OLL		lgc-38	lgc-38			lgc-38
	URY
inter-neuron (22 classes)	AIB		lgc-38					lgc-38
	AIN		lgc-38
	AIZ		lgc-37, lgc-38, gab-1					lgc-37, lgc-38, gab-1
	ALN
	AUA
	AVA		lgc-37, gab-1					lgc-37, gab-1
	AVB
	AVD	lgc-35	lgc-35
	AVE	gab-1	gab-1	gab-1	gab-1			gab-1
	AVK
	DVC
	PVP
	PVR							lgc-37, gab-1
	PVW				lgc-37, gab-1
	RIA
	RIB
	RIG
	RIH
	RIP
	RIS
	SAA
Motor neuron (16 classes)	AVL
	DA					lgc-37, gab-1, lgc-35
	DD
	DVB
	HSN				lgc-37, gab-1
	PDA					exp-1, lgc-35
	RIM
	RIV							lgc-38
	RME
	RMD*	gab-1, lgc-37	gab-1, lgc-37	gab-1, lgc-37			gab-1, lgc-37	gab-1, lgc-37
	RMH
	SAB				exp-1, lgc-37, gab-1, lgc-36
	SIA							lgc-37, gab-1
	SIB
	SMD		lgc-37, lgc-38, gab-1	lgc-37, lgc-38, gab-1			lgc-37, lgc-38, gab-1	lgc-37, lgc-38, gab-1
	VC				lgc-37, gab-1
	VD

elife-17686-v1.xml

10.7554/eLife.17686.014

Table 5.

Genetic characterization of tab-1 function in the RME neurons. Expression in RME can not always be unambiguously assigned to the dorsal, ventral, left or right RME neuron, hence only the total number of RME neurons was counted. otEx6804-6806 are tab-1-rescuing arrays (see Material and methods).

DOI: http://dx.doi.org/10.7554/eLife.17686.014

marker	Genotype	Expression observed in:
marker	Genotype	4 RMEs	3 RMEs	2 RMEs	1 RME	0 RME	n
unc-47^prom::gfp (otIs509)	wild type	100%	0%	0%	0%	0%	31
unc-47^prom::gfp (otIs509)	ot796	0%	26.7%	70%	3.3%	0%	30
unc-47^prom::gfp (oxIs12)	wild type	100%	0%	0%	0%	0%	30
unc-47^prom::gfp (oxIs12)	gk753	16.7%	30%	53.3%	3.3%	0%	30
unc-25^prom::gfp (otIs549)	wild type	100%	0%	0%	0%	0%	30
	ot796/+	100%	0%	0%	0%	0%	22
	ot796	0%	23.3%	76.7%	0%	0%	30
	gk753	0%	20%	80%	0%	0%	30
	ot796 otIs549/+	6.7%	36.7%	56.6%	0%	0%	30
	ot796/ok2198	0%	42.8%	57.2%	0%	0%	28
	ot796/u271	3.3%	36.7%	60%	0%	0%	30
	ot796/gk753	3.3%	36.7%	60%	0%	0%	30
unc-46^prom::gfp(otIs575)	wild type	93.3%	6.7%	0%	0%	0%	30
unc-46^prom::gfp(otIs575)	gk753	13.3%	36.7%	46.7%	3.3%	0%	30
anti-GABA staining	wild type	70%	16.7%	10%	0%	3.3%	30
anti-GABA staining	ot796	10%	20%	63.4%	3.3%	3.3%	30
tab-1(gk753); otIs549; Ex[tab-1(+),ttx-3::gfp]	without otEx6804	13.3%	16.7%	70%	0%	0%	30
	with otEx6804	80%	8%	12%	0%	0%	25
	without otEx6805	5%	25%	65%	0%	5%	20
	with otEx6805	41.9%	9.7%	48.4%	0%	0%	31
	without otEx6806	5.6%	16.7%	77.8%	0%	0%	18
	with otEx6806	66.7%	10%	23.3%	0%	0%	30

elife-18096-v2.xml

10.7554/eLife.18096.025

Table 4.

TEC assembly ratios and reaction buffers.

DOI: http://dx.doi.org/10.7554/eLife.18096.025

	Concentrations during assembly, µM				Assembly buffer	Reaction buffer*
	RNA	tDNA	ntDNA	RNAP	Assembly buffer	TEC	additive
Nucleotide addition (gel)	1	1.4	2	1.5	TB10	TB10	TB10	Figure 2B
RNA cleavage (gel)	1	1.4	2	1.5	TB0	TB0	TB2	Figure 3B
Forward translocation (nucleotide addition)	1.4	1	2	1.5	TB10	TB10	TB10	Figure 2B
Backward translocation (pyrophosphorolysis)	1.4	1	2	1.5	TB10	TB10	TB10	Figure 2C
Backtracking (RNA cleavage)	1.4	1	2	1.5	TB0	TB0	TB2	Figure 3B
NusG binding	1.4	1	2	1	TB1	TB1	TB1	Figure 6C
Equilibrium 6-MI assays	1.4	1	2	1.5	TB10	TB10		Figures 2D,6–7
Dinucleotide release (RNA cleavage)	1	1.4	2	1.5	TB0	TB0	TB2	Figure 3
8-MP crosslinking	1.2	1	1	1.5	TB10	TB10		Figures 4,7A
6-TG crosslinking	1	1	2	1.5	TB10	TB10		Figure 5

* In time resolved assays the equal volumes of the TEC and the additive solutions were mixed to initiate the reaction.

elife-18096-v2.xml

10.7554/eLife.18096.026

Table 5.

The number of repeats for each experiment.

DOI: http://dx.doi.org/10.7554/eLife.18096.026

Figure	Data	Number of experiments
Figure	Data	with independently assembled TECs		including the experiments with the same TEC preparation		with independently assembled TECs not in the figures
		control	+NusG	control	+NusG	control	+NusG
2B	WT catalysis WT translocation	4 3	3 2	8 >12	6 >8
2C	WT pyrophosphorolysis	2	2	>8	>8
2D	WT TGT binding	2	2
3BC	WT RNA cleavage WT 6-MI WT 2-AP ΔRL 2-AP ΔLL 2-AP ΔGL 2-AP WT mm1 2-AP WT mm1-2 2-AP WT 3’mm 2-AP	2 2 2 2 2 2 2 2 2	2 2 2 2 2 2 2 2 2	3 >8 >8 >8 >8 >8 >8 >8 >8	4 >8 >8 >8 >8 >8 >8 >8 >8	6	2
3S3	WT 6-MI WT 2-AP WT mm1-2 AA 2-AP WT mm1-2 GG 2-AP	2 1 1 2	2 1 1 2	5 3 7 >8	5 3 8 >8	1	1
	The experiments reported in the figures were performed with the same batch of GreA. The older and the newer experiments cannot be directly combined with the reported experiments due to the variations in the specific activity of the GreA preparations. However, the relative effect of NusG on the reactions involving backtracking can be estimated from all available data. In the WT TEC NusG inhibits reactions that involve backtracking: 2.61 ± 0.28 fold (n = 5, 2 µM GreA); 2.62 ± 0.22 fold (n = 6, 8 µM GreA)
4AB	WT 8-MP ΔRL 8-MP ΔLL 8-MP WT TEC18+TGT 8-MP	7 3 3 2	3 2 2
5AB 5S2	WT 6-TG ΔRL 6-TG ΔLL 6-TG WT TEC18+TGT 6-TG	7 2 3 2	3 2 2
6AB,C(Left)	WT 6-MI ΔRL 6-MI ΔLL 6-MI	2 2 2	2 2 2	>5 5* 5*	>3 3* >3	>7	>7
6AB,C(Left)	* Except TEC19. SD of the fluorescence measurements with the same TEC preparation = 2.3 ± 1.3% (n = 122). SD of the fluorescence measurements with the independently assembled TECs = 16% (n = 8, WT TEC17 measured with different batches of the fluorescent oligonucleotides). Accordingly, the primary data from all fluorescent experiments cannot be directly combined with a figure but some NusG effects can be estimated with the highest accuracy and precision from all available data. NusG effects on the fluorescence intensity of the WT TECs: (TEC17NusG–TEC16NusG)/(TEC17-TEC16) = 1.45 ± 0.09 (n = 9) (TEC18NusG–TEC16NusG)/(TEC18-TEC16) = 0.99 ± 0.02 (n = 7) (TEC19NusG–TEC16NusG)/(TEC19-TEC16) = 0.50 ± 0.35 (n=3)
6C (Right)	WT+NusG 6-MI	2		>6
7A	TEC16-19 6-MI	2		9 (except TEC19)
	TEC16-19 6-MI	2		4 (except TEC19)
	TEC16-18 8-MP	2		2

elife-18432-v2.xml

10.7554/eLife.18432.025

Table 2.

Interactions^* of sterols at the three high-affinity cholesterol-binding sites.

DOI: http://dx.doi.org/10.7554/eLife.18432.025

Cholesterol/Cholesterol analogue	High-affinity cholesterol interaction sites
	IC1		IC2		EC1
	vdW interaction energy (kJ/mol)	No. of contacts	vdW interaction energy (kJ/mol)	No. of contacts	vdW interaction energy (kJ/mol)	No. of contacts
Cholesterol^†	−138.04 ± 0.20	141.02 ± 0.22	−95.06 ± 0.12	90.65 ± 0.16	−129.51 ± 0.29	104.38 ± 0.28
CHS	−29.63 ± 0.14	28.78 ± 0.16	−98.75 ± 0.11	96.30 ± 0.16	-	-
27-OH-Chol	−32.17 ± 0.30	34.95 ± 0.33	−22.69 ± 0.23	28.41 ± 0.28	−132.85 ± 0.27	120.20 ± 0.30
4β-OH-Chol	-	-	-	-	−41.80 ± 0.48	33.41 ± 0.42

^* Shown are the total van der Waals (vdW) interaction energy and the number of contacts between cholesterol and β₂AR, when cholesterol is in the IC1, IC2, or EC1 binding site (and similarly for the cholesterol analogues).

^† Calculations are based on systems having ≥10 mol% cholesterol. Shown here are the average values over different trajectories.

elife-18566-v2.xml

10.7554/eLife.18566.076

Appendix 1—table 5.

Structural connection parameters for Pyramidal cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.076

Other type	Other cell to pyr				Pyr to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Axo	6	6	36	axon	1	3	2	apical dendrite
Bis	10	10	100	any dendrite	3	3	7	apical dendrite
CCK+B	13	8	104	any dendrite
Ivy	42	10	420	any dendrite	0	3	0	apical dendrite
NGF	14	10	140	apical dendrite
O-LM	8	10	80	apical dendrite	13	3	37	basal dendrite
Pyr	197	1	197	apical dendrite	197	1	197	apical dendrite
PV+B	17	11	187	soma	8	3	22	apical dendrite
SC-A					0	3	0	apical dendrite
CA3	5985	2	11970	any dendrite
ECIII	1299	2	2598	any dendrite

elife-18566-v2.xml

10.7554/eLife.18566.079

Appendix 1—table 8.

Model synaptic parameters for Pyramidal cells in the control network.

DOI: http://dx.doi.org/10.7554/eLife.18566.079

Type	Other cell to pyr				Pyr to other cell
Type	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)
Axo	−60.0	1.150e-03	0.28	8.40	0.0	4.000e-05	0.30	0.60
Bis	−60.0	5.100e-04	0.11	9.70	0.0	1.900e-03	0.11	0.25
CCK+B	−60.0	5.200e-04	0.20	4.20
Ivy	−60.0	4.100e-05	1.10	11.00	0.0	4.050e-04	0.30	0.60
NGF	−60.0	6.500e-05	9.00	39.00
O-LM	−60.0	3.000e-04	0.13	11.00	0.0	2.000e-04	0.30	0.60
Pyr	0.0	7.000e-02	0.10	1.50	0.0	7.000e-02	0.10	1.50
PV+B	−60.0	2.000e-04	0.30	6.20	0.0	7.000e-04	0.07	0.20
SC-A					0.0	4.050e-04	0.30	0.60
CA3	0.0	2.000e-04	0.50	3.00
ECIII	0.0	2.000e-04	0.50	3.00

elife-18566-v2.xml

10.7554/eLife.18566.080

Appendix 1—table 9.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.080

Type	Other cell to pyr					Pyr to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)
Axo	−50.0	−60.0	36.45	0.85	11.57	−50.0	0.0	1.85	0.78	2.53
Bis	−50.0	−60.0	13.47	2.17	15.20	−50.0	0.0	64.48	0.28	1.42
CCK+B	−50.0	−60.0	24.86	0.52	6.03
Ivy	−50.0	−60.0	1.63	3.63	15.35	−50.0	0.0	40.70	0.58	1.28
NGF	−50.0	−60.0	1.10	65.58	0.00
O-LM	−50.0	−60.0	0.54	3.70	14.10	−50.0	0.0	17.47	0.60	1.53
Pyr	−50.0	0.0	22.13	2.22	9.65	−50.0	0.0	22.13	2.22	9.65
PV+B	−50.0	−60.0	20.56	0.50	6.70	−50.0	0.0	14.75	0.25	1.77
SC-A						−50.0	0.0	17.42	0.68	3.05
CA3	−50.0	0.0	7.15	1.83	7.08
ECIII	−50.0	0.0	1.41	3.25	13.63

elife-18566-v2.xml

10.7554/eLife.18566.085

Appendix 1—table 12.

Structural connection parameters for Axo-axonic cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.085

Other type	Other cell to axo				Axo to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Bis	16	10	160	any dendrite
CCK+B	12	8	96	any dendrite
Ivy	24	10	240	any dendrite
O-LM	8	10	80	apical dendrite
Pyr	162	3	486	apical dendrite	1271	6	7628	axon
PV+B	39	1	39	soma
SC-A	1	6	6	any dendrite
CA3	4170	2	8340	any dendrite
ECIII	485	2	970	any dendrite

elife-18566-v2.xml

10.7554/eLife.18566.087

Appendix 1—table 14.

Model synaptic parameters for Axo-axonic cells in the control network.

DOI: http://dx.doi.org/10.7554/eLife.18566.087

Type	Other cell to axo				Axo to other cell
Type	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)
Bis	−60.0	6.000e-04	0.29	2.67
CCK+B	−60.0	7.000e-04	0.43	4.49
Ivy	−60.0	5.700e-05	2.90	3.10
O-LM	−60.0	1.200e-04	0.73	10.00
Pyr	0.0	4.000e-05	0.30	0.60	−60.0	1.150e-03	0.28	8.40
PV+B	−60.0	1.200e-04	0.29	2.67
SC-A	−60.0	6.000e-04	0.42	4.99
CA3	0.0	1.200e-04	2.00	6.30
ECIII	0.0	1.200e-04	2.00	6.30

elife-18566-v2.xml

10.7554/eLife.18566.088

Appendix 1—table 15.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.088

Type	Other cell to axo					Axo to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)
Bis	−50.0	−60.0	36.77	0.70	3.70
CCK+B	−50.0	−60.0	47.29	0.75	5.27
Ivy	−50.0	−60.0	4.34	2.13	6.57
O-LM	−50.0	−60.0	4.76	2.55	12.03
Pyr	−50.0	0.0	1.85	0.78	2.53	−50.0	−60.0	36.45	0.85	11.57
PV+B	−50.0	−60.0	1.08	0.45	3.13
SC-A	−50.0	−60.0	24.00	1.00	6.13
CA3	−50.0	0.0	10.85	2.30	8.80
ECIII	−50.0	0.0	8.74	3.08	9.20

elife-18566-v2.xml

10.7554/eLife.18566.093

Appendix 1—table 18.

Structural connection parameters for Bistratified cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.093

Other type	Other cell to bis				Bis to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Axo					11	10	106	any dendrite
Bis	16	10	160	any dendrite	16	10	160	any dendrite
CCK+B	12	8	96	any dendrite	26	10	260	any dendrite
Ivy	24	10	240	any dendrite	12	10	119	any dendrite
O-LM	8	10	80	apical dendrite	29	10	289	any dendrite
Pyr	366	3	1098	apical dendrite	1410	10	14095	any dendrite
PV+B	39	1	39	soma	40	10	400	any dendrite
SC-A	1	6	6	any dendrite	3	10	30	any dendrite
CA3	5782	2	11564	any dendrite
ECIII	432	2	864	any dendrite

elife-18566-v2.xml

10.7554/eLife.18566.096

Appendix 1—table 21.

Model synaptic parameters for Bistratified cells in the control network.

DOI: http://dx.doi.org/10.7554/eLife.18566.096

Type	Other cell to bis				Bis to other cell
Type	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)
Axo					−60.0	6.000e-04	0.29	2.67
Bis	−60.0	5.100e-04	0.29	2.67	−60.0	5.100e-04	0.29	2.67
CCK+B	−60.0	7.000e-04	0.43	4.49	−60.0	8.000e-04	0.29	2.67
Ivy	−60.0	7.700e-05	2.90	3.10	−60.0	5.000e-04	0.29	2.67
O-LM	−60.0	1.100e-04	0.60	15.00	−60.0	2.000e-05	1.00	8.00
Pyr	0.0	1.900e-03	0.11	0.25	−60.0	5.100e-04	0.11	9.70
PV+B	−60.0	2.900e-03	0.18	0.45	−60.0	9.000e-03	0.29	2.67
SC-A	−60.0	6.000e-04	0.42	4.99	−60.0	8.000e-04	0.29	2.67
CA3	0.0	1.500e-04	2.00	6.30
ECIII	0.0	1.500e-04	2.00	6.30

elife-18566-v2.xml

10.7554/eLife.18566.097

Appendix 1—table 22.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.097

Type	Other cell to bis					Bis to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)
Axo						−50.0	−60.0	36.77	0.70	3.70
Bis	−50.0	−60.0	34.34	0.70	3.72	−50.0	−60.0	34.34	0.70	3.72
CCK+B	−50.0	−60.0	48.13	0.78	5.35	−50.0	−60.0	48.55	0.73	4.15
Ivy	−50.0	−60.0	6.39	2.15	6.63	−50.0	−60.0	43.40	0.60	3.17
O-LM	−50.0	−60.0	6.31	2.70	17.05	−50.0	−60.0	1.86	1.78	8.13
Pyr	−50.0	0.0	64.48	0.28	1.42	−50.0	−60.0	13.47	2.17	15.20
PV+B	−50.0	−60.0	24.45	0.17	0.73	−50.0	−60.0	429.34	0.57	4.13
SC-A	−50.0	−60.0	26.43	1.02	6.20	−50.0	−60.0	50.35	0.70	4.10
CA3	−50.0	0.0	13.81	2.38	8.82
ECIII	−50.0	0.0	12.04	3.05	9.30

elife-18566-v2.xml

10.7554/eLife.18566.102

Appendix 1—table 25.

Structural connection parameters for CCK+ Basket cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.102

Other type	Other cell to CCK+B				CCK+B to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Axo					5	8	39	any dendrite
Bis	16	10	160	any dendrite	7	8	58	any dendrite
CCK+B	35	8	280	any dendrite	35	8	280	any dendrite
Ivy	96	10	960	any dendrite	20	8	156	any dendrite
O-LM	40	10	400	apical dendrite	9	8	72	any dendrite
Pyr					1125	8	8998	any dendrite
PV+B	38	1	38	soma	18	8	147	any dendrite
SC-A	6	6	36	any dendrite	3	8	24	any dendrite
CA3	2000	2	4000	any dendrite
ECIII	559	2	1118	any dendrite

elife-18566-v2.xml

10.7554/eLife.18566.104

Appendix 1—table 27.

Model synaptic parameters for CCK+ Basket cells in the control network.

DOI: http://dx.doi.org/10.7554/eLife.18566.104

Type	Other cell to CCK+B				CCK+B to other cell
Type	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)
Axo					−60.0	7.000e-04	0.43	4.49
Bis	−60.0	8.000e-04	0.29	2.67	−60.0	7.000e-04	0.43	4.49
CCK+B	−60.0	4.500e-04	0.43	4.49	−60.0	4.500e-04	0.43	4.49
Ivy	−60.0	3.700e-05	2.90	3.10	−60.0	3.000e-04	0.43	4.49
O-LM	−60.0	1.200e-03	0.73	20.20	−60.0	7.000e-04	1.00	8.00
Pyr					−60.0	5.200e-04	0.20	4.20
PV+B	−60.0	1.200e-03	0.29	2.67	−60.0	9.000e-03	0.43	4.49
SC-A	−60.0	8.500e-04	0.42	4.99	−60.0	7.000e-04	0.43	4.49
CA3	0.0	6.500e-04	2.00	6.30
ECIII	0.0	6.500e-04	2.00	6.30

elife-18566-v2.xml

10.7554/eLife.18566.105

Appendix 1—table 28.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.105

Type	Other cell to CCK+B					CCK+B to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)
Axo						−50.0	−60.0	47.29	0.75	5.27
Bis	−50.0	−60.0	48.55	0.73	4.15	−50.0	−60.0	48.13	0.78	5.35
CCK+B	−50.0	−60.0	32.19	0.73	5.30	−50.0	−60.0	32.19	0.73	5.30
Ivy	−50.0	−60.0	3.00	2.25	6.95	−50.0	−60.0	22.34	0.80	5.05
O-LM	−50.0	−60.0	40.32	3.10	28.42	−50.0	−60.0	54.98	1.35	9.05
Pyr						−50.0	−60.0	24.86	0.52	6.03
PV+B	−50.0	−60.0	11.31	0.42	3.08	−50.0	−60.0	523.11	0.68	5.70
SC-A	−50.0	−60.0	33.81	1.05	6.90	−50.0	−60.0	49.55	0.70	5.38
CA3	−50.0	0.0	55.24	2.53	9.35
ECIII	−50.0	0.0	43.27	3.40	10.87

elife-18566-v2.xml

10.7554/eLife.18566.110

Appendix 1—table 31.

Structural connection parameters for Ivy cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.110

OtherType	Other cell to ivy				Ivy to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Axo					4	10	40	any dendrite
Bis	3	10	30	any dendrite	6	10	60	any dendrite
CCK+B	8	8	64	any dendrite	39	10	392	any dendrite
Ivy	24	10	240	any dendrite	24	10	240	any dendrite
NGF					11	10	113	any dendrite
O-LM					25	10	253	any dendrite
Pyr	9	3	27	apical dendrite	1485	10	14850	any dendrite
PV+B	8	1	8	soma	15	10	150	any dendrite
SC-A	2	6	12	any dendrite	5	10	46	any dendrite
CA3	1923	2	3846	any dendrite

elife-18566-v2.xml

10.7554/eLife.18566.059

Table 5.

Preferred theta firing phases for each model cell type.

DOI: http://dx.doi.org/10.7554/eLife.18566.059

Cell type	Firing rate (Hz)	Modulation		Phase (0o=trough)
Cell type	Firing rate (Hz)	Level	p	Phase (0o=trough)
Axo.	8.9	0.07	4.58e − 130	163.4
Bis.	18.0	0.76	0.00e + 00	340.0
CCK+ B.	54.4	0.10	0.00e + 00	202.8
Ivy	43.3	0.33	0.00e + 00	142.1
NGF.	55.1	0.07	1.46e − 32	176.3
O-LM	17.4	0.76	0.00e + 00	334.7
Pyr.	6.0	0.74	0.00e + 00	339.7
PV+ B.	0.9	0.46	0.00e + 00	356.8
S.C.-A.	5.2	0.03	1.13e − 07	197.9

elife-18566-v2.xml

10.7554/eLife.18566.113

Appendix 1—table 34.

Model synaptic parameters for Ivy cells in the control network.

DOI: http://dx.doi.org/10.7554/eLife.18566.113

Type	Other cell to ivy				Ivy to other cell
Type	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)	Erev (mV)	Gmax (nS)	τrise (ms)	τdecay (ms)
Axo					−60.0	5.700e-05	2.90	3.10
Bis	−60.0	5.000e-04	0.29	2.67	−60.0	7.700e-05	2.90	3.10
CCK+B	−60.0	3.000e-04	0.43	4.49	−60.0	3.700e-05	2.90	3.10
Ivy	−60.0	5.700e-05	2.90	3.10	−60.0	5.700e-05	2.90	3.10
NGF					−60.0	5.700e-05	2.90	3.10
O-LM					−60.0	5.700e-05	2.90	3.10
Pyr	0.0	4.050e-04	0.30	0.60	−60.0	4.100e-05	1.10	11.00
PV+B	−60.0	1.600e-04	0.29	2.67	−60.0	7.000e-04	2.90	3.10
SC-A	−60.0	8.500e-04	0.42	4.99	−60.0	3.700e-05	2.90	3.10
CA3	0.0	3.000e-04	2.00	6.30

elife-18566-v2.xml

10.7554/eLife.18566.114

Appendix 1—table 35.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.114

Type	Other cell to ivy					Ivy to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	τdecay (ms)
Axo						−50.0	−60.0	4.34	2.13	6.57
Bis	−50.0	−60.0	43.40	0.60	3.17	−50.0	−60.0	6.39	2.15	6.63
CCK+B	−50.0	−60.0	22.34	0.80	5.05	−50.0	−60.0	3.00	2.25	6.95
Ivy	−50.0	−60.0	5.48	1.88	6.42	−50.0	−60.0	5.48	1.88	6.42
NGF						−50.0	−60.0	5.48	1.88	6.42
O-LM						−50.0	−60.0	5.32	2.10	6.33
Pyr	−50.0	0.0	40.70	0.58	1.28	−50.0	−60.0	1.63	3.63	15.35
PV+B	−50.0	−60.0	1.44	0.55	3.13	−50.0	−60.0	51.35	2.05	6.75
SC-A	−50.0	−60.0	46.62	0.85	5.58	−50.0	−60.0	3.09	2.22	6.88
CA3	−50.0	0.0	29.42	2.05	8.60

elife-18566-v2.xml

10.7554/eLife.18566.119

Appendix 1—table 38.

Structural connection parameters for Neurogliaform cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.119

Other type	Other cell to NGF				NGF to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Ivy	28	10	280	any dendrite
NGF	17	10	170	apical dendrite	17	10	170	apical dendrite
O-LM	13	10	130	apical dendrite
Pyr					1218	10	12181	apical dendrite
ECIII	523	2	1046	any dendrite

elife-18566-v2.xml

10.7554/eLife.18566.122

Appendix 1—table 41.

Model synaptic parameters for Neurogliaform cells in the control network.

DOI: http://dx.doi.org/10.7554/eLife.18566.122

Type	Other cell to NGF				NGF to other cell
Type	Erev (mV)	Gmax (nS)	𝛕rise (ms)	𝛕decay (ms)	Erev (mV)	Gmax (nS)	𝛕rise (ms)	𝛕decay (ms)
Ivy	−60.0	5.700e-05	2.90	3.10
NGF	−60.0	1.600e-04	3.10	42.00	−60.0	1.600e-04	3.10	42.00
O-LM	−60.0	9.800e-05	1.30	10.20
Pyr					−60.0	6.500e-05	9.00	39.00
ECIII	0.0	3.500e-03	2.00	6.30

elife-18566-v2.xml

10.7554/eLife.18566.123

Appendix 1—table 42.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.123

Type	Other cell to NGF					NGF to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	𝛕decay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	𝛕decay (ms)
Ivy	−50.0	−60.0	5.48	1.88	6.42
NGF	−50.0	−60.0	17.52	5.67	14.32	−50.0	−60.0	17.52	5.67	14.32
O-LM	−50.0	−60.0	9.14	1.98	11.63
Pyr						−50.0	−60.0	1.10	65.58	0.00
ECIII	−50.0	0.0	324.35	2.13	8.80

elife-18566-v2.xml

10.7554/eLife.18566.060

Table 6.

Firing rates and theta phase preferences for various cell types in various conditions. Theta phase is relative to the LFP recorded in the pyramidal layer, where 0^o and 360^o are at the trough of the oscillation. non: non-theta/non-SWR state. SWR: sharp wave/ripple. u+k and x: urethane + supplemental doses of ketamine and xylazine.

DOI: http://dx.doi.org/10.7554/eLife.18566.060

Cell type	Firing rate (Hz)			Theta phase (o)	State of animal	Animal	Ref.
Cell type	Theta	Non	SWR	Theta phase (o)	State of animal	Animal	Ref.
ADI	8.60	0.06	0.25	156	anesth: u+k and x	rat	(Klausberger et al., 2005)
Axo-axonic	17.10	3.50	2.95	185	anesth: u+k and x	rat	(Klausberger et al., 2003)
Axo-axonic	27		27	251	awake, head restraint	mouse	(Varga et al., 2014)
Bistratified	5.90	0.90	42.80	1	anesth: u+k and x	rat	(Klausberger et al., 2004)
Bistratified	34		36	0	awake, head restraint	mouse	(Varga et al., 2014)
Bistratified	30.42	27.65	35.82	2	awake	rat	(Katona et al., 2014)
CCK+ Basket	9.40	1.60	2.70	174	anesth: u+k and x	rat	(Klausberger et al., 2005)
Ivy	0.70	1.70	0.80	31	anesth: u+k and x	rat	(Fuentealba et al., 2008)
Ivy	2.80	2.10	5.20	46	awake, free	rat	(Lapray et al., 2012)
Ivy	2.40	3.00	6.70		awake, free	rat	(Fuentealba et al., 2008)
NGF	6.00	2.65	2.30	196	anesth: u+k and x	rat	(Fuentealba et al., 2010)
O-LM	4.90	2.30	0.23	19	anesth: u+k and x	rat	(Klausberger et al., 2003)
O-LM	29.80	10.40	25.40	346	awake, head restraint	mouse	(Varga et al., 2012)
O-LM	17.30	11.88	18.95	342	awake	rat	(Katona et al., 2014)
PPA	5.75	1.95	1.50	100	anesth: u+k and x	rat	(Klausberger et al., 2005)
PV+ Basket	7.30	2.74	32.68	271	anesth: u+k and x	rat	(Klausberger et al., 2003)
PV+ Basket				234	anesth: u+k and x	rat	(Klausberger et al., 2005)
PV+ Basket	21.00	6.50	122.00	289	awake, free	rat	(Lapray et al., 2012)
PV+ Basket	25.00	8.20	75.00	307	awake, head restraint	mouse	(Varga et al., 2012)
PV+ Basket	28		77	310	awake, head restraint	mouse	(Varga et al., 2014)
Pyramidal				20	anesth: u+k and x	rat	(Klausberger et al., 2003)
Trilaminar	0.20	0.10	69.00	trough	anesth: u+k and x	rat	(Ferraguti et al., 2005)
Double Proj.	0.90	0.55	26.93	77	anesth: u+k and x	rat	(Jinno et al., 2007)
Oriens Retro.	0.53	0.37	53.37	28	anesth: u+k and x	rat	(Jinno et al., 2007)
Radiatum Retro.	5.15	1.90	0.70	298	anesth: u+k and x	rat	(Jinno et al., 2007)

elife-18566-v2.xml

10.7554/eLife.18566.128

Appendix 1—table 45.

Structural connection parameters for O-LM cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.128

Other type	Other cell to O-LM				O-LM to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Axo					7	10	71	apical dendrite
Bis	39	10	390	any dendrite	11	10	107	apical dendrite
CCK+B	20	8	160	any dendrite	88	10	878	apical dendrite
Ivy	136	10	1360	any dendrite
NGF					28	10	283	apical dendrite
O-LM	6	10	60	basal dendrite	6	10	60	basal dendrite
Pyr	2379	3	7137	basal dendrite	1520	10	15195	apical dendrite
PV+B					27	10	269	apical dendrite
SC-A					10	10	97	apical dendrite

elife-18566-v2.xml

10.7554/eLife.18566.130

Appendix 1—table 47.

Model synaptic parameters for O-LM cells in the control network.

DOI: http://dx.doi.org/10.7554/eLife.18566.130

Type	Other cell to O-LM				O-LM to other cell
Type	Erev (mV)	Gmax (nS)	𝛕rise (ms)	𝛕decay (ms)	Erev (mV)	Gmax (nS)	𝛕rise (ms)	𝛕decay (ms)
Axo					−60.0	1.200e-04	0.73	10.00
Bis	−60.0	2.000e-05	1.00	8.00	−60.0	1.100e-04	0.60	15.00
CCK+B	−60.0	7.000e-04	1.00	8.00	−60.0	1.200e-03	0.73	20.20
Ivy	−60.0	5.700e-05	2.90	3.10
NGF					−60.0	9.800e-05	1.30	10.20
O-LM	−60.0	1.200e-03	0.25	7.50	−60.0	1.200e-03	0.25	7.50
Pyr	0.0	2.000e-04	0.30	0.60	−60.0	3.000e-04	0.13	11.00
PV+B					−60.0	1.100e-03	0.25	7.50
SC-A					−60.0	1.500e-04	0.07	29.00

elife-18566-v2.xml

10.7554/eLife.18566.131

Appendix 1—table 48.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.131

Type	Other cell to O-LM					O-LM to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	𝛕decay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	𝛕decay(ms)
Axo						−50.0	−60.0	4.76	2.55	12.03
Bis	−50.0	−60.0	1.86	1.78	8.13	−50.0	−60.0	6.31	2.70	17.05
CCK+B	−50.0	−60.0	54.98	1.35	9.05	−50.0	−60.0	40.32	3.10	28.42
Ivy	−50.0	−60.0	5.32	2.10	6.33
NGF						−50.0	−60.0	9.14	1.98	11.63
O-LM	−50.0	−60.0	78.69	1.05	9.30	−50.0	−60.0	78.69	1.05	9.30
Pyr	−50.0	0.0	17.47	0.60	1.53	−50.0	−60.0	0.54	3.70	14.10
PV+B						−50.0	−60.0	35.53	1.65	10.18
SC-A						−50.0	−60.0	7.91	3.90	29.83

elife-18566-v2.xml

10.7554/eLife.18566.136

Appendix 1—table 51.

Structural connection parameters for PV+ Basket cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.136

Other type	Other cell to PV+B				PV+B to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Axo					10	1	10	soma
Bis	16	10	160	any dendrite	16	1	15	soma
CCK+B	12	8	96	any dendrite	25	1	24	soma
Ivy	24	10	240	any dendrite	13	1	12	soma
O-LM	8	10	80	apical dendrite
Pyr	424	3	1272	apical dendrite	958	11	10533	soma
PV+B	39	1	39	soma	39	1	39	soma
SC-A					2	1	1	soma
CA3	6047	2	12094	any dendrite

elife-18566-v2.xml

10.7554/eLife.18566.139

Appendix 1—table 54.

Model synaptic parameters for PV+ Basket cells in the control network.

DOI: http://dx.doi.org/10.7554/eLife.18566.139

Type	Other cell to PV+B				PV+B to other cell
Type	Erev (mV)	Gmax(nS)	𝛕rise (ms)	𝛕decay (ms)	Erev (mV)	Gmax (nS)	𝛕rise (ms)	𝛕decay (ms)
Axo					−60.0	1.200e-04	0.29	2.67
Bis	−60.0	9.000e-03	0.29	2.67	−60.0	2.900e-03	0.18	0.45
CCK+B	−60.0	9.000e-03	0.43	4.49	−60.0	1.200e-03	0.29	2.67
Ivy	−60.0	7.000e-04	2.90	3.10	−60.0	1.600e-04	0.29	2.67
O-LM	−60.0	1.100e-03	0.25	7.50
Pyr	0.0	7.000e-04	0.07	0.20	−60.0	2.000e-04	0.30	6.20
PV+B	−60.0	1.600e-03	0.08	4.80	−60.0	1.600e-03	0.08	4.80
SC-A					−60.0	6.000e-04	0.29	2.67
CA3	0.0	2.200e-04	2.00	6.30

elife-18566-v2.xml

10.7554/eLife.18566.140

Appendix 1—table 55.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.140

Type	Other cell to PV+B					PV+B to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	𝛕decay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	𝛕decay (ms)
Axo						−50.0	−60.0	1.08	0.45	3.13
Bis	−50.0	−60.0	429.34	0.57	4.13	−50.0	−60.0	24.45	0.17	0.73
CCK+B	−50.0	−60.0	523.11	0.68	5.70	−50.0	−60.0	11.31	0.42	3.08
Ivy	−50.0	−60.0	51.35	2.05	6.75	−50.0	−60.0	1.44	0.55	3.13
O-LM	−50.0	−60.0	35.53	1.65	10.18
Pyr	−50.0	0.0	14.75	0.25	1.77	−50.0	−60.0	20.56	0.50	6.70
PV+B	−50.0	−60.0	13.94	0.23	5.25	−50.0	−60.0	13.94	0.23	5.25
SC-A						−50.0	−60.0	5.71	0.42	3.08
CA3	−50.0	0.0	19.71	2.38	8.78

elife-18566-v2.xml

10.7554/eLife.18566.145

Appendix 1—table 58.

Structural connection parameters for Schaffer Collateral-Associated cells, based on Bezaire and Soltesz (2013).

DOI: http://dx.doi.org/10.7554/eLife.18566.145

Other type	Other cell to SC-A				SC-A to other cell
	#	Syn.s	#	Post	#	Syn.s	#	Post
	Conn.s	/Conn.	#	Loc.	Conn.s	/Conn.	#	Loc.
Axo					4	6	22	any dendrite
Bis	17	10	170	any dendrite	6	6	33	any dendrite
CCK+B	27	8	216	any dendrite	54	6	324	any dendrite
Ivy	102	10	1020	any dendrite	44	6	264	any dendrite
O-LM	40	10	400	apical dendrite
Pyr	105	3	315	apical dendrite
PV+B	24	1	24	soma
CA3	1940	2	3880	any dendrite
ECIII	573	2	1146	any dendrite

elife-18566-v2.xml

10.7554/eLife.18566.149

Appendix 1—table 62.

Model synaptic properties under voltage clamp at −50 mV with physiological reversal potentials

DOI: http://dx.doi.org/10.7554/eLife.18566.149

Type	Other cell to SC-A					SC-A to other cell
Type	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	𝛕decay (ms)	Hold (mV)	Erev (mV)	Amp. (pA)	t10-90 (ms)	𝛕decay (ms)
Axo						−50.0	−60.0	24.00	1.00	6.13
Bis	−50.0	−60.0	50.35	0.70	4.10	−50.0	−60.0	26.43	1.02	6.20
CCK+B	−50.0	−60.0	49.55	0.70	5.38	−50.0	−60.0	33.81	1.05	6.90
Ivy	−50.0	−60.0	3.09	2.22	6.88	−50.0	−60.0	46.62	0.85	5.58
O-LM	−50.0	−60.0	7.91	3.90	29.83
Pyr	−50.0	0.0	17.42	0.68	3.05
PV+B	−50.0	−60.0	5.71	0.42	3.08
CA3	−50.0	0.0	27.10	2.35	9.13
ECIII	−50.0	0.0	31.82	3.38	10.47

elife-18566-v2.xml

10.7554/eLife.18566.151

Appendix 1—table 63.

Measured dendritic lengths and somatic diameters for ivy and neurogliaform cells from the hippocampal CA1 area in Wistar rats, with calculation of somatic surface area included. Cells were characterized in our lab and their function has been reported in Krook-Magnuson et al. (2011). Source Data available in Appendix 1—table 1 - Source Data.

DOI: http://dx.doi.org/10.7554/eLife.18566.151

Cell type	Cell name		Dendritic length (μM))				Somatic dia-meter (μm)	Calculated synap-tic Area (μ⁢m2)
Cell type	Cell name	# Sections	SO	SP	SR	SLM	Somatic dia-meter (μm)	Calculated synap-tic Area (μ⁢m2)
Ivy	0217–1 DAB 3_2_10 left slice	1	129.2	64.5	1200.6	0	38.9	1188.5
Ivy	9 n23-7 DAB 12_16_09 left+middle slice	2	0	0	2703.2	300.3	45.2	1604.6
Ivy	9 n23-6 DAB 06_10 left slice	1	75.4	133.8	2115.4	0	36.6	1052.1
Ivy	9 n16-3 DAB 12_29_09 left slice	1	0	0	1015.2	0	52.5	2164.8
Ivy	Average		51.15	49.575	1758.6	75.075		1502.5
Neurogliaform	9n 12–5 DAB 1_06_09	1	0	0	2097.7	525	34.4	929.4
Neurogliaform	91021 DAB 3_18_10 second,third,fourth from left slice	3	0	0	1230.7	780.1	28	615.8
Neurogliaform	9d 8–3 DAB 1_15_10 left and right slice	2	0	0	2328.2	1382.4	32.2	814.3
Neurogliaform	Average		0	0	1885.5	895.8		786.5

elife-18566-v2.xml

10.7554/eLife.18566.152

Appendix 1—table 64.

Estimated or observed somatic area and dendritic length. Experimental observations of the dendritic length of broad interneuron classes were used as the basis for these estimations. The relative lengths for PV+ basket cells and axo-axonic cells were further differentiated based on experimental observations in region CA3 Papp et al. (2013). The observations published in Mátyás et al. (2004) for CCK+ basket cells were also applied to the CCK+ Schaffer Collateral-Associated cells, based on the discussion in Mátyás et al. (2004). The data for ivy and neurogliaform cells were based on measurements from filled cells from slices. Due to the compact nature of their morphology, especially the neurogliaform cells, the dendritic lengths within the slices were assumed to comprise most or all of the dendritic extents of those cells. See section below for raw data. The O-LM cell morphological measurements were taken from Blasco-Ibáñez and Freund (1995).

DOI: http://dx.doi.org/10.7554/eLife.18566.152

Interneuron	Soma area (100 μ⁢m2)	Dendritic length (μ⁢m2)					Reference
Interneuron	Soma area (100 μ⁢m2)	Total	SO	SP	SR	SLM	Reference
Ivy	1502	1934.4	51.15	49.575	1758.6	75.075	See below
Neurogliaform	786	2781.4	0	0	1885.5	895.8	See below
PV+ basket	3428	4359	1493	697	1877	292	(Papp et al., 2013)
Bistratified	1006	4347.75	1074.57	248.28	2369.24	655.66	(Gulyás et al., 1999)
Axo-axonic	2329	2825	570	659	1259	337	(Papp et al., 2013)
CCK+ basket	966	6338.31	1213.92	310.61	3522.6	1291.18	(Mátyás et al., 2004)
SCA	966	6338.31	1213.92	310.61	3522.6	1291.18	(Mátyás et al., 2004)
O-LM	3007.78	4165.68	4165.68	0	0	0	(Blasco-Ibáñez and Freund, 1995)

elife-18566-v2.xml

10.7554/eLife.18566.155

Appendix 1—table 67.

Ion channels included in the model. GHK: based on Goldman-Hodgkin-Katz equation; Q-O: quasi-ohmic; Hyperpol.-act: Hyperpolarization-activated; Nucleo.-gated: Nucleotide-gated; voltage-act.: voltage activated; voltage-dep.: voltage dependent; Calcium-act.: Calcium-activated; Pyr.: pyramidal; NGF: neurogliaform; dist.: distal; prox.: proximal.

DOI: http://dx.doi.org/10.7554/eLife.18566.155

Ion		Model
Channel	Description	Type	Pyramidal	Axo-axonic	Bistratified	CCK+ Basket	Ivy	Neurogliaform	O-LM	PV+ Basket	S.C.-Assoc.
Cav,L	L-type Calcium	GHK		∙	∙	∙	∙	∙		∙	∙
Cav,N	N-type Calcium	Q-O		∙	∙	∙	∙	∙		∙	∙
HCN	Hyperpol.-act, Cyclic Nucleo.-gated	Q-O				∙					∙
HCNO⁢L⁢M	Hyperpol.-act, Cyclic Nucleo.-gated for O-LM cells	Q-O							∙
HCNp	Hyperpol.-act, Cyclic Nucleo.-gated for Pyr. cells	Q-O	∙
KC⁢a,S	Small (SK) Calcium-activated potassium	Q-O		∙	∙	∙	∙	∙		∙	∙
Kd⁢r,f⁢a⁢s⁢t	Fast delayed rectifier potassium	Q-O		∙	∙	∙			∙	∙	∙
Kd⁢r,f⁢a⁢s⁢t,n⁢g⁢f	Fast delayed rectifier potassium for NGF-family cells	Q-O					∙	∙
Kd⁢r,p	Delayed rectifier potassium for Pyr. cells	Q-O	∙
Kv,A	A-type voltage-act. potassium	Q-O		∙	∙	∙				∙	∙
Kv,A,d⁢i⁢s⁢t,p	A-type voltage-act. potassium for dist. Pyr. dendrites	Q-O	∙
Kv,A,n⁢g⁢f	A-type voltage-act. potassium for NGF-family cells	Q-O					∙	∙
Kv,A,o⁢l⁢m	A-type voltage-act. potassium for O-LM cells	Q-O							∙
Kv,A,p⁢r⁢o⁢x,p	A-type voltage-act. potassium for prox. Pyr. dendrites	Q-O	∙
Kv,C⁢a,B	Big (BK) Calcium-act., voltage-dep. potassium	Q-O		∙	∙	∙	∙	∙		∙	∙
Kv,G⁢r⁢o⁢u⁢p	Multiple slower voltage-dep. potassium	Q-O				∙					∙
leak	Leak	Q-O		∙	∙	∙	∙	∙	∙	∙	∙
Nav	Voltage-dep. sodium	Q-O		∙				∙		∙
Nav,b⁢i⁢s	Voltage-dep. sodium for bistratified cells	Q-O			∙
Nav,c⁢c⁢k	Voltage-dep. sodium for CCK+ cells	Q-O				∙					∙
Nav,n⁢g⁢f	Voltage-dep. sodium for NGF-family cells	Q-O					∙	∙
Nav,p	Voltage-dep. sodium for Pyr. cells	Q-O	∙
pas	Leak	Q-O	∙

elife-18566-v2.xml

10.7554/eLife.18566.069

Appendix 1—table 2.

AxoClamp raw data files. Sch. Coll.-Assoc.: Schaffer Collateral-Associated; Super: superficial. Current sweep injection levels are reported as minimum (most hyperpolarized) : step size : maximum (depolarized) level in units of pA.

DOI: http://dx.doi.org/10.7554/eLife.18566.069

Cell type	Lab	Cell name	Current inj.		Original use and methods reference
Cell type	Lab	Cell name	Species	Levels (pA)	Original use and methods reference
Axo-axonic	Soltesz	CA203LF57	mouse	−200:50:+500	unpublished
Axo-axonic	Soltesz	CA204LF59	mouse	−200:50:+300	unpublished
Axo-axonic	Soltesz	CA204RF59	mouse	−200:50:+400	unpublished
Bistratified	Soltesz	PV16IM	mouse	−300:50:+400	unpublished
Bistratified	Soltesz	PV74	mouse	−300:50:+350	unpublished
Bistratified	Soltesz	PV27IM	mouse	−300:50:+450	unpublished
PV+ Basket	Soltesz	PV34	mouse	−300:50:+500	Lee et al. (2014)
PV+ Basket	Soltesz	PV36	mouse	−300:50:+800	Lee et al. (2014)
PV+ Basket	Soltesz	PV37	mouse	−300:50:+500	Lee et al. (2014)
PV+ Basket	Soltesz	PV38	mouse	−300:50:+300	Lee et al. (2014)
PV+ Basket	Soltesz	PV72	mouse	−300:50:+400	Lee et al. (2014)
PV+ Basket	Soltesz	PV80	mouse	−300:50:+450	Lee et al. (2014)
Deep Pyramidal	Soltesz	D1_25abf	mouse	−400:50:+550	Lee et al. (2014)
Deep Pyramidal	Soltesz	D1_45abf	mouse	−400:50:+550	Lee et al. (2014)
Deep Pyramidal	Soltesz	D2_06abf	mouse	−400:50:+550	Lee et al. (2014)
Deep Pyramidal	Soltesz	D2_49abf	mouse	−400:50:+550	Lee et al. (2014)
Deep Pyramidal	Soltesz	D3_55abf	mouse	−400:50:+550	Lee et al. (2014)
Deep Pyramidal	Soltesz	D4_11abf	mouse	−400:50:+550	Lee et al. (2014)
Deep Pyramidal	Soltesz	D5_15abf	mouse	−400:50:+550	Lee et al. (2014)
Deep Pyramidal	Soltesz	D6_19abf	mouse	−400:50:+550	Lee et al. (2014)
Deep Pyramidal	Soltesz	D7	mouse	−400:50:+550	Lee et al. (2014)
Super. Pyramidal	Soltesz	S1_04abf	mouse	−400:50:+550	Lee et al. (2014)
Super. Pyramidal	Soltesz	S1_47abf	mouse	−400:50:+550	Lee et al. (2014)
Super. Pyramidal	Soltesz	S2_08abf	mouse	−400:50:+550	Lee et al. (2014)
Super. Pyramidal	Soltesz	S2_31abf	mouse	−400:50:+550	Lee et al. (2014)
Super. Pyramidal	Soltesz	S2_51abf	mouse	−400:50:+550	Lee et al. (2014)
Super. Pyramidal	Soltesz	S3_13abf	mouse	−400:50:+550	Lee et al. (2014)
Super. Pyramidal	Soltesz	S4	mouse	−400:50:+550	Lee et al. (2014)
Super. Pyramidal	Soltesz	S5_21abf	mouse	−400:50:+550	Lee et al. (2014)
Ivy	Soltesz	0422–1 (File 5)	rat	−100:20:+890	Krook-Magnuson et al. (2011)
Ivy	Soltesz	0428–1 (File 4)	rat	−100:20:+300	Krook-Magnuson et al. (2011)
Neurogliaform	Soltesz	09o21 (File 4)	rat	−100:20:+120	Krook-Magnuson et al. (2011)
Neurogliaform	Soltesz	09o27 (File 7)	rat	−100:20:+490	Krook-Magnuson et al. (2011)
CCK+ Basket	Soltesz	sh108_BC	rat	−100:20:+80	Lee et al. (2010)
Sch. Coll.-Assoc.	Soltesz	sh114_SCA	rat	−100:20:+60	Lee et al. (2010)
Sch. Coll.-Assoc.	Soltesz	sh153_SCA	rat	−100:20:+60	Lee et al. (2010)
O-LM	Maccaferri	1May2012_P3	mouse	−100:30:+250	Quattrocolo and Maccaferri (2013)
O-LM	Maccaferri	20Sept2011_P2	mouse	−100:30:+250	Quattrocolo and Maccaferri (2013)
O-LM	Maccaferri	24October2012_C2	mouse	−100:30:+250	Quattrocolo and Maccaferri (2013)

elife-18659-v1.xml

10.7554/eLife.18659.007

Table 1.

Measured and calculated values (µm) for the FWHM of the PSF in laser scanning confocal mode and wide-field epi-fluorescence mode for a conventional 5x/0.15 N.A. lens and the 4x/0.47 N.A. Mesolens used with oil immersion. We have assumed emission λ=550 nm for the calculations.

DOI: http://dx.doi.org/10.7554/eLife.18659.007

	5x/0.15 N.A.		Mesolens (4x/0.47 N.A.)
	Theoretical	Measured	Theoretical	Measured
XY FWHM, epi	1.9	1.9	0.6	0.7
Z FWHM, epi	41	51	6.3	7
XY FWHM, confocal	1.8	1.7	0.6	0.8
Z FWHM, confocal	25	38	3.7	8

elife-18972-v3.xml

10.7554/eLife.18972.006

Table 1.

Determination of the Fe/EncFtn_sH protein ratio by ICP-MS. EncFtn_sH was purified as a SeMet derivative from E. coli B834(DE3) cells grown in SeMet medium with 1 mM Fe(NH₄)₂(SO₄)₂. Fractions from SEC were collected, acidified and analysed by ICP-MS. EncFtn_sH concentration was calculated based on the presence of two SeMet per mature monomer. Samples where the element was undetectable are labelled with n.d. These data were collected from EncFtn_sH fractions from a single gel-filtration run.

DOI: http://dx.doi.org/10.7554/eLife.18972.006

Peak	EncFtn_sH retention volume (ml)	Element concentration (µM)				Derived EncFtn_sHconcentration (µM)	Derived Fe/ EncFtn_sH monomer
Peak	EncFtn_sH retention volume (ml)	Ca	Fe	Zn	Se	Derived EncFtn_sHconcentration (µM)	Derived Fe/ EncFtn_sH monomer
Decamer	66.5	n.d.	6.7	n.d.	24.6	12.3	0.5
	68.3	n.d.	28.4	n.d	124.5	62.3	0.5
	70.1	2.9	93.7	2.4	301.7	150.9	0.6
	71.9	6.9	120.6	3.7	379.8	189.9	0.6
	73.7	1.9	64.4	0.8	240.6	120.3	0.5
	75.5	0.9	21.1	n.d.	101.7	50.8	0.4
	77.3	n.d.	6.2	n.d.	42.6	21.3	0.3
	79.1	0.1	2.4	n.d.	26.5	13.3	0.2
	80.9	1.0	1.5	n.d.	22.3	11.2	0.1
	82.7	n.d.	0.2	n.d.	29.2	14.6	n.d
Monomer	84.5	n.d.	0.1	n.d.	34.9	17.5	n.d
	86.3	n.d.	n.d	n.d.	28.9	14.4	n.d
	88.1	n.d.	n.d.	n.d.	17.4	8.7	n.d.
	89.9	n.d.	n.d.	n.d.	5.5	2.8	n.d.
	91.7	n.d.	n.d.	n.d.	0.1	0.07	0.2

elife-19089-v2.xml

10.7554/eLife.19089.005

Table 1.

Patient details and movement-related modulated in beta and gamma bands.

DOI: http://dx.doi.org/10.7554/eLife.19089.005

Patient ID	Age (yrs)	Gender	PD duration (yrs)	Main symptoms	Daily dose (mg)	UPDRS part III (Pre-op)		Movement related power change (%) and electrode localisation												Stimulation effect
						UPDRS part III (Pre-op)		Left STN						Right STN
						OFF	ON	Bipoloar channel	Beta ERD	Gamma ERS	Localisation	Most %beta	Stim setting	Bipoloar channel	Beta ERD	Gamma ERS	Localisation	Most % beta	Stim setting
1 QS	49	M	13	Stiffness, bradykinesia, bilateral tremor, freezing	Levodopa 800 Apomorphine (6.5 mg/hour) Rotigotine 8	38	13	L1L2	−4.52 (*)	17.99 (*)	L1,L2 border MED	L1	Case: + L1: -	R1R2	1.15	33.2 (*)	R0:inside/border/MED; R1: border/MED	R0	Case: + R1: -	UPDRS OFF Med, Stim ON/OFF: 13/38
2 Ox	69	M	11	Rigidity, bradykinesia, freezing	Ropinirole 8 Pramipexole 0.75 Levodopa 900	38	18		--	--	Electrode was not in target and therefore not recorded			R0R1	−4.79	0.92	R0,R1 inside only	R1	None	Stimulation was discontinued shortly after surgery due to unsatisfactory clinical effect
3 King	65	F	17	Rigidity, tremor	Amantadine 400 Levodopa 600	55	49	L0L1	−5.12 (*)	7.44 (*)	All inside	L1	Case: + L0: -	R0R1	−29.03 (*)	3.29 (*)	All inside	R1	Case: + R1: -	Not evaluated
4 QS	56	M	10	Bradykinesia, rigidity, tremor limping gait	Levodopa 1000 Rasagiline 1 Citalopram 20	40	12	L1L2	−2.48 (*)	37.73 (*)	L1,L2,L3 inside; L2 dorsolat	L2	Case: + L1: -	R0R1	−18.92 (*)	2.98 (*)	R0 inside; R1 border/dorsolat	R1	Case: + R0, R1 (alternating): -	UPDRS OFF Med, Stim ON/OFF: 29/40
5 QS	60	F	11	Tremor@Left; poor coordination, bended gait	Levodopa 600 Pramipexole 0.75	53	16	L1L2	−4.94 (*)	6.68 (*)	All inside; L1 dorsolat	L1	Case: + L1: -	R2R3	−0.049	2.14	R1 inside; R2 border	R2	Case: + R1: -	Not evaluated
6 Kings	65	M	5	Rigidity, bradykinesia, motor fluctuation, tremor	Levodopa 400 Entacapone 800 Rotigotine 8	41	29	L1L2	3.33	1.81	All inside	None	Case + L2: -	R1R2	−7.37 (*)	0.66	All inside	R2	Case + R1: -	Not evaluated
7 QS	56	M	10	tremor@all four limbs	Levodopa 600 Rotigotine 8 Selegiline 10	52	19	L0L1	−10.68 (*)	8.42 (*)	L2, L3 in superior STN	L0	Case: + L1: -	R0R1	−22.76 (*)	14.02 (*)	R0, R1 in STN, R2 lateral border of superior STN	R1	Case + R1: -	Relocation after recording due to side effects on speech
8 Kings	73	M	14	Bradykinesia, tremor	Rotigotine 16 Selegeline 10 Levodopa 700	35	15	L0L1	0.157	−0.186	All inside	None	Case: + L1: -	R1R2	−4.93 (*)	5.57 (*)	All inside	R1	Case: + R1: -	Not evaluated
9 Ox	63	F	14	Rigidity, bradykinesia	Ropinirole 23 Levodopa 150	35	24		3.197	−1.14	None inside	None	None		−2.59	7.20	None inside	None	None	Post-op imaging show mis-location, and electrodes were relocated to GPi
10 QS	66	F	16	Shuffle, poor balance, NO tremor	Levodopa 600 Amantadine 200 Ropinirole 24 Rasagiline 1	32	13	L0L2(L1 no signal)	4.33	2.95	L0,L1 inside	L0	Case: + L1: -	R0R1 (bipolar reduced modulation)	−1.37	7.41 (*)	R1,R2 inside	R1	Case: + R1: -	UPDRS OFF Med, Stim ON/OFF: 26/32
11 QS	52	M	7	Freezing, falls, postural instability, tremor@right side	Levodopa 1300 Citalopram 20 Trihexyphenidyl 6	58	13	L1L2 (bipolar reduced modulation)	38.77	13.22		L2	Case: + L1: -	R1R2 (bipolar reduced modulation)	−1.05	1.11		R1	Case: + R1: -	Relocation after recording
Mean	61.3		11.3			43.4	20.1

(*) Indicate significant movement-related modulation in the power of the activity of the specific frequency band; Ox, Kings, QS indicate the three neurosurgical centres where the data were recorded: Ox = John Radcliffe Hospital, University of Oxford; Kings = Department of Neurosurgery, Kings College Hospital, Kings College London; QS = Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology.

elife-19130-v2.xml

10.7554/eLife.19130.013

Table 2.

Amino acid levels showing consistent positive correlation with longevity traits.

For the mammalian fibroblast dataset, the number of longevity traits (out of Maximum Lifespan; Female Time to Maturity; Maximum Lifespan Residual; and Female Time to Maturity Residual) with significant positive correlation with the amino acid levels at two different cut-offs (p value.robust < 0.01 and p value.robust < 0.05) are shown. For the primate and bird fibroblast dataset, the regression was performed using primate data only, bird data only, and the pooled data of both. The regression slope p value < 0.05 are in bold.

DOI: http://dx.doi.org/10.7554/eLife.19130.013

10.7554/eLife.19130.014Table 2—source data 1.Phylogenetic regression of metabolite levels against longevity traits.

Regression against (A) Adult Weight; (B) Maximum Lifespan; (C) Female Time to Maturity; (D) Maximum Lifespan Residual; and (E) Female Time to Maturity Residual. ‘coef.all’, ‘p value.all’, and ‘q value.all’ refer to the regression slope, p value, and FDR-adjusted q value using all the species. ‘p value.robust’ and ‘q value.robust’ refer to the statistics after removing the potential outlier point. ‘p value.max’ and ‘q value.max’ refer to the maximal (least significant) regression p value and q value when each one of the species was left out, one at a time. Only genes with p value.robust < 0.01 and p value.max < 0.05 are shown. (F) Top hits identified by two or more longevity traits. The p value.robust against each of the four longevity traits (ML, FTM, MLres, and FTMres) as well as adult weight (AW) are shown. These metabolites were the input for pathway enrichment analysis. Pathway enrichment analysis of metabolites showing (G) positive and (H) negative correlation with longevity traits. Enrichment was performed based on hypergeometric statistics. (I) Top hits identified by two or more longevity traits, using cut-off of p value.robust < 0.05. The p value.robust against each of the four longevity traits (ML, FTM, MLres, and FTMres) as well as adult weight (AW) are shown.

DOI: http://dx.doi.org/10.7554/eLife.19130.014

Amino acid	Mammalian fibroblasts		Primate and bird fibroblasts
	No. of longevity traits (out of four) with significant correlation		Regression slope p value with species maximum lifespan			Regression slope p value with species maximum lifespan residual
	p value.robust < 0.01	p value.robust < 0.05	Primates only	Birds only	Primates and birds	Primates only	Birds only	Primates and birds
arginine	3	4	3.4 × 10⁻²	8.6 × 10⁻²	3.1 × 10⁻²	3.8 × 10⁻¹	1.1 × 10⁻²	2.1 × 10⁻²
glutamate	2	4	6.5 × 10⁻²	1.8 × 10⁻²	1.1 × 10⁻²	4.6 × 10⁻²	2.8 × 10⁻¹	1.3 × 10⁻¹
histidine	0	4	9.4 × 10⁻²	6.0 × 10⁻²	4.3 × 10⁻²	2.3 × 10⁻¹	1.4 × 10⁻¹	1.7 × 10⁻¹
leucine	2	4	2.9 × 10⁻³	6.0 × 10⁻²	4.8 × 10⁻³	1.4 × 10⁻²	5.9 × 10⁻¹	2.3 × 10⁻¹
lysine	3	3	9.8 × 10⁻³	8.2 × 10⁻²	1.4 × 10⁻²	9.1 × 10⁻²	2.9 × 10⁻¹	2.5 × 10⁻¹
methionine	1	3	3.2 × 10⁻¹	1.4 × 10⁻²	2.7 × 10⁻²	3.0 × 10⁻¹	3.0 × 10⁻²	4.9 × 10⁻²
phenylalanine	1	4	9.8 × 10⁻³	1.2 × 10⁻³	2.1 × 10⁻⁴	8.2 × 10⁻²	1.3 × 10⁻¹	1.2 × 10⁻¹
proline	1	4	4.4 × 10⁻³	3.9 × 10⁻⁴	3.6 × 10⁻⁵	3.5 × 10⁻²	1.2 × 10⁻¹	5.4 × 10⁻²
tryptophan	2	4	9.2 × 10⁻³	7.8 × 10⁻⁴	1.2 × 10⁻⁴	2.6 × 10⁻²	2.5 × 10⁻¹	1.5 × 10⁻¹
tyrosine	1	3	3.2 × 10⁻¹	8.8 × 10⁻³	1.8 × 10⁻²	4.3 × 10⁻¹	1.7 × 10⁻¹	2.9 × 10⁻¹
valine	0	3	1.2 × 10⁻²	5.4 × 10⁻³	1.0 × 10⁻³	2.0 × 10⁻¹	2.8 × 10⁻¹	3.2 × 10⁻¹

elife-19469-v2.xml

10.7554/eLife.19469.004

Table 1.

Susceptibility of E. coli strains determined by the disk diffusion assay.

DOI: http://dx.doi.org/10.7554/eLife.19469.004

Antibiotic	Load (µg)	BW25113	Diameter of inhibition zones (mm) for the indicated strains*
Antibiotic	Load (µg)	BW25113	BW25113Δ4	M1IPTG 50 µM	M1_cured	M1_curedpJEH12(ycbB)	M1_curedpJEH12(ycbB)IPTG 50 µM
Amoxicillin	25	23	24	13	28	28	16
Ampicillin	10	21	21	ND^§	27	26	ND
Amox+Clav^†	20+10	20	23	13	27	30	11
Piperacillin	75	29	28	ND	36	36	ND
Pip+Tazo^‡	75+10	29	30	ND	37	37	ND
Ticarcillin	75	26	27	ND	37	31	ND
Mecillinam	10	17	22	ND	ND	ND	ND
Aztreonam	30	33	36	ND	49	47	ND
Cefalotin	30	16	18	ND	23	23	ND
Cefoxitin	30	20	25	29	30	30	30
Cefotetan	30	30	31	25	41	41	27
Ceftazidime	30	29	30	ND	39	37	9
Cefotaxime	30	33	36	ND	44	44	9
Cefixime	10	28	30	ND	37	38	ND
Cefpirome	30	31	33	ND	41	41	9
Cefoperazone	30	27	28	ND	41	40	ND
Moxalactam	30	31	32	15	43	40	17
Ceftriaxone	30	33	32	15	42	42	18
Carbapenems
Doripenem	10	31	34	32	38	37	38
Meropenem	10	30	34	35	40	41	34
Imipenem	10	26	30	35	25	27	28
Ertapenem	10	30	35	37	49	47	37

*BW25113Δ4 is a derivative of E. coli BW25113 that does not harbor the ynhG, ybiS, erfK, and ycfS genes encoding YcbB paralogues. M1 is a β-lactam-resistant mutant of BW25113Δ4 harboring pJEH11-1(ycbB). M1_cured is a derivative of M1 resulting from the spontaneous loss of pJEH11-1(ycbB). Plasmid pJEH12(ycbB) was obtained by replacing the origin of replication (ColE1) and resistance marker (kanamycin) of pJEH11-1(ycbB) by the p15A replication origin and tetracycline resistance marker of plasmid pACY184. The L,D-transpeptidase gene ycbB of pJEH11-1 and pJEH12 are expressed under the control of the IPTG-inducible trc promoter and regulated by the LacI Arg¹²⁷Leu repressor.

^†Combination of amoxicillin (20 µg) and clavulanate (10 µg).

^‡Combination of piperacillin (75 µg) and tazobactam (10 µg).

^§ND, not detected as the strains grew at the contact of the disk.

elife-19469-v2.xml

10.7554/eLife.19469.016

Table 5.

Minimal inhibitory concentration of β-lactams against E. coli strains harboring various plasmids^*.

DOI: http://dx.doi.org/10.7554/eLife.19469.016

β-lactam	Inducer^†	Strains
β-lactam	Inducer^†	BW25113	BW25113pJEH12(ycbB)	M1cured	M1curedpJEH12(ycbB)	BW25113pKT8(relA')	BW25113pKT8(relA')pKT2(ycbB)	BW25113ΔrelApKT8(relA')	BW25113ΔrelApKT8(relA')pKT2(ycbB)
Ampicillin	None	8	8	8	8	8	4	8	4
	IPTG	8	8	8	128	8	4	8	4
	Ara	8	8	8	8	8	8	8	4
	IPTG+Ara	8	8	8	128	8	64	8	128
Ceftriaxone	None	0,05	0,05	0,05	0,05	0,05	0,05	0,05	0,05
	IPTG	0,05	0,05	0,05	32	0,05	0,05	0,05	0,05
	Ara	0,05	0,05	0,05	0,05	0,05	0,1	0,05	0,05
	IPTG+Ara	0,05	0,05	0,05	32	0,05	32	0,05	32

^*Minimal inhibitory concentrations were determined by the agar dilution method with an inoculum of 10⁵ colony forming units per spot in brain heart infusion agar after 24 hr of incubation at 37°C. The same results were obtained with 10⁴ and 10⁶ colony forming units, indicating that YcbB in combination with elevated (p)ppGpp rendered the bulk of the population resistant.

^†Induction was performed with 50 mM IPTG, 1% arabinose (Ara), and a combination of both inducers (IPTG+Ara). IPTG induces expression of the ycbB gene of plasmids pJEH12(ycbB) and pKT2(ycbB). Arabinose induces expression of relA’ encoding the first 455 residues of RelA.

elife-19568-v1.xml

10.7554/eLife.19568.019

Table 2.

Dimensional parameters measured and derived from the Laetoli Site S tracks and stature and body mass estimates for S1 and S2.

DOI: http://dx.doi.org/10.7554/eLife.19568.019

Footprint	Side	Length (mm)	Max width (mm)	Foot index (%)	Heel width (mm)	Angle of gait (degrees)	Estimated stature (cm)			Estimated body mass (kg)
Footprint	Side	Length (mm)	Max width (mm)	Foot index (%)	Heel width (mm)	Angle of gait (degrees)	H. sapiens^§	H. sapiens^°	Au. afarensis^‡	H. sapiens^°	Au. afarensis^‡
TP2/S1-1	right	271	101	37.2	83	6	194–170	175.4	167–175	53.8	42.9–50.0
TP2/S1-2	left	271	99	36.6	81	4	193–169	175.1	167–175	53.1	42.8–49.8
M9/S1-1	left	250	102	40.6	73	2	179–156	167.5	154–161	51.6	39.6–46.0
M9/S1-2	right	264	105	39.7	80	3	189–165	172.8	163–171	54.2	41.8–48.7
M9/S1-3	left	268	111	41.2	91	4	192–168	174.3	166–173	56.3	42.5–49.4
M9/S1-4	right	245	101	41.2	71	4	175–153	165.6	151–158	50.9	38.8–45.1
L8/S1-1	right	245	104	42.4	78	8	175–153	165.6	151–158	51.7	38.8–45.1
L8/S1-2	left	265	106	40.0	82	11	189–166	173.1	164–171	54.5	41.9–48.8
L8/S1-3	right	260	103	39.6	77	3	186–163	171.3	161–168	53.1	41.2–47.9
L8/S1-4	left	274	106	38.6	81	10	196–171	176.5	169–177	55.6	43.4–50.5
L8/S1-5	right	-	-	-	-	-	-	-	-	-	-
L8/S1-6	left	-	-	-	86	3	-	-	-	-	-
L8/S1-7	right	258	110	42.7	90	8	184–161	170.3	159–166	54.8	40.7–47.4
Average S1	-	261	104	40.0	81	6	184–163	171.6	161–168	53.6	41.3–48.1
TP2/S2-1	right	231	120^*	51.9^*	86	-	165–144	160	142–149	46.7	36.5–42.4

Step length			Stride length
Footprints	Side	Step length (mm)	Footprints	Side	Stride length (mm)
TP2/S1-1 → 2	right → left	553	M9/S1-1 → 3	left	1044
M9/S1-1 → 2	left → right	548	M9/S1-2 → 4	right	1069
M9/S1-2 → 3	right → left	505	L8/S1-1 → 3	right	1140
M9/S1-3 → 4	left → right	571	L8/S1-2 → 4	left	1159
L8/S1-1 → 2	right → left	552	L8/S1-4 → 6	left	1284
L8/S1-2 → 3	left → right	587	Average right		1105
L8/S1-3 → 4	right → left	573	Average left		1162
L8/S1-6 → 7	left → right	660	Average		1139
Average right → left		545
Average left → right		591
Average		568

*Values overestimated because of the enlarged morphology of the only preserved track of S2. ^§Estimation based on the relationship between foot length and stature in Homo sapiens (Tuttle, 1987). ^°Estimation based on the relationship between footprint length and stature/body mass in H. sapiens (Dingwall et al., 2013). ^‡Estimation based on the relationship between foot length and stature/body mass in Au. afarensis (Dingwall et al., 2013). See Materials and methods for details.

elife-19720-v1.xml

10.7554/eLife.19720.005

Table 1.

FLIM analysis of the PS1 NT-CT proximity in phosphorylation-inhibited PS1 mutants.

DOI: http://dx.doi.org/10.7554/eLife.19720.005

Construct	^*Relative FRET efficiency (%)		p value
Construct	DMSO	A23187	^‡vs WT (in DMSO)	^§DMSO vs A23187
PS1 Wild type (WT)	100 ± 8.9 (n = 18)	134.7 ± 7.5 (n = 25)	-	^†p<0.05
PS1 S28A	106.9 ± 7.0 (n = 19)	143.4 ± 8.6 (n = 19)	n.s.	^†p<0.05
PS1 T74A	96.5 ± 13.9 (n = 14)	98.5 ± 8.3 (n = 22)	n.s.	n.s.
PS1 S310A	88.8 ± 10.2 (n = 17)	95.1 ± 8.6 (n = 24)	n.s.	n.s.
PS1 S313A	92.7 ± 8.4 (n = 15)	108.0 ± 8.8 (n = 21)	n.s.	n.s.
PS1 S310A/S313A	84.2 ± 6.7 (n = 26)	87.8 ± 9.0 (n = 17)	n.s.	n.s.
PS1 S319A/T320A	106.2 ± 8.1 (n = 20)	131.8 ± 8.1 (n = 20)	n.s.	^†p<0.05
PS1 S324A	93.8 ± 6.2 (n = 19)	129.9 ± 8.4 (n = 15)	n.s.	^†p<0.05
PS1 S337A	99.9 ± 8.8 (n = 13)	132.4 ± 10.9 (n = 16)	n.s.	^†p<0.05
PS1 S346A	100.1 ± 8.9 (n = 18)	135.0 ± 5.2 (n = 19)	n.s.	^†p<0.05
PS1 S353A	89.6 ± 7.4 (n = 18)	129.8 ± 8.3 (n = 23)	n.s.	^†p<0.05
PS1 T354A	74.4 ± 5.6 (n = 14)	113.4 ± 7.7 (n = 23)	n.s.	^†p<0.05
PS1 S357A	91.2 ± 7.9 (n = 18)	119.8 ± 9.2 (n = 23)	n.s.	^†p<0.05
PS1 S353A/S357A	98.9 ± 9.1 (n = 14)	125.9 ± 7.1 (n = 13)	n.s.	^†p<0.05
PS1 S365A	102.3 ± 6.4 (n = 19)	87.3 ± 9.9 (n = 21)	n.s.	n.s.
PS1 S366A	102.8 ± 6.7 (n = 16)	101.6 ± 12.6 (n = 16)	n.s.	n.s.
PS1 S367A	99.7 ± 6.1 (n = 10)	99.1 ± 11.4 (n = 15)	n.s.	n.s.
PS1 S365A/S367A	104.1 ± 6.7 (n = 19)	102.8 ± 8.4 (n = 19)	n.s.	n.s.
PS1 S366A/S367A	102.7 ± 11.2 (n = 10)	108.2 ± 9.9 (n = 19)	n.s.	n.s.

*The FRET efficiency in DMSO-treated cells expressing WT PS1 is set as 100%, and relative FRET efficiency in phosphorylation-inhibited mutants of PS1 is shown. Mean ± SEM, Student’s t-test, n: cell number, ^†: p<0.05, n.s.: not significant.

^‡p-value is shown for the comparison between WT PS1 and phosphorylation-inhibited mutants of PS1 in DMSO-treated conditions, or ^§for the comparison between DMSO-treated and A23187 (5 µM for 15 min)-treated cells expressing the same PS1 construct.

elife-20147-v2.xml

10.7554/eLife.20147.019

Appendix 1—table 1.

Parameters used for simulations. For the serial, two state and multistate models, the plasticity parameter listed is the transition probability between adjacent states. For the pooled resource model, the plasticity parameters are the minimum and maximum transition probability for the constituent two-state synapses. For the cascade and non-uniform multistate models, the plasticity parameter is the ratio of adjacent transition probabilities.

DOI: http://dx.doi.org/10.7554/eLife.20147.019

Model	# states	Plasticity parameter			fdep			rtpre
Model	# states	Pot	WT dep	DKO dep	Base	Inc	Dec	rtpre
Serial	10	0.12	0.14	0.2	0.5	0.89	0.11	100
Two-state	2	0.1	0.1	0.2	0.5	0.6	0.4	5
Multistate	10	0.3	0.3	0.4	0.5	0.8	0.2	5
Pooled res.	7	0.008	[0.0006, 0.6]	[0.001, 1]	0.5	0.9	0.1	20
Cascade	14	0.386	0.398	0.466	0.478	0.63	0.002	200
Non-uni.	12	0.4	0.4	0.53	0.5	0.7	0.1	500

elife-20147-v2.xml

10.7554/eLife.20147.024

Appendix 1—table 2.

DOI: http://dx.doi.org/10.7554/eLife.20147.024

Model	# states	Plasticity parameter		fdep			rtpre
Model	# states	Pot	Dep	Base	Inc	CF stim	rtpre
Serial	10	0.12	0.14	0.5	0.89	0.9879	100
Two-state	2	0.1	0.4	0.5	0.7	0.91	5
Multistate	10	0.3	0.3	0.5	0.8	0.96	5
Pooled res.	7	0.08	[0.006, 0.6]	0.5	0.9	0.99	20
Cascade	14	0.386	0.398	0.522	0.63	0.99	200
Non-uni.	12	0.4	0.4	0.5	0.7	0.99	500

elife-20198-v2.xml

10.7554/eLife.20198.005

Table 1.

Activity of T. brucei AdoMetDC and AdoMetDC/prozyme complexes.

DOI: http://dx.doi.org/10.7554/eLife.20198.005

TbAdoMetDC proteins	Prozyme proteins	k_cat/K_m (s⁻¹M⁻¹)
		TbAdoMetDC monomer		TbAdoMetDC/prozyme heterodimer
		(+) Put	(−) Put	(+) Put	(−) Put
Wild-type	Wild-type	9.7 ± 3.5	0.48 ± 0.08	3.2 ± 0.6×10³	2.6 ± 0.3×10³
Δ16	Wild-type	16±3^*	16±11^*	28±5^*	18±3^*
Δ26	Wild-type	0.32 ± 0.07	0.11 ± 0.02	7.6 ± 1.7	2.2 ± 0.3
H172A	Wild-type	ND	ND	2.1 ± 0.4×10³	93 ± 42
W137A/M146A	Wild-type	ND	ND	87 ± 8	5.0 ± 0.9
Wild-type	M148'A/Y152'A	as above	as above	0.66 ± 0.23×10³	16 ± 4

^* data taken from (Velez et al., 2013). Data were collected in the presence of 4 mM putrescine (Put), except for the Δ16 mutant (5 mM putrescine^*). In all cases, the heterodimer with the wild-type counterpart formed with sufficient affinity that the subunits could be copurified as a stable complex. Error represents the standard deviation for the fit of triplicate data points. ND, not determined.

elife-20600-v1.xml

10.7554/eLife.20600.008

Table 2.

αSMA stress fiber localization and expression levels in assorted naïve pancreatic fibroblasts (stellate cells) cultured overnight within different D-ECMs.

DOI: http://dx.doi.org/10.7554/eLife.20600.008

(#X naïve cell) / (#Y D-ECM)	αSMA
	Stress fiber localization			Expression
	25% percentile	Median	75% percentile	25% percentile	Median	75% percentile
(2)/(1)	0.35	1.00	1.26	0.65	1.00	1.19
(2)/(2)	0.90	1.15	1.38	0.87	1.10	1.30
(3)/(2)	0.92	1.08	1.36	0.86	1.20	1.72
(4)/(1)	0.08	0.85	1.03	0.79	2.62	3.04
(4)/(5)	0.06	0.83	1.36	0.29	1.15	2.40
(2)/(5)	0.52	1.24	1.33	0.60	1.44	2.31
(2)/(1 +TGFβi)	0.00	0.00	0.04	0.04	0.07	0.10
(2)/(5 +TGFβi)	0.00	0.06	1.20	0.01	0.14	0.76
(3)/(1 +TGFβi)	0.01	0.06	0.23	0.01	0.15	0.28
(4)/(5 +TGFβi)	0.11	0.22	0.71	0.25	0.74	1.66

Values obtained from naïve cells (e.g., inactive stellate cells) isolated from patient number ‘#2’ cultured overnight within D-ECMs made from CAFs isolated from patient #1 were used for normalization and assigned an arbitrary unit of 1.00. Assorted, naïve cells (patient numbers indicated) were cultured within D-ECMs derived from the indicated CAFs, while experimental conditions included assorted D-ECMs treated with SB-431542 (D+TGFβi) during ECM production. Note that quantitative immunofluorescent obtained values of αSMA and F-actin were used to calculate stress fiber localization and expression of αSMA. P values, listed below, were all calculated using the Mann Whitney test, compared to the normalized (2)/(1) experimental condition, to account for non-paired, two-tailed and non-Gaussian distributions of the data.

(2)/(1) vs. (2)/(2); p=0.0836 stress fiber localization; p=0.3825 expression

(2)/(1) vs. (3)/(2); p=0.1680 stress fiber localization; p=0.1736 expression

(2)/(1) vs. (4)/(1); p=0.4266 stress fiber localization; p=0.0755 expression

(2)/(1) vs. (4)/(5); p=0.8927 stress fiber localization; p=0.7509 expression

(2)/(1) vs. (2)/(5); p=0.1885 stress fiber localization; p=0.4192 expression

(2)/(1) vs. (2)/(1+TGFβi); p<0.0001 stress fiber localization; p<0.0001 expression

(2)/(1) vs. (2)/(5+TGFβi); p=0.0909 stress fiber localization; p=0.0040 expression

(2)/(1) vs. (3)/(1+TGFβi); p=0.0018 stress fiber localization; p<0.0001 expression

(2)/(1) vs. (4)/(5+TGFβi); p=0.1018 stress fiber localization; p=0.5181 expression

elife-20707-v2.xml

10.7554/eLife.20707.014

Table 3.

Time course of pathway enrichment relating to affected and unaffected developmental and functional phenotypes.

DOI: http://dx.doi.org/10.7554/eLife.20707.014

Phenotype^†	Development stage*
Phenotype^†	3 dpf/E1	6 dpf/E2	10 dpf/E3	11 dpf/E4	0 Dph/E5	three Dph/E6
Cardiovascular	0 (0/8)	22.4 (11/49)	5.7 (4/70)	7.0 (4/57)	4.7 (2/43)	2.1 (1/48)
Craniofacial	0 (0/8)	12.2 (6/49)	10 (7/70)	5.3 (3/57)	7.0 (3/43)	2.1 (1/48)
Liver	12.5 (1/8)	0 (0/49)	5.7 (4/70)	8.8 (5/57)	0 (0/43)	0 (0/48)
Eye	0 (0/8)	4.1 (2/49)	20 (14/70)	48.6 (17/35)	51.2 (22/43)	50.0 (24/48)
Osmoregulation	--	43.3 (13/30)	29.3 (12/41)	15.0 (3/20)	16 (4/25)	--
Cholesterol	0/30	0 (0/27)	27.1 (13/48)	31.3 (10/32)	25.5 (12/47)	--
Lipid	0/30	40.7 (11/27)	35.4 (17/48)	50.0 (16/32)	48.9 (23/47)	--

*Percentage of total enriched pathways (absolute values).

^†Numbers of affected pathways representing Cardiovascular, Craniofacial, Liver and Eye were extracted from the combined Development category in IPA results; numbers of pathways representing osmoregulation/ion transport were extracted from the Molecular Transport category; numbers of pathways affecting Cholesterol/sterol metabolism and other non-cholesterol lipids (Lipid) were extracted from the Lipid Metabolism category.

elife-20713-v1.xml

10.7554/eLife.20713.007

Table 1.

Cell counts for dsx-intersected neurons in male and female adult CNS. Male and female dsx/elav, dsx/vGlut and dsx/Gad1 cell counts are listed in black. Subsets of neurons that co-express Fru^M in males are listed in italics.

DOI: http://dx.doi.org/10.7554/eLife.20713.007

dsx neuronal clusters	dsx/elav		dsx/vGlut		dsx/Gad1
dsx neuronal clusters	Male	Female	Male	Female	Male	Female
Brain
pC1*	52.8 ± 4.1 (12)	8.3 ± 1.6 (12)	0 ± 0 (12)	0 ± 0 (12)	0 ± 0 (12)	0 ± 0 (12)
pC2*	78.3 ± 4.8 (12)	14.2 ± 1.5 (12)	0 ± 0 (12)	0 ± 0 (12)	1.0 ± 0(12) 0.9 ± 0.3 (10)	0 ± 0 (12)
pC3*	13.8 ± 0.9 (12)	8.0 ± 1.0 (12)	0 ± 0 (12)	0 ± 0 (12)	3.5 ± 0.5 (12) 0.5 ± 0.5 (10)	3.0 ± 0 (12)
aDN*	2.0 ± 0 (12)	2.0 ± 0 (12)	1.9 ± 0.3 (12)0 ± 0 (10)	2.0 ± 0 (12)	0 ± 0 (12)	0 ± 0 (12)
SN*	1.0 ± 0 (12)	n.a.	0 ± 0 (12)	n.a.	0 ± 0 (12)	n.a.
Ventral Nerve Cord
TN1*	23.0 ± 1.5 (12)	n.a.	0 ± 0 (12)	n.a.	0 ± 0 (12)	n.a.
TN2*	7.9 ± 0.3 (12)	n.a.	0 ± 0 (12)	n.a.	0 ± 0 (12)	n.a.
Abg^†	275.0 ± 21.7 (10)	314.8 ± 18.9 (10)	79.8 ± 2.3 (10)7.4 ± 3.1 (10)	101.8 ± 6.7 (10)	151.2 ± 3.8 (10)30.0 ± 4.8 (10)	213.1 ± 2.1 (10)

*Neuronal cluster away from CNS midline. Count represents one cluster per hemisegment of the CNS.

^†Neuronal cluster spans the CNS midline. Count given is for the entire Abg. Counts represent mean ± S.D. n’s listed in parentheses.

elife-20718-v4.xml

10.7554/eLife.20718.004

Table 1.

Comparison of PSICOV predictions for Tat component contacts with those of other co-evolutionary methods. The programs PSICOV (Jones et al., 2012), CCMPRED (Seemayer et al., 2014), and FreeContact (mfDCA) (Hopf et al., 2012; Kaján et al., 2014) use methodologically distinct algorithms to calculate sequence co-evolution. Contacts predicted by all three of the co-evolutionary methods are colored green. Meta-PSICOV (Jones et al., 2015) aggregates information from the other three prediction methods as well as other sequence information in Stage 1, then weights by vicinity to other contacts in Stage 2. The table is divided to include the co-evolutionary contacts for TatA_All, TatA, TatB, TatA with TatA_basal, TatA with TatB_basal, and TatC-TatC contacts with separations greater than 20 Å. For the TatC-TatC contacts the three high-probabilty contacts identified by the three distinct methods suggest plausible contacts between the TM2-3 linker and residues at the C-terminal end of TM3 (green).

DOI: http://dx.doi.org/10.7554/eLife.20718.004

	PSICOV				FreeContact (mfDCA)				CCMPRED				Meta-PSICOV Stage 1				Meta-PSICOV Stage 2
	TMH	TatC	Score	Rank	TMH	TatC	Score	Rank	TMH	TatC	Score	Rank	TMH	TatC	Score	Rank	TMH	TatC	Score	Rank
TatA_All	12	202	0.71	51	12	202	1.46	108	12	202	0.30	28	12	202	0.75	22	12	202	0.46	112
	16	198	0.56	88	15	201	1.00	305	16	198	0.27	59	16	198	0.71	30	15	201	0.40	145
	15	201	0.5	109	16	198	0.95	335	15	201	0.23	117	15	201	0.64	49	16	198	0.34	191
	8	215	0.48	123	8	215	0.84	422	12	215	0.21	175	12	215	0.19	414	12	201	0.15	444
	12	215	0.38	189	12	215	0.75	549	18	21	0.19	313	15	198	0.14	609	12	198	0.08	771
	7	213	0.23	497	18	21	0.56	1010	11	212	0.18	323	18	21	0.14	611	8	215	0.05	1171
	8	208	0.22	578	8	208	0.53	1128	8	215	0.18	388	8	215	0.11	734	4	205	0.04	1332
	19	194	0.22	591	14	172	0.45	1577	15	198	0.18	400	8	208	0.09	860	8	205	0.04	1593
	5	208	0.22	619	8	205	0.44	1630	5	208	0.18	404	12	201	0.06	1072	5	208	0.03	1726
	18	21	0.21	670	5	126	0.43	1717	11	174	0.16	674	12	198	0.06	1083	15	198	0.03	1897
	11	25	0.2	768	15	198	0.42	1761	8	208	0.15	753	14	203	0.05	1175	8	208	0.03	1963
	8	205	0.19	772	17	85	0.42	1851	4	205	0.15	793	4	205	0.05	1176	11	202	0.03	2044
	8	166	0.19	855	5	124	0.39	2105	17	227	0.15	802	5	208	0.04	1367	8	198	0.02	2299
	12	198	0.18	911	5	132	0.38	2131	19	194	0.15	960	11	25	0.04	1424	15	202	0.02	2569
	17	227	0.17	1003	12	194	0.33	2870	8	214	0.15	979	11	174	0.04	1544	4	208	0.02	2846
	15	198	0.17	1150	12	75	0.32	2995	12	198	0.15	1036	15	219	0.03	1574	8	202	0.02	3287
	12	201	0.16	1183	12	198	0.32	3008	12	201	0.14	1158	10	25	0.03	1607	4	206	0.01	3437
TatA	12	202	0.71	18	12	202	1.81	16	12	202	0.21	10	12	202	0.72	12	12	202	0.46	91
	16	198	0.55	39	16	198	1.12	124	16	198	0.19	15	16	198	0.72	13	9	206	0.27	229
	14	216	0.38	122	12	215	1.06	155	9	206	0.14	49	9	206	0.40	82	16	198	0.27	230
	16	82	0.37	133	5	136	0.91	246	15	163	0.14	67	15	163	0.35	98	4	206	0.18	378
	9	206	0.34	162	5	210	0.86	287	3	205	0.14	72	15	202	0.29	137	9	202	0.11	630
	5	162	0.29	262	15	163	0.86	297	12	215	0.14	74	16	82	0.28	146	8	206	0.09	830
	5	136	0.29	270	8	212	0.77	408	13	197	0.14	79	15	201	0.24	184	5	210	0.09	835
	9	39	0.28	290	19	170	0.74	470	16	82	0.14	86	19	20	0.20	271	15	202	0.09	866
	12	215	0.26	339	15	202	0.72	530	2	219	0.13	121	12	215	0.18	317	18	232	0.09	880
TatB	18	21	0.83	7	18	21	2.19	6	18	21	0.23	9	12	198	0.72	12	12	198	0.61	41
	12	215	0.60	30	12	215	1.45	22	12	198	0.18	14	12	202	0.63	23	12	202	0.47	97
	12	202	0.56	36	12	198	1.39	24	18	24	0.17	16	18	21	0.61	29	18	21	0.41	125
	20	185	0.46	65	12	202	1.13	63	12	202	0.16	17	18	24	0.53	47	18	24	0.32	194
	12	198	0.39	110	19	13	1.04	89	12	215	0.16	21	12	215	0.49	55	5	212	0.20	350
	5	213	0.36	127	5	212	0.97	117	17	227	0.14	71	19	13	0.39	79	12	215	0.20	355
	7	204	0.35	141	5	126	0.87	164	14	167	0.14	72	14	24	0.25	175	4	206	0.16	462
	5	212	0.28	281	18	24	0.81	221	5	213	0.13	88	19	198	0.22	225	5	208	0.14	529
TatA with TatA_basal	12	202	0.75	28	12	202	1.85	26	16	198	0.31	10	16	198	0.80	8	12	202	0.47	94
	16	198	0.70	35	16	198	1.26	62	12	202	0.30	11	12	202	0.77	14	16	198	0.43	111
	15	201	0.60	58	8	215	1.01	130	15	201	0.22	40	15	201	0.68	36	15	201	0.39	136
	8	215	0.58	64	15	201	1.01	131	11	212	0.17	126	8	215	0.18	309	12	201	0.08	644
	19	194	0.38	141	12	215	0.69	378	8	215	0.16	143	14	203	0.14	419	8	215	0.06	832
	8	205	0.27	309	5	136	0.67	426	12	215	0.16	159	8	208	0.09	605	4	205	0.06	852
TatB with TatA_basal	18	21	0.48	72	18	21	1.42	44	18	21	0.23	19	12	198	0.65	36	12	198	0.48	94
	12	198	0.46	79	12	198	0.99	173	12	198	0.19	37	12	202	0.56	55	4	206	0.43	119
	12	202	0.38	123	12	202	0.84	281	12	202	0.19	39	18	21	0.56	56	18	21	0.28	214
	20	185	0.37	134	12	215	0.76	383	18	24	0.18	44	15	201	0.34	122	12	202	0.28	218
	12	215	0.33	180	15	201	0.73	427	14	167	0.17	69	4	206	0.28	168	4	207	0.28	225
	5	213	0.30	252	5	212	0.68	514	5	213	0.17	88	18	24	0.27	175	4	205	0.16	415
TatC-TatC	64	134	0.79	33	27	199	2.04	39	64	134	0.28	51	64	134	0.6	62	64	134	0.64	60
	71	140	0.77	41	65	137	1.72	62	71	140	0.26	75	71	140	0.54	84	27	199	0.47	108
	65	137	0.64	69	71	140	1.63	72	65	137	0.21	191	27	199	0.48	103	65	137	0.3	227
	28	203	0.51	10864	64	134	1.51	93	113	228	0.19	319	65	137	0.39	150	64	137	0.24	283
	72	217	0.42	155	64	157	1.05	284	67	140	0.18	345	28	203	0.37	162	33	167	0.23	289

elife-20954-v2.xml

10.7554/eLife.20954.008

Table 1.

Characteristics of nanodiscs and contained bilayer for used combinations of different scaffold proteins with various lipids.

DOI: http://dx.doi.org/10.7554/eLife.20954.008

Scaffold	Nanodisc diameter [nm]	Lipid	Protein:lipid ratio in nanodisc reaction mix	Attached lipids (LILBID)	Transition tempature [°C]	Headgroup charge Σ charges	Hydrophobic tail
Scaffold	Nanodisc diameter [nm]	Lipid	Protein:lipid ratio in nanodisc reaction mix	Attached lipids (LILBID)	Transition tempature [°C]	Headgroup charge Σ charges	Double bonds	Length
MSP1D1ΔH5	8	DMPC	1:50	15	24	0	0	14
MSP1D1ΔH5	8	DMPG	1:45	6	23	−1	0	14
MSP1	10	DMPC	1:80	17	24	0	0	14
MSP1	10	DMPG	1:70	9	23	−1	0	14
MSP1E3D1	12	DMPC	1:115	19	24	0	0	14
		DMPG	1:110	11	23	−1	0	14
		DPPC	1:100	18	41	0	0	16
		POPG	1:90	15	−2	−1	0/1	16/18
		DOPC	1:80	21	−17	0	2	18
		DOPG	1:80	20	−18	−1	2	18
		DOPS	1:90	20	−11	−1	2	18
		DOPE	1:80	8	−16	0	2	18
		Mixtures			Lipid ratio
		DMPG/DMPC	1:115	11	50/50	−1/0	0/0	14/14
		DMPG/Cardiolipin	1:120	12	90/10	−1/–2	0/0	14/14
		DMPG/Inositol	1:110	15	50/50	−1/–1	0/0;1	14/16;18
		DMPC/Cholesterol	1:115	23	90/10	0/0	0/ n.d.	14/ n.d.
		E. coli total lipids	1:50	n.i.	n.d.	n.d.	n.d.	n.d.

n.d. = not defined.

n.i. = not investigated.

elife-20954-v2.xml

10.7554/eLife.20954.011

Table 2.

Construct list combining full name, size and expression system with the abbreviation. The theoretical masses of the different constructs are calculated by the Expasy tool protparam according to the primary sequence. Based on that the theoretical molecular weights of labeled proteins are calculated by the addition of masses of the single amino acids subtracted by the number of water molecules corresponding to the number of peptide bonds.

DOI: http://dx.doi.org/10.7554/eLife.20954.011

Protein	Molecular weight [kDa]		Full name	Reference
Protein	Theoretical	Experimental	Full name	Reference
PR	27.09*	27.19*	Proteorhodopsin (green variant)	(Reckel et al., 2011)
KcsA	21.33/22.70^†	21.38/22.77^†	pH-gated potassium channel KcsA	-
Emre	13.00	13.09	Multidrug transporter EmrE	(Roos et al., 2012)
LspA	21.52/22.83^†	21.63/22.84^†	Lipoprotein signal peptidase	(Laguerre et al., 2016)
hHv1-VSD	20.80/22.28^†	20.89/22.20^†	Human proton channel - voltage sensing domain	(Li et al., 2015)
Bs-MraY	37.88	37.93	Phospho-N-acetylmuramyl-pentapeptide-transferase B.subtilis	(Henrich et al., 2016)
Ec-MraY	42.22	42.29	Phospho-N-acetylmuramyl-pentapeptide-transferase E.coli	(Henrich et al., 2016)
MSP1	25.3	25.40	Membrane scaffold protein	(Denisov et al., 2004)
MSP1E3D1	31.96	32.08	Membrane scaffold protein	(Denisov et al., 2004)
MSP1D1ΔH5	19.49^‡/21.46	19.53^‡/21.50	Membrane scaffold protein	(Hagn et al., 2013)

* Molecular mass according to covalent coupling of all trans-retinal.

† Molecular mass according to heavy isotope labeling.

‡ Molecular mass according to cleavage of the His₆-tag.

elife-21350-v2.xml

10.7554/eLife.21350.008

Table 2.

Comparison of results on HR activity and drug response of the BRCA1 variants analyzed in this study obtained from previous and this studies.

DOI: http://dx.doi.org/10.7554/eLife.21350.008

	Domain	HR activity (%)						Cisplatin response		Olaparib response
	Domain	Sy et al., 2009	Ransburgh et al. (2010)	Towler et al. (2013)	Bouwman et al. (2013)	Lu et al., 2015	This study	Bouwman et al. (2013)	This study	Bouwman et al. (2013)	This study
Vector		N/A	~10	~9	~20	~18	17.3	S	S	S	S
WT		98	100	100	100	100	100	R	R	R	R
C61G	RING	-	~17	-	-	23.6	21.2	S	S	-	S
C64R	RING	-	-	-	-	-	22.3	-	S	-	S
Y179C		-	-	~95	-	157.1	92.7	-	R	-	R
L246V		-	-	-	-	-	91.5	R	R	-	R
Q356R		-	-	-	-	-	95.5	-	R	-	R
F486L		-	-	-	-	160	95.8	-	R	-	R
R496H		-	-	-	-	-	95.9	-	R	-	R
N550H		-	-	-	-	90.8	88.4	-	R	-	R
L668F		-	-	-	-	96.8	93.6	R	R	-	R
D693N		-	-	-	-	-	111.5	R	R	-	R
V772A		-	-	-	-	110.4	84.5	-	R	-	R
R841W		-	-	-	-	-	98.2	-	R	-	R
P871L		-	-	-	-	-	wt	-	wt	-	wt
M1008I		-	-	-	-	-	99.2	R	R	-	R
E1038G		-	-	-	-	-	wt	-	wt	-	wt
S1040N		-	-	-	-	-	98.0	-	R	-	R
S1101N		-	-	-	-	-	97.3	R	R	-	R
S1140G		-	-	-	-	-	106.2	R	R	-	R
K1183R		-	-	-	-	-	wt	-	wt	-	wt
R1347G		-	-	-	-	-	106.5	-	R	-	R
M1400V	CC	56	-	-	-	-	74.8	R	S	R	S
L1407P	CC	24	-	-	-	-	24	S	S	S	S
M1411T	CC	25	-	-	-	-	26	R	S	R	S
S1512I		-	-	-	-	-	95.3	-	R	-	R
T1561I		-	-	-	-	133.2	102.3	-	R	-	R
S1613G		-	-	-	-	-	wt	-	wt	-	wt
M1628T		-	-	-	-	107	107.6	R	R	-	R
P1637L		-	-	-	-	98.8	99.5	-	R	-	R
5055△G	BRCT	-	-	-	-	-	22.5	-	S	-	S
M1652I	BRCT	-	-	-	-	-	106.2	R	R	-	R
S1655F	BRCT	-	-	-	~30	-	8.4	S	S	-	S
C1697R	BRCT	-	-	-	-	-	8.0	-	S	-	S
R1699Q	BRCT	-	-	-	~45	-	16.9	S	S	S	S
A1708E	BRCT	-	-	-	-	-	10.7	-	S	-	S
S1715R	BRCT	-	-	-	-	-	9.3	-	S	-	S
M1775R	BRCT	36	-	~6	-	-	10.2	-	S	-	S

R, resistant; S, sensitive. See Figure 1—source data 1, Figure 2—source data 1 and Figure 3—source data 1 for details.

elife-21350-v3.xml

10.7554/eLife.21350.008

Table 2.

Comparison of results on HR activity and drug response of the BRCA1 variants analyzed in this study obtained from previous and this studies.

DOI: http://dx.doi.org/10.7554/eLife.21350.008

	Domain	HR activity (%)						Cisplatin response		Olaparib response
	Domain	Sy et al., 2009	Ransburgh et al. (2010)	Towler et al. (2013)	Bouwman et al. (2013)	Lu et al., 2015	This study	Bouwman et al. (2013)	This study	Bouwman et al. (2013)	This study
Vector		N/A	~10	~9	~20	~18	17.3	S	S	S	S
WT		98	100	100	100	100	100	R	R	R	R
C61G	RING	-	~17	-	-	23.6	21.2	S	S	-	S
C64R	RING	-	-	-	-	-	22.3	-	S	-	S
Y179C		-	-	~95	-	157.1	92.7	-	R	-	R
L246V		-	-	-	-	-	91.5	R	R	-	R
Q356R		-	-	-	-	-	95.5	-	R	-	R
F486L		-	-	-	-	160	95.8	-	R	-	R
R496H		-	-	-	-	-	95.9	-	R	-	R
N550H		-	-	-	-	90.8	88.4	-	R	-	R
L668F		-	-	-	-	96.8	93.6	R	R	-	R
D693N		-	-	-	-	-	111.5	R	R	-	R
V772A		-	-	-	-	110.4	84.5	-	R	-	R
R841W		-	-	-	-	-	98.2	-	R	-	R
P871L		-	-	-	-	-	wt	-	wt	-	wt
M1008I		-	-	-	-	-	99.2	R	R	-	R
E1038G		-	-	-	-	-	wt	-	wt	-	wt
S1040N		-	-	-	-	-	98.0	-	R	-	R
S1101N		-	-	-	-	-	97.3	R	R	-	R
S1140G		-	-	-	-	-	106.2	R	R	-	R
K1183R		-	-	-	-	-	wt	-	wt	-	wt
R1347G		-	-	-	-	-	106.5	-	R	-	R
M1400V	CC	56	-	-	-	-	74.8	R	S	R	S
L1407P	CC	24	-	-	-	-	24	S	S	S	S
M1411T	CC	25	-	-	-	-	26	R	S	R	S
S1512I		-	-	-	-	-	95.3	-	R	-	R
T1561I		-	-	-	-	133.2	102.3	-	R	-	R
S1613G		-	-	-	-	-	wt	-	wt	-	wt
M1628T		-	-	-	-	107	107.6	R	R	-	R
P1637L		-	-	-	-	98.8	99.5	-	R	-	R
5055△G	BRCT	-	-	-	-	-	22.5	-	S	-	S
M1652I	BRCT	-	-	-	-	-	106.2	R	R	-	R
S1655F	BRCT	-	-	-	~30	-	8.4	S	S	-	S
C1697R	BRCT	-	-	-	-	-	8.0	-	S	-	S
R1699Q	BRCT	-	-	-	~45	-	16.9	S	S	S	S
A1708E	BRCT	-	-	-	-	-	10.7	-	S	-	S
S1715R	BRCT	-	-	-	-	-	9.3	-	S	-	S
M1775R	BRCT	36	-	~6	-	-	10.2	-	S	-	S

R, resistant; S, sensitive. See Figure 1—source data 1, Figure 2—source data 1 and Figure 3—source data 1 for details.

elife-21459-v3.xml

10.7554/eLife.21459.004

Table 1.

Relative gene expression level of selected WNT pathway regulators in HAP1 cells. RPKM values from duplicate RNAseq datasets generated as described in Materials and methods from two different passages of WT HAP1 cells are shown. Groups of paralogues and genes with similar functions are shaded in alternating colors to facilitate comparisons.

DOI: http://dx.doi.org/10.7554/eLife.21459.004

Gene	RPKM
Gene	Replicate 1	Replicate 2	Average
LGR4	160.61	174.69	167.65
LGR5	0.02	0.00	0.01
LGR6	0.02	0.00	0.01
ZNRF3	30.90	33.30	32.10
RNF43	0.12	0.08	0.10
LRP5	55.92	64.38	60.15
LRP6	109.51	121.08	115.30
FZD1	19.57	18.85	19.21
FZD2	19.56	21.09	20.33
FZD3	48.02	55.82	51.92
FZD4	19.60	22.10	20.85
FZD5	31.85	34.52	33.19
FZD6	33.53	31.95	32.74
FZD7	13.89	14.89	14.39
FZD8	4.02	4.48	4.25
FZD9	3.66	2.80	3.23
FZD10	10.40	9.86	10.13
DVL1	73.91	69.61	71.76
DVL2	51.74	48.80	50.27
DVL3	88.84	90.25	89.54
APC	80.47	85.22	82.84
APC2	2.94	3.69	3.32
AXIN1	55.97	54.07	55.02
AXIN2	10.04	12.51	11.27
CSNK1A1	111.18	109.57	110.37
GSK3A	75.97	69.21	72.59
GSK3B	62.79	69.98	66.39
TCF7L2	23.89	27.69	25.79
LEF1	12.34	14.80	13.57
CTNNB1	324.05	308.53	316.29
CREBBP	141.92	165.58	153.75
PIGL	4.07	4.51	4.29
GPC4	209.39	229.86	219.63
GPC6	13.88	14.90	14.39
TFAP4	36.99	41.94	39.46
SERBP1	721.65	698.99	710.32
HUWE1	631.58	777.06	704.32

elife-21459-v4.xml

10.7554/eLife.21459.005

Table 1.

DOI: http://dx.doi.org/10.7554/eLife.21459.005

Gene	RPKM
Gene	Replicate 1	Replicate 2	Average
LGR4	160.61	174.69	167.65
LGR5	0.02	0.00	0.01
LGR6	0.02	0.00	0.01
ZNRF3	30.90	33.30	32.10
RNF43	0.12	0.08	0.10
LRP5	55.92	64.38	60.15
LRP6	109.51	121.08	115.30
FZD1	19.57	18.85	19.21
FZD2	19.56	21.09	20.33
FZD3	48.02	55.82	51.92
FZD4	19.60	22.10	20.85
FZD5	31.85	34.52	33.19
FZD6	33.53	31.95	32.74
FZD7	13.89	14.89	14.39
FZD8	4.02	4.48	4.25
FZD9	3.66	2.80	3.23
FZD10	10.40	9.86	10.13
DVL1	73.91	69.61	71.76
DVL2	51.74	48.80	50.27
DVL3	88.84	90.25	89.54
APC	80.47	85.22	82.84
APC2	2.94	3.69	3.32
AXIN1	55.97	54.07	55.02
AXIN2	10.04	12.51	11.27
CSNK1A1	111.18	109.57	110.37
GSK3A	75.97	69.21	72.59
GSK3B	62.79	69.98	66.39
TCF7L2	23.89	27.69	25.79
LEF1	12.34	14.80	13.57
CTNNB1	324.05	308.53	316.29
CREBBP	141.92	165.58	153.75
PIGL	4.07	4.51	4.29
GPC4	209.39	229.86	219.63
GPC6	13.88	14.90	14.39
TFAP4	36.99	41.94	39.46
SERBP1	721.65	698.99	710.32
HUWE1	631.58	777.06	704.32

elife-21477-v2.xml

10.7554/eLife.21477.015

Table 1.

Overview of crosslinks formed by ISWI_H483B.

DOI: http://dx.doi.org/10.7554/eLife.21477.015

ID	Mass (D a)	Error (ppm)	Bpa peptide		Target peptide
ID	Mass (D a)	Error (ppm)	Sequence^*,†	Site	Sequence^†	Site
XL1	3220.4946	−1.9	LDGQTPBEDRNR	483	QTEIFTHFM^oxTNSAK^‡	59–60
XL2	3204.5056	−3.7	LDGQTPBEDRNR	483	QTEIFTHFMTNSAK^‡	60–61
XL3	2950.3474	−1.0	LDGQTPBEDR	483	QTEIFTHFM^oxTNSAK^‡	55–59
XL4	2934.3571	−2.6	LDGQTPBEDR	483	QTEIFTHFMTNSAK^‡	59–61
XL5	2207.0968	+0.2	LDGQTPBEDRNR	483	SPTKPK^‡	69–72
XL6	1936.9645	−6.1	LDGQTPBEDR	483	SPTKPK^‡	71–72
XL7	1736.8594	−6.1	LDGQTPBEDR	483	GRPK	75

^*B symbolizes Bpa.

^†Crosslinked amino acids are underlined; ^oxindicates oxidized methionine (+15.9949 Da).

^‡Precise attachment sites not distinguishable from data.

elife-21477-v2.xml

10.7554/eLife.21477.016

Table 2.

Overview of H4-tail mediated crosslinks.

DOI: http://dx.doi.org/10.7554/eLife.21477.016

ID	Reliability	H4	Remodeler construct	Mass (Da)	Error (ppm)	H4 peptide		Remodeler peptide
ID	Reliability	H4	Remodeler construct	Mass (Da)	Error (ppm)	Sequence^*	Site	Sequence^†	Site
XL11	high	nucleosomal	ISWI_WT	2034.8571	−0.2	XGR	1	QIQEFNMDNSAK	495
XL12	high	nucleosomal	SNF2H	2251.9753	−0.4	GXGK	10	VLDILEDYCMWR	520
XL13a	high	peptide	ISWI_26-648	1648.7601	−0.4	BGR	1	LDGQTPHEDR	482
XL13b	high	peptide	ISWI_26-648	1918.9052	−0.9	BGR	1	LDGQTPHEDRNR	482
XL13c	high	peptide	ISWI_26-648	3340.5374	−2.8	BGR	1	LDGQTPHEDRNRQIQEFNMDNSAK	482
XL14	medium	nucleosomal	SNF2H	2222.9624	−1.5	XGR	1	VLDILEDYCMWR^‡	519–22
XL15	medium	peptide	ISWI_26-648	1257.6261	+2.3	BGR	1	MVIQGGR	578
XL16	medium	peptide	ISWI_26-648	1424.7832	−3.9	BGR	1	IVERAEVK	568
XL17	medium	peptide	ISWI_26-648	1453.7998	−4.6	GBGK	10	IVERAEVK	568

^*B symbolizes Bpa; X symbolizes Benzophenone-labeled cysteine.

^†Crosslinked amino acids are underlined.

^‡Precise attachment sites not distinguishable from data.

elife-22069-v2.xml

10.7554/eLife.22069.005

Table 2.

Number and origin of blood meals according to the fly species (Fsp), park and climatic season.

DOI: http://dx.doi.org/10.7554/eLife.22069.005

			Number of identified blood meals by fly species (Fsp)
			Moukalaba-Doudou											Lopé
			Rainy season					Dry season						Rainy season					Dry season
Taxonomic group/Order/Family	Host species	N° Identified	Fsp1	Fsp2	Fsp3	Fsp4	Fsp5	Fsp1	Fsp2	Fsp3	Fsp4	Fsp5	Fsp8	Fsp1	Fsp2	Fsp3	Fsp4	Fsp5	Fsp1	Fsp2	Fsp3	Fsp4	Fsp5	Fsp6	Fsp7
Mammals
Artiodactyla		295		1	4	3	8	1	1	7	1	14			2	1		2	3	3	4	1	3
Bovidae	Cephalophus silvicultor	65
	kobus ellipsiprymnus	4					3					1
	Syncerus caffer	126	3		5		7	1	1	3	2	9		2	1	10	5	7	1	2	8	1	6		1
	Tragelaphus spekii	95								1		6		4	1	5	1	3	7	6	9	4	12	1
Hippopotamidae	Hippopotamus amphibius	2					1					1
Suidae	Potamochoerus porcus	3					1					2
Carnivora		1
Herpestidae	Herpestinae sp	1					1
Primates		67
Hominidae	Gorilla gorilla	3					2					1
	Homo sapiens	64			1	1	13			2		22	1		3		1	2			1		4		1
Proboscidae		10
Elephantidae	Loxodonta cyclotis	10										7				1		2
Reptiles
Crocodilia		23										3
Crocodylidae	Crocodylus niloticus	3
	Mecistops cataphractus	19			1		1					6
	Osteolaemus tetraspis	1										1
Squamata		12
Pythonidae	Python sebae	8										2
Varanidae	Varanus sp	4								2		1				1
Testudines		16
Testunidae	Kinixys erosa	1										1
Pelomedusidae	Pelusios castaneus	3								1	1	1
	Pelusios chapini	1										1
	Pelusios marani	11					3					8
Birds
Ciconiformes		4
Ciconiidae	Ciconia sp	4					1					2
8 orders/12 families	20 species	428	3	1	11	4	41	2	2	16	4	89	1	6	7	18	7	16	11	11	22	6	25	1	2

Fsp1 = Glossina caliginea; Fsp2 = G. fusca congolensis; Fsp3 = G. fuscipes fuscipes; Fsp4 = G. pallicera newsteadi; Fsp5 = G. palpalis palpalis; Fsp6 = Stomoxys calcitrans; Fsp7 = S. niger niger; Fsp8 = Chrysops sp.

elife-22069-v2.xml

10.7554/eLife.22069.006

Table 3.

Number and origin of blood meals according to the fly species (Fsp), park and climatic season.

DOI: http://dx.doi.org/10.7554/eLife.22069.006

			Number of identified blood meals by fly species (Fsp)
			La Lékédi										Ivindo
			Rainy season					Dry season					Dry season
Taxonomic group/Order/Family	Host species	N° Identified	Fsp1	Fsp3	Fsp4	Fsp5	Fsp6	Fsp1	Fsp2	Fsp3	Fsp4	Fsp5	Fsp1	Fsp2	Fsp3	Fsp5
Mammals
Artiodactyla		295		2	1	3
Bovidae	Cephalophus silvicultor	65
	kobus ellipsiprymnus	4
	Syncerus caffer	126	2	1		1		6	10	8	8	13			1	1
	Tragelaphus spekii	95		1		3	1	2	8	5	5	9		1
Hippopotamidae	Hippopotamus amphibius	2
Suidae	Potamochoerus porcus	3
Carnivora		1
Herpestidae	Herpestinae sp	1
Primates		67
Hominidae	Gorilla gorilla	3
	Homo sapiens	64				4				1		5			1	1
Proboscidae		10
Elephantidae	Loxodonta cyclotis	10
Reptiles
Crocodilia		23
Crocodylidae	Crocodylus niloticus	3
	Mecistops cataphractus	19							2	4	2	3
	Osteolaemus tetraspis	1
Squamata		12
Pythonidae	Python sebae	8				2				2		2
Varanidae	Varanus sp	4
Testudines		16
Testunidae	Kinixys erosa	1
Pelomedusidae	Pelusios castaneus	3
	Pelusios chapini	1
	Pelusios marani	11
Birds
Ciconiformes		4
Ciconiidae	Ciconia sp	4											1
8 orders/12 families	20 species	428	2	4	1	13	1	8	20	20	15	32	1	1	2	2

elife-22152-v1.xml

10.7554/eLife.22152.019

Table 2.

Voltage-clamp protocol parameters for the five ion type classes. Times are stated in units of ms, voltages in units of mV. See Figure 3—figure supplement 1 for graphical description. Items TA* and TB* represent the starting and ending times, respectively, of the regions used for analysis (dashed areas in Figure 3 of the main text, as well as Figure 3—figure supplement 1).

DOI: http://dx.doi.org/10.7554/eLife.22152.019

Act	Ion type	V0	V1	V2	Δ⁢V	T1	T2	T3	TA*	TB*
	Kv	−80	−80	70	10	100	500	100	100	700
	Nav	−80	−80	70	10	20	50	30	18	100
	Cav	−80	−80	70	10	100	500	100	98	700
	KCa	−80	−80	70	10	100	500	100	95	605
	Ih	−40	−150	0	10	100	2000	100	95	2105
Inact	Ion Type	V0	V1	V2	V3	Δ⁢V	T1	T2	T3	T4	TA*	TB*
	Kv	−80	−40	70	30	10	100	1500	50	100	1600	1700
	Nav	−80	−40	70	30	10	100	1500	50	100	1580	1750
	Cav	−80	−40	70	30	10	100	1500	50	100	1580	1750
	KCa	−80	−40	70	30	10	100	1500	50	100	1595	1700
	Ih	−40	−150	−40	−120	10	100	1000	300	100	1095	1405
Deact	Ion Type	V0	V1	V2	V3	Δ⁢V	T1	T2	T3	T4	TA*	TB*
	Kv	−80	70	−100	40	10	100	300	200	100	400	600
	Nav	−80	70	−100	40	10	20	10	30	20	29	80
	Cav	−80	70	−100	40	10	100	300	200	100	380	700
	KCa	−80	70	−100	40	10	100	300	200	100	395	605
	Ih	−40	−140	−110	0	10	100	1500	500	400	1595	2105
Ramp	Ion Type	V0	V1	T1	T2	T3	T4	T5	T6	T7	T8	T9	TA*	TB*
	Kv	−80	70	100	800	400	400	400	200	400	100	100	100	2800
	Nav	−80	70	100	800	400	400	400	200	400	100	100	98	2800
	Cav	−80	70	100	800	400	400	400	200	400	100	100	98	2800
	KCa	−80	70	100	800	400	400	400	200	400	100	100	100	2800
	Ih	−80	70	100	800	400	400	400	200	400	100	100	100	2800
AP	Ion Type	T1	TA*	TB*
	Kv	1800	100	1800
	Nav	1800	98	1800
	Cav	1800	98	1800
	KCa	1800	95	1655
	Ih	1800	95	1655

elife-22352-v2.xml

10.7554/eLife.22352.023

Table 3.

Minimal spanning trees (MSTs) simulation parameters. 16 STG neuronal structures were simulated using MST analyses from the TREES toolbox (Cuntz et al., 2010). Carrier point numbers (column 4) were tuned to generate MSTs with branch point numbers within 20% of the branch point counts in the actual neurons (column 2, gray shaded). MSTs were generated for balancing factors between 0 and 0.6, at increments of 0.1. Columns 5–18 show branch point numbers and cable lengths for each of these MSTs. The MSTs often had cable lengths within 20% of that measured in the actual neurons (column 3), but in some cases, the MSTs were not a close approximation of the actual cable length.

DOI: http://dx.doi.org/10.7554/eLife.22352.023

Cell	Actual neuron		Minimum spanning trees
	Branch Points	Cable length(x 10⁴ µm)	Carrier Points	Branch point numbers							Cable length (x 10⁴ µm)
	Branch Points	Cable length(x 10⁴ µm)	Carrier Points	0	0.1	0.2	0.3	0.4	0.5	0.6	0	0.1	0.2	0.3	0.4	0.5	0.6
GM1	2671	6.1	8500	2416	2477	2512	2576	2727	2916	2971	16.8	17.2	17.7	18.2	19.0	19.9	20.7
GM2	7125	8.9	23000	6296	6789	7030	7271	7592	7773	7994	2.5	2.6	2.7	2.8	2.9	3.1	3.3
GM3	2675	4.6	8800	2384	2537	2665	2749	2827	2959	3026	5.5	5.7	5.9	6.1	6.4	6.8	7.3
GM4	5984	10.4	19000	5274	5574	5762	5969	6187	6379	6571	14.3	14.7	15.2	15.8	16.6	17.5	18.8
LG1	2002	2.0	6500	1746	1860	1976	2092	2154	2209	2302	1.7	1.8	1.9	1.9	2.0	2.1	2.3
LG2	705	1.0	2300	641	672	696	710	750	768	815	1.5	1.5	1.6	1.7	1.7	1.8	2.0
LG3	2460	4.3	8000	2168	2302	2389	2498	2559	2612	2707	4.3	4.4	4.6	4.8	5.0	5.3	5.7
LG4	2311	4.9	7500	2050	2189	2282	2346	2430	2502	2603	2.4	2.4	2.5	2.6	2.8	2.9	3.1
LP1	2015	4.1	6550	1825	1957	1998	2059	2126	2195	2263	3.3	3.3	3.5	3.6	3.8	4.0	4.3
LP2	704	1.8	2330	649	666	706	716	748	773	788	2.0	2.1	2.1	2.2	2.3	2.5	2.6
LP3	499	1.4	1705	452	493	509	534	531	560	574	1.6	1.7	1.7	1.8	1.9	2.0	2.1
LP4	1708	2.4	5650	1574	1639	1697	1743	1819	1883	1921	3.8	3.9	4.0	4.2	4.4	4.6	5.0
PD1	424	1.9	1400	370	398	422	444	442	464	501	1.6	1.7	1.8	1.8	1.9	2.0	2.2
PD2	418	1.5	1400	383	406	426	425	455	460	477	1.2	1.2	1.3	1.3	1.4	1.5	1.6
PD3	1597	3.0	5000	1344	1462	1519	1587	1667	1724	1776	3.3	3.4	3.5	3.7	3.8	4.1	4.3
PD4	410	1.7	1300	363	389	397	396	429	442	451	1.2	1.3	1.3	1.4	1.4	1.5	1.6

elife-22519-v1.xml

10.7554/eLife.22519.010

Table 1.

Molecular evolution analyses of the provirus containing hsaHTenv in its orthologs. (1) Divergence measured in substitutions per site. (2) Integration dates inferred from the divergence of the paired LTRs for human, gorilla and orangutan proviruses. Age is calculated assuming a human neutral substitution rate of 2.2 × 10⁻⁹ substitutions per site per year. (3) Pairwise dN/dS ratios for the env genes calculated using codeml (CodonFreq = F3 × 4, Kappa and Omega estimated). (**) Significantly different from dN/dS = 1 (p<0.01).

DOI: http://dx.doi.org/10.7554/eLife.22519.010

10.7554/eLife.22519.011Table 1—source data 1.Likelihood ratio tests on dN/dS estimates for hsaHTenv and its orthologs. dN/dS ratios (ω) were estimated on a pairwise basis using codeml.

Likelihood ratio tests were performed comparing the log likelihood of the estimated ω (L₁) to the log likelihood when ω was fixed to 1 (L₀, neutral selection). The probability (P) of twice the difference (D = 2(L₁−L₀)) was calculated using a chi-squared distribution (degrees of freedom = 1). The single nucleotide frame-shift insertion in the gorilla sequence was artificially deleted in order to compare orthologous codons.

DOI: http://dx.doi.org/10.7554/eLife.22519.011

Locus	LTR divergence⁽¹⁾	Age (MY)⁽²⁾	Env dN/dS ratio⁽³⁾
Locus	LTR divergence⁽¹⁾	Age (MY)⁽²⁾	Gorilla	Orangutan
Human	0.0317	7.20	1.4860	0.5184**
Gorilla	0.0414	9.41	−	0.7592
Orangutan	0.0855	19.43	0.7592	−

elife-22679-v2.xml

10.7554/eLife.22679.021

Table 2.

Biochemical characterization of PriA, SubHisA2 and SubTrpF homologs.

DOI: http://dx.doi.org/10.7554/eLife.22679.021

Enzymes	In vivo activity		In vitro activity ^*
			ProFAR isomerase (HisA)			PRA isomerase (TrpF)
	HisA	TrpF	K_M (µM)	k_cat (s⁻¹)	k_cat/K_M (s⁻¹µM⁻¹)	K_M (µM)	k_cat (s⁻¹)	k_cat/K_M (s⁻¹µM⁻¹)
PriA_Org3_B. longum	+	+	2.7 ± 0.5	0.4 ± 0.1	0.1	6.1 ± 0.1	2.1 ± 0.5	0.3
PriA_Org1_B. gallicum	+	+	1.7 ± 0.3	0.3 ± 0.1	0.2	40 ± 9	3.5 ± 0.1	0.09
PriA_Org6_B. adolescentis	+	+	17 ± 4.3	2.3 ± 0.01	0.1	21 ± 5	0.9 ± 0.2	0.04
PriA_Org15_A. urogenitalis	+	+	4.0 ± 0.9	0.2 ± 0.03	0.04	23 ± 6.5	0.5 ± 0.05	0.02
PriA_Org22_A. sp. oral taxon 171	+	+	3 ± 0.3	0.3 ± 0.09	0.1	8 ± 2	0.4 ± 0.1	0.04
PriA_Org21_A. oris MG-1	+	+	10 ± 2	0.2 ± 0.09	0.02	30 ± 7	0.3 ± 0.03	0.01
SubHisA2_Org34_A. vaccimaxillae	+	+
SubHisA2_Org36_A. cardiffensis	+	+	56 ± 17	0.14 ± 0.05	0.002	n.d.	n.d.	n.d.
SubTrpF_Org10_A. sp. oral taxon 848	−	+	n.d.	n.d.	n.d.	n.d.	n.d.	0.0001
SubTrpF_Org13_A. graevenitzii	−	+
SubTrpF_Org39_A. sp. oral taxon 180	−	+
SubTrpF_Org41_A. odontolyticus	−	+	n.d.	n.d.	n.d.	8.5 ± 0.9	0.15 ± 0.06	0.02

^* Each data point comes from at least three independent determinations using freshly purified enzyme. n.d., activity not detected, even using active-site saturation conditions. Empty entries reflect our inability to properly express and/or solubilize these proteins. The detection limits for the PRA and ProFAR isomerase assay used in the present study are 0.0001 μM⁻¹s⁻¹ and 0.001 μM⁻¹s⁻¹, respectively (Noda-García et al., 2013; Verduzco-Castro et al., 2016; Noda-García et al., 2010).

elife-22767-v2.xml

10.7554/eLife.22767.009

Table 1.

Ikaros represses transcription by interfering with RNAP2 recruitment rather than elongation. Analysis of differential gene expression (adj. p<0.05) 360 min after 4-OHT-induced nuclear translocation of Ikaros in B3 cells, RNAP2 ChIP-seq, and the distribution of RNAP2 over the TSS and the gene body derived from RNAP2 ChIP-seq. RNAP2 occupancy was significantly decreased at only 40.3% (372 of 924) of genes downregulated at adj. p<0.05 but increased to 62% when considering only genes downregulated with adj. p<0.01 and a minimal log2 fold-change of 2. This suggests that the failure to detect decreased RNAP2 occupancy at the majority of downregulated genes may be due to the limited sensitivity of RNAP2 ChIP-seq compared to RNA-seq.

DOI: http://dx.doi.org/10.7554/eLife.22767.009

10.7554/eLife.22767.010Table 1—source data 1.Numerical data used to generate <xref ref-type="table" rid="tbl1">Table 1</xref>.

DOI: http://dx.doi.org/10.7554/eLife.22767.010

Gene expression	RNAP2 occupancy by ChIP
Gene expression	Global	TSS~gene body	TSS>gene body	TSS<gene body
Unchanged: 8799	Unchanged: 8125	8019	49	57
	Reduced: 405	378	11	16
	Increased: 269	256	10	3
Downregulated by Ikaros: 924	Unchanged: 549	520	12	17
	Reduced: 372	324	15	33
	Increased: 3	3	0	0
Upregulated by Ikaros: 855	Unchanged: 634	615	15	4
	Reduced: 6	6	0	0
	Increased: 215	200	13	2

elife-22772-v2.xml

10.7554/eLife.22772.079

Appendix 2—table 1.

Parameter values in the reaction-diffusion system: Appendix 2-Equations (1–4). (1) In Figure 1C, βI ranges from −11 to 2, and Figure 1B is obtained under βI=0; both are noise-free, thus λA=λI=0. (2) In Appendix 2—figure 6, low, medium and high inhibitor L correspond to βI=-6,-3,0, respectively, and weak, medium and strong noise correspond to λA=λI=2,4,6 – the same for both multiplicative and additive noise. (3) In Appendix 2—figure 8 and 9, low R and high R correspond to RtotA=RtotI=R=6 or 60, respectively, while low, medium and high inhibitor L correspond to βI=-6,-3,0, respectively, which is the same as in Appendix 2—figure 6. Appendix 2—figure 8 and 9 again show noise-free results, hence λA=λI=0. Also see Appendix 2—table 2 for supplementary parameter values.

DOI: http://dx.doi.org/10.7554/eLife.22772.079

Reaction - Diffusion System
Parameters		1D	2D	3D
Parameters		1D	2D	Dorsal	Ventral
Preservation of Receptors	RtotA	10	10	15	50
Preservation of Receptors	RtotI	10	10	15	50
Diffusion	DA	1	0.5	0.5
Diffusion	DI	1	0.5	0.5
Reaction	konA	0.3
	koffA	0
	konI	0.5
	koffI	0
Degradation	kdegA	2
Degradation	kdegI	4	6.5	7
Concentration Threshold	Δ+	1.5	2.25	2.6
Concentration Threshold	Δ-	0
Noise	λA	2/4/6	3.2	See Appendix 2—table 2.
Noise	λI	2/4/6	3.2	See Appendix 2—table 2.
Others	βA	4
Others	βI	−11 → 2	2.3

elife-22772-v2.xml

10.7554/eLife.22772.082

Appendix 2—table 4.

Activity strength of activator/inhibitor ligands (L), antagonists (A), receptors (R) and ligand-bond receptors (LR) in different phases within a full HF growth cycle.

DOI: http://dx.doi.org/10.7554/eLife.22772.082

		Activator		Inhibitor
		Region I	Region II	Region I	Region II
		(Bulge)	(sHG, Matrix, DP)	(Bulge)	(sHG, Matrix, DP)
Late Competent Telogen (late C)	L	3	(3,0,4)	2	(2,0,3)
	A	2	(2,0,1)	0	(0,0,3)
	R	2	(2,0,4)	3	(3,0,3)
	LR	4	(4,0,4)	1	(1,0,3)
Propagating Anagen (P)	L	2	(0,4,4)	2	(0,3,3)
	A	2	(0,2,3)	0	(0,2,2)
	R	2	(0,3,4)	3	(0,3,3)
	LR	4	(0,4,4)	1	(0,3,3)
Autonomous Anagen (A)	L	2	(0,4,4)	2	(0,4,4)
	A	2	(0,4,4)	0	(0,2,2)
	R	2	(0,3,4)	3	(0,3,3)
	LR	2	(0,4,4)	3	(0,3,3)
Catagen (Cat)	L	2	(2,0,2)	2	(2,0,4)
	A	2	(2,0,4)	0	(0,0,1)
	R	2	(2,0,4)	3	(3,0,3)
	LR	1	(1,0,1)	3	(3,0,3)
Refractory Telogen (R)	L	2	(2,0,1)	2	(2,0,4)
	A	2	(2,0,4)	0	(0,0,1)
	R	2	(2,0,4)	3	(3,0,3)
	LR	1	(1,0,1)	4	(4,0,4)
Early Competent Telogen (early C)	L	Similar to refractory telogen		Similar to late competent telogen
	A
	R
	LR

elife-22835-v2.xml

10.7554/eLife.22835.031

Table 1.

Concentrations of DAPG, pyoluteorin, and expression of pltL::gfp in pure cultures and co-culture of the ΔphlAΔpltM mutant and the ΔphlAΔphlDΔpltA mutant of P. protegens Pf-5.

DOI: http://dx.doi.org/10.7554/eLife.22835.031

Product/expression*	Amendment^†	Bacterial cultures^‡
Product/expression*	Amendment^†	ΔphlAΔpltM	ΔphlAΔpltM + ΔphlAΔphlDΔpltA	ΔphlAΔphlDΔpltA
Pyoluteorin	None	BD	6.2 ± 1.8 nmol/g	BD
DAPG	None	BD	BD	BD
Relative GFP	None	34.6 ± 2.3	137.4 ± 3.4^§; 214.7 ± 11.2^¶	27.6 ± 1.9
	PG (10 nM)	37.6 ± 3.1	NT	133.3 ± 6.4
	PG-Cl (1 µM)	261.0 ± 13.3	NT	308.6 ± 21.8
	PG-Cl₂ (10 nM)	128.2 ± 10.7	NT	268.4 ± 16.2

*The mutants were cultured for 3 d on a NAGly plate to determine production of secondary metabolites, and for 20 hr in NBGly broth to determine expression of pltL::gfp from the reporter construct pL-gfp (Figure 1E). The co-culture was prepared by mixing the two mutants at a 1:1 ratio.

^†PG, PG-Cl or PG-Cl₂ was amended in the mutant cultures to test their influences on the expression of pltL::gfp. The concentrations of the tested compounds are shown in parenthesis.

^‡Secondary metabolites were extracted from the agar plate and the concentrations of DAPG and pyoluteorin were determined by HPLC. Expression of pltL::gfp was monitored and recorded as relative GFP (fluorescence of GFP divided by OD₆₀₀). ^§The ΔphlAΔpltM mutant, but not the ΔphlAΔphlDΔpltA mutant, contains pL-gfp in the co-culture. ^¶The ΔphlAΔphlDΔpltA mutant, but not the ΔphlAΔpltM mutant, contains pL-gfp in the co-culture. Data are presented as mean ± standard derivation. Mean values are calculated from three biological replicates. BD = below detection. NT = not tested.

elife-22900-v2.xml

10.7554/eLife.22900.012

Table 1.

Impact of phospho-mimicking or phospho-blocking mutations on the thermodynamics parameters of XRCC4-XLF protein-protein interaction by micro-calorimetry.

DOI: http://dx.doi.org/10.7554/eLife.22900.012

10.7554/eLife.22900.013Table 1—source data 1.Thermograms of XRCC4-XLF WT-WT, Ala-Ala, and Asp-Asp experiments.

DOI: http://dx.doi.org/10.7554/eLife.22900.013

	T (°C)	2-Me (mM)	[XRCC4] (μM)	[XLF] (μM)	Ratio	N	K_a (M⁻¹)	ΔH⁰ (kcal/mol)	K_d (μM)	−ΔG⁰ (kcal/mol)	−TΔS⁰ (kcal/mol)	Thermogram shown in	Source data	<K_d> (μM)	<ΔH⁰> (kcal/mol)	<-ΔG⁰> (kcal/mol)	<-TΔS⁰> (kcal/mol)
	T (°C)	2-Me (mM)	ITC cell	ITC syringe	Ratio	N	K_a (M⁻¹)	ΔH⁰ (kcal/mol)	K_d (μM)	−ΔG⁰ (kcal/mol)	−TΔS⁰ (kcal/mol)	Thermogram shown in	Source data	<K_d> (μM)	<ΔH⁰> (kcal/mol)	<-ΔG⁰> (kcal/mol)	<-TΔS⁰> (kcal/mol)
XRCC4-WT XLF-WT	10	10	17	168	10	n.d.	n.d.	n.d.	n.d.	n.d.	n.d.	Figure 5—figure supplement 1A	A
	25	10	17	168	10	0.97	536000	−1.7	1.8	−7.8	−6.1	--	B	3.2 ± 0.8	−2.4 ± 0.4	−7.5 ± 0.2	−5.2 ± 0.5
	25	10	33	330	10	0.91	306000	−2.9	3.2	−7.5	−4.6	Figure 5—figure supplement 1B	C
	25	10	25	330	13	0.84	222000	−2.6	4.5	−7.3	−4.7	--	D
	37	0	23	300	13	0.85	273000	−6.0	3.7	−7.7	−1.7	--	E	2.4 ± 0.7	−7.1 ± 1	−8.0 ± 0.2	−1.0 ± 0.8
	37	0	23	300	13	0.89	278000	−4.9	3.6	−7.7	−2.9	--	F
	37	0	12	154	13	0.92	848000	−8.6	1.2	−8.4	0.2	Figure 5A	G
	37	0	12	154	13	0.84	760000	−8.8	1.3	−8.3	0.4	--	H
XRCC4-Ala XLF-Ala	25	10	25	330	13	1.21	300000	−1.7	3.3	−7.5	−5.8	Figure 5—figure supplement 1C	I
	37	0	25	325	13	1.07	637000	−3.1	1.6	−8.2	−5.1	--	J	2.3 ± 0.4	−5.8 ± 1.4	−8.0 ± 0.1	−2.2 ± 1.4
	37	0	25	325	13	1	343000	−3.7	2.9	−7.8	−4.1	--	K
	37	0	19	250	13	0.92	345000	−8.4	2.9	−7.8	0.6	--	L
	37	0	19	250	13	0.92	582000	−8.1	1.7	−8.2	−0.1	Figure 5B	M
XRCC4-Asp XLF-Asp	25	10	35	350	10	1.27	672000	−0.9	1.5	−7.9	−7.0	--	N
	25	10	25	330	13	0.82	263000	−1.2	3.8	−7.4	−6.2	Figure 5—figure supplement 1D	O
	37	0	32	416	13	1.06	289000	−2.4	3.4	−7.8	−5.4	--	P	2.4 ± 0.4	−3.7 ± 0.8	−8.0 ± 0.1	−4.3 ± 0.7
	37	0	32	416	13	0.95	425000	−2.3	2.4	−8.0	−5.7	--	Q
	37	0	19	250	13	0.88	566000	−4.7	1.8	−8.2	−3.5	Figure 5C	R
	37	0	17	220	13	0.85	538000	−5.5	1.8	−8.1	−2.6	--	S

2-Me stands for 2-Mercaptoethanol

Ratio indicates the titrant over analyte concentration ([XLF]/[XRCC4])

Source data specifies the column corresponding to each thermogram in Table 1—source data 1.

Last four columns report mean values ± Standard Error of the Mean (SEM) from four experimental runs at 37°C (grey cells) and 3 runs at 25°C (white cells)

n.d. denotes no detectable heat transfer (at 10°C)

elife-22900-v3.xml

10.7554/eLife.22900.012

Table 1.

Impact of phospho-mimicking or phospho-blocking mutations on the thermodynamics parameters of XRCC4-XLF protein-protein interaction by micro-calorimetry.

DOI: http://dx.doi.org/10.7554/eLife.22900.012

10.7554/eLife.22900.013Table 1—source data 1.Thermograms of XRCC4-XLF WT-WT, Ala-Ala, and Asp-Asp experiments.

DOI: http://dx.doi.org/10.7554/eLife.22900.013

	T (°C)	2-Me (mM)	[XRCC4] (μM)	[XLF] (μM)	Ratio	N	K_a (M⁻¹)	ΔH⁰ (kcal/mol)	K_d (μM)	−ΔG⁰ (kcal/mol)	−TΔS⁰ (kcal/mol)	Thermogram shown in	Source data	<K_d> (μM)	<ΔH⁰> (kcal/mol)	<-ΔG⁰> (kcal/mol)	<-TΔS⁰> (kcal/mol)
	T (°C)	2-Me (mM)	ITC cell	ITC syringe	Ratio	N	K_a (M⁻¹)	ΔH⁰ (kcal/mol)	K_d (μM)	−ΔG⁰ (kcal/mol)	−TΔS⁰ (kcal/mol)	Thermogram shown in	Source data	<K_d> (μM)	<ΔH⁰> (kcal/mol)	<-ΔG⁰> (kcal/mol)	<-TΔS⁰> (kcal/mol)
XRCC4-WT XLF-WT	10	10	17	168	10	n.d.	n.d.	n.d.	n.d.	n.d.	n.d.	Figure 5—figure supplement 1A	A
	25	10	17	168	10	0.97	536000	−1.7	1.8	−7.8	−6.1	--	B	3.2 ± 0.8	−2.4 ± 0.4	−7.5 ± 0.2	−5.2 ± 0.5
	25	10	33	330	10	0.91	306000	−2.9	3.2	−7.5	−4.6	Figure 5—figure supplement 1B	C
	25	10	25	330	13	0.84	222000	−2.6	4.5	−7.3	−4.7	--	D
	37	0	23	300	13	0.85	273000	−6.0	3.7	−7.7	−1.7	--	E	2.4 ± 0.7	−7.1 ± 1	−8.0 ± 0.2	−1.0 ± 0.8
	37	0	23	300	13	0.89	278000	−4.9	3.6	−7.7	−2.9	--	F
	37	0	12	154	13	0.92	848000	−8.6	1.2	−8.4	0.2	Figure 5A	G
	37	0	12	154	13	0.84	760000	−8.8	1.3	−8.3	0.4	--	H
XRCC4-Ala XLF-Ala	25	10	25	330	13	1.21	300000	−1.7	3.3	−7.5	−5.8	Figure 5—figure supplement 1C	I
	37	0	25	325	13	1.07	637000	−3.1	1.6	−8.2	−5.1	--	J	2.3 ± 0.4	−5.8 ± 1.4	−8.0 ± 0.1	−2.2 ± 1.4
	37	0	25	325	13	1	343000	−3.7	2.9	−7.8	−4.1	--	K
	37	0	19	250	13	0.92	345000	−8.4	2.9	−7.8	0.6	--	L
	37	0	19	250	13	0.92	582000	−8.1	1.7	−8.2	−0.1	Figure 5B	M
XRCC4-Asp XLF-Asp	25	10	35	350	10	1.27	672000	−0.9	1.5	−7.9	−7.0	--	N
	25	10	25	330	13	0.82	263000	−1.2	3.8	−7.4	−6.2	Figure 5—figure supplement 1D	O
	37	0	32	416	13	1.06	289000	−2.4	3.4	−7.8	−5.4	--	P	2.4 ± 0.4	−3.7 ± 0.8	−8.0 ± 0.1	−4.3 ± 0.7
	37	0	32	416	13	0.95	425000	−2.3	2.4	−8.0	−5.7	--	Q
	37	0	19	250	13	0.88	566000	−4.7	1.8	−8.2	−3.5	Figure 5C	R
	37	0	17	220	13	0.85	538000	−5.5	1.8	−8.1	−2.6	--	S

2-Me stands for 2-Mercaptoethanol

Ratio indicates the titrant over analyte concentration ([XLF]/[XRCC4])

Source data specifies the column corresponding to each thermogram in Table 1—source data 1.

Last four columns report mean values ± Standard Error of the Mean (SEM) from four experimental runs at 37°C (grey cells) and 3 runs at 25°C (white cells)

n.d. denotes no detectable heat transfer (at 10°C)

elife-23013-v2.xml

10.7554/eLife.23013.011

Table 1.

Estimated rates of replacement of CD4 effector and central memory through influx of new cells in 14 week-old mice. We quote both absolute influx (cells per day as a percentage of the pool size) and percent replaced per week. The latter is slightly less than 7 × the daily rate of influx because immigrant cells are assumed to be lost at the same rate as existing displaceable cells (see Methods). AIC differences (ΔAIC) are quoted relative to the best-fitting model for each cell type. These differences reflect the relative support for two models, with exp(-ΔAIC/2) being the relative probability that it is the model with the lower penalised likelihood (larger AIC value) that minimises the information lost in describing the data. For CD4 T_EM the two models have equal support, but for CD4 T_CM the resistant memory model is favoured (ΔAIC = 8.3, exp(-ΔAIC/2)=0.02). Models considered most plausible are highlighted.

DOI: http://dx.doi.org/10.7554/eLife.23013.011

		Resistant memory model					Declining recruitment model
	Source	% Input/day		% Replaced/wk		ΔAIC	% Input/day		% Replaced/wk		ΔAIC
CD4 T_EM	Naive	1.0	(0.7, 1.4)	6.3	(4.4, 8.6)	0.16	1.0	(0.7, 1.6)	6.4	(4.3, 9.7)	0
	CM	4.1	(2.6, 7.5)	23.0	(16, 35)	11	3.6	(2.1, 6.2)	21	(13, 30)	11
CD4 T_CM	Naive	1.5	(1.0, 2.8)	9.8	(6.5, 17)	0	2.3	(1.3, 4.1)	13.5	(8.4, 22)	8.3

elife-23013-v2.xml

10.7554/eLife.23013.019

Table 2.

Parameters describing homeostasis of murine CD4 memory subsets, using a two-population model of kinetic heterogeneity and the best estimates of the magnitudes of the influx into each subset from the naive pool. Pool-average lifetimes and interdivision times are defined to be the mean of the corresponding quantities for the fast and slow subpopulations weighted by their size estimates. The best-fitting models were those that assumed no difference in death rates of Ki67^high and Ki67^low cells (indicated by rows in which ratio of loss rates = 1).

DOI: http://dx.doi.org/10.7554/eLife.23013.019

Parameter	Ratio of loss rates	CD4 effector memory		CD4 central memory
Parameter	Ki67^high:Ki67^low	Estimate	95% CI	Estimate	95% CI
Pool-average lifetime (days)	1 10 0.1	29 41 55	(28, 30) (39, 42) (54, 56)	21 27 44	(19, 24) (26, 35) (39, 51)
Pool-average interdivision time (days)	1 10 0.1	88 63 84	(83, 158) (53, 353) (80, 108)	86 59 51	(47, 144) (35, 74) (38, 84)
Ki67 lifetime (days)	1 10 0.1	3.28 3.23 3.28	(3.14, 3.39) (3.03, 3.30) (3.18, 3.41)	3.59 3.74 3.32	(3.47, 3.70) (3.57, 3.82) (3.31, 3.52)
Efficiency of BrdU uptake (%)	1 10 0.1	76 75 78	(74, 79) (73, 78) (76, 81)	77 78 78	(76, 79) (76, 79) (78, 81)
Delay before source switches to BrdU⁻ post-labelling (days)	1 10 0.1	2.5 2.6 2.1	(1.7, 3.0) (1.9, 3.5) (1.3, 2.3)	0.085 0.006 0.14	(0.002, 1.16) (0.003, 1.43) (0.003, 0.66)
Source contribution to peripheral production (fraction)	1 10 0.1	0.12 0.11 0.15	(0.12, 0.13) (0.099, 0.11) (0.15, 0.16)	0.092 0.085 0.12	(0.088, 0.096) (0.08, 0.088) (0.11, 0.12)
Fraction of source enteringslow subpopulation	1 10 0.1	1 1 1	(0.98, 1) (0.95, 1) (0.98, 1)	0.69 1 0.46	(0.38, 0.85) (0.45, 1) (0.19, 0.62)
Mean lifetime offast subpopulation (days)	1 10 0.1	5.7 17 18	(5.5, 6.8) (15, 20) (18, 21)	3.3 7.1 6.4	(3.1, 3.4) (6.2, 7.5) (6.4, 6.9)
Mean lifetime ofslow subpopulation (days)	1 10 0.1	43 61 75	(43, 48) (60, 65) (74, 77)	38 48 76	(34, 44) (47, 65) (68, 90)
Mean interdivision time offast subpopulation (days)	1 10 0.1	5.7 5.7 6.8	(5.5, 6.9) (5.1, 6.7) (6.8, 7.6)	3.4 3.3 4.2	(3.2, 3.5) (3.0, 3.4) (4.2, 4.4)
Mean interdivision time ofslow subpopulation (days)	1 10 0.1	138 113 125	(130, 275) (90, 750) (119, 169)	167 118 92	(89, 280) (72, 151) (69, 151)
Size of fast subpopulation(fraction of total)	1 10 0.1	0.38 0.46 0.35	(0.37, 0.44) (0.43, 0.54) (0.34, 0.38)	0.49 0.52 0.47	(0.47, 0.51) (0.49, 0.53) (0.45, 0.48)

elife-23013-v3.xml

10.7554/eLife.23013.011

Table 1.

DOI: http://dx.doi.org/10.7554/eLife.23013.011

		Resistant memory model					Declining recruitment model
	Source	% Input/day		% Replaced/wk		ΔAIC	% Input/day		% Replaced/wk		ΔAIC
CD4 T_EM	Naive	1.0	(0.7, 1.4)	6.3	(4.4, 8.6)	0.16	1.0	(0.7, 1.6)	6.4	(4.3, 9.7)	0
	CM	4.1	(2.6, 7.5)	23.0	(16, 35)	11	3.6	(2.1, 6.2)	21	(13, 30)	11
CD4 T_CM	Naive	1.5	(1.0, 2.8)	9.8	(6.5, 17)	0	2.3	(1.3, 4.1)	13.5	(8.4, 22)	8.3

elife-23013-v3.xml

10.7554/eLife.23013.019

Table 2.

DOI: http://dx.doi.org/10.7554/eLife.23013.019

Parameter	Ratio of loss rates	CD4 effector memory		CD4 central memory
Parameter	Ki67^high:Ki67^low	Estimate	95% CI	Estimate	95% CI
Pool-average lifetime (days)	1 10 0.1	29 41 55	(28, 30) (39, 42) (54, 56)	21 27 44	(19, 24) (26, 35) (39, 51)
Pool-average interdivision time (days)	1 10 0.1	88 63 84	(83, 158) (53, 353) (80, 108)	86 59 51	(47, 144) (35, 74) (38, 84)
Ki67 lifetime (days)	1 10 0.1	3.28 3.23 3.28	(3.14, 3.39) (3.03, 3.30) (3.18, 3.41)	3.59 3.74 3.32	(3.47, 3.70) (3.57, 3.82) (3.31, 3.52)
Efficiency of BrdU uptake (%)	1 10 0.1	76 75 78	(74, 79) (73, 78) (76, 81)	77 78 78	(76, 79) (76, 79) (78, 81)
Delay before source switches to BrdU⁻ post-labelling (days)	1 10 0.1	2.5 2.6 2.1	(1.7, 3.0) (1.9, 3.5) (1.3, 2.3)	0.085 0.006 0.14	(0.002, 1.16) (0.003, 1.43) (0.003, 0.66)
Source contribution to peripheral production (fraction)	1 10 0.1	0.12 0.11 0.15	(0.12, 0.13) (0.099, 0.11) (0.15, 0.16)	0.092 0.085 0.12	(0.088, 0.096) (0.08, 0.088) (0.11, 0.12)
Fraction of source enteringslow subpopulation	1 10 0.1	1 1 1	(0.98, 1) (0.95, 1) (0.98, 1)	0.69 1 0.46	(0.38, 0.85) (0.45, 1) (0.19, 0.62)
Mean lifetime offast subpopulation (days)	1 10 0.1	5.7 17 18	(5.5, 6.8) (15, 20) (18, 21)	3.3 7.1 6.4	(3.1, 3.4) (6.2, 7.5) (6.4, 6.9)
Mean lifetime ofslow subpopulation (days)	1 10 0.1	43 61 75	(43, 48) (60, 65) (74, 77)	38 48 76	(34, 44) (47, 65) (68, 90)
Mean interdivision time offast subpopulation (days)	1 10 0.1	5.7 5.7 6.8	(5.5, 6.9) (5.1, 6.7) (6.8, 7.6)	3.4 3.3 4.2	(3.2, 3.5) (3.0, 3.4) (4.2, 4.4)
Mean interdivision time ofslow subpopulation (days)	1 10 0.1	138 113 125	(130, 275) (90, 750) (119, 169)	167 118 92	(89, 280) (72, 151) (69, 151)
Size of fast subpopulation(fraction of total)	1 10 0.1	0.38 0.46 0.35	(0.37, 0.44) (0.43, 0.54) (0.34, 0.38)	0.49 0.52 0.47	(0.47, 0.51) (0.49, 0.53) (0.45, 0.48)

elife-23049-v2.xml

10.7554/eLife.23049.003

Table 1.

Selected proteins identified in IgG-sepharose pulldowns on ZZ-TAPBPR

Affinity chromatography with IgG-sepharose was performed on HeLaM cells expressing a protein-A-tagged TAPBPR molecule (ZZ-TAPBPR) or HeLaM cells transduced with an empty vector (control). Immunoprecipitates were analysed by in gel tryptic digest followed by liquid chromatography-tandem mass spectrometry and data were processed using Scaffold. Identified proteins are shown with their exclusive unique peptide count, percentage coverage, and exclusive unique spectrum count as determined by Scaffold. Rank denotes the position when data are sorted by exclusive unique peptide count with all proteins present in the control removed. Pep: exclusive unique peptide count; Cov: percentage coverage; Count: exclusive unique spectrum count.

DOI: http://dx.doi.org/10.7554/eLife.23049.003

Protein	Gene name	Control		ZZ-TAPBPR		Rank
Protein	Gene name	Pep (Cov)	Count	Pep (Cov)	Count	Rank
Tapasin-related protein	TAPBPL	–	–	8 (16)	11	2
HLA class 1, A-68	HLA-A	–	–	14 (35)	21	1
β-2-microglobulin	β2M	–	–	1 (8.4)	1	95
UDP-glucose:glycoprotein glucosyltransferase 1	UGGT1	–	–	10 (7.3)	10	3

elife-23049-v2.xml

10.7554/eLife.23049.009

Table 2.

Selected proteins identified in TAPBPR co-immunoprecipitates

TAPBPR was immunuoprecipitated using PeTe4 from IFN-γ-treated HeLaM-TAPBPR^KO(HeLaM^KO) cells reconstituted with either TAPBPR^WT or TAPBPR^C94A. Immunoprecipitates were analysed by in gel tryptic digest followed by liquid chromatography-tandem mass spectrometry and data were processed using Scaffold. Identified proteins are shown with their exclusive unique peptide count, total percentage coverage, and exclusive unique spectrum count as determined by Scaffold. Pep: exclusive unique peptide count; Cov: percentage coverage; Count: exclusive unique spectrum count.

DOI: http://dx.doi.org/10.7554/eLife.23049.009

Protein	Gene name	TAPBPR^WT		TAPBPR^C94A
Protein	Gene name	Pep (Cov)	Count	Pep (Cov)	Count
Tapasin-related protein	TAPBPL	32 (43)	54	29 (47)	50
HLA class 1, A-68	HLA-A	50 (64)	88	41 (59)	70
β-2-microglobulin	β2M	4 (46)	7	1 (8.4)	1
UDP-glucose:glycoprotein glucosyltransferase 1	UGGT1	19 (11)	25	–	–

elife-23481-v2.xml

10.7554/eLife.23481.006

Table 1.

Numbers of IL17 genes by subfamily in echinoderm species.

DOI: http://dx.doi.org/10.7554/eLife.23481.006

	Echinodermata
	Echinoidea					Asteroidea
	Euechinoidea				Cidaroidea
	Strongylocentrotidae			Toxopneustidae	Cidaroidea
Subfamily	S. purpuratus	S. fragilis* (5–7 myr)^†	M. franciscanus*^a (20 myr)^†	L. variegatus (50 myr)^†	E. tribuloides (268 myr)^†	P. miniata (480 myr)^†
1	11	8.6	10.0	2	6	0
2	1	0.5	0.4	1	1	0
3	1	0.5	0.9	2	0	0
4	1	1.9	0.4	1	3	0
5	2	3.3	3.5	2	2	0
6	3	4.4	4.4	2	3	0
7	1	2.9	7.8	1	2	0
8	1	1.9	6.5	1	2	0
9	7	13.8	7.1	1	0	0
10	2	1.0	5.2	1	0	0
Other	-	-	-	-	4	12^‡
Total	30	38.6	47.0	15	22	12

*Estimates are based on the number of best reciprocal blast hits using the SpIL17 sequences against the unassembled genomic trace sequences (Buckley and Rast, 2012).

^†Estimated divergence times shown in million years from S. purpuratus (Thompson et al., 2015; Pisani et al., 2012; Biermann et al., 2003; Smith et al., 2006).

^‡See Figure 2—figure supplement 1 for the phylogenetic analysis of these genes.

elife-23551-v2.xml

10.7554/eLife.23551.003

Table 1.

Mean offspring numbers, TFT haplotype frequencies, and genotyping outcomes for the two experiments (regulated conditions and fluctuating conditions).

DOI: http://dx.doi.org/10.7554/eLife.23551.003

10.7554/eLife.23551.004Table 1—source data 1.Raw data for offspring number and TFT frequency for Experiments 1 and 2.

Offspring number per population for each of 10 generations in Experiment 1 and 2. TFT frequency for each population at generations 1, 5 and 10 for Experiment 1 and at generation 10 for Experiment 2.

DOI: http://dx.doi.org/10.7554/eLife.23551.004

		TFT treatment (starting frequency)	0% TFT	25% TFT	50% TFT	75% TFT
		Populations [n]	21	21	21	21
Experiment	Regulated	F₁ Frequency	0.00	0.26 ± 0.03	0.44 ± 0.03	0.63 ± 0.03
		F₅ Frequency	0.00	0.15 ± 0.03	0.63 ± 0.03	0.71 ± 0.02
		F₁₀ Frequency	0.00	0.17 ± 0.03	0.67 ± 0.03	0.80 ± 0.03
		Loss	-	4	0	0
		Fixation	-	0	0	3
		Heteroplasmy	-	0	0	0
		Mean offspring number (F₁₀)	74.15 ± 1.00	72.05 ± 0.89	67.43 ± 0.99	66.38 ± 0.70
		Population extinction	1	0	0	0
	Fluctuating	F₁₀frequency	0.00	0.35 ± 0.06	0.59 ± 0.06	0.75 ± 0.05
		Loss	-	4	1	0
		Fixation	-	1	4	4
		Heteroplasmy	-	0	2	0
		Mean offspring number (F₁₀)	80.47 ± 5.12	81.19 ± 4.59	78.56 ± 5.63	85.86 ± 3.73
		Population extinction	2	0	2	0

elife-23584-v4.xml

10.7554/eLife.23584.009

Table 1.

Comparison between the response rate for different sensory stimuli applied to the fore– or hindlimb of a rat standing on four or two limbs. Results of Fisher Exact test, 2 × 2 contingency tables. Values in red are significant. Values in black are not significant. In parenthesis is the rate for full withdrawal for each condition.

DOI: http://dx.doi.org/10.7554/eLife.23584.009

10.7554/eLife.23584.010Table 1—source data 1.Proportion of withdrawals for different sensory stimuli applied to the fore- or hindlimb of a rat standing on four or two limbs.

Source data and Column histogram presenting the number of trials the rats responded with a full withdrawal to a stimulus. Each column presents the total number of trials. (Black: full withdrawal; Gray: no withdrawal). l-laser stimulus; s-sharp stimulus; 4-animal on all four limbs; 2-animal on two hind limbs; f -forelimb stimulation; h -hindlimb stimulation.

DOI: http://dx.doi.org/10.7554/eLife.23584.010

			Laser				Sharp
			Standing on four		Standing on two		Standing on four		Standing on two
			Forelimb (%100)	Hindlimb (%82.8)	Hindlimb (%48.7)	Hindlimb+NL (%63.2)	Forelimb (%100)	Hindlimb (%100)	Hindlimb (%66.7)	Hindlimb+NL (%55)
Laser	Standing on four	Forelimb (%100)
	Standing on four	Hindlimb (%82.8)	1.0
	Standing on two	Hindlimb (%48.7)	>0.05	<0.01
	Standing on two	Hindlimb+NL (%63.2)	>0.2	>0.1	>0.4
Sharp	Standing on four	Forelimb (%100)	1.0	>0.1	<0.001	<0.05
	Standing on four	Hindlimb (%100)	1.0	<0.05	<0.001	<0.001	1.0
	Standing on two	Hindlimb (%66.7)	>0.3	>0.1	>0.1	>0.7	<0.05	<0.001
	Standing on two	Hindlimb+NL (%55)	>0.1	>0.5	>0.7	>0.7	<0.001	<0.001	>0.4

elife-23608-v2.xml

10.7554/eLife.23608.009

Table 2.

Results from voxelwise GBC analysis.

DOI: http://dx.doi.org/10.7554/eLife.23608.009

Label	Volume	t-value	Peak activation (LPI)
Label	Volume	t-value	x	y	z
Right Angular Gyrus	158	3.45	48	−51	27
Right Intraparietal Sulcus	83	3.42	21	−60	66
Left Intraparietal Sulcus	81	3.6	−18	−63	66

elife-23608-v2.xml

10.7554/eLife.23608.012

Table 3.

Results from voxelwise IPS connectivity analysis.

DOI: http://dx.doi.org/10.7554/eLife.23608.012

Label	Volume	t-value	Peak activation (LPI)
Label	Volume	t-value	x	y	z
Left Thalamus	342	3.92	-9	6	12
Right Inferior Parietal Lobule	208	3.67	57	−57	39
Left Superior Medial Gyrus	184	3.65	3	36	42
Left Precuneus	179	3.59	3	−69	48
Right Middle Frontal Gyrus	137	3.64	33	15	60
Left Angular Gyrus	113	3.51	−57	−54	30
Left Middle Frontal Gyrus	96	3.69	−24	15	60
Left Middle Frontal Gyrus	90	3.48	−45	51	-3

elife-23708-v2.xml

10.7554/eLife.23708.004

Table 2.<italic>Plasmodium</italic> infection status at enrolment by village.

Village	P. falciparum					P. vivax					P. malariae			P. ovale
Village	N pos.	Prevalence by qPCR (CI₉₅)	% mixed^*	Mean^† density (IQR)	Mean MOI^‡ (range)	N pos.	Prevalence by qPCR (CI₉₅)	% mixed^*	Mean^† density (IQR)	Mean MOI^‡ (range)	N pos.	Prevalence by qPCR (CI₉₅)	% mixed^*	N pos.	Prevalence by qPCR (CI₉₅)	% mixed^*
Albinama	18	18 (11–27)	72	131 (38–189)	1.4 (1–4)	54	55 (44–65)	24	3 (1–17)	1.8 (1–7)	9	9 (5–17)	67	5	5 (2–12)	100
Amahup	14	12 (7–19)	57	56 (14–105)	1.6 (1–5)	46	39 (30–48)	24	3 (1–29)	2.2 (1–7)	12	10 (6–17)	83	0	0
Balanga	15	28 (17–42)	67	79 (30–848)	1.7 (1–5)	23	43 (30–57)	43	2 (1–28)	2.0 (1–7)	9	17 (8–30)	56	2	3 (0–14)	50
Balif	8	9 (4–17)	63	64 (10–325)	2.0 (1–4)	35	38 (30–48)	14	2 (1–14)	1.9 (1–6)	7	8 (3–15)	57	0	0
Bolumita	50	71 (59–81)	80	331 (62–1988)	2.2 (1–8)	47	67 (55–78)	81	3 (2–27)	2.9 (1–10)	28	40 (29–52)	89	8	11 (5–22)	100
Numangu	8	26 (13–45)	75	192 (30–848)	1.1 (1–2)	18	58 (39–75)	28	3 (1–25)	1.6 (1–5)	4	13 (4–31)	50	0	0
Overall	113	24 (20–28)	73	163 (20–1103)	1.9 (1–8)	223	48 (43–52)	37	3 (1–23)	2.2 (1–10)	69	15 (12–18)	75	15	3 (2–5)	93
p-value^§		<0.001	0.034	0.086	0.047		<0.001	<0.001	0.947	0.020		<0.001	0.086		<0.001	0.133

* % of infections by qPCR that are mixed-species infections.

† Geometric mean of species-specific 18S rRNA copy numbers per µl blood.

‡ MOI, multiplicity of infection: number of Pf-msp2 and Pv-msp1F3 alleles per infection.

§ Differences between villages were tested for using Chi² and Fisher’s exact test (prevalence, proportion mixed) or Kruskal-Wallis test (MOI, log₁₀-transformed parasite density).

elife-23708-v2.xml

10.7554/eLife.23708.008

Table 3.Multivariable predictors for time to recurrent blood-stage infection with <italic>Plasmodium</italic> species by qPCR

Variable	P. vivax			P. falciparum			P. malariae			P. ovale
Variable	AHR^*	CI₉₅	p-value	AHR^*	CI₉₅	p-value	AHR^*	CI₉₅	p-value	AHR^*	CI₉₅	p-value
PQ treatment	0.18	0.13–0.25	<0.001	0.73	0.52–1.02	0.064	0.51	0.22–1.19	0.121	0.31	0.12–0.75	0.010
Age	0.95	0.87–1.04	0.247	1.05	0.94–1.17	0.361	0.98	0.75–1.29	0.905	0.96	0.74–1.26	0.793
LLIN use at enrolment	0.62	0.39–0.98	0.043	0.84	0.49–1.44	0.531	1.33	0.33–6.09	0.715	0.95	0.26–3.43	0.936
Hb at enrolment (g/dl)	0.88	0.80–0.98	0.019	0.90	0.80–1.02	0.099	0.83	0.61–1.12	0.224	0.92	0.66–1.28	0.634
Village
Albinama (ref)	1			1			1			1
Amahup	0.45	0.29–0.71	0.001	0.58	0.31–1.11	0.101	0.34	0.07–1.79	0.205	2.83	0.29–27.48	0.370
Balanga	2.15	1.40–3.31	<0.001	1.81	0.99–3.30	0.054	0.92	0.24–3.60	0.910	7.74	0.85–70.45	0.070
Balif	1.00	0.66–1.54	0.983	0.60	0.30–1.19	0.145	0.24	0.03–2.07	0.193	4.60	0.51–41.41	0.173
Bolumita	3.34	2.09–5.33	<0.001	4.73	2.69–8.30	<0.001	1.21	0.34–4.31	0.770	19.43	2.19–172.37	0.008
Numangu	0.83	0.44–1.59	0.583	2.29	1.17–4.50	0.015	0.82	0.15–4.53	0.823	3.17	0.19–52.41	0.420
Infection status at enrolment (by qPCR)
Uninfected (ref)	1			1			1			1
P. vivax	1.27	0.91–1.78	0.165	1.37	0.86–2.20	0.186	0.92	0.20–4.18	0.913	2.17	0.68–6.97	0.192
P. falciparum	1.36	0.84–2.19	0.205	1.56	0.86–2.82	0.145	3.54	0.85–14.72	0.083	1.25	0.26–5.90	0.779
P. malariae	0.83	0.38–1.85	0.655	0.99	0.38–2.56	0.977	6.35	1.31–30.81	0.022	1.58	0.17–14.30	0.676
Mixed P.f. or P.v.^†	1.74	1.14–2.65	0.010	2.08	1.25–3.48	0.005	3.37	0.88–12.90	0.076	2.03	0.55–7.53	0.287

* AHRs were modeled using Cox proportional hazard regression.

† Mixed infection including P. falciparum or P. vivax infection in conjunction with one or more other Plasmodium spp.

PQ: Primaquine; LLIN: long-lasting insecticide-treated net; Hb: haemoglobin.

elife-23708-v2.xml

10.7554/eLife.23708.011

Table 4.Multivariable predictors of <italic>Pv-</italic> and <italic>Pf-</italic>molFOB per follow-up interval.

Model predictions from this model were used for mapping _molFOB in Figure 3A.

Variable	P. vivax						P. falciparum
	PQ arm			Placebo arm			Combined arms
	IRR^*	CI₉₅	p-value	IRR^*	CI₉₅	p-value	IRR^*	CI₉₅	p-value
PQ treatment	n.a.^†	n.a.	n.a.	n.a.	n.a.	n.a.	0.89	0.65–1.22	0.474
New P. falc. infections in interval^‡	1.32	0.92–1.89	0.134	1.10	0.85–1.42	0.466	n.a.	n.a.	n.a.
New P. vivax infections in interval^‡	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	1.15	0.97–1.36	0.100
Age	0.86	0.74–1.01	0.059	0.95	0.87–1.04	0.305	1.03	0.92–1.14	0.640
LLIN use at enrolment	0.96	0.51–1.79	0.897	0.62	0.43–0.91	0.013	1.07	0.7–1.62	0.755
Hb at enrolment (g/dl)	0.85	0.72–1.01	0.063	0.91	0.85–0.99	0.025	0.85	0.75–0.97	0.013
Village
Albinama (ref)	1			1			1
Amahup	0.02	0–0.11	<0.001	0.56	0.34–0.91	0.020	0.52	0.25–1.07	0.074
Balif	0.85	0.4–1.8	0.664	1.74	1.16–2.61	0.007	1.81	0.98–3.35	0.059
Balanga	0.28	0.1–0.82	0.020	1.13	0.73–1.73	0.590	0.75	0.37–1.52	0.423
Bolumita	1.52	0.73–3.17	0.268	2.67	1.83–3.9	<0.001	6.05	3.32–11.05	<0.001
Numangu	0.5	0.15–1.68	0.264	0.76	0.4–1.43	0.394	2.8	1.39–5.64	0.004
Study Day
Day 0–35 (ref)	1			1			1
Day 36–80	1.37	0.54–3.48	0.509	1.99	1.39–2.84	<0.001	2.42	1.44–4.07	0.001
Day 81–175	1.34	0.57–3.12	0.503	0.89	0.61–1.3	0.538	1.13	0.7–1.84	0.616
Day > 175	0.65	0.25–1.69	0.374	0.56	0.38–0.83	0.004	0.87	0.48–1.56	0.643

*IRRs were modeled per sampling interval using negative binomial generalized estimating equations allowing for repeated visits with log-link and an exchangeable correlation structure.

† n.a., not applicable.

‡_molFOB in the follow-up interval (time-varying covariate).

PQ: Primaquine; LLIN: long-lasting insecticide-treated net; Hb: haemoglobin.

elife-23708-v2.xml

10.7554/eLife.23708.013

Table 5.Multivariable predictors for time to <italic>P. vivax</italic> and <italic>P. falciparum</italic> clinical episodes.

Model predictions from this model were used for mapping the relative risk of clinical malaria episodes in Figure 3C and D.

Variable	P. vivax			P. falciparum
Variable	AHR^*	CI₉₅	p-value	AHR^*	CI₉₅	p-value
PQ treatment	0.76	0.34–1.68	0.497	1.79	1.05–3.03	0.031
P. vivax _molFOB^‡	1.07	1.04–1.09	<0.001	n.a.	n.a.	n.a.
P. falciparum _molFOB^‡	n.a.	n.a.	n.a.	1.15	1.11–1.21	<0.001
Age	0.62	0.46–0.84	0.002	0.98	0.85–1.13	0. 799
LLIN use at enrolment	0.84	0.24–2.88	0.778	0.44	0.22–0.87	0.018
Hb at enrolment (g/dl)	0.95	0.74–0.67	0.668	0.85	0.71–1.01	0.070
Village
Albinama (ref)	1			1
Amahup	0.89	0.23–3.46	0.871	0.65	0.20–2.08	0.465
Balif	1.48	0.45–4.86	0.518	1.26	0.50–3.14	0.626
Balanga	0.85	0.21–3.53	0.827	1.39	0.59–3.30	0.455
Bolumita	0.99	0.24–4.03	0.987	1.32	0.58–3.03	0.508
Numangu	1.00	0.23–4.31	0.997	4.29	2.06–8.97	<0.001
Infection status at enrolment (by qPCR)
Uninfected (ref)	1			1
P. vivax	0.77	0.29–2.07	0.608	1.64	0.91–2.95	0.101
P. falciparum	1.74	0.59–5.11	0.316	0.97	0.34–2.77	0.954
Mixed P.f. or P.v.	1.59	0.56–4.50	0.381	1.24	0.57–2.68	0.582

* AHRs were modeled using multiple failure Cox proportional hazard regression.

† n.a., not applicable

‡ Average _molFOB until the time of failure (time-varying covariate).

PQ: Primaquine; LLIN: long-lasting insecticide-treated net; Hb: haemoglobin.

elife-24001-v2.xml

10.7554/eLife.24001.022

Author response table 1.

Protein concentration estimation.

DOI: http://dx.doi.org/10.7554/eLife.24001.022

Protein Name	Concentration of protein taken (mg/ml) measured using A₂₈₀	Protein concentration estimation (mg/ml) using
Protein Name	Concentration of protein taken (mg/ml) measured using A₂₈₀	Bicinchoninic acid Assay	Bradford Assay
E. coli AlaRS	4	3.82	5.22
E. coli AlaRS	8	7.45	9.02
E. coli DTD	4	4.36	4.83
E. coli DTD	8	8.08	7.93

elife-24192-v2.xml

10.7554/eLife.24192.007

Table 1.Shisa7 is a native interactor of hippocampal AMPARs.

Shisa7 complexes were immunoprecipitated from the hippocampi of Shisa7 WT and KO animals (DDM-extracted crude synaptic membranes; n = 3 IPs per genotype) and subjected to mass spectrometric analysis. The following protein categories are highlighted: Shisa7 (dark blue), AMPAR subunits (light blue), established non-PDZ AMPAR-interacting proteins (Schwenk et al., 2012) (dark yellow), PDZ domain-containing interactors (light yellow). Percent coverage, percent of the database protein sequence covered by all matching peptides. Green background highlights values of statistical significance upon performing a Student’s t-test with permutation-based FDR analysis (S0 = 1, FDR = 0.01 (dark green) or FDR = 0.05 (light green)). Note the identification of a peptide specific for exon 4 containing Shisa7 (NLYNTMKPSNLDwNLHYNVNSPK; diamond indicates exon3-exon4 boundary). The full list of identified protein groups is reported in Table 1—source data 1, and the statistical analysis is provided in Table 1—source data 2, which includes a volcano-plot of differentially IP-ed proteins.

10.7554/eLife.24192.008Table 1—source data 1.Maxquant analysis of hippocampal Shisa7 immunoprecipitation experiments, as detailed in the Materials and methods section.

The Maxquant ‘proteinGroups.txt’ output file was supplemented with ‘LFQ intensity _ Average KO’, ‘LFQ intensity _ Average WT’, and the ‘KO/WT’ and ‘WT/KO’ ratios thereof.

10.7554/eLife.24192.009Table 1—source data 2.Statistical analysis of hippocampal Shisa7 immunoprecipitation data, as detailed in the Materials and methods section.

Tab 1: In summary, the Maxquant ‘proteinGroups.txt’ output file was imported into Perseus, and processed in the following manner: (1) Removal of ‘Reverse’, ‘Potential contaminant’, and ‘Only identified by site’ protein groups; (2) Log(2) transformation of all LFQ intensity values; (3) Removal of protein groups with less than three valid ‘Log(2) LFQ intensity’ values in either the WT or KO groups; (4) Imputation of missing values (8.6% of the population) from a normal distribution (width 0.3, down shift 1.8, whole matrix); (5) Performing a Student's t-test followed by permutation-based FDR analysis (S0 = 1, FDR = 0.01, 2500 permutations). Tab 2: Visualization of the data by means of Histogram and Vulcanoplot is presented in the additional sheets. Tab 3: Distribution of LFQ intensities after replacing missing values from a normal distribution. The imputed value distribution is depicted in red.

Gene name	Uniprot recommendedprotein name(s)	Uniprot ID	PDZ-domains	Number of unique peptides						LFQ intensity						Average KO LFQ intensity	Average WT LFQ intensity	Average KO/WT LFQ intensity	Average WT/KO LFQ intensity	T-test significant FDR0.01 = ++ DR0.05 = +	T-test q-value	Percent cover-age
Gene name	Uniprot recommendedprotein name(s)	Uniprot ID	PDZ-domains	KO1	KO2	KO3	WT1	WT2	WT3	KO1	KO2	KO3	WT1	WT2	WT3	Average KO LFQ intensity	Average WT LFQ intensity	Average KO/WT LFQ intensity	Average WT/KO LFQ intensity	T-test significant FDR0.01 = ++ DR0.05 = +	T-test q-value	Percent cover-age
Shisa7	Protein Shisa-7	Q8C3Q5	0	1	1	2	17	18	16	865	873	1750	319820	305190	346730	1163	323913	0.4%	278.58	++	0.0000	39.2
Shisa7	Protein Shisa-7:Exon4-specificpeptideNLYNTMKPSNLDNLHYNVNSPK	-	-	0	0	0	1	0	0	-	-	-	-	-	-	-	-	-	-	-	-	-
Gria1	Glutamatereceptor 1	P23818	0	0	0	0	10	12	12	5921	0	3217	17828	52304	54212	4569	41448	11.0%	9.07	++	0.0000	22.8
Gria2	Glutamatereceptor 2	P23819	0	2	1	0	17	17	17	2743	0	0	104860	101430	93097	2743	99796	2.7%	36.39	++	0.0000	36.4
Gria3	Glutamatereceptor 3	Q9Z2W9	0	0	0	0	4	4	5	0	0	0	6529	7068	10102	0	7900	0.0%	NaN	++	0.0000	17.7
Cacng8	Voltage-dependentcalciumchannelgamma-8subunit;TARPgamma-8	Q8VHW2	0	2	2	1	2	1	5	4023	0	0	0	0	3962	4023	3962	101.5%	0.98	-	N/A	30.5
Olfm1	Noelin	O88998	0	1	1	0	0	2	2	0	1076	0	0	1004	779	1076	892	120.6%	0.83	-	N/A	7.0
Prrt1	Proline-richtransmem-braneprotein 1;SynDIG4	O35449	0	0	0	0	1	1	0	0	0	0	969	0	0	0	969	0.0%	NaN	-	N/A	7.2
Prrt2	Proline-richtransmem-braneprotein 2	E9PUL5	0	0	1	0	1	1	1	0	333	0	318	0	202	333	260	127.9%	0.78	-	N/A	3.8
Rap2b	Ras-relatedproteinRap-2b	P61226	0	0	1	1	1	0	0	0	0	2588	0	0	0	2588	0	NaN	0.00	-	N/A	12.0
Shisa6	Proteinshisa-6homolog	Q3UH99	0	1	0	0	3	3	1	0	0	0	2666	3580	2136	0	2794	0.0%	NaN	+	0.0306	9.9
Dlg1	Disks largehomolog 1;SAP97	Q811D0	3	0	1	1	3	0	0	0	0	0	2126	0	0	0	2126	0.0%	NaN	-	N/A	4.4
Dlg3	Disks largehomolog 3;SAP102	P70175	3	0	0	0	0	2	2	0	0	0	0	2441	0	0	2441	0.0%	NaN	-	N/A	4.8
Dlg4	Disks largehomolog 4;PSD95	Q62108	3	0	0	0	9	8	7	0	0	0	11835	13410	9284	0	11510	0.0%	NaN	++	0.0000	21.7
Magi2	Membrane-associatedguanylatekinase,WW and PDZdomain-containingprotein 2	Q9WVQ1	6	0	0	0	1	1	0	0	0	0	0	1558	0	0	1558	0.0%	NaN	-	N/A	1.6

elife-24192-v4.xml

10.7554/eLife.24192.007

Table 1.Shisa7 is a native interactor of hippocampal AMPARs.

Shisa7 complexes were immunoprecipitated from the hippocampi of Shisa7 WT and KO animals (DDM-extracted crude synaptic membranes; n = 3 IPs per genotype) and subjected to mass spectrometric analysis. The following protein categories were indicated: Shisa7, AMPAR subunits, established non-PDZ AMPAR-interacting proteins (Schwenk et al., 2012), PDZ domain-containing interactors. Percent coverage, percent of the database protein sequence covered by all matching peptides. Values of statistical significance upon performing a Student’s t-test with permutation-based FDR analysis (S0 = 1, FDR < 0.05 (bold)) are indicated. Note the identification of a peptide specific for exon 4 containing Shisa7 (NLYNTMKPSNLDwNLHYNVNSPK; diamond indicates exon3-exon4 boundary). The full list of identified protein groups is reported in Table 1—source data 1, and the statistical analysis is provided in Table 1—source data 2, which includes a volcano-plot of differentially IP-ed proteins.

10.7554/eLife.24192.008Table 1—source data 1.Maxquant analysis of hippocampal Shisa7 immunoprecipitation experiments, as detailed in the Materials and methods section.

The Maxquant ‘proteinGroups.txt’ output file was supplemented with ‘LFQ intensity _ Average KO’, ‘LFQ intensity _ Average WT’, and the ‘KO/WT’ and ‘WT/KO’ ratios thereof.

10.7554/eLife.24192.009Table 1—source data 2.Statistical analysis of hippocampal Shisa7 immunoprecipitation data, as detailed in the Materials and methods section.

Gene name	Uniprot recommendedprotein name(s)	Uniprot ID	PDZ-domains	Number of unique peptides						LFQ intensity						Average KO LFQ intensity	Average WT LFQ intensity	Average KO/WT LFQ intensity	Average WT/KO LFQ intensity	T-test significant FDR0.01 = ++ DR0.05 = +	T-test q-value	Percent cover-age
Gene name	Uniprot recommendedprotein name(s)	Uniprot ID	PDZ-domains	KO1	KO2	KO3	WT1	WT2	WT3	KO1	KO2	KO3	WT1	WT2	WT3	Average KO LFQ intensity	Average WT LFQ intensity	Average KO/WT LFQ intensity	Average WT/KO LFQ intensity	T-test significant FDR0.01 = ++ DR0.05 = +	T-test q-value	Percent cover-age
Shisa7	Protein Shisa-7	Q8C3Q5	0	1	1	2	17	18	16	865	873	1750	319820	305190	346730	1163	323913	0.4%	278.58	++	0.0000	39.2
Shisa7	Protein Shisa-7:Exon4-specificpeptideNLYNTMKPSNLDNLHYNVNSPK	-	-	0	0	0	1	0	0	-	-	-	-	-	-	-	-	-	-	-	-	-
Gria1	Glutamatereceptor 1	P23818	0	0	0	0	10	12	12	5921	0	3217	17828	52304	54212	4569	41448	11.0%	9.07	++	0.0000	22.8
Gria2	Glutamatereceptor 2	P23819	0	2	1	0	17	17	17	2743	0	0	104860	101430	93097	2743	99796	2.7%	36.39	++	0.0000	36.4
Gria3	Glutamatereceptor 3	Q9Z2W9	0	0	0	0	4	4	5	0	0	0	6529	7068	10102	0	7900	0.0%	NaN	++	0.0000	17.7
Cacng8	Voltage-dependentcalciumchannelgamma-8subunit;TARPgamma-8	Q8VHW2	0	2	2	1	2	1	5	4023	0	0	0	0	3962	4023	3962	101.5%	0.98	-	N/A	30.5
Olfm1	Noelin	O88998	0	1	1	0	0	2	2	0	1076	0	0	1004	779	1076	892	120.6%	0.83	-	N/A	7.0
Prrt1	Proline-richtransmem-braneprotein 1;SynDIG4	O35449	0	0	0	0	1	1	0	0	0	0	969	0	0	0	969	0.0%	NaN	-	N/A	7.2
Prrt2	Proline-richtransmem-braneprotein 2	E9PUL5	0	0	1	0	1	1	1	0	333	0	318	0	202	333	260	127.9%	0.78	-	N/A	3.8
Rap2b	Ras-relatedproteinRap-2b	P61226	0	0	1	1	1	0	0	0	0	2588	0	0	0	2588	0	NaN	0.00	-	N/A	12.0
Shisa6	Proteinshisa-6homolog	Q3UH99	0	1	0	0	3	3	1	0	0	0	2666	3580	2136	0	2794	0.0%	NaN	+	0.0306	9.9
Dlg1	Disks largehomolog 1;SAP97	Q811D0	3	0	1	1	3	0	0	0	0	0	2126	0	0	0	2126	0.0%	NaN	-	N/A	4.4
Dlg3	Disks largehomolog 3;SAP102	P70175	3	0	0	0	0	2	2	0	0	0	0	2441	0	0	2441	0.0%	NaN	-	N/A	4.8
Dlg4	Disks largehomolog 4;PSD95	Q62108	3	0	0	0	9	8	7	0	0	0	11835	13410	9284	0	11510	0.0%	NaN	++	0.0000	21.7
Magi2	Membrane-associatedguanylatekinase,WW and PDZdomain-containingprotein 2	Q9WVQ1	6	0	0	0	1	1	0	0	0	0	0	1558	0	0	1558	0.0%	NaN	-	N/A	1.6

elife-24414-v2.xml

10.7554/eLife.24414.007

Table 2.

Summary of mutations detected following experimental evolution of V. fischeri using Illumina genome resequencing and targeted Sanger sequencing. For culture-evolved populations of V. fischeri MJ11, five isolates from each evolved population were combined to generate five metagenomes. For squid-evolved populations of MJ11, EM17, WH1 and H905, individual isolates were sequenced from lineages that ultimately survived 15 host passages. Isolates saved from early evolutionary time-points (host passage 2) are shown along with isolate genomes from the endpoint (host passage 15). Mean read depth and genome coverage for isolates analyzed with WGS are also provided.

DOI: http://dx.doi.org/10.7554/eLife.24414.007

Ancestor	Evolved Passage (EP)	Population	Isolate^†	Detected mutations^‡				Illumina sequencing statistics
				binK (VFMJ11_A0397)		tadC1 (MJ11_0520); mutation (reads)	All other mutations detectected by WGS gene (locus); mutation (reads)	Reads	% Mapped to ancestor	Coverage
				allele/mutation	Method (reads)^§	tadC1 (MJ11_0520); mutation (reads)		Reads	% Mapped to ancestor	ChI	ChII
MJ11	2	1	1	binK3/S311L	WGS (35)	–	–	3753352	99.5	135.2	118
MJ11	2	1	3	binK3/S311L	WGS (32)	–	–	3717088	99.6	134.2	113.5
MJ11	15	1	4	binK3/S311L	WGS (17)	–	–	1716144	99.5	46.8	42.5
MJ11	2	3	3	binK4/N292T	PCR/SS	n.d.	n.d.
MJ11	2	3	4	binK4/N292T	PCR/SS	n.d.	n.d.
MJ11	2	3	5	binK4/N292T	PCR/SS	n.d.	n.d.
MJ11	2	3	6	binK4/N292T	PCR/SS	n.d.	n.d.
MJ11	2	3	7	binK4/N292T	PCR/SS	n.d.	n.d.
MJ11	2	3	8	binK4/N292T	PCR/SS	n.d.	n.d.
MJ11	15	3	1	binK4/N292T	WGS (42)	–	–	3031149	98.9	104.3	93.5
MJ11	15	3	3	binK4/N292T	WGS (63)	–	–	3777714	99.4	114.6	105.2
MJ11	15	3	4	binK4/N292T	WGS (42)	–	–	3420212	99.5	106.4	97.1
MJ11	15	3	7	binK4/N292T	WGS (41)	–	–	3304891	99.5	90.3	82.5
MJ11	15	3	8	binK4/N292T	WGS (63)	–	–	2948743	99.6	85.5	81.2
MJ11	2	4	1	binK1/R537C	WGS (62)	–	–	2511256	99	84	78
MJ11	2	4	3	binK1/R537C	PCR/SS	n.d.	n.d.
MJ11	2	4	4	binK1/R537C	PCR/SS	n.d.	n.d.
MJ11	2	4	5	binK1/R537C	PCR/SS	n.d.	n.d.
MJ11	2	4	6	binK1/R537C	PCR/SS	n.d.	n.d.
MJ11	2	4	7	binK1/R537C	PCR	n.d.	n.d.
MJ11	2	4	8	binK1/R537C	PCR	n.d.	n.d.
MJ11	2	4	9	binK1/R537C	PCR	n.d.	n.d.
MJ11	2	4	10	binK1/R537C	PCR	n.d.	n.d.
MJ11	2	4	11	binK1/R537C	PCR	n.d.	n.d.
MJ11	2	4	12	binK1/R537C	PCR	n.d.	n.d.
MJ11	2	4	13	binK1/R537C	PCR	n.d.	n.d.
MJ11	2	4	14	binK1/R537C	PCR/SS	n.d.	n.d.
MJ11	2	4	15	binK1/R537C	PCR/SS	n.d.	n.d.
MJ11	2	4	16	binK1/R537C	PCR/SS	n.d.	n.d.
MJ11	15	4	1	binK1/R537C	WGS (131)	G198V (85)	–	4126149	99.4	117.8	106.1
MJ11	15	4	6	binK1/R537C	WGS (61)	G198V (55)	–	2266821	99.2	60.8	52.5
MJ11	15	4	7	binK1/R537C	WGS (89)	G198V (93)	–	3074437	99.6	92	83.6
MJ11	15	4	8	binK1/R537C	WGS (47)	G198V (96)	–	2902977	99.5	84	77.5
MJ11	2	5	2	binK3/S311L	WGS (26)	–	–	3771048	99.6	132.4	123.7
MJ11	2	5	3	binK3/S311L	WGS (46)	–	–	2595518	99.6	84.2	83.7
MJ11	2	5	4	binK3/S311L	WGS (20)	–	–	1785713	99.5	60.6	57.2
MJ11	2	5	5	binK3/S311L	WGS (62)	–	–	3641346	99.6	117.4	113.1
MJ11	2	5	6	binK3/S311L	WGS (81)	–	–	4128751	99.6	141.1	134.8
MJ11	15	5	2	binK4/N292T	WGS (89)	–	–	4430823	99.1	152.3	138.4
MJ11	15	5	3	binK3/S311L	WGS (10)	–	–	3248580	99.3	88	81.1
MJ11	15	5	4	binK3/S311L	WGS (59)	–	–	3609382	99.5	106.8	97.1
MJ11	15	5	5	binK3/S311L	WGS (28)	–	–	2915570	99.5	87.4	82.6
MJ11	2	6	1	binK2/K482N	WGS (104)	–	–	4748569	99.1	164.6	147
MJ11	2	6	2	binK2/K482N	PCR/SS	n.d.	n.d.
MJ11	15	6	1	binK2/K482N	WGS (75)	–	–	2764910	99.4	83.2	75.5
MJ11	15	6	2	binK2/K482N	WGS (63)	–	–	3240968	99.2	88	72.6
MJ11	15	6	3	binK2/K482N	WGS (93)	–	–	3814367	99.5	108.1	101.7
MJ11	15	6	4	binK2/K482N	WGS (108)	–	–	3714638	99.5	121.4	85.7
MJ11	15	6	5	binK2/K482N	WGS (90)	–	–	3006362	99.4	85.5	72
MJ11	15	Culture1	mg	–		–	–	10319291	98	272.8	237.8
MJ11	15	Culture3	mg	–		–	–	7496847	98.2	196.7	195
MJ11	15	Culture4	mg	–		–	fliA (VF_1834); G80D (63)	2894160	98.3	76.6	67.4
MJ11	15	Culture5	mg	–		–	fliP (VF_1842); ∆1 @ 476/870nt (110)	5571439	97.9	148.5	132.1
MJ11	15	Culture2	mg	–		–	–	5411032	98	144.2	129.4
WH1	15	4	1	–		–	–	7273244	98.6	257.8	251.1
WH1	15	4	2	–		–	–	2144381	99.6	61.4	65.1
WH1	15	4	3	–		–	–	2260232	99.6	62.1	66.6
WH1	15	4	4	–		–	–	2341428	99.7	61.6	65
WH1	15	5	1	–		–	NADH oxidase (VF_A0027); A402T (62)	1732106	99.5	60.8	64.7
WH1	15	5	2	–		–	NADH oxidase (VF_A0027); A402T (61)	1737095	99.4	61.9	64.9
WH1	15	5	3	–		–	NADH oxidase (VF_A0027); A402T (80)	2194847	96	60.8	63.4
WH1	15	5	4	–		–	–	2191986	99.8	61.9	64.9
WH1	15	6	1	–		–	–	9256547	99.3	212.6	220.3
WH1	15	6	2	–		–	–	2131144	99.6	62	64.7
WH1	15	6	3	–		–	–	1908857	99.5	62.4	60.5
EM17	15	6	2	–		–	–	2611609	99.6	93.3	89.3
EM17	15	7	1	–		–	–	6690137	98.6	225.8	227.1
EM17	15	7	4	–		–	–	2977429	99.5	83.4	82.1
EM17	15	7	5	–		–	icmF (VF_0992);S171N, (72)	2414288	99.5	71.6	71.5
EM17	15	8	1	–		–	–	3177981	99.5	97.5	94.6
EM17	15	8	2	–		–	–	3138175	99.5	92.4	92.3
EM17	15	8	3	–		–	–	2810099	99.5	81.2	80
EM17	15	8	5	–		–	–	5230411	99.6	144.9	143.2
EM17	15	9	1	–		–	–	8022935	99.4	184.2	173.5
EM17	15	9	2	–		–	–	3346216	99.6	113.7	106.9
EM17	15	9	3	–		–	gdh2 (VF_1284); E732D (72)	3484188	99.5	95.7	93.2
EM17	15	9	5	–		–	–	2445758	99.5	72.8	72.6
H905	15	1	1	(∆37168 bp/25 genes)	WGS (230)	–	IlvY (VF_2529); M25I (233)	7645508	94.2	250.4	222.1
H905	15	1	2	(∆37168 bp/25 genes)	WGS (167)	–	IlvY (VF_2529); M25I (112)	3531114	96.8	117.5	104.4
H905	15	1	3	(∆37168 bp/25 genes)	WGS (175)	–	IlvY (VF_2529); M25I (97)	3596689	97	122.3	109.1
H905	15	2	2	∆16 bp@ 498/2595	WGS (75)	–	purR (VF_1572); N71T (60)	2819387	97.6	91.4	79.6
H905	15	2	4	∆16 bp@ 498/2595	WGS (94)	–	purR (VF_1572); N71T (52)	2992978	96.9	103.3	91.4
H905	15	2	5	∆16 bp@ 498/2595	WGS (90)	–	purR (VF_1572); N71T (95)	3844830	96.3	123.6	109
H905	2	3	1	–		–	tadF2 (VF_A0228); G21D (68)	3393611	90.7	99.5	92.2
H905	15	3	1	–		–	tadF2 (VF_A0228); G21D (140)	7974773	91.5	147.9	143.9
H905	15	3	2	T195I	WGS (65)	–	tadF2 (VF_A0228); G21D (28)	1989875	95.5	65.4	58.2
H905	15	3	3	–		–	tadF2 (VF_A0228); G21D (77)	3253899	96.7	103.8	94.4
H905	15	3	4	–		–	tadF2 (VF_A0228); G21D (58)	3242749	97.1	103.3	94.7
H905	15	3	5	–		–	tadF2 (VF_A0228); G21D (25)	2190771	95.9	67.5	59
H905	15	4	1	E43*	WGS (102)	–	–	6651385	92	125.1	130
H905	15	4	3	E43*	WGS (111)	–	–	4032373	96.4	135.9	120.4
H905	15	4	4	E43*	WGS (187)	–	–	6122168	95.8	203.4	179.4
H905	15	4	5	E43*	WGS (90)	–	–	3177817	96.7	100.8	90.6
H905	15	5	1	∆1 bp @ 2325/2595nt	WGS (113)	–	–	7166870	90.4	134.5	130.9
H905	15	5	2	∆1 bp @ 2325/2595nt	WGS (94)	–	–	3703946	96.7	118.6	108.3
H905	15	5	3	∆1 bp @ 2325/2595nt	WGS (66)	–	–	2828102	97.4	98.6	90.4
H905	15	5	4	∆1 bp @ 2325/2595nt	WGS (109)	–	–	4721575	97	158.9	143.8
H905	2	6	1	T195I	WGS (105)	–	tadF2 (VF_A0228); G21D (28)	2743693	94	83.3	73.6
H905	15	6	3	T195I	WGS (142)	–	tadF2 (VF_A0228); G21D (49)	5594771	97.5	191.7	175.3
H905	15	6	4	T195I	WGS (105)	–	tadF2 (VF_A0228); G21D (37)	3361206	96	115.9	101.4

^†Individual characterized strain collection names assigned to isolates were derived from their ancestral lineage (e.g. MJ11), evolved passage (e.g. EP2), the population (e.g. 1), and isolate number (e.g. 1), which in the preceding example would give rise to strain collection name of MJ11EP2-1-1. Isolates in bold served as allelic binK representatives for further assays. mg: metagenome sequencing by pooling five isolates from a population.

^‡The presence of mutations was determined from Illumina short read (100PE) whole genome sequencing (WGS), by allele-specific PCR (PCR), and/or by locus PCR-amplification, followed by Sanger sequencing (SS). ‘–' indicates that no mutations were identified at this locus by breseq (Deatherage and Barrick, 2014) in this isolate using WGS. ‘n.d.’ indicates that the presence of mutations at this locus was not determined.

^§The number of reads supporting the mutation call from WGS data is provided. Mutations were called for sites with minimum coverage of 20 mappable reads. Mutations identified by Sanger sequencing (SS) of PCR-generated amplicons were confirmed from alignments of both forward and reverse reads. Coding genes reference V. fischeri ES114 locus tags.

elife-24502-v2.xml

10.7554/eLife.24502.005

Table 2.Activity of novel indole compounds against DYRK1A and related kinases relative to ID-8.

Compound	R₁	R₂	R₃	IC₅₀ (μM)
Compound	R₁	R₂	R₃	DYRK1A	DYRK1B	DYRK2	CLK1	CLK4	GSK3α	GSK3β	LRRK2	PIM1	PIM3
ID-8	6-OH	NO₂	p-OCH₃	0.104	0.040	NC	1.37	1.05	0.428	0.153	0.100	0.376	0.176
34	6-OCOCH₃	NHCOCH₃	p-OCH3	NC	NC	NC	NC	NC	NC	NC	NC	NC	NC
28	6-OCH₃	NO₂	p-OCH₃	0.346	0.695	NC	NC	2.23	2.36	3.44	0.854	0.176	0.259
29	6-OCH₂C₆H₅	NO₂	p-OCH₃	6.52	3.57	NC	NC	NC	18.0	14.3	8.16	18.5	8.28
30	6-OCOCH₃	NO₂	p-OCH₃	0.680	0.299	NC	NC	11.95	22.15	1.71	0.891	4.15	1.21
45	6-OH	NO₂	p-OH	0.122	0.060	2.30	0.364	0.163	0.375	0.233	0.046	0.243	0.180
48	6-OH	NO₂	m-OCH₃	0.594	0.257	NC	13.0	4.77	2.32	0.692	2.17	0.654	0.593
49	6-OH	NO₂	o-OCH₃	0.829	0.341	41.9	10.7	8.59	6.12	3.82	1.98	1.44	0.892
51	5-NO₂	NO₂	p-OCH₃	NC	NC	NC	NC	NC	NC	NC	NC	7.62	4.57
38	H	NO₂	p-OCH₃	NC	NC	NC	NC	NC	NC	NC	NC	NC	20.74

elife-24669-v2.xml

10.7554/eLife.24669.036

Table 11.

Rich medium replicate 3: All mutations detected in rounds 5, 10 and 15 of rich medium replicate 3. See Table 9 caption. Note low coverage on Δ1 bp mutation at 523086 noted in bold.

DOI: http://dx.doi.org/10.7554/eLife.24669.036

Rich medium replicate 3
Round, (coverage)	5, (291×)	10, (45×)	15, (186×)
Mutation (loc., mut., frac., cov.)	457978, clpX E185*, 100%, 300	457978, clpX E185*, 100%, 43	457978, clpX E185*, 100%, 185
Mutation (loc., mut., frac., cov.)	523086, IG Δ1 bp, 50%, 38	523086, IG Δ1 bp, 100%, 8	523086, IG Δ1 bp, 100%, 16
	950518, pflA T188I, 26.3%, 332	950518, pflA T188I, 53.3%, 53	950518, pflA T188I, 30.6%, 190
		321263, IG T→C, 25%, 16	1968653, cheR Q238K, 29.6%, 190
		382794, yaiX +9bp insertion, 64%, NA	382794, yaiX +9bp insertion, 25.8%, NA
			4161562, fabR Δ⁢17bp, 46.2%, 67

elife-24669-v2.xml

10.7554/eLife.24669.037

Table 12.

Rich medium replicate 4: All mutations detected in rounds 5, 10 and 15 of rich medium replicate 4. See Table 9 caption. Note low coverage on Δ1 bp mutation at 523086 noted in bold.

DOI: http://dx.doi.org/10.7554/eLife.24669.037

Rich medium replicate 4
Round, (coverage)	5, (384×)	10, (555×)	15, (333×)
Mutation (loc., mut., frac., cov.)	457978, clpX E185*, 100%, 370	457978, clpX E185*, 100%, 559	457978, clpX E185*, 100%, 339
	523086, IG Δ1 bp, 50%, 72	523086, IG Δ1 bp, 100%, 34/83	523086, IG Δ1 bp, 100%, 19/33
	950518, pflA T188I, 31.7%, 446		3619915, rhsB W242G, 24.9%, 20

elife-24669-v2.xml

10.7554/eLife.24669.026

Table 5.

Minimal medium replicate 1: All mutations detected in rounds 5 and 10 of minimal medium replicate 1. The galSL22R mutation in rounds 5 and 10 was confirmed by Sanger sequencing. See Table 9 caption.

DOI: http://dx.doi.org/10.7554/eLife.24669.026

Minimal medium replicate 1
round, (coverage)	5, (71×)	10, (214×)
Mutation (loc., mut., frac., cov.)	1196220, icd H366H,78.4%, 46	1196220, icd H366H, 100%, 141
Mutation (loc., mut., frac., cov.)	1196232, icd T370T, 71.1%, 34	1196232, icd T370T, 100%, 101
	1196247, icd L375L, 72.0%, 25	1196247, icd L375L, 100%, 75
	1196277, icd N385N, 47.1%, 17	2015871, fliG V331D, 100%, 111
	1196280, icd A386A, 47.1%, 17	2241604, galS L22R, 100%, 184
	1196283, icd K387K, 47.2%, 17	2685013, glyA H165H, 100%, 197
	1196292, icd T390T, 46.2%, 13	3815859, rph Δ82 bp, 100%, 260
	1196304, icd E394E, 46.2%, 13
	2015871, fliG V331D, 70.0%, 60
	2241604, galS L22R, 100%, 45
	2685013, glyA H165H, 100%, 62

elife-24669-v2.xml

10.7554/eLife.24669.027

Table 6.

Minimal medium replicate 2: All mutations detected in rounds 5 and 10 of minimal medium replicate 2. The galSL22R mutation in rounds 5 and 10 was confirmed by Sanger sequencing. See Table 9 caption.

DOI: http://dx.doi.org/10.7554/eLife.24669.027

Minimal medium replicate 2
round, (coverage)	5, (67×)	10, (64×)
Mutation (loc., mut., frac., cov.)	2241604, galS L22R, 100%, 70	1757419, IG +17 bp insertion, 94.9%, 37
Mutation (loc., mut., frac., cov.)	2685013, glyA H165H, 100%, 65	2241604, galS L22R, 100%, 47
		2685013, glyA H165H, 100%, 79
		3815828, IG T→G, 43.5%, 62

elife-24669-v2.xml

10.7554/eLife.24669.028

Table 7.

Minimal medium replicate 3: All mutations detected in rounds 5 and 10 of minimal medium replicate 3. See Table 9 caption.

DOI: http://dx.doi.org/10.7554/eLife.24669.028

Minimal medium replicate 3
round, (coverage)	5, (208×)	10, (229×)
Mutation (loc., mut., frac., cov.)	1291079, rssB A280T, 29.7%, 54	2241595, galS Δ1bp, 100%, 218
Mutation (loc., mut., frac., cov.)	2241595, galS Δ1bp, 64.7%, 102	3277264, prlF +CATTCAA insertion, 93.6%, 109
	3762200, rhsA A6A, 23.5%, 181	3350529, IG T→C, 100%, 117
	3762212, rhsA G10G, 23.1%, 164	3762200, rhsA A6A, 45.8%, 320
		3762212, rhsA G10G, 42.0%, 292

elife-24669-v2.xml

10.7554/eLife.24669.029

Table 8.

Minimal medium replicate 4: All mutations detected in rounds 5 and 10 of minimal medium replicate 4. See Table 9 caption.

DOI: http://dx.doi.org/10.7554/eLife.24669.029

Minimal medium replicate 4
round, (coverage)	5, (256×)	10, (230×)
Mutation (loc., mut., frac., cov.)	2241232, galS R146L, 72.4%, 274	2020519, fliM E145K, 100%, 205
Mutation (loc., mut., frac., cov.)		2241665, galS I2L, 100%, 304

elife-24669-v2.xml

10.7554/eLife.24669.034

Table 9.

Rich medium replicate 1: All mutations detected above a frequency of 0.2 in rounds 5, 10 and 15 of rich medium selection replicate 1. The first number in each cell denotes the distance in base pairs from ori (location). The second entry (mutation) identifies the mutations with ‘IG’ denoting an intergenic mutation. The third entry (fraction) is the fraction of the population carrying this mutation (as inferred by breseq in polymorphism mode). The fourth entry (coverage) is the number of reads that aligned to this location. In the round 15 strain, the clpX SNP and Δ1 bp deletion at position 523,086 were confirmed by Sanger sequencing.

DOI: http://dx.doi.org/10.7554/eLife.24669.034

Rich medium replicate 1
Round, (coverage)	5, (172×)	10, (213×)	15, (180×)
Mutation (loc., mut., frac., cov.)	457978, clpX E185*, 75.2%, 179	457978, clpX E185*, 100%, 199	457978, clpX E185*, 100%, 164
Mutation (loc., mut., frac., cov.)	523086, IG Δ1 bp, 100%, 194	523086, IG Δ1 bp, 100%, 266	523086, IG Δ1 bp, 100%, 168
	950518, pflA T188I, 22.2%, 144	990379, IG A→C, 100%, 201	663115, dacA Δ1 bp, 100%, 150
	1978458, IG G→T, 21.2%, 156		990379, IG A→C, 100%, 156
	3618863, nikR H92H, 20.7%, 189

elife-24669-v2.xml

10.7554/eLife.24669.035

Table 10.

Rich medium replicate 2: All mutations detected in rounds 5, 10 and 15 of rich medium replicate 2. See Table 9 caption. Note low coverage on Δ1 bp mutation at 523086 noted in bold.

DOI: http://dx.doi.org/10.7554/eLife.24669.035

Rich medium replicate 2
Round, (coverage)	5, (218×)	10, (100×)	15, (166×)
Mutation (loc., mut., frac., cov.)	457978, clpX E185*, 100%, 220	457978, clpX E185*, 100%, 109	457978, clpX E185*, 100%, 184
Mutation (loc., mut., frac., cov.)	950518, pflA T188I, 27.2%, 210	523086, IG Δ1 bp, 100%, 16	523086, IG Δ1 bp, 100%, 24
	523086, IG Δ1 bp, 100%, 10/18		667259, mrdA R320H, 39.5%, 159
			794472, modE L58*, 42.4%, 136

elife-24998-v2.xml

10.7554/eLife.24998.004

Table 1.

Summary of kinetic analysis of ARPP-16 phosphorylation by MAST3 and PKA.

DOI: http://dx.doi.org/10.7554/eLife.24998.004

	MAST3	Vm	Km	Catalytic efficiency
	MAST3	³²P-incorporation/minute	nM	Vm/Km
Figure 1b	ARPP-16	1388 ± 27	90 ± 5	15.4
	P-S88-ARPP-16	866 ± 59	158 ± 26	5.5
Figure 1—figure supplement 1	ARPP-16	1391 ± 34	92 ± 6	15.1
	P-S88D-ARPP-16	465 ± 32	138 ± 24	3.4
	PKA	Vm	Km	Catalytic efficiency
	PKA	³²P-incorporation/minute	nM	Vm/Km
Figure 1d	ARPP-16	6999 ± 127	1685 ± 51	4.1
	P-S46-ARPP-16	1027 ± 39	870 ± 47	1.2

elife-25068-v1.xml

10.7554/eLife.25068.003

Table 1.

Binding affinities of the different YAP^50-151 proteins for wt hTEAD4^217-434. The affinities were measured at 298°K by Surface Plasmon Resonance in n ≥ 3 independent experiments. N-Avitagged hTEAD4^217-434 was immobilized on sensor chips. The K_d values were obtained from equilibrium data (K_d^eq). Averages and standard errors (SE) are given. ΔΔG = ΔG_mutant – ΔG_wt and SE_ΔΔG = (SE_ΔGmutant² + SE_ΔGwt²)^1/2.

DOI: http://dx.doi.org/10.7554/eLife.25068.003

Mutation site	YAP^50-171	K_d^eq (nM)	ΔG (kcal/mol)	ΔΔG (kcal/mol)
Mutation site	Wild type	18 ± 0	−10.56 ± 0.01
α-helix	Leu65Ala	794 ± 4	−8.31 ± 0.01	2.24 ± 0.01
	Leu68Ala	464 ± 4	−8.63 ± 0.01	1.92 ± 0.01
	Phe69Ala	6447 ± 400	−7.08 ± 0.04	3.48 ± 0.04
Ω-loop	Met86Ala	2080 ± 69	−7.74 ± 0.02	2.81 ± 0.02
	Arg89Ala	27423 ± 381	−6.22 ± 0.01	4.34 ± 0.01
	Leu91Ala	30550 ± 2250	−6.15 ± 0.04	4.40 ± 0.05
	Ser94Ala	5623 ± 341	−7.16 ± 0.04	3.40 ± 0.04
	Phe95Ala	26045 ± 755	−6.25 ± 0.02	4.31 ± 0.02
	Phe96Ala	4755 ± 245	−7.25 ± 0.03	3.30 ± 0.03

elife-25068-v1.xml

10.7554/eLife.25068.004

Table 2.

Properties of the different hTEAD4^217-434 proteins. The melting temperatures (T_m) of the proteins were determined in n ≥ 3 independent experiments in a fluorescence-based thermal shift assay. Averages and standard errors (SE) are given. ΔT_m = T_m^mutant – T_m^wt and SE_ΔTm = (SE_Tmmutant² + SE_Tmwt²)^1/2. For dissociation constant measurements, the different N-Avitagged hTEAD4^217-434 proteins were immobilized on sensor chips and their affinity for wt hYAP^50-171 was measured at 298°K by Surface Plasmon Resonance in n ≥ 3 independent experiments. K_d values were obtained from equilibrium data (K_d^eq). Averages and standard errors (SE) are given. ΔΔG = ΔG_mutant – ΔG_wt and SE_ΔΔG = (SE_ΔGmutant + SE_ΔGwt)^1/2. n. d.: not determined.

DOI: http://dx.doi.org/10.7554/eLife.25068.004

Mutation site	hTEAD4^217-434	T_m (°C)	ΔT_m (°C)	K_d^eq (nM)	ΔG (kcal/mol)	ΔΔG (kcal/mol)
Mutation site	Wild type	54.0 ± 0.1		18 ± 0	−10.56 ± 0.01
α-helix	Phe337Ala	53.1 ± 0.1	−0.9 ± 0.1	202 ± 8	−9.12 ± 0.02	1.43 ± 0.02
	Tyr369Ala	49.9 ± 0.2	−4.2 ± 0.3	n. d.
	Phe373Ala	53.0 ± 0.3	−1.0 ± 0.3	12 ± 0	−10.79 ± 0.00	−0.24 ± 0.01
	Lys376Ala	53.4 ± 0.1	−0.7 ± 0.1	203 ± 9	−9.13 ± 0.03	1.43 ± 0.03
	Leu377Ala	49.8 ± 0.1	−4.3 ± 0.2	n. d.
	Leu380Ala	52.8 ± 0.1	−1.3 ± 0.2	162 ± 7	−9.26 ± 0.03	1.30 ± 0.03
	Val389Ala	53.0 ± 0.0	−1.0 ± 0.1	304 ± 5	−8.88 ± 0.01	1.67 ± 0.01
Ω-loop	Glu263Ala	53.0 ± 0.2	−1.1 ± 0.2	220 ± 9	−9.07 ± 0.02	1.48 ± 0.03
	Val265Ala	52.0 ± 0.0	−2.0 ± 0.1	106 ± 3	−9.51 ± 0.02	1.05 ± 0.02
	Asp272Ala	54.1 ± 0.1	0.1 ± 0.1	6995 ± 317	−7.03 ± 0.03	3.53 ± 0.03
	Lys273Ala	48.1 ± 0.2	−5.9 ± 0.3	n. d.
	Leu295Ala	47.4 ± 0.1	−6.6 ± 0.1	n. d.
	Lys297Ala	48.4 ± 0.2	−5.7 ± 0.3	n. d.
	Val414Ala	50.9 ± 0.1	−3.2 ± 0.1	14 ± 1	−10.73 ± 0.02	−0.17 ± 0.02
	Tyr429Phe	52.3 ± 0.1	−1.7 ± 0.1	71 ± 6	−9.75 ± 0.05	0.81 ± 0.05

elife-25068-v1.xml

10.7554/eLife.25068.007

Table 3.

Summary of the coupling energy (ΔΔG_int) measured for each pair of residues. ΔΔG_int values are in kcal/mol and were calculated according to the description given in the Materials and methods section. Average and standard errors (SE) are shown. The gray cells indicate mutations of YAP and TEAD in the same binding pocket. n. m. (not measured) indicates that ΔΔG_int could not be determined experimentally because the K_d values for the mutant YAP:mutant TEAD interaction in the corresponding double mutant cycles were above our assay limit (>200 µM).

DOI: http://dx.doi.org/10.7554/eLife.25068.007

			hYAP^50-171
			α-helix			Ω-loop
			Leu65	Leu68	Phe69	Met86	Arg89	Leu91	Ser94	Phe95	Phe96
hTEAD^217-434	α-helix	Phe337	−0.34 ±0.04	−0.65 ±0.04	−0.96 ±0.04	0.17 ±0.04	−0.44 ±0.03	n. m.	−0.09 ±0.05	n. m.	0.02 ±0.06
		Lys376	−0.65 ±0.04	−0.41 ±0.05	−1.28 ±0.06	0.13 ±0.04	−0.62 ±0.03	−0.41 ±0.06	−0.22 ±0.06	−0.30 ±0.04	−0.14 ±0.05
		Leu380	−0.36 ±0.05	−0.29 ±0.04	−1.01 ±0.06	0.07 ±0.03	−0.29 ±0.03	−0.26 ±0.05	−0.08 ±0.05	−0.18 ±0.03	−0.02 ±0.06
		Val389	−0.52 ±0.06	−0.29 ±0.05	−1.11 ±0.05	0.16 ±0.03	n. m.	n. m.	0.03 ±0.05	n. m.	−0.06 ±0.04
	Ω-loop	Glu263	−0.05 ±0.05	−0.09 ±0.03	−0.10 ±0.06	0.07 ±0.05	−0.59 ±0.06	−0.62 ±0.05	−0.96 ±0.05	−0.51 ±0.05	−0.04 ±0.07
		Val265	0.26 ±0.03	0.15 ±0.03	0.13 ±0.05	0.09 ±0.03	−0.58 ±0.02	−0.28 ±0.06	−0.06 ±0.06	−0.61 ±0.04	−0.22 ±0.06
		Asp272	n. m.	−0.02 ±0.04	n. m.	−1.85 ±0.04	−3.49 ±0.05	−2.74 ±0.06	−1.65 ±0.05	−2.50 ±0.07	−1.67 ±0.06

elife-25069-v1.xml

10.7554/eLife.25069.007

Table 1.

CP behavioral scores ordered by severity as indicated by performance on the CFMT.

DOI: http://dx.doi.org/10.7554/eLife.25069.007

Participant	Sex	Age	Famous faces questionnaire		CFMT (total)
Participant	Sex	Age	% corr.	Z- score	CFMT (total)
BL	F	18	20	-4.88	28	-4.15
BQ	F	29	16	-4.92	30	-3.89
KG	F	49	75	-0.69	33	-3.5
ON (Avidan et al., 2014)	F	48	60.7	-1.77	35	-3.23
MT (Nishimura et al., 2010), (Avidan et al., 2011), (Behrmann and Avidan, 2005), (Thomas et al., 2009), (Avidan and Behrmann, 2008), (Humphreys et al., 2007) , (Behrmann et al., 2007), (Avidan et al., 2014)	M	50	62.5	-1.64	36	-3.11
WA (Nishimura et al., 2010), (Avidan et al., 2014)	F	23	45.7	-2.91	40	-2.58
KE (Avidan et al., 2011), (Thomas et al., 2009), (Avidan et al., 2014)	F	67	42.9	-3.12	40	-2.58
TD (Nishimura et al., 2010), (Avidan et al., 2011), (Avidan et al., 2014)	F	38	46.4	-2.85	41	-2.45
MN (Nishimura et al., 2010), (Avidan et al., 2014)	F	50	60.7	-1.77	52	-1
BT (Avidan et al., 2011), (Avidan et al., 2014)	M	32	55.3	-2.18	58	-0.21
CP Mean ± s.d		40.4± 15.03	48.52 ± 18.72		39.3 ± 9.41
Control Mean ± s.d		39.3 ± 13.4	91.57±6.24		58.28 ± 5.87

The table shows the age and gender of participants and their performance (raw values and z-normalized scores relative to a large control group) on the famous faces questionnaire and CFMT. Note that 7 of the 10 CPs have participated in previous behavioral (3 CPs), and imaging (7 CPs) studies; additional behavioral measures for the CP individuals can be found in these references. Specific details regarding diagnostic and inclusion criteria can be found in the Materials and methods section and in the related studies. The average performance on the famous faces questionnaire and the CFMT of the controls who participated in the present study is also provided (t-test comparing performance across the CP and the controls, for famous faces questionnaire p<0.0005 and CFMT p<0.0005).

elife-25069-v2.xml

10.7554/eLife.25069.007

Table 1.

CP behavioral scores ordered by severity as indicated by performance on the CFMT.

DOI: http://dx.doi.org/10.7554/eLife.25069.007

Participant	Sex	Age	Famous faces questionnaire		CFMT (total)
Participant	Sex	Age	% corr.	Z- score	CFMT (total)
BL	F	18	20	-4.88	28	-4.15
BQ	F	29	16	-4.92	30	-3.89
KG	F	49	75	-0.69	33	-3.5
ON (Avidan et al., 2014)	F	48	60.7	-1.77	35	-3.23
MT (Nishimura et al., 2010), (Avidan et al., 2011), (Behrmann and Avidan, 2005), (Thomas et al., 2009), (Avidan and Behrmann, 2008), (Humphreys et al., 2007) , (Behrmann et al., 2007), (Avidan et al., 2014)	M	50	62.5	-1.64	36	-3.11
WA (Nishimura et al., 2010), (Avidan et al., 2014)	F	23	45.7	-2.91	40	-2.58
KE (Avidan et al., 2011), (Thomas et al., 2009), (Avidan et al., 2014)	F	67	42.9	-3.12	40	-2.58
TD (Nishimura et al., 2010), (Avidan et al., 2011), (Avidan et al., 2014)	F	38	46.4	-2.85	41	-2.45
MN (Nishimura et al., 2010), (Avidan et al., 2014)	F	50	60.7	-1.77	52	-1
BT (Avidan et al., 2011), (Avidan et al., 2014)	M	32	55.3	-2.18	58	-0.21
CP Mean ± s.d		40.4± 15.03	48.52 ± 18.72		39.3 ± 9.41
Control Mean ± s.d		39.3 ± 13.4	91.57±6.24		58.28 ± 5.87

elife-25069-v3.xml

10.7554/eLife.25069.007

Table 1.

CP behavioral scores ordered by severity as indicated by performance on the CFMT.

DOI: http://dx.doi.org/10.7554/eLife.25069.007

Participant	Sex	Age	Famous faces questionnaire		CFMT (total)
Participant	Sex	Age	% corr.	Z- score	CFMT (total)
BL	F	18	20	-4.88	28	-4.15
BQ	F	29	16	-4.92	30	-3.89
KG	F	49	75	-0.69	33	-3.5
ON (Avidan et al., 2014)	F	48	60.7	-1.77	35	-3.23
MT (Nishimura et al., 2010), (Avidan et al., 2011), (Behrmann and Avidan, 2005), (Thomas et al., 2009), (Avidan and Behrmann, 2008), (Humphreys et al., 2007) , (Behrmann et al., 2007), (Avidan et al., 2014)	M	50	62.5	-1.64	36	-3.11
WA (Nishimura et al., 2010), (Avidan et al., 2014)	F	23	45.7	-2.91	40	-2.58
KE (Avidan et al., 2011), (Thomas et al., 2009), (Avidan et al., 2014)	F	67	42.9	-3.12	40	-2.58
TD (Nishimura et al., 2010), (Avidan et al., 2011), (Avidan et al., 2014)	F	38	46.4	-2.85	41	-2.45
MN (Nishimura et al., 2010), (Avidan et al., 2014)	F	50	60.7	-1.77	52	-1
BT (Avidan et al., 2011), (Avidan et al., 2014)	M	32	55.3	-2.18	58	-0.21
CP Mean ± s.d		40.4± 15.03	48.52 ± 18.72		39.3 ± 9.41
Control Mean ± s.d		39.3 ± 13.4	91.57±6.24		58.28 ± 5.87

elife-25078-v2.xml

10.7554/eLife.25078.007

Table 1.

Statistical properties of all KV analyzed. Table summarizing some of the cilia features collected from the 3D-CiliaMap for individual KV at 3-, 8- and 9–14- somite stage (SS).

DOI: http://dx.doi.org/10.7554/eLife.25078.007

stage	KV number	N cilia	% immotile cilia	Ellipsoid axis		Axis ratio a / b	Volume (pl)	Average motile cilium			Ellipsoid fit RMS residue (µm)	Ω (s^-1)
stage	KV number	N cilia	% immotile cilia	a (µm)	b (µm)	Axis ratio a / b	Volume (pl)	r	θ (°)	φ (°)	Ellipsoid fit RMS residue (µm)	Ω (s^-1)
3-SS	1	56	11%	27	12	2.3	35	0.8	37	6	2.07	0.423
	2	23	39%	21	12	1.8	21	0.8	44	2	1.56	0.207
	3	35	3%	23	12	1.9	27	0.8	42	-11	2.38	0.457
	4	21	33%	18	11	1.6	15	0.8	22	12	2.14	0.350
	5	19	100%	15	9	1.7	8	NA	NA	NA	1.5	0.000
	6	24	54%	15	10	1.5	9	0.7	28	3	1.78	0.230
	7	23	61%	14	12	1.2	10	0.8	18	-46	1.92	0.110
	8	40	53%	18	11	1.6	16	0.7	8	22	2.05	0.034
	mean ± SD	30 ± 13	44% ± 31%	19 ± 5	11 ± 1	1.7 ± 0.3	17 ± 10	0.8 ± 0.1	28 ± 13	-2 ± 22	1.9 ± 0.3	0.226 ± 0.173
8-SS	1	50	4%	29	18	1.6	64	0.8	37	-14	1.2	0.270
	2	49	2%	22	8	2.8	15	0.8	35	6	1.1	0.595
	3	43	0%	25	11	2.3	30	0.7	46	12	2.3	0.561
	4	50	4%	27	12	2.3	39	0.7	41	16	2.5	0.329
	5	71	0%	26	13	2.0	36	0.8	35	16	1.8	0.469
	6	47	0%	30	22	1.4	85	0.7	21	39	1.7	0.110
	mean ± SD	52 ± 10	2% ± 2%	26 ± 3	14 ± 5	2.0 ± 0.5	45 ± 25	0.7 ± 0.1	36 ± 8	13 ± 17	1.7 ± 0.5	0.389 ± 0.186
9-14-SS	1	89	16%	37	31	1.2	174	0.7	49	12	2.1	0.271
	2	78	6%	27	15	1.8	47	0.7	46	18	2.0	0.600
	3	80	3%	33	20	1.7	93	0.8	54	13	2.2	0.412
	4	50	0%	33	20	1.7	91	0.7	47	14	2.6	0.290
	5	78	6%	31	17	1.8	70	0.7	36	20	2.0	0.393
	6	94	4%	36	21	1.7	111	0.8	52	10	1.7	0.424
	7	62	11%	34	26	1.3	124	0.8	46	11	1.8	0.216
	8	39	3%	24	20	1.2	48	0.7	54	36	4.4	0.378
	9	35	0%	31	13	2.4	52	0.8	50	10	2.6	0.245
	10	49	4%	32	17	1.9	74	0.8	53	2	2.3	0.275
	11	50	2%	30	22	1.4	82	0.9	64	3	2.9	0.433
	12	55	2%	30	23	1.3	85	0.8	61	11	2.6	0.388
	13	49	4%	33	10	3.3	47	0.7	40	32	2.1	0.224
	14	79	5%	27	19	1.4	56	0.7	51	22	1.8	0.521
	mean ± SD	63 ± 19	5% ± 4%	31 ± 4	19 ± 5	1.7 ± 0.6	82 ± 36	0.8 ± 0.05	50 ± 7	15 ± 10	2.3 ± 0.7	0.362 ± 0.114

elife-25100-v1.xml

10.7554/eLife.25100.026

Table 1.

Differences in amplification cost indicated by the extinction risk of populations with amplifications. Populations with amplifications of higher (strain BΔIS5I) or lower (strain E) expected cost of amplifications have a higher or lower risk of becoming extinct, respectively. n = initial number of replicate populations used for analysis (n = 285 includes replicate evolution experiments to increase statistical power), ‘Extinct’ and ‘Rescued’ = numbers of extinct and rescued populations with amplifications as indicated by (transiently) increased CFP fluorescence (see Materials and methods), sample odds ratio compared to strain B, p-values: 2 × 2 Fisher’s exact test.

DOI: http://dx.doi.org/10.7554/eLife.25100.026

n	Strain	Populations with (transiently) increased CFP fluorescence		Sample Odds Ratio	P-value
n	Strain	Extinct	Rescued	Sample Odds Ratio	P-value
95	BΔIS5I	12	5	10.1	10⁻⁴
95	B	18	76	1 (ref)	–
95	E	0	95	0	10⁻⁶

285	A	8	4	5.8	10⁻³
285	B	58	168	1 (ref)	–
285	C	0	1	0	n.s.
285	D	0	7	0	n.s.

elife-25624-v2.xml

10.7554/eLife.25624.026

Table 2.

Minimum inhibitory concentrations (MICs) of cell wall targeting drugs for different Mycobacterium tuberculosis strains.

Source data file for the calculation of MIC values is available in Table 2–source data 1.

DOI: http://dx.doi.org/10.7554/eLife.25624.026

10.7554/eLife.25624.027Table 2—source data 1.Percentage growth inhibition values for <italic>Mtb</italic>, <italic>MtbΔwhiB4 </italic>and <italic>whiB4-OE </italic>in presence of different drugs for calculation of minimum inhibitory concentration (MIC).

DOI: http://dx.doi.org/10.7554/eLife.25624.027

Drugs	µg/ml
Drugs	Mtb	MtbΔwhib4B4	whiB4-OE
Amoxicillin	80	>160	40
Ampicillin	500	4000	250
Cloxacillin	400	800	200
Carbenicillin	1024	4096	512
Meropenem	5	20	2.5
Penicillin	200	800	100
Lysozyme	50	200	25
Vancomycin	10	80	2.5
Isoniazid	0.0625	0.0625	0.03125
Rifampicin	0.0625	0.0625	0.0625

elife-25923-v2.xml

10.7554/eLife.25923.009

Table 2.Circumcision levels and commitment for MC, by segment.

Country	Segment	All men in segment*		Uncircumcised men in segment^†
Country	Segment	Circumcised % (n)	Uncircumcised % (n)	Not committed % (n)	Committed % (n)
Zimbabwe	Enthusiasts	42.6 (211)	57.4 (284)	15.5 (44)	84.5 (240)
	Champions	76.2 (269)	23.8 (84)	8.3 (7)	91.7 (77)
	Neophytes	6.1 (17)	93.9 (260)	43.1 (112)	56.9 (148)
	Scared rejecters	2.6 (6)	97.4 (228)	78.1 (178)	21.9 (50)
	Embarrassed rejecters	32.7 (112)	67.3 (230)	56.1 (129)	43.9 (101)
	Highly resistant	0.7 (2)	99.3 (298)	92.6 (276)	7.4 (22)
Zambia	Socially-supported believers	56.1 (160)	43.9 (125)	20.0 (25)	80.0 (100)
	Self-reliant believers	71.2 (272)	28.8 (110)	14.5 (16)	85.5 (94)
	Knowledgeable hesitant	49.8 (119)	50.2 (120)	41.7 (50)	58.3 (70)
	Friends-driven hesitant	14.1 (38)	85.9 (231)	29.0 (67)	71.0 (164)
	Scared rejecters	9.7 (22)	90.3 (204)	62.7 (128)	37.3 (76)
	Indifferent resisters	5.5 (19)	94.5 (325)	79.4 (258)	20.6 (67)
	Traditional believers	70.6 (180)	29.4 (75)	16.0 (12)	84.0 (63)

*No. of circumcised OR uncircumcised men in segment/no. total men in segment; Zambia, N = 2000; Zimbabwe, N = 2001

^†uncircumcised committed OR not-committed men in segment/all uncircumcised men in segment; Zimbabwe, N = 1384; Zambia, N = 1189

elife-26117-v1.xml

10.7554/eLife.26117.072

Appendix 6—table 1.Response latency to dot motion analyses in <italic>Calliphora</italic> R1-R6s (Mean ± SD).

Intracellular recordings were performed at 19°C. The tested moving dot (point-object) velocities were: 334.6, 167.3, 111.53, 83.65, 66.92, 55.77, 47.8, 41.83, 37.18 and 33.46 ^o/sec.

Animal	Flash response time-to-peak (ms)	Peaks corresponding to the receptive field center		Peaks corresponding to the light-point No.22
Animal	Flash response time-to-peak (ms)	Lag-time b (ms)	Adj. R-Sqr	Lag-time b' (ms)	Adj. R-Sqr
Calliphora	14.85 ± 0.78	14.6 ± 0.64	0.99985 ± 0.00012	13.9 ± 3.59	0.99985 ± 0.00017
Calliphora	14.85 ± 0.78	n = 7		n = 5

elife-26117-v1.xml

10.7554/eLife.26117.073

Appendix 6—table 2.Response latency to dot motion analyses in <italic>Drosophila</italic> wild-type and hdcJK910 R1-R6s (Mean ± SD).

Intracellular recordings were performed at 19°C. The tested point-object velocities were: 818.4, 409.2, 272.8, 204.6, 163.68, 136.4, 116.91, 102.3, 90.93 and 81.84 ^o/s. Note, these statistics are collected from individual recordings, not from paired data.

Animal	Flash response time-to-peak (ms)	Front-to-back		Back-to-front
Animal	Flash response time-to-peak (ms)	Lag-time b (ms)	Adj. R-Sqr	Lag-time b (ms)	Adj. R-Sqr
Wild-type Drosophila	23.81 ± 1.41	21.41 ± 4.5	0.99649 ± 0.0065	22.54 ± 4.15	0.99378 ± 0.007
Wild-type Drosophila	23.81 ± 1.41	n = 12		n = 5
hdc^JK910	24.4 ± 1.08	21.82 ± 1.36	0.9992 ± 0.0008	23.79 ± 5.72	0.9978 ± 0.003
hdc^JK910	24.4 ± 1.08	n = 3

elife-26117-v2.xml

10.7554/eLife.26117.072

Appendix 6—table 1.Response latency to dot motion analyses in <italic>Calliphora</italic> R1-R6s (Mean ± SD).

Intracellular recordings were performed at 19°C. The tested moving dot (point-object) velocities were: 334.6, 167.3, 111.53, 83.65, 66.92, 55.77, 47.8, 41.83, 37.18 and 33.46 ^o/sec.

Animal	Flash response time-to-peak (ms)	Peaks corresponding to the receptive field center		Peaks corresponding to the light-point No.22
Animal	Flash response time-to-peak (ms)	Lag-time b (ms)	Adj. R-Sqr	Lag-time b' (ms)	Adj. R-Sqr
Calliphora	14.85 ± 0.78	14.6 ± 0.64	0.99985 ± 0.00012	13.9 ± 3.59	0.99985 ± 0.00017
Calliphora	14.85 ± 0.78	n = 7		n = 5

elife-26117-v2.xml

10.7554/eLife.26117.073

Appendix 6—table 2.Response latency to dot motion analyses in <italic>Drosophila</italic> wild-type and hdcJK910 R1-R6s (Mean ± SD).

Animal	Flash response time-to-peak (ms)	Front-to-back		Back-to-front
Animal	Flash response time-to-peak (ms)	Lag-time b (ms)	Adj. R-Sqr	Lag-time b (ms)	Adj. R-Sqr
Wild-type Drosophila	23.81 ± 1.41	21.41 ± 4.5	0.99649 ± 0.0065	22.54 ± 4.15	0.99378 ± 0.007
Wild-type Drosophila	23.81 ± 1.41	n = 12		n = 5
hdc^JK910	24.4 ± 1.08	21.82 ± 1.36	0.9992 ± 0.0008	23.79 ± 5.72	0.9978 ± 0.003
hdc^JK910	24.4 ± 1.08	n = 3

elife-26487-v2.xml

10.7554/eLife.26487.020

Table 1.Dimeric and trimeric dUTPases induce PICIs from other species encoding SaPIbov1-like Stl repressorsa.

10.7554/eLife.26487.021Table 1—source data 1.β-lactamase assay data and statistical analysis for the SaPIbov1 Stl homologues.

	Phage Duts
	Dimeric		Trimeric
	ϕNM1 S. aureus	ϕO11 S. aureus	ϕIPLA6 S. epidermidis	ϕ11 S. aureus
PICIs
SaPIbov1	++	++	++	+++
ShoCI794_SEPI	++	++	++	+++
ShaCI51-48	+	+	+	+

^aResults are from 5 independent β-lactamase/Nitrocefin assay experiments, using the dual plasmid system described in the text. Levels of induction were based on the calculated units/ml with the following ranges: (-): no induction, <1 Units/ml; (+): low induction, 1–5 Units/ml; (++): moderate induction, 5–10 Units/ml; (+++): high induction, >10 Units/ml. A 2-way ANOVA with Sidak's multiple comparisons test was performed to compare mean differences within rows. The differences observed among the +,++or +++ samples, compared with the controls or the - samples, were in all cases statistically significant (p<0.05).

elife-26487-v2.xml

10.7554/eLife.26487.022

Table 2.Unrelated SSAPs differentially induce PICIs from other species encoding SaPI2-like Stl repressorsa.

10.7554/eLife.26487.023Table 2—source data 1.β-lactamase assay data and statistical analysis for the SaPI2 Stl homologues.

			SSAPs
	Sak (80α) S. aureus	Chimera (80α) S. aureus	Sak (PH15) S. epidermidis	Sak4 (52A) S. aureus	Erf (SLT) S. aureus	Redβ (N315) S. aureus
PICIs
SaPI2	++	-	++	+++	++	+
SeCINIHLM095	++	-	++	-	++	-
ShaCI137133	++	-	++	-	-	-
ScCIUMC-CNS990	-	-	-	+++	-	-

^aResults are from 3 independent β-lactamase/Nitrocefin assay experiments, using the dual plasmid system described in the text. Levels of induction were based on the calculated units/ml with the following ranges: (-): no induction, <1 Units/ml; (+): low induction, 1–5 Units/ml; (++): moderate induction, 5–10 Units/ml; (+++): high induction,>10 Units/ml. A 2-way ANOVA with Sidak's multiple comparisons test was performed to compare mean differences within rows. The differences observed among the +,++or +++ samples, compared with the controls or the - samples, were in all cases statistically significant (p<0.05).

elife-26526-v2.xml

10.7554/eLife.26526.010

Table 1.Populations and lifetimes of hydrogen-bonded turns.

Turn	Population (%)		Lifetime (ns)
Turn	SC	MC	SC	MC
VPGV^*	18 ± 1	16 ± 2	0.18 ± 0.02	0.19 ± 0.01
VPGVG	5.9 ± 0.9	4.6 ± 0.7	0.9 ± 0.3	0.8 ± 0.1
PGV	1.5 ± 0.1	2.0 ± 0.2	0.008 ± 0.002	0.009 ± 0.001
PGVG	2.3 ± 0.2	2.9 ± 0.3	0.30 ± 0.05	0.39 ± 0.03
GVGV	20 ± 3	17 ± 2	0.15 ± 0.02	0.24 ± 0.07

^*A hydrogen-bonded turn refers to a hydrogen bond between the first and last residue in the sequences shown. For example, the VPGV turn has a hydrogen bond between valine 1 and valine 4.

elife-26653-v2.xml

10.7554/eLife.26653.009

Table 1.Regions of interest used in this study and their BOLD activity during the gambling task.

Brain regions	X	Y	Z	Brain Activity (T-score)
Brain regions	X	Y	Z	Reward	Punishment	RPE
SN subdivisions
vSN	±9	−13	−12	11.12 **	8.63 **	1.85
medial SNc	±8	−16	−12	17.45 **	12.48 **	3.96 **
lateral SNc	±12	−17	-9	9.72 **	8.87 **	0.93
Ventral Striatum	±12	15	-6	8.91 **	- 9.33 **	16.25 **
vmPFC	±6	45	-9	- 26.72 **	- 32.37 **	8.75 **
Anterior insula	±32	22	-6	35.54 **	36.62 **	1.07
dACC	±4	40	24	8.43 **	7.64 **	1.37

Notes: **p-value<0.01; *p-value<0.05 with FDR correction

SN: substantia nigra; vSN: ventral subregion of SN; SNc: SN pars compacta; vmPFC: ventral medial prefrontal cortex; dACC: dorsal anterior cingulate cortex; RPE: reward prediction error

elife-26973-v2.xml

10.7554/eLife.26973.009

Table 1.Response strength during episodes of singing.

Standardized response strength (mean ± s.e.m.) for core and shell neurons in LMAN that showed significant excitation or suppression during song production compared with quiet baseline periods (see Materials and methods).

	CORE		SHELL
	Fraction	Response strength	Fraction	Response strength
Excited	0.72 (66/92)	7.06 ± 0.71	0.65 (66/102)	7.28 ± 0.44
Suppressed	0.28 (26/92)	−7.32 ± 1.15	0.35 (36/102)	−5.82 ± 0.45

elife-27038-v2.xml

10.7554/eLife.27038.020

Table 1.Model Parameters.

	Parameter	Unit	Description	Acceptable range		Default
	Parameter	Unit	Description	Max.	Min.	Default
BOR	ϵB	-	Time constant for transporter regulation	-	-	1
	αB	μm s^-2	Production rate of transporter activity	4.9×102	3.7×10-9	2.0×10-1
	ξB	s^-1	Basal degradation rate		1.6×10-6	7.6×10-2
	kB	μM	Boron concentration for half-maximum in Hill’s function	1000	1	600
	dB	-	Amplitude of increased degradation rate by boron	100	0	50
	nB	-	Hill’s coefficient	-	-	2
	cB	μM	Boron concentration at which the flux reaches its half-maximum value	∞	500	1000
NIP	ϵN	-	Time constant for transporter regulation	-	-	1
	αN	μm s^-2	Production rate of transporter activity	4.9×102	3.7×10-9	2.0×10-1
	ξN	s^-1	Basal degradation rate		1.6×10-6	7.6×10-2
	kN	μM	Boron concentration for half-maximum in Hill’s function	1000	1	20
	nN	-	Hill’s coefficient	-	-	2
Cell size	l⁢c	μm	Cell width	20	5	10
	l⁢w	μm	Cell wall width	2	0.2	0.5
	h⁢c	μm	Cell height	150	5	20
Other	p	μm s^-1	Membrane background permeability of boron	8×10-2	2.3×10-3	3×10-2
	a	μm s^-1	Xylem loading rate (in the last cell)	500	0	0.5
	c0	μm	Boron concentration in medium	5000	0	300

elife-27167-v2.xml

10.7554/eLife.27167.013

Table 2.Average fitness increments of populations in home and away environments, in percent.

Numbers in parentheses denote 95% confidence intervals.

	Kre33 -RM		Kre33 -BY
	Evolved at OT	Evolved at HT	Evolved at OT	Evolved at HT
Fitnessat OT, %	8.33(8.27, 8.38)	8.86(8.81, 8.92)	5.01(4.94, 5.07)	4.834.76, 4.90
Fitnessat HT, %	9.57(9.42, 9.77)	20.33(20.18, 20.53)	6.25(6.12, 6.38)	11.51(11.38, 11.64)

elife-27441-v1.xml

10.7554/eLife.27441.011

Table 1.Fractions and molecular properties of diffusional particles of Syt1C2AB generated various conditions as measured by fluorescence correlation spectroscopy.

Averages and standard errors from three independent trials are shown.

Proteins	Total protein conc. (nM)	Mg²⁺ + polyphosphate	Readout channel	Component 1			Component 2
Proteins	Total protein conc. (nM)	Mg²⁺ + polyphosphate	Readout channel	Fraction (%)	Diffusion time (µs)	Diffusion coefficient (μm²/s)	Fraction (%)	Diffusion time (µs)	Diffusion coefficient (μm²/s)
Syt1-Alexa488	~30	No	Alexa488	100	620 ± 35	70 ± 4	n/a	n/a	n/a
Syt1-Alexa647	~30	No	Alexa647	100	616 ± 22	70 ± 3	n/a	n/a	n/a
Syt1-Alexa488 + Syt1-Alexa647 + unlabeled Syt1	~5000	No	Alexa488	100	583 ± 20	74 ± 8	n/a	n/a	n/a
Syt1-Alexa488 + Syt1-Alexa647 + unlabeled Syt1	~5000	No	Alexa647	100	577 ± 20	75 ± 8	n/a	n/a	n/a
Syt1-Alexa488 + Syt1-Alexa647 + unlabeled Syt1	~5000	Yes	Alexa488	77 ± 2	527 ± 20	82 ± 4	23 ± 2	4168 ± 194	10 ± 1
Syt1-Alexa488 + Syt1-Alexa647 + unlabeled Syt1	~5000	Yes	Alexa647	76 ± 2	567 ± 26	77 ± 4	24 ± 2	3862 ± 196	11 ± 1

elife-27451-v2.xml

10.7554/eLife.27451.009

Table 2.Copy number data.

Mean average and SD of copy number in pool and foci in each compartment.

	Mig1-GFP				Msn2-GFP
	Glucose (+)		Glucose (−)		Glucose (+)		Glucose (−)
	Mean	SD	Mean	SD	Mean	SD	Mean	SD
Cytoplasmic Pool	509	274	949	394	1422	977	2487	1360
Nuclear Pool	77	101	140	97	551	608	1692	1221
Total Pool	586	336	1088	392	1973	1585	4179	2581
Cytoplasmic Spots	57	79	311	212	333	196	776	635
Nuclear Spots	190	99	35	63	81	138	320	269
Total Spots	246	100	345	203	414	334	1096	904
Total Cytoplasm	580	276	1156	399	1755	1173	3263	1995
Total Nuclear	226	155	176	124	632	746	2012	1490
Total Cell	806	353	1331	352	2387	1919	5274	3485

elife-27451-v2.xml

10.7554/eLife.27451.010

Table 3.Foci tracking data.

Mean average, SD and mean number detected per cell (N) of stoichiometry values (molecules), and microscopic diffusion coefficients D in each compartment detected within the depth of field.

	Mig1-GFP						Msn2-GFP
	Glucose (+)			Glucose (−)			Glucose (+)			Glucose (−)
	Mean	SD	N	Mean	SD	N	Mean	SD	N	Mean	SD	N
Stoichiometry of Nuclear Spots	19.0	16.2	7.2	8.5	4.8	5.8	34.5	26.6	3.5	46.5	31.6	4.7
Diffusion Constant of Nuclear Spots (µm²/s)	0.8	0.8	7.2	1.3	1.5	5.8	0.7	0.9	3.5	0.9	0.9	4.7
Stoichiometry of Trans-Nuclear Spots	10.6	10.2	1.0	8.7	5.3	5.1	21.8	16.7	1.9	43.9	35.0	0.9
Diffusion Constant of Trans-Nuclear Spots (µm²/s)	1.3	1.2	1.0	1.5	1.6	5.1	1.5	1.2	1.9	1.1	1.1	0.9
Stoichiometry of Cytoplasmic Spots	6.6	4.9	1.1	7.2	3.7	17.8	25.7	19.5	4.8	30.1	17.5	4.0
Diffusion Constant of Cytoplasmic Spots (µm²/s)	1.4	1.4	1.1	1.2	1.2	17.8	1.2	1.1	4.8	1.0	1.4	4.0

elife-27451-v2.xml

10.7554/eLife.27451.015

Table 4.<italic>snf1Δ</italic> foci tracking and copy number data.

Upper panel: Mean average, SD and mean number detected per cell (N) of stoichiometry values (molecules), and microscopic diffusion coefficients D in each compartment detected within the depth of field. Lower panel: Mean average and SD of copy number in pool and foci in each compartment.

	Mig1-GFP snf1Δ
	Glucose (+)			Glucose (−)
	Mean	SD	N	Mean	SD	N
Stoichiometry of Nuclear Spots	17.5	10.9	13.2	23.5	15.4	10.9
Diffusion Constant of Nuclear Spots (µm²/s)	1.1	1.1	13.2	0.7	0.8	10.9
Stoichiometry of Trans-Nuclear Spots	8.9	6.0	1.2	12.7	6.1	0.5
Diffusion Constant of Trans-Nuclear Spots (µm²/s)	1.9	2.0	1.2	1.1	1.4	0.5
Stoichiometry of Cytoplasmic Spots	6.2	2.2	5.0	8.3	4.1	9.1
Diffusion Constant of Cytoplasmic Spots (µm²/s)	1.3	1.2	5.0	1.0	1.2	9.1
Copy Numbers
Cytoplasmic Pool	947	728	30	608	450	30
Nuclear Pool	807	398	30	611	325	30
Total Pool	1754	1127	30	1219	775	30
Cytoplasmic Spots	118	169	30	334	374	30
Nuclear Spots	162	69	30	164	71	30
Total Spots	280	238	30	498	445	30
Total Cytoplasm	1065	897	30	941	824	30
Total Nuclear	969	467	30	775	396	30
Total Cell	2034	1364	30	1717	1220	30

elife-27451-v3.xml

10.7554/eLife.27451.009

Table 2.Copy number data.

Mean average and SD of copy number in pool and foci in each compartment.

	Mig1-GFP				Msn2-GFP
	Glucose (+)		Glucose (−)		Glucose (+)		Glucose (−)
	Mean	SD	Mean	SD	Mean	SD	Mean	SD
Cytoplasmic Pool	509	274	949	394	1422	977	2487	1360
Nuclear Pool	77	101	140	97	551	608	1692	1221
Total Pool	586	336	1088	392	1973	1585	4179	2581
Cytoplasmic Spots	57	79	311	212	333	196	776	635
Nuclear Spots	190	99	35	63	81	138	320	269
Total Spots	246	100	345	203	414	334	1096	904
Total Cytoplasm	580	276	1156	399	1755	1173	3263	1995
Total Nuclear	226	155	176	124	632	746	2012	1490
Total Cell	806	353	1331	352	2387	1919	5274	3485

elife-27451-v3.xml

10.7554/eLife.27451.010

Table 3.Foci tracking data.

Mean average, SD and mean number detected per cell (N) of stoichiometry values (molecules), and microscopic diffusion coefficients D in each compartment detected within the depth of field.

	Mig1-GFP						Msn2-GFP
	Glucose (+)			Glucose (−)			Glucose (+)			Glucose (−)
	Mean	SD	N	Mean	SD	N	Mean	SD	N	Mean	SD	N
Stoichiometry of Nuclear Spots	19.0	16.2	7.2	8.5	4.8	5.8	34.5	26.6	3.5	46.5	31.6	4.7
Diffusion Constant of Nuclear Spots (µm²/s)	0.8	0.8	7.2	1.3	1.5	5.8	0.7	0.9	3.5	0.9	0.9	4.7
Stoichiometry of Trans-Nuclear Spots	10.6	10.2	1.0	8.7	5.3	5.1	21.8	16.7	1.9	43.9	35.0	0.9
Diffusion Constant of Trans-Nuclear Spots (µm²/s)	1.3	1.2	1.0	1.5	1.6	5.1	1.5	1.2	1.9	1.1	1.1	0.9
Stoichiometry of Cytoplasmic Spots	6.6	4.9	1.1	7.2	3.7	17.8	25.7	19.5	4.8	30.1	17.5	4.0
Diffusion Constant of Cytoplasmic Spots (µm²/s)	1.4	1.4	1.1	1.2	1.2	17.8	1.2	1.1	4.8	1.0	1.4	4.0

elife-27451-v3.xml

10.7554/eLife.27451.015

Table 4.<italic>snf1Δ</italic> foci tracking and copy number data.

	Mig1-GFP snf1Δ
	Glucose (+)			Glucose (−)
	Mean	SD	N	Mean	SD	N
Stoichiometry of Nuclear Spots	17.5	10.9	13.2	23.5	15.4	10.9
Diffusion Constant of Nuclear Spots (µm²/s)	1.1	1.1	13.2	0.7	0.8	10.9
Stoichiometry of Trans-Nuclear Spots	8.9	6.0	1.2	12.7	6.1	0.5
Diffusion Constant of Trans-Nuclear Spots (µm²/s)	1.9	2.0	1.2	1.1	1.4	0.5
Stoichiometry of Cytoplasmic Spots	6.2	2.2	5.0	8.3	4.1	9.1
Diffusion Constant of Cytoplasmic Spots (µm²/s)	1.3	1.2	5.0	1.0	1.2	9.1
Copy Numbers
Cytoplasmic Pool	947	728	30	608	450	30
Nuclear Pool	807	398	30	611	325	30
Total Pool	1754	1127	30	1219	775	30
Cytoplasmic Spots	118	169	30	334	374	30
Nuclear Spots	162	69	30	164	71	30
Total Spots	280	238	30	498	445	30
Total Cytoplasm	1065	897	30	941	824	30
Total Nuclear	969	467	30	775	396	30
Total Cell	2034	1364	30	1717	1220	30

elife-27451-v4.xml

10.7554/eLife.27451.009

Table 2.Copy number data.

Mean average and SD of copy number in pool and foci in each compartment.

	Mig1-GFP				Msn2-GFP
	Glucose (+)		Glucose (−)		Glucose (+)		Glucose (−)
	Mean	SD	Mean	SD	Mean	SD	Mean	SD
Cytoplasmic Pool	509	274	949	394	1422	977	2487	1360
Nuclear Pool	77	101	140	97	551	608	1692	1221
Total Pool	586	336	1088	392	1973	1585	4179	2581
Cytoplasmic Spots	57	79	311	212	333	196	776	635
Nuclear Spots	190	99	35	63	81	138	320	269
Total Spots	246	100	345	203	414	334	1096	904
Total Cytoplasm	580	276	1156	399	1755	1173	3263	1995
Total Nuclear	226	155	176	124	632	746	2012	1490
Total Cell	806	353	1331	352	2387	1919	5274	3485

elife-27451-v4.xml

10.7554/eLife.27451.010

Table 3.Foci tracking data.

Mean average, SD and mean number detected per cell (N) of stoichiometry values (molecules), and microscopic diffusion coefficients D in each compartment detected within the depth of field.

	Mig1-GFP						Msn2-GFP
	Glucose (+)			Glucose (−)			Glucose (+)			Glucose (−)
	Mean	SD	N	Mean	SD	N	Mean	SD	N	Mean	SD	N
Stoichiometry of Nuclear Spots	19.0	16.2	7.2	8.5	4.8	5.8	34.5	26.6	3.5	46.5	31.6	4.7
Diffusion Constant of Nuclear Spots (µm²/s)	0.8	0.8	7.2	1.3	1.5	5.8	0.7	0.9	3.5	0.9	0.9	4.7
Stoichiometry of Trans-Nuclear Spots	10.6	10.2	1.0	8.7	5.3	5.1	21.8	16.7	1.9	43.9	35.0	0.9
Diffusion Constant of Trans-Nuclear Spots (µm²/s)	1.3	1.2	1.0	1.5	1.6	5.1	1.5	1.2	1.9	1.1	1.1	0.9
Stoichiometry of Cytoplasmic Spots	6.6	4.9	1.1	7.2	3.7	17.8	25.7	19.5	4.8	30.1	17.5	4.0
Diffusion Constant of Cytoplasmic Spots (µm²/s)	1.4	1.4	1.1	1.2	1.2	17.8	1.2	1.1	4.8	1.0	1.4	4.0

elife-27451-v4.xml

10.7554/eLife.27451.015

Table 4.<italic>snf1Δ</italic> foci tracking and copy number data.

	Mig1-GFP snf1Δ
	Glucose (+)			Glucose (−)
	Mean	SD	N	Mean	SD	N
Stoichiometry of Nuclear Spots	17.5	10.9	13.2	23.5	15.4	10.9
Diffusion Constant of Nuclear Spots (µm²/s)	1.1	1.1	13.2	0.7	0.8	10.9
Stoichiometry of Trans-Nuclear Spots	8.9	6.0	1.2	12.7	6.1	0.5
Diffusion Constant of Trans-Nuclear Spots (µm²/s)	1.9	2.0	1.2	1.1	1.4	0.5
Stoichiometry of Cytoplasmic Spots	6.2	2.2	5.0	8.3	4.1	9.1
Diffusion Constant of Cytoplasmic Spots (µm²/s)	1.3	1.2	5.0	1.0	1.2	9.1
Copy Numbers
Cytoplasmic Pool	947	728	30	608	450	30
Nuclear Pool	807	398	30	611	325	30
Total Pool	1754	1127	30	1219	775	30
Cytoplasmic Spots	118	169	30	334	374	30
Nuclear Spots	162	69	30	164	71	30
Total Spots	280	238	30	498	445	30
Total Cytoplasm	1065	897	30	941	824	30
Total Nuclear	969	467	30	775	396	30
Total Cell	2034	1364	30	1717	1220	30

elife-27469-v1.xml

10.7554/eLife.27469.017

Table 6.Phenotypic alterations as a function of time spent in quiescence

Time	# of colonies w/phenotype	18°C	37°C	KCl 1M	Ca(NO₃)2 0.15M	CaCl₂0.3M	TBZ 15 μg/ml	HU 4 mM	SDS 0.01%
in G0	# of colonies w/phenotype	18°C	37°C	KCl 1M	Ca(NO₃)2 0.15M	CaCl₂0.3M	TBZ 15 μg/ml	HU 4 mM	SDS 0.01%
1 day	0/384	-	-	-	-	-	-	-	-
1 month	0/384	-	-	-	-	-	-	-	-
2 months	4/376	-	-	1	1	4	-	-	-
3 months	6/334	1	1	1	1	3	3	2	1

(-) indicates the absence of a selected phenotype (all the cells form colonies) The numbers in the columns indicate the number of colonies exhibiting a sensitivity to a given treatment (some mutants display a sensitivity to multiple treatments).

Serial dilutions were spotted on rich medium plates containing (or not) the drugs at the indicated concentrations. (TBZ): Thiabendazole; (HU): Hydroxyurea; (SDS): Sodium Dodecyl Sulfate

elife-27702-v2.xml

10.7554/eLife.27702.021

Table 2.Proportion of units that have stable neural dynamics and motor representations in the striatum and motor cortex.

Activity metric	Dorsolateral striatum		Motor cortex
Activity metric	% stable	n	% stable	n
Firing rate	90.3	186	88.1	42
ISI histogram	97.9	187	97.6	42
State tuning	93.9	163	92.7	41
STA	93.6	202	95.0	80
PETH	89.4	113	89.5	57

elife-27711-v1.xml

10.7554/eLife.27711.012

Table 2.

Cβ-Cβ and N-Cβ interresidue distance restraints, measured in the molecular models of the CRF- and ^dFXCRF(12-41)-CRF1R complexes.

DOI: http://dx.doi.org/10.7554/eLife.27711.012

CRF1R bound to agonist CRF
No	CRF-CRF1R residue pair	Region of CRF	Region of CRF1R	Cβ-Cβ distance [Å]
No	CRF-CRF1R residue pair	Region of CRF	Region of CRF1R	Constraint	Measured
1	H13-F330	N-term	Helix VI	10.0	5.1
2	H13-F344	N-term	Helix VII	10.0	9.4
3	L15-Q173	N-term	Helix II	10.0	7.1
4	E17-I345	N-term	Helix VII	10.0	9.2
5	V18-V120	C-term	Helix I	10.0	6.4
6	A31-E104	C-term	Hinge	10.0	8.6
7	S33-Y73	C-term	ECD	10.0	6.7
CRF1R bound to Antagonist ^dFXCRF(12-41)
No	CRF1R-^dFXCRF(12-41) residue pair	Region of ^dFXCRF(12-41)	Region of CRF1R	Cβ-Cβ or N-Cβ* distance [Å]
No	CRF1R-^dFXCRF(12-41) residue pair	Region of ^dFXCRF(12-41)	Region of CRF1R	Constraint	Measured
1	F12-L329	N-term	Helix VI	5.0*	4.4*
2	F12-F330	N-term	Helix VI	5.0*	4.6*
3	F12-N348	N-term	Helix VII	5.0*	4.8*
4	H13-L329	N-term	Helix VI	10.0	6.7
5	H13-F330	N-term	Helix VI	10.0	5.5
6	H13-F344	N-term	Helix	10.0	5.0
7	L14-N123	N-term	Helix I	10.0	9.1
8	L15-R341	N-term	Helix VII	10.0	5.9
9	L15-I345	N-term	Helix VII	10.0	6.8
10	E17-N123	N-term	Helix I	10.0	7.4
11	E17-Q173	N-term	Helix II	10.0	6.3
12	E17-I345	N-term	Helix VII	10.0	6.1
13	V18-V120	C-term	Helix I	10.0	4.7
14	A31-E104	C-term	Hinge	10.0	4.3
15	S33-Y73	C-term	ECD	10.0	6.7

^*Pair-wise crosslinking between N-terminal ClAc in the peptide and Cys thiol in CRF1R.

elife-27793-v2.xml

10.7554/eLife.27793.005

Table 1.Kinetic and affinity data of monomeric Kinesin-1,–3, and −5 compared to MKLP2-MD.

A summary of steady state ATPase activities and MT affinities of monomeric Kin1 (Atherton et al., 2014; Woehlke et al., 1997; Hackney, 1988; Gilbert et al., 1995; Ma and Taylor, 1995; Rosenfeld et al., 1996; Nitta et al., 2004; Gigant et al., 2013), whose structures were used to compared with MKLP2, as well as Kin3 (Nitta et al., 2004). Kin5’s MT-stimulated ATPase activity has similar values as MKLP2 (Cochran et al., 2004; Cochran et al., 2006).

Monomeric motor	MT-stimulated ATPase		MT affinity; K_d (μM)
Monomeric motor	K_{0.5, MT} (μM)	k_cat (S⁻¹)	ADP	NN	ADP.AlFx	AMPPNP
MKLP2-MD	1.07 ± 0.18	4.38 ± 0.20	0.363 ± 0.057	0.043 ± 0.002	0.355 ± 0.073	0.043 ± 0.035
Kin1 (Kif5a/b)	12.7 ± 4.0 (Atherton et al., 2014) 26.0 ± 5.8 (Rosenfeld et al., 1996)	34.2 ± 5.7 (Atherton et al., 2014) 43.6 ± 7.8 (Rosenfeld et al., 1996) 50.3 ± 1.6 (26)	20.8 ± 2.4 (Rosenfeld et al., 1996) 2.0 ± 0.3 (Gigant et al., 2013)	n.a.	1.4 ± 0.2 (Rosenfeld et al., 1996) 0.3 ± 0.006 (Gigant et al., 2013)	1.1 ± 0.1 (Rosenfeld et al., 1996) 0.045 ± 0.012 (Gigant et al., 2013)
Kin3 (Kif1a)	0.0537 ± 0.0057 (Atherton et al., 2014)	43.4 ± 1.0 (Atherton et al., 2014)	0.0068 ± 0.0025 (Nitta et al., 2004)	n.a.	0.0059 ± 0.0015 (Nitta et al., 2004)	0.0042 ± 0.0013 (Nitta et al., 2004)
Kin5 (Eg5)	4.5 (Cochran et al., 2004) 0.29 ± 0.02 (Cochran et al., 2006)	2.9 (Cochran et al., 2004) 5.5 ± 0.1 (Cochran et al., 2006)	n.a.	n.a.	n.a.	n.a.

n.a.: not available.

elife-27793-v2.xml

10.7554/eLife.27793.011

Table 2.MKLP2 Homology modelling and validation.

Columns 2–3 show the list of PDB IDs that were used as templates for specific structural regions of each MKLP2 nucleotide state (4LNU (Cao et al., 2014), 4HNA (Gigant et al., 2013), 4OZQ (Arora et al., 2014), 1VFV (Nitta et al., 2004), 3GBJ and 4Y05 are structures from the Structural Genomics Consortium). Columns 4–5 show the overall QMEAN scores calculated before, and after refinement and show that model quality is maintained following refinement. Columns 6–7 show the global cross-correlation scores before and after refinement.

Nucleotide state	Templates used for homology modelling		QMEAN scores		Global Cross-correlation scores
Nucleotide state	MKLP2 Structure	Template	Homology Model	Refined Model	Homology Model	Refined Model
ADP	Main template	3GBJ	0.636	0.623	0.908	0.931
	Helix α4, helix α5, loop 8	4LNU
	Helix α4/loop 12	4OZQ
	Loop 2	4Y05
NN	Main template	4LNU	0.669	0.663	0.913	0.930
	Helix α4/loop 12	4OZQ
	Loop 2	4Y05
	Loop 5	3GBJ
ADP.AlFx	Main template	4HNA	0.671	0.689	0.860	0.890
	Helix α4/loop 12	4OZQ
	Loop 2	4Y05
	Loop 5	3GBJ
AMPPNP	Main template	1VFV	0.658	0.679	0.925	0.943
	Helix α4, helix α5, loop 8	4LNU
	Helix α4/loop 12	4OZQ
	Loop 2	4Y05

elife-27793-v3.xml

10.7554/eLife.27793.005

Table 1.Kinetic and affinity data of monomeric Kinesin-1,–3, and −5 compared to MKLP2-MD.

Monomeric motor	MT-stimulated ATPase		MT affinity; K_d (μM)
Monomeric motor	K_{0.5, MT} (μM)	k_cat (S⁻¹)	ADP	NN	ADP.AlFx	AMPPNP
MKLP2-MD	1.07 ± 0.18	4.38 ± 0.20	0.363 ± 0.057	0.043 ± 0.002	0.355 ± 0.073	0.043 ± 0.035
Kin1 (Kif5a/b)	12.7 ± 4.0 (Atherton et al., 2014) 26.0 ± 5.8 (Rosenfeld et al., 1996)	34.2 ± 5.7 (Atherton et al., 2014) 43.6 ± 7.8 (Rosenfeld et al., 1996) 50.3 ± 1.6 (26)	20.8 ± 2.4 (Rosenfeld et al., 1996) 2.0 ± 0.3 (Gigant et al., 2013)	n.a.	1.4 ± 0.2 (Rosenfeld et al., 1996) 0.3 ± 0.006 (Gigant et al., 2013)	1.1 ± 0.1 (Rosenfeld et al., 1996) 0.045 ± 0.012 (Gigant et al., 2013)
Kin3 (Kif1a)	0.0537 ± 0.0057 (Atherton et al., 2014)	43.4 ± 1.0 (Atherton et al., 2014)	0.0068 ± 0.0025 (Nitta et al., 2004)	n.a.	0.0059 ± 0.0015 (Nitta et al., 2004)	0.0042 ± 0.0013 (Nitta et al., 2004)
Kin5 (Eg5)	4.5 (Cochran et al., 2004) 0.29 ± 0.02 (Cochran et al., 2006)	2.9 (Cochran et al., 2004) 5.5 ± 0.1 (Cochran et al., 2006)	n.a.	n.a.	n.a.	n.a.

n.a.: not available.

elife-27793-v3.xml

10.7554/eLife.27793.011

Table 2.MKLP2 Homology modelling and validation.

Nucleotide state	Templates used for homology modelling		QMEAN scores		Global Cross-correlation scores
Nucleotide state	MKLP2 Structure	Template	Homology Model	Refined Model	Homology Model	Refined Model
ADP	Main template	3GBJ	0.636	0.623	0.908	0.931
	Helix α4, helix α5, loop 8	4LNU
	Helix α4/loop 12	4OZQ
	Loop 2	4Y05
NN	Main template	4LNU	0.669	0.663	0.913	0.930
	Helix α4/loop 12	4OZQ
	Loop 2	4Y05
	Loop 5	3GBJ
ADP.AlFx	Main template	4HNA	0.671	0.689	0.860	0.890
	Helix α4/loop 12	4OZQ
	Loop 2	4Y05
	Loop 5	3GBJ
AMPPNP	Main template	1VFV	0.658	0.679	0.925	0.943
	Helix α4, helix α5, loop 8	4LNU
	Helix α4/loop 12	4OZQ
	Loop 2	4Y05

elife-27860-v2.xml

10.7554/eLife.27860.009

Table 1.AltORF and alternative protein annotations in different organisms.

Genomes	Features
	Transcripts		Current annotations		Annotations of alternative protein coding sequences
	mRNAs	Others1*	CDSs	Proteins	AltORFs	Alternative proteins
H. sapiens GRCh38 RefSeq GCF_000001405.26	67,765	11,755	68,264	54,498	539,134	183,191
P. troglodytes 2.1.4 RefSeq GCF_000001515.6	55,034	7527	55,243	41,774	416,515	161,663
M. musculus GRCm38p2, RefSeq GCF_000001635.22	73,450	18,886	73,55 1	53,573	642,203	215,472
B. Taurus UMD3.1.86	22,089	838	22,089	21,915	79,906	73,603
X. tropicalis Ensembl JGI_4.2	28,462	4644	28,462	22,614	141,894	69,917
D. rerio Ensembl ZV10.84	44,198	8196	44,198	41,460	214,628	150,510
D. melanogaster RefSeq GCA_000705575.1	30,255	3474	30,715	20,995	174,771	71,705
C. elegans WBcel235, RefSeq GCF_000002985.6	28,653	25,256	26,458	25,750	131,830	45,603
S. cerevisiae YJM993_v1, RefSeq GCA_000662435.1	5471	1463	5463	5423	12,401	9492

^*Other transcripts include miRNAs, rRNAs, ncRNAs, snRNAs, snoRNAs, tRNAs.

^†Annotated retained-intron and processed transcripts were classified as mRNAs.

elife-28020-v1.xml

10.7554/eLife.28020.004

Table 2.Antiviral activity of GRL-121 and −142 against cHIVNL4-3WT and two HIV-2 strains and their cytotoxicities in vitro.

Drug	Mean IC₅₀(nM) ± SD			CC₅₀ (μM)	Selectivity index*
Drug	cHIV_NL4-3^WT	HIV-2_ROD	HIV-2_EHO	CC₅₀ (μM)	Selectivity index*
SQV	12 ± 3	9.0 ± 5.0	8.8 ± 2.1	33	2750
IDV	18 ± 5	31 ± 3	55 ± 25	75	4167
NFV	23 ± 5	27 ± 0.4	84 ± 20	32	1391
RTV	34 ± 10	136 ± 165	278 ± 88	35	1.029
TPV	330 ± 13	293 ± 45	313 ± 48	34	103
APV	26 ± 8	170 ± 82	305 ± 78	>150	>4167
LPV	13 ± 8	40 ± 28	11 ± 2	33	2538
ATV	4.0 ± 2.3	28 ± 6	10 ± 8	80	20,000
DRV	3.2 ± 0.7	8.5 ± 0.7	6.2 ± 0.7	133	41,562
GRL-121	0.26 ± 0.05	0.020 ± 0.014	0.071 ± 0.071	34	130,769
GRL-142	0.019 ± 0.017	0.00032 ± 0.00015	0.000059 ± 0.000025	47	2,473,684

*Each selectivity index denotes a ratio of CC₅₀ to IC₅₀ against cHIV_NL4-3^WT.

The data shown represent mean values (±1 standard deviation) derived from the results of three independent experiments.

elife-28020-v1.xml

10.7554/eLife.28020.009

Table 5.van der Waals interaction energies between GRL-142 or DRV with the protease dimer and selected active site residues.

	GRL-142	DRV
	(kcal/mol)	(kcal/mol)
Protease dimer	−67.5	−57.8
Asp29 & Asp29’	−7.4	−4.2
Asp30 & Asp30’	−5.4	−2.9
Val82 & Val82’	−2.2	−2.3
Ile84 & Ile84’	−4.3	−4.6
Ile47 & Ile47’	−6.5	−3.6
Gly48 & Gly48’	−3.3	−2.8
Gly49 & Gly49’	−3.7	−3.3
Ile50 & Ile50’	−8.7	−9.2
Pro81 & Pro81’	−1.6	−1.9
Arg8 & Arg8’	−2.2	−2

Average van der Waals energies were calculated by analyzing the trajectories from a 1.2 ns molecular dynamics simulation using Desmond molecular dynamics system (D.E. Shaw Research, New York, NY 2017).

elife-28257-v2.xml

10.7554/eLife.28257.016

Table 2.

Specific pairwise overlap between activator C-terminal BioID datasets. Twelve activator BioID datasets were contrasted (6 N-terminal and 6 C-terminal) to determine for each activator which of its C-terminal hits were specifically shared with other datasets. Those shared with N-terminal datasets were removed. The specific pairwise overlap of the remaining hits with each activator is reported (n and %). Input n = BICD1 (92), BICD2 (87), HOOK1 (39), HOOK3 (37), NIN (74), NINL (53). Only pairwise overlap is represented in this analysis; overlap with multiple activators (e.g. BICD1 overlap with both BICD2 and HOOK1) is not shown.

DOI: http://dx.doi.org/10.7554/eLife.28257.016

	BICD1		BICD2		HOOK1		HOOK3		NIN		NINL
	N	%	N	%	N	%	N	%	N	%	N	%
BICD1			44	50.6	4	10.3	0	0	5	6.8	5	9.4
BICD2	44	47.8			4	10.3	7	18.9	6	8.1	0	0
HOOK1	4	4.3	4	4.6			14	37.8	3	4.1	1	1.9
HOOK3	0	0	7	8.0	14	35.9			2	2.7	1	1.9
NIN	5	5.4	6	6.9	3	7.7	2	5.4			27	50.9
NINL	5	5.4	0	0	1	2.6	1	2.7	27	36.5

elife-28275-v2.xml

10.7554/eLife.28275.008

Table 2.Number of overlapping Bcd ChIP peaks and Vienna Tile-GAL4 enhancer reporters.

Note that some Bcd peaks overlap with more than one Vienna Tile, and vice versa. The reporters expressed at stage 4–6 that overlapped with more than one Bcd peak were excluded from the plot in Figure 2B.

Overlaps with Vienna Tile-GAL4 reporters
	Total Vienna tiles	Total overlaps		Single overlaps
	Total Vienna tiles	Vienna tiles	Bcd peaks	Single overlaps
Active (all stages)	3604	238	193	127
Active (stage 4–6)	666	163	151	115
Patterned (stage 4–6)	627*	159	147	112
Not Active	4189	55	41	28
Total	7793	293	234	155

*The patterned expression from the 666 Vienna Tiles that drive expression at stage 4–6 was determined by subtracting the number of tiles scored as ‘ubiquitous’ (39) from the total number of tiles.

elife-28275-v2.xml

10.7554/eLife.28275.009

Table 3.Number of Bcd ChIP-seq peaks in each class overlapping with Vienna Tile-GAL4 reporters.

Queried Bcd peaks are peaks that are present in the Fly Enhancer database, whose expression can be assessed.

Overlaps of peak classes with active enhancers and transcription start sites
Bcd peak class	Overlaps with Vienna tiles		Overlaps with Vienna tiles active at stg. 4–6			Total bcd peaks
Bcd peak class	N	% of Total Bcd Peaks	N	% of Queried Bcd Peaks	% of Total Bcd Peaks	Total bcd peaks
Concentration-Sensitive I	52	34.2%	38	73.1%	25.0%	152
Concentration-Sensitive II	38	27.5%	29	73.7%	21.0%	138
Concentration-Sensitive III	109	18.4%	57	52.3%	9.6%	593
Concentration-Insensitive	34	23.8%	26	76.5%	18.2%	143

elife-28275-v2.xml

10.7554/eLife.28275.010

Table 4.Number of Bcd ChIP-seq peaks in each class within 500 bp Transcription Start Sites.

Bcd peak class	Overlaps with TSS		Total bcd peaks
Bcd peak class	N	%	Total bcd peaks
Concentration-Sensitive I	29	19.1%	152
Concentration-Sensitive II	35	25.4%	138
Concentration-Sensitive III	291	49.1%	593
Concentration-Insensitive	74	51.7%	143

elife-28298-v2.xml

10.7554/eLife.28298.028

Table 2.Effect of early growth (<italic>tlag</italic>, <italic>µ</italic> and <italic>σb</italic>) and control (<italic>t̄c</italic>, <italic>Vc</italic> and <italic>ntip</italic>) parameters on the capacity of the model to predict survival.

Log-likelihood is computed either on bacterial load data (i.e. on the data set we used to fit the model) or on survival data. In this latter case, we used the probability of control predicted by the model as an offset in a binomial general linear model (glm) fitted to survival data. This glm includes an intercept which quantifies the difference between predicted control probability and observed survival. p-values indicate whether keeping a parameter constant for all bacteria significantly alters survival prediction.

		Complete data set			Intermediate survival
		Bacterial load	Survival		Bacterial load	Survival
	df	logLik	logLik	p-value	logLik	logLik	p-value
Full		−1243.119	−17.85860		−800.0603	−11.48770
Control	24	−1629.965	−21.68408	0.999	−839.5523	−17.18319	0.496
t̄^c	8	−1660.396	−19.18941	0.954	−839.5791	−16.82534	0.030
V^c	8	−1643.985	−17.37663	1	−826.4296	−14.67760	0.173
n^tip	8	−1634.382	−25.23397	0.064	−832.8896	−12.85596	0.603
Growth	24	−1798.630	−81.13355	6.512e-16	−854.1100	−11.37739	1
t^lag	8	−1692.743	−16.49076	1	−835.3833	−11.30397	1
µ	8	−1705.175	−61.56015	1.564e-15	−836.3794	−11.75406	0.970
σ_b	8	−1704.156	−21.95270	0.415	−848.2682	−12.28487	0.810

elife-28477-v2.xml

10.7554/eLife.28477.007

Table 1.Summary of sequence data used in this paper.

Putative subfamilies within each TcR alpha V family share at least 85% nucleotide identity using nearest-neighbor consensus trees of V segments. Number of TcR alpha nucleotide (NUC), amino acid (AA) sequences or sequence groups within each category. Highlighted columns specifically refer to data used in this study. (See results for detailed descriptions of sequences included within each column.)

10.7554/eLife.28477.008Table 1–source data 1.Tab-delimited text file containing sequences used in this paper for analysis of somatic hypermutation of TcR alpha chain.

Alpha V segment	Putative # Sub-families	All cloned sequences	Complete CDR3-J junction^*	Unique V Region ^†		Unique V segment^‡		Unique CDR3-J^§		Groups with identical CDR3-J^#	CDR3-J groups in Study^**	Sequences in each dataset^††
Alpha V segment	Putative # Sub-families	All cloned sequences	Complete CDR3-J junction^*	NUC	AA	NUC	AA	NUC	AA	Groups with identical CDR3-J^#	CDR3-J groups in Study^**	Sequences in each dataset^††
TRA V1	1	40	40	35	34	24	16	34	32	7	4	2, 3, 3, 5
TRA V2	3	18	18	13	13	13	10	12	12	3	1	5
TRA V3	3	217	194	55	52	35	34	51	50	5	1	4
TRA V4	3	60	28	22	22	21	21	21	21	6	2	2, 2
TRA V5	4	35	34	15	13	9	8	13	13	3	1	2
TRA V6	2	9	9	7	7	5	6	7	7	1	0	0
TRA V7	5	96	60	49	48	39	38	48	48	9	2	2, 2
TRA V9	3	19	19	14	14	12	11	13	13	4	0	0
TRA V10	2	45	45	29	26	21	19	27	26	10	2	4, 9
		539	447	239	229	179	163	226	224	48	13	45

^*A full list of these sequences can be found in Table 1—source data 1.

^†V Region includes all bases between the 1 st predicted nucleotide of the V segment to the last predicted nucleotide of the J segment (V and J).

‡V Segment includes all bases between the 1 st predicted nucleotide of the V segment to the last predicted nucleotide of the V segment (V only).

^§CDR3-J includes all bases after the last predicted nucleotide of the V segment to the last predicted nucleotide of the J segment.

#Number of groups with identical CDR3-J sequences, which we used to determine sequence relatedness (see text for details).

**Number of groups with identical CDR3-J sequences used in this study. (Those not used contained no mutation with V segments.)

††Total number of sequences for each alpha V used to assess somatic hypermutation within this study (e.g., for aV1, 4 different clonal groups contained 2, 3, 3, and 5 identical CDR3-J regions, respectively).

elife-28477-v2.xml

10.7554/eLife.28477.010

Table 2.Frequencies of somatic hypermutation in nurse shark alpha V groups (αV G) containing the same CDR3.

Mutation frequency is the total number of nucleotide changes to a Geneious-derived consensus sequence divided by the total number of nucleotides. We counted synonymous (S) and nonsynymous (N) mutations separately for each FR and CDR for 11 different CDR3 groups in seven predicted alpha V genes. [FR: framework region; CDR: complementarity-determining region; Seqs: sequences; Nuc: nucleotides; Freq: frequency]

		FR1						FR2						FR3						FR Means
αV Group	# Seqs	# Codons	Total	Mutations		Total	Mutation	# Codons	Total	Mutations		Total	Mutation	# Codons	Total	Mutations		Total	Mutation	FR Means
αV Group	# Seqs	# Codons	Nuc	S	N	Mutation	Freq (%)	# Codons	Nuc	S	N	Mutation	Freq (%)	# Codons	Nuc	S	N	Mutation	Freq (%)	S	N	ALL
αV1.1	3	25	225	2	12	14	6.222	17	153	0	2	2	1.307	41	369	4	4	8	2.168	6	18	24
αV1.2	5	25	375	10	8	18	4.800	17	255	1	8	9	3.529	41	615	5	5	10	1.626	16	21	37
αV1.4	3	25	225	1	0	1	0.444	17	153	1	3	4	2.614	41	369	4	5	9	2.439	6	8	14
αV2.1	5	25	375	0	0	0	0.000	17	255	1	0	1	0.392	42	630	0	0	0	0.000	1	0	1
αV3.1	4	25	300	0	4	4	1.333	17	204	0	0	0	0.000	40	480	0	1	1	0.208	0	5	5
αV4.1	2	25	150	1	2	3	2.000	17	102	0	2	2	1.961	43	258	11	7	18	6.977	12	11	23
αV4.2	2	25	150	0	0	0	0.000	17	102	1	1	2	1.961	43	258	2	7	9	3.488	3	8	11
αV5.1	2	25	150	0	6	6	4.000	17	102	2	3	5	4.902	42	252	1	2	3	1.190	3	11	14
αV7.2	2	25	150	4	7	11	7.333	17	102	1	3	4	3.922	41	246	1	6	7	2.846	6	16	22
αV10.1	4	25	300	0	0	0	0.000	17	204	1	1	2	0.980	41	492	4	0	4	0.813	5	1	6
αV10.2	9	25	675	2	11	13	1.926	17	459	4	4	8	1.743	40	1080	3	11	14	1.296	9	26	35
Sum	41	275	3075	20	50	70		187	2091	12	27	39		455	5049	35	48	83		67	125	192
Mean Mutation Freq (%)				0.65	1.63	2.28				0.57	1.29	1.87				0.69	0.95	1.64		0.66	1.22	1.88
Standard Deviation				2.994	4.547	6.531				1.136	2.252	2.841				3.125	3.414	5.429		4.742	8.201	11.861

		CDR1						CDR2						CDR3						CDR Means
AlphaV Group	# Seqs	# Codons	Total	Mutations		Total	Mutation	# Codons	Total	Mutations		Total	Mutation	# Codons	Total	Mutations		Total	Mutation	CDR Means
AlphaV Group	# Seqs	# Codons	Nuc	S	N	Mutation	Freq (%)	# Codons	Nuc	S	N	Mutation	Freq (%)	# Codons	Nuc	S	N	Mutation	Freq (%)	S	N	ALL
αV1.1	3	8	72	2	2	4	5.556	5	45	1	0	1	2.222	10	90	1	6	7	7.778	4	8	12
αV1.2	5	8	120	5	4	9	7.500	5	75	1	2	3	4.000	8	120	1	4	5	4.167	7	10	17
αV1.4	3	8	72	0	1	1	1.389	5	45	0	0	0	0.000	5	45	0	2	2	4.444	0	3	3
αV2.1	5	7	105	0	1	1	0.952	5	75	0	0	0	0.000	3	45	0	0	0	0.000	0	1	1
αV3.1	4	6	72	0	3	3	4.167	6	72	0	0	0	0.000	1	12	0	0	0	0.000	0	3	3
αV4.1	2	7	42	3	1	4	9.524	6	36	0	1	1	2.778	6	36	2	0	2	5.556	5	2	7
αV4.2	2	7	42	1	1	2	4.762	6	36	0	0	0	0.000	6	36	0	0	0	0.000	1	1	2
αV5.1	2	7	42	0	3	3	7.143	6	36	0	7	7	19.444	7	42	0	0	0	0.000	0	10	10
αV7.2	2	5	30	0	0	0	0.000	7	42	1	1	2	4.762	6	36	0	2	2	5.556	1	3	4
αV10.1	4	7	84	3	0	3	3.571	6	72	0	0	0	0.000	7	84	0	3	3	3.571	3	3	6
αV10.2	9	7	189	1	8	9	4.762	6	162	2	2	4	2.469	7	189	3	0	3	1.587	6	10	16
Sum	41	77	870	15	24	39		63	696	5	13	18		66	735	7	17	24		27	54	81
Mean Mutation Freq (%)				1.72	2.76	4.48				0.72	1.87	2.59				0.95	2.31	3.27		1.17	2.35	3.52
Standard Deviation				1.690	2.316	2.979				0.688	2.089	2.248				1.027	2.067	2.272		2.659	3.754	5.626

elife-28477-v2.xml

10.7554/eLife.28477.011

Table 3.Number and frequency of DNA mutations that occur in tandem within framework regions (FR) and complementarity determining regions (CDR) in nurse shark alpha V (αV) groups.

All mutations include both tandem and point mutations within a region. [Seqs: sequences]

		FR						CDR
		# Nucleotides Tandemly Mutated				All mutation	Frequency of tandem mutation	# Nucleotides Tandemly Mutated				All mutation	Frequency of tandem mutation
αV Group	# Seqs	2	3	4	Sum	All mutation	Frequency of tandem mutation	2	3	4	Sum	All mutation	Frequency of tandem mutation
αV1.1	3	1	0	1	6	24	25.0	3	0	0	6	12	50.0
αV1.2	5	4	1	0	11	37	29.7	5	1	0	13	17	76.5
αV1.4	3	3	0	0	6	14	42.9	0	0	0	0	3	0.0
αV2	5	0	0	0	0	1	0.0	0	0	0	0	1	0.0
αV3	4	2	0	0	4	5	80.0	1	0	0	2	3	66.7
αV4.1	2	4	1	0	11	23	47.8	0	1	0	3	7	42.9
αV4.2	2	1	1	0	5	11	45.5	0	1	0	3	2	150.0
αV5	2	1	0	0	2	14	14.3	1	1	0	5	10	50.0
αV7.2	2	4	1	0	11	22	50.0	1	0	0	2	4	50.0
αV10.1	4	3	0	0	6	6	100.0	0	0	0	0	6	0.0
αV10.2	9	4	1	0	11	35	31.4	2	1	0	7	16	43.8
Total	41	27	5	1	73	192	38.0	13	5	0	41	81	50.6

elife-28477-v2.xml

10.7554/eLife.28477.017

Table 6.Frequencies of somatic hypermutation in nurse shark thymus and peripheral lymphoid tissue (blood and spiral valve).

Mutations were analyzed only in alpha V groups containing the same third complementarity-determining region (CDR). Mutation frequency was measured as the total number of nucleotide changes to a Geneious-derived consensus sequence divided by the total number of nucleotides in all sequences. Nonsynymous (N) and synonymous (S) mutations (mut) were counted separately for each framework (FR) and CDR for two predicted alpha V genes. [FR1, FR2, FR3, CDR1, CDR2, and CDR3 refer to the first, second, or third FR or CDR region, respectively.]

Tissue type	Mut type	FR Mutations (#)				CDR Mutations (#)				FR mutation frequency			CDR mutation frequency
Tissue type	Mut type	FR1	FR2	FR3	All FR	CDR1	CDR2	CDR3	All CDR	FR1	FR2	FR3	CDR1	CDR2	CDR3
Thymus (6 sequences)	N	8	8	7	23	1	3	3	7	0.570	0.871	0.317	0.071	0.327	0.136
	S	8	2	6	16	1	0	0	1	0.570	0.218	0.272	0.071	0.000	0.000
	ALL	16	10	13	39	2	3	3	8	1.140	1.089	0.590	0.529	1.075	1.235
Total Nucleotides		1404	918	2205	4527	378	279	243	900
Periphery (2 sequences)	N	7	4	6	17	0	2	2	4	1.496	1.307	0.833	0.000	1.852	1.587
	S	4	0	1	5	0	0	0	0	0.855	0.000	0.139	0.000	0.000	0.000
	ALL	11	4	7	22	0	2	2	4	2.350	1.307	0.972	0.000	1.852	1.587
Total Nucleotides		468	306	720	1494	126	108	126	360

elife-28477-v3.xml

10.7554/eLife.28477.007

Table 1.Summary of sequence data used in this paper.

10.7554/eLife.28477.008Table 1–source data 1.Tab-delimited text file containing sequences used in this paper for analysis of somatic hypermutation of TcR alpha chain.

Alpha V segment	Putative # Sub-families	All cloned sequences	Complete CDR3-J junction^*	Unique V Region ^†		Unique V segment^‡		Unique CDR3-J^§		Groups with identical CDR3-J^#	CDR3-J groups in Study^**	Sequences in each dataset^††
Alpha V segment	Putative # Sub-families	All cloned sequences	Complete CDR3-J junction^*	NUC	AA	NUC	AA	NUC	AA	Groups with identical CDR3-J^#	CDR3-J groups in Study^**	Sequences in each dataset^††
TRA V1	1	40	40	35	34	24	16	34	32	7	4	2, 3, 3, 5
TRA V2	3	18	18	13	13	13	10	12	12	3	1	5
TRA V3	3	217	194	55	52	35	34	51	50	5	1	4
TRA V4	3	60	28	22	22	21	21	21	21	6	2	2, 2
TRA V5	4	35	34	15	13	9	8	13	13	3	1	2
TRA V6	2	9	9	7	7	5	6	7	7	1	0	0
TRA V7	5	96	60	49	48	39	38	48	48	9	2	2, 2
TRA V9	3	19	19	14	14	12	11	13	13	4	0	0
TRA V10	2	45	45	29	26	21	19	27	26	10	2	4, 9
		539	447	239	229	179	163	226	224	48	13	45

^*A full list of these sequences can be found in Table 1—source data 1.

^†V Region includes all bases between the 1 st predicted nucleotide of the V segment to the last predicted nucleotide of the J segment (V and J).

‡V Segment includes all bases between the 1 st predicted nucleotide of the V segment to the last predicted nucleotide of the V segment (V only).

^§CDR3-J includes all bases after the last predicted nucleotide of the V segment to the last predicted nucleotide of the J segment.

#Number of groups with identical CDR3-J sequences, which we used to determine sequence relatedness (see text for details).

**Number of groups with identical CDR3-J sequences used in this study. (Those not used contained no mutation with V segments.)

elife-28477-v3.xml

10.7554/eLife.28477.010

Table 2.Frequencies of somatic hypermutation in nurse shark alpha V groups (αV G) containing the same CDR3.

		FR1						FR2						FR3						FR Means
αV Group	# Seqs	# Codons	Total	Mutations		Total	Mutation	# Codons	Total	Mutations		Total	Mutation	# Codons	Total	Mutations		Total	Mutation	FR Means
αV Group	# Seqs	# Codons	Nuc	S	N	Mutation	Freq (%)	# Codons	Nuc	S	N	Mutation	Freq (%)	# Codons	Nuc	S	N	Mutation	Freq (%)	S	N	ALL
αV1.1	3	25	225	2	12	14	6.222	17	153	0	2	2	1.307	41	369	4	4	8	2.168	6	18	24
αV1.2	5	25	375	10	8	18	4.800	17	255	1	8	9	3.529	41	615	5	5	10	1.626	16	21	37
αV1.4	3	25	225	1	0	1	0.444	17	153	1	3	4	2.614	41	369	4	5	9	2.439	6	8	14
αV2.1	5	25	375	0	0	0	0.000	17	255	1	0	1	0.392	42	630	0	0	0	0.000	1	0	1
αV3.1	4	25	300	0	4	4	1.333	17	204	0	0	0	0.000	40	480	0	1	1	0.208	0	5	5
αV4.1	2	25	150	1	2	3	2.000	17	102	0	2	2	1.961	43	258	11	7	18	6.977	12	11	23
αV4.2	2	25	150	0	0	0	0.000	17	102	1	1	2	1.961	43	258	2	7	9	3.488	3	8	11
αV5.1	2	25	150	0	6	6	4.000	17	102	2	3	5	4.902	42	252	1	2	3	1.190	3	11	14
αV7.2	2	25	150	4	7	11	7.333	17	102	1	3	4	3.922	41	246	1	6	7	2.846	6	16	22
αV10.1	4	25	300	0	0	0	0.000	17	204	1	1	2	0.980	41	492	4	0	4	0.813	5	1	6
αV10.2	9	25	675	2	11	13	1.926	17	459	4	4	8	1.743	40	1080	3	11	14	1.296	9	26	35
Sum	41	275	3075	20	50	70		187	2091	12	27	39		455	5049	35	48	83		67	125	192
Mean Mutation Freq (%)				0.65	1.63	2.28				0.57	1.29	1.87				0.69	0.95	1.64		0.66	1.22	1.88
Standard Deviation				2.994	4.547	6.531				1.136	2.252	2.841				3.125	3.414	5.429		4.742	8.201	11.861

		CDR1						CDR2						CDR3						CDR Means
AlphaV Group	# Seqs	# Codons	Total	Mutations		Total	Mutation	# Codons	Total	Mutations		Total	Mutation	# Codons	Total	Mutations		Total	Mutation	CDR Means
AlphaV Group	# Seqs	# Codons	Nuc	S	N	Mutation	Freq (%)	# Codons	Nuc	S	N	Mutation	Freq (%)	# Codons	Nuc	S	N	Mutation	Freq (%)	S	N	ALL
αV1.1	3	8	72	2	2	4	5.556	5	45	1	0	1	2.222	10	90	1	6	7	7.778	4	8	12
αV1.2	5	8	120	5	4	9	7.500	5	75	1	2	3	4.000	8	120	1	4	5	4.167	7	10	17
αV1.4	3	8	72	0	1	1	1.389	5	45	0	0	0	0.000	5	45	0	2	2	4.444	0	3	3
αV2.1	5	7	105	0	1	1	0.952	5	75	0	0	0	0.000	3	45	0	0	0	0.000	0	1	1
αV3.1	4	6	72	0	3	3	4.167	6	72	0	0	0	0.000	1	12	0	0	0	0.000	0	3	3
αV4.1	2	7	42	3	1	4	9.524	6	36	0	1	1	2.778	6	36	2	0	2	5.556	5	2	7
αV4.2	2	7	42	1	1	2	4.762	6	36	0	0	0	0.000	6	36	0	0	0	0.000	1	1	2
αV5.1	2	7	42	0	3	3	7.143	6	36	0	7	7	19.444	7	42	0	0	0	0.000	0	10	10
αV7.2	2	5	30	0	0	0	0.000	7	42	1	1	2	4.762	6	36	0	2	2	5.556	1	3	4
αV10.1	4	7	84	3	0	3	3.571	6	72	0	0	0	0.000	7	84	0	3	3	3.571	3	3	6
αV10.2	9	7	189	1	8	9	4.762	6	162	2	2	4	2.469	7	189	3	0	3	1.587	6	10	16
Sum	41	77	870	15	24	39		63	696	5	13	18		66	735	7	17	24		27	54	81
Mean Mutation Freq (%)				1.72	2.76	4.48				0.72	1.87	2.59				0.95	2.31	3.27		1.17	2.35	3.52
Standard Deviation				1.690	2.316	2.979				0.688	2.089	2.248				1.027	2.067	2.272		2.659	3.754	5.626

elife-28477-v3.xml

10.7554/eLife.28477.011

Table 3.Number and frequency of DNA mutations that occur in tandem within framework regions (FR) and complementarity determining regions (CDR) in nurse shark alpha V (αV) groups.

All mutations include both tandem and point mutations within a region. [Seqs: sequences]

		FR						CDR
		# Nucleotides Tandemly Mutated				All mutation	Frequency of tandem mutation	# Nucleotides Tandemly Mutated				All mutation	Frequency of tandem mutation
αV Group	# Seqs	2	3	4	Sum	All mutation	Frequency of tandem mutation	2	3	4	Sum	All mutation	Frequency of tandem mutation
αV1.1	3	1	0	1	6	24	25.0	3	0	0	6	12	50.0
αV1.2	5	4	1	0	11	37	29.7	5	1	0	13	17	76.5
αV1.4	3	3	0	0	6	14	42.9	0	0	0	0	3	0.0
αV2	5	0	0	0	0	1	0.0	0	0	0	0	1	0.0
αV3	4	2	0	0	4	5	80.0	1	0	0	2	3	66.7
αV4.1	2	4	1	0	11	23	47.8	0	1	0	3	7	42.9
αV4.2	2	1	1	0	5	11	45.5	0	1	0	3	2	150.0
αV5	2	1	0	0	2	14	14.3	1	1	0	5	10	50.0
αV7.2	2	4	1	0	11	22	50.0	1	0	0	2	4	50.0
αV10.1	4	3	0	0	6	6	100.0	0	0	0	0	6	0.0
αV10.2	9	4	1	0	11	35	31.4	2	1	0	7	16	43.8
Total	41	27	5	1	73	192	38.0	13	5	0	41	81	50.6

elife-28477-v3.xml

10.7554/eLife.28477.017

Table 6.Frequencies of somatic hypermutation in nurse shark thymus and peripheral lymphoid tissue (blood and spiral valve).

Tissue type	Mut type	FR Mutations (#)				CDR Mutations (#)				FR mutation frequency			CDR mutation frequency
Tissue type	Mut type	FR1	FR2	FR3	All FR	CDR1	CDR2	CDR3	All CDR	FR1	FR2	FR3	CDR1	CDR2	CDR3
Thymus (6 sequences)	N	8	8	7	23	1	3	3	7	0.570	0.871	0.317	0.071	0.327	0.136
	S	8	2	6	16	1	0	0	1	0.570	0.218	0.272	0.071	0.000	0.000
	ALL	16	10	13	39	2	3	3	8	1.140	1.089	0.590	0.529	1.075	1.235
Total Nucleotides		1404	918	2205	4527	378	279	243	900
Periphery (2 sequences)	N	7	4	6	17	0	2	2	4	1.496	1.307	0.833	0.000	1.852	1.587
	S	4	0	1	5	0	0	0	0	0.855	0.000	0.139	0.000	0.000	0.000
	ALL	11	4	7	22	0	2	2	4	2.350	1.307	0.972	0.000	1.852	1.587
Total Nucleotides		468	306	720	1494	126	108	126	360

elife-28721-v2.xml

10.7554/eLife.28721.003

Table 1.Transmission chain size distribution and model parameters.

	Subtype						Overall
	B	C	01_AE	02_AG	A	Other	Overall
Total number of chains, n (%)	1643 (53%)	322 (10%)	239 (7.7%)	331 (11%)	327 (11%)	238 (7.7%)	3100 (100%)
Chain size, n (%)
1	1437 (87%)	280 (87%)	206 (86%)	272 (82%)	269 (82%)	195 (82%)	2659 (86%)
2	158 (9.6%)	34 (11%)	31 (13%)	40 (12%)	44 (13%)	36 (15%)	343 (11%)
3	30 (1.8%)	7 (2.2%)	1 (0.42%)	10 (3.0%)	10 (3.1%)	6 (2.5%)	64 (2.1%)
4	12 (0.73%)	-	1 (0.42%)	6 (1.8%)	3 (0.92%)	1 (0.42%)	23 (0.74%)
5	1 (0.06%)	1 (0.31%)	-	2 (0.6%)	1 (0.31%)	-	5 (0.16%)
6	1 (0.06%)	-	-	1 (0.3%)	-	-	2 (0.06%)
7	1 (0.06%)	-	-	-	-	-	1 (0.03%)
8	2 (0.12%)	-	-	-	-	-	2 (0.06%)
9	1 (0.06%)	-	-	-	-	-	1 (0.03%)
Sampling probability, p (SD)	0.39	0.29	0.34	0.26	0.33	0.29	0.35 (0.05)
Chain origin, n (%)
Swiss (ρindex=1)	948 (58%)	36 (11%)	36 (15%)	36 (11%)	47 (14%)	30 (13%)	1133 (37%)
non-Swiss (ρindex=0.35)	695 (42%)	286 (89%)	203 (85%)	295 (89%)	280 (86%)	208 (87%)	1967 (63%)

elife-28721-v2.xml

10.7554/eLife.28721.006

Table 2.Patients’ demographic characteristics.

	Patients	Transmission chains
	Patients	Index case
Total number, n	3698	3100
Age at estimated date of infection [in years], median (IQR)	29.2 (23.1—37.8)	28.8 (22.8—37.4)
Estimated date of infection, median (IQR)	Jun 1996 (Sep 1990—Nov 2001)	Nov 1995 (Sep 1989—May 2001)
Time to diagnosis [in years], median (IQR)	3.40 (1.66—5.24)	3.54 (1.78—5.43)
Reported sex with occasional partner [as fraction of FUPs*], median (IQR)	0.53 (0.09—0.89)	0.50 (0.07—0.88)
No available FUP^†, n (%)	250 (6.8%)	226 (7.3%)
Earliest CD4 count [per μL]^‡, median (IQR)	310 (143—510)	300 (134—507)

*Follow-up visit (FUP).

^†Patients without FUP questionnaire regarding the sexual risk behavior. See Sensitivity analyses.

^‡One patient did not have any available CD4 cell count. The missing value was imputed with the mean CD4 cell count.

elife-28721-v2.xml

10.7554/eLife.28721.021

Appendix 1—table 1.Overview of all the parameters, their estimates and the <inline-formula><mml:math id="inf309"><mml:mrow><mml:mn mathsize="125%">95</mml:mn><mml:mo lspace="0pt" mathsize="125%" rspace="3.5pt" stretchy="false">%</mml:mo></mml:mrow></mml:math></inline-formula>-confidence intervals fitted in all the models presented in this study.

Subtypes	Parameter number	Parameter name	Parameter estimate	Wald-type 95%-CI	Profile likelihood 95%-CI
Overall	1	log⁡(R0)	-0.823	(-0.876,-0.770)	(-0.878,-0.772)
B	2	log⁡(R0)	-1.037	(-1.121,-0.952)	(-1.124,-0.955)
C	3	log⁡(R0)	-0.719	(-0.879,-0.559)	(-0.892,-0.571)
01_AE	4	log⁡(R0)	-0.826	(-1.036,-0.615)	(-1.057,-0.632)
02_AG	5	log⁡(R0)	-0.483	(-0.587,-0.378)	(-0.594,-0.384)
A	6	log⁡(R0)	-0.618	(-0.751,-0.485)	(-0.760,-0.492)
other	7	log⁡(R0)	-0.605	(-0.758,-0.451)	(-0.771,-0.461)
Overall	8	log⁡(R0,𝑟𝑒𝑓)	-0.839	(-0.894,-0.784)	(-0.895,-0.785)
Overall	9	𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10	-0.112	(-0.187,-0.037)	(-0.188,-0.037)
B	10	log⁡(R0,𝑟𝑒𝑓)	-1.070	(-1.165,-0.975)	(-1.169,-0.979)
B	11	𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10	-0.112	(-0.234,0.010)	(-0.236,0.008)
C	12	log⁡(R0,𝑟𝑒𝑓)	-0.692	(-0.851,-0.533)	(-0.864,-0.544)
C	13	𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10	-0.209	(-0.466,0.049)	(-0.473,0.046)
01_AE	14	log⁡(R0,𝑟𝑒𝑓)	-0.781	(-0.991,-0.570)	(-1.013,-0.588)
01_AE	15	𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10	-0.255	(-0.616,0.106)	(-0.629,0.101)
02_AG	16	log⁡(R0,𝑟𝑒𝑓)	-0.434	(-0.539,-0.329)	(-0.545,-0.333)
02_AG	17	𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10	-0.415	(-0.609,-0.222)	(-0.615,-0.226)
A	18	log⁡(R0,𝑟𝑒𝑓)	-0.725	(-0.892,-0.558)	(-0.907,-0.571)
A	19	𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10	-0.430	(-0.660,-0.199)	(-0.672,-0.209)
other	20	log⁡(R0,𝑟𝑒𝑓)	-0.600	(-0.754,-0.446)	(-0.767,-0.456)
other	21	𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10	-0.162	(-0.397,0.073)	(-0.403,0.072)
Overall	22	log⁡(R0,𝑟𝑒𝑓)	-0.710	(-0.780,-0.640)	(-0.782,-0.641)
	23	(𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10)2	-0.313	(-0.451,-0.176)	(-0.457,-0.182)
	24	(𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10)3	-0.184	(-0.283,-0.086)	(-0.288,-0.091)
Overall	25	log⁡(R0,𝑟𝑒𝑓)	-1.252	(-1.366,-1.137)	(-1.369,-1.140)
	26	𝑆𝑢𝑏𝑡𝑦𝑝𝑒C	0.352	(0.167,0.538)	(0.158,0.531)
	27	𝑆𝑢𝑏𝑡𝑦𝑝𝑒01⁢_⁢𝐴𝐸	0.274	(0.046,0.502)	(0.029,0.490)
	28	𝑆𝑢𝑏𝑡𝑦𝑝𝑒02⁢_⁢𝐴𝐺	0.575	(0.428,0.721)	(0.426,0.720)
	29	𝑆𝑢𝑏𝑡𝑦𝑝𝑒A	0.430	(0.271,0.588)	(0.266,0.584)
	30	𝑆𝑢𝑏𝑡𝑦𝑝𝑒𝑜𝑡ℎ𝑒𝑟	0.426	(0.247,0.606)	(0.238,0.600)
	31	𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10	-0.214	(-0.301,-0.127)	(-0.301,-0.128)
	32	𝐴𝑔𝑒-3210	0.007	(-0.045,0.058)	(-0.046,0.057)
	33	CD4-350100	0.000	(-0.018,0.019)	(-0.019,0.018)
	34	𝑅𝑎𝑡𝑒𝑟𝑖𝑠𝑘	0.230	(0.095,0.364)	(0.096,0.365)
	35	𝑌𝑒𝑎𝑟𝑠𝑑𝑖𝑎𝑔𝑛𝑜𝑠𝑖𝑠-310	0.351	(0.210,0.492)	(0.207,0.490)
Overall	36	log⁡(R0,𝑟𝑒𝑓)	-1.173	(-1.301,-1.045)	(-1.304,-1.048)
	37	110⁢log⁡(𝑌𝑒𝑎𝑟𝑠𝑑𝑖𝑎𝑔𝑛𝑜𝑠𝑖𝑠3)	1.727	(1.049,2.405)	(1.064,2.420)
	38	𝑆𝑢𝑏𝑡𝑦𝑝𝑒C	0.322	(0.140,0.505)	(0.131,0.498)
	39	𝑆𝑢𝑏𝑡𝑦𝑝𝑒01⁢_⁢𝐴𝐸	0.246	(0.020,0.472)	(0.004,0.460)
	40	𝑆𝑢𝑏𝑡𝑦𝑝𝑒02⁢_⁢𝐴𝐺	0.516	(0.374,0.659)	(0.372,0.658)
	41	𝑆𝑢𝑏𝑡𝑦𝑝𝑒A	0.404	(0.246,0.562)	(0.241,0.558)
	42	𝑆𝑢𝑏𝑡𝑦𝑝𝑒𝑜𝑡ℎ𝑒𝑟	0.401	(0.223,0.580)	(0.214,0.574)
	43	(𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10)3	-0.231	(-0.337,-0.124)	(-0.345,-0.131)
	44	𝑅𝑎𝑡𝑒𝑟𝑖𝑠𝑘	0.230	(0.094,0.366)	(0.096,0.368)
	45	(𝐷𝑎𝑡𝑒𝑖𝑛𝑓𝑒𝑐𝑡𝑖𝑜𝑛-1.1.1996365⋅10)4	-0.129	(-0.227,-0.031)	(-0.235,-0.038)

elife-28721-v2.xml

10.7554/eLife.28721.025

Appendix 2—table 1.Establishment date models obtained with the AIC/BIC forward selection and backward elimination and their respective AIC and BIC values as well as the <inline-formula><mml:math id="inf508"><mml:mi>p</mml:mi></mml:math></inline-formula>-values from the likelihood ratio test compared to the null model without any covariates.

Terms that were part of the respective final model are marked by ×.

	AIC		BIC
	Forward	Backward	Forward	Backward
Dateinfection−1.1.1996365⋅10
(Dateinfection−1.1.1996365⋅10)2		×		×
(Dateinfection−1.1.1996365⋅10)3	×	×	×	×
(Dateinfection−1.1.1996365⋅10)4	×		×
AIC	3364.3	3364.2	3364.3	3364.2
BIC	3382.4	3382.3	3382.4	3382.3
p-value from LR test	<0.0001	<0.0001	<0.0001	<0.0001

elife-28721-v2.xml

10.7554/eLife.28721.026

Appendix 2—table 2.Multivariate models obtained with the AIC/BIC forward selection and backward elimination algorithms.

The terms listed in the table are the terms identified from the single determinant model selections and the crosses indicate the terms entering the multivariate models. The null model from the likelihood ratio test refers to the baseline model without any covariates (not even the subtype).

	AIC		BIC
	Forward	Backward	Forward	Backward
Subtype	×	×	×	×
(Dateinfection−1.1.1996365⋅10)2
(Dateinfection−1.1.1996365⋅10)3	×	×	×	×
(Dateinfection−1.1.1996365⋅10)4	×	×	×
𝑅𝑎𝑡𝑒𝑟𝑖𝑠𝑘	×	×	×	×
Raterisk	×	×	×
110log⁡(Yearsdiagnosis3)		×		×
Yearsdiagnosis−310	×		×
Yearsdiagnosis−310	×	×	×
(Yearsdiagnosis−310)3		×		×
CD4−35010
(Age−3210)2
AIC	3254	3252	3254	3262
BIC	3314	3331	3314	3316
p-value from LR test	<0.0001	<0.0001	<0.0001	<0.0001

elife-28751-v2.xml

10.7554/eLife.28751.009

Table 1.Correlation between mGluR5 availability in distinct brain regions and the EEG <1 Hz activity.

Brain region		Correlation between mGluR5 availability and EEG < 1 Hz activity
		Baseline		Sleep deprivation
		r_P, p	r_S, p	r_P, p	r_S, p
Medial superior frontal cortex *	Left	0.75,<0.0001	0.73, <0.0001	0.60, 0.0022	0.63, 0.0011
Medial superior frontal cortex *	Right	0.79,<0.0001	0.76, <0.0001	0.60, 0.0024	0.66, 0.0006
Orbitofrontal cortex	Left	0.60, 0.0027	0.60, 0.0026	0.58, 0.0036	0.57, 0.0046
Orbitofrontal cortex	Right	0.68, 0.0003	0.69, 0.0002	0.57, 0.0046	0.56, 0.0051
Dorsolateral prefrontal cortex *	Left	0.76, <0.0001	0.77, <0.0001	0.67, 0.0005	0.66, 0.0006
Dorsolateral prefrontal cortex *	Right	0.75, 0.0001	0.76, <0.0001	0.67, 0.0004	0.72, 0.0001
Anterior cingulate cortex	Left	0.67, 0.0004	0.70, 0.0002	0.51, 0.0126	0.59, 0.0032
Anterior cingulate cortex	Right	0.66, 0.0007	0.64, 0.001	0.55, 0.0061	0.61, 0.0021
Inferior parietal cortex *	Left	0.80, <0.0001	0.79, <0.0001	0.77, <0.0001	0.76, <0.0001
Inferior parietal cortex *	Right	0.79, <0.0001	0.78, <0.0001	0.71, 0.0002	0.75, <0.0001
Precuneus *	Left	0.82, <0.0001	0.77,<0.0001	0.78, <0.0001	0.80, <0.0001
Precuneus *	Right	0.77, <0.0001	0.76, <0.0001	0.76, <0.0001	0.82, <0.0001
Insula	Left	0.63, 0.0014	0.63, 0.0012	0.47, 0.0244	0.41, 0.0532
Insula	Right	0.69, 0.0003	0.67, 0.0004	0.58, 0.0041	0.58, 0.004
Striatum	Left	0.62, 0.0016	0.63, 0.0013	0.50, 0.0147	0.49, 0.0176
Striatum	Right	0.68, 0.0004	0.66, 0.0006	0.52, 0.0104	0.58, 0.0037
Parahippocampal gyrus	Left	0.41, 0.0536	0.46, 0.0267	0.33, 0.1296	0.28, 0.1897
Parahippocampal gyrus	Right	0.53, 0.0093	0.53, 0.01	0.38, 0.0728	0.40, 0.0585
Hippocampus	Left	0.52, 0.0101	0.47, 0.0245	0.36, 0.0886	0.37, 0.0853
Hippocampus	Right	0.53, 0.009	0.48, 0.0198	0.43, 0.0413	0.37, 0.0835

r_P = Pearson Product Moment Correlation coefficient; r_S = Spearman Rank Correlation coefficient. Those brain regions that showed a significant (p_corr <0.00278) correlation between mGluR5 availability and EEG <1 Hz activity on left and right hemisphere in both baseline and sleep deprivation conditions are highlighted by a star (*).

elife-28877-v1.xml

10.7554/eLife.28877.007

Table 1.Active fractions of each chromatography and the amino acid sequences of the purified peptides.

Ion-exchange- HPLC Elution time (min)		Reversed-phase- HPLC Retention time (min)	Observed mass (MH⁺)	Theoretical mass (MH⁺)	Sequence	Precursor gene	Peptide name*
pH 6.5	pH4.8	Reversed-phase- HPLC Retention time (min)	Observed mass (MH⁺)	Theoretical mass (MH⁺)	Sequence	Precursor gene	Peptide name*
48–52 (Fr. A)	46–48	13–13.5	717.25	717.42	AVLPRY-NH₂	lury-1	LURY-1-2
48–52 (Fr. A)	46–48	17–18	818.34	818.46	PALLSRY-NH₂	lury-1	LURY-1-1
60–62 (Fr. B)	56–60	25.5–26.5	792.29	792.43	PNFLRF-NH₂	flp-1	FLP-1-6
92–94 (Fr. C)	108–112	27.5–28.5	1255.45	1255.68	RNKFEFIRF-NH₂	flp-12	FLP-12
94–96 (Fr. D)	86–88	15.5–16.5	901.27	901.45	KSAYMRF-NH₂	flp-6	FLP-6-1
94–96 (Fr. D)	90–92	23–23.5	1108.33	1108.55	SPSAKWMRF-NH₂	flp-22	FLP-22

*Peptide names other than LURY-1 peptides are taken from Li and Kim, 2008.

elife-28921-v3.xml

10.7554/eLife.28921.015

Table 1.Additive null predictions for interactions between mutations.

Most interactions result in high expression phenotypes because the wildtype in the presence of CI has no expression, meaning that mutations are either neutral or increase wildtype expression. If an effect of a mutation is positive, the additive model states that the effect remains positive (and the same), independent of the genetic background. As such, these predictions are true only for a system that is tightly repressed, where the wildtype has no expression. ‘High +’ indicates predictions that result in expression levels above the biologically meaningful limit, which is defined by the unrepressed P_R promoter (shown in Figure 2A). We treat these predictions as high expression phenotypes. We consider three categorical single component effects (‘no expression’, ‘intermediate expression’, and ‘high expression’), and show the categorical effect predicted by the additive null model for the system. We use categorical effects only to provide an intuition for what the additive model predicts - to obtain actual predictions of system DMEs, we use convolution (as explained in detail in Materials and methods section Naïve convolution of component distributions as the null model for additivity between mutations).

		Effects of mutations in trans
		No expression	Intermediate expression	High expression
Effects of mutations in cis	No expression	No	Intermediate	High
	Intermediate expression	Intermediate	Intermediate +high	High +
	High expression	High	High +	High +

elife-28939-v2.xml

Treatment	Stg (hpf)	n	heg1			krit1			klf2a
Treatment	Stg (hpf)	n	Mean	SEM	p	Mean	SEM	p	Mean	SEM	p
tnnt2a MO	54	3	0.85	0.008	0.013	1.06	0.009	0.103	-	-	-
klf2a/b MO	54	4	0.77	0.034	0.045	1.17	0.029	0.103	-	-	-
hs:Klf2a	54	3	2.56	0.089	0.044	1.38	0.061	0.151	-	-	-
hs:Krit1	48	4	-	-	-	9.77	0.063	0.001	0.63	0.059	0.044
heg1 mRNA	24	3	4.01	0.059	0.0095	-	-	-	0.31	0.107	0.04
heg1 mRNA	48	3	2.47	0.036	0.0082	-	-	-	0.68	0.023	0.019
egfp-krit1 mRNA	24	3	-	-	-	7.06	0.125	0.021	-	-	-
egfp-krit1 mRNA	48	3	-	-	-	3.24	0.053	0.011	-	-	-
egfp-krit1 mRNA	96	3	-	-	-	1.20	0.161	0.675	-	-	-

elife-28939-v2.xml

	Within each row, compare columns (simple effects within rows)
	Uncorrected Fisher's LSD	Mean diff.	Summary	Individual P value
48 hpf	WT vs. krit1	100.0	****	<0.0001
	WT vs. WT + egfp-krit1 mRNA	0.0	ns	>0.9999
	WT vs. krit1 + egfp-krit1 mRNA	0.0	ns	>0.9999
96 hpf	WT vs. krit1	100.0	****	<0.0001
	WT vs. WT + egfp-krit1 mRNA	1.590	ns	0.7212
	WT vs. krit1 + egfp-krit1 mRNA	76.44	****	<0.0001

elife-29023-v2.xml

10.7554/eLife.29023.021

Table 3.Retrospective test cases.

Columns indicate the PDB ID of each Ab-Ag pair; the number of residues for various subsets of the Ag; the number and success of EpiScope designs based on crystal and model Ag structures; a measure of the quality of the closest native-like docking model among ClusPro generated models (f_nat[Lensink et al., 2007]); the quality of the homology models built for Ab and Ags (TM-score [Zhang and Skolnick, 2004]); and the number of docking decoys generated by ClusPro.

PDB code	Number of residues			Crystal structure		Model structure		Fnat		TM-score		Number of docking decoys
PDB code	Whole	Surface	Epitopes	Number of designs	Overlap with epitopes	Number of designs	Overlap with epitopes	Crystal	Model	Antibody	Antigen	Crystal	Model
1FE8	196	124	27	4	Y	3	N	0.1	0.04	0.96	0.84	30	24
1FNS	196	120	12	5	Y	2	Y	0.39	0.09	0.96	0.86	26	20
1H0D	123	96	14	3	N	2	Y	0	0.05	0.98	0.79	30	30
1LK3	160	102	26	3	Y	3	Y	0.73	0.44	0.97	0.74	23	29
1OAZ	123	101	14	2	N	2	N	0.1	0.1	0.97	0.77	30	29
1OB1	99	74	13	3	Y	4	Y	0.62	0.61	0.97	0.85	30	29
1RJL	95	82	13	3	Y	2	Y	0.29	0.3	0.96	0.89	30	27
1V7M	163	113	20	6	Y	3	Y	0.45	0.19	0.96	0.78	27	24
1YJD	140	86	14	2	Y	3	Y	0.42	0.13	0.98	0.77	25	30
2ARJ	123	90	17	3	Y	3	Y	0.63	0.26	0.97	0.75	24	30
2VXQ	96	71	21	3	Y	3	Y	0.32	0.21	0.89	0.89	30	30
2VXT	157	116	19	3	Y	3	Y	0.83	0.13	0.95	0.93	13	19
2XQB	114	87	18	2	Y	3	Y	0.16	0.25	0.92	0.89	17	21
3D9A	129	93	19	3	Y	2	Y	0.09	0.63	0.93	0.93	22	29
3HI1	290	246	20	4	N	3	N	0.28	0.02	0.97	0.83	30	29
3L5X	113	83	8	6	Y	3	Y	0.18	0.24	0.98	0.83	30	30
3MXW	169	108	22	2	Y	2	Y	0.52	0.47	0.96	0.92	20	23
3QWO	57	48	10	3	Y	4	Y	0.32	0.53	0.96	0.86	30	30
3RKD	146	105	18	5	Y	3	Y	0.55	0.48	0.97	0.49	30	30
4DN4	76	50	12	2	Y	2	Y	0.49	0.28	0.92	0.88	20	27
4DW2	222	175	20	4	Y	3	Y	0.1	0.35	0.92	0.85	30	30
4ETQ	226	186	22	4	Y	3	Y	0.45	0.57	0.96	0.94	30	30
4G3Y	157	114	12	3	Y	4	Y	0.35	0.12	0.94	0.86	30	30
4G6J	158	109	13	3	Y	3	Y	0.57	0.15	0.97	0.85	30	30
4I3S	190	163	23	4	Y	4	Y	0.05	0.09	0.81	0.82	30	30
4JZJ	252	210	18	4	Y	6	Y	0.31	0.25	0.95	0.33	30	30
4KI5	183	108	7	1	Y	1	Y	0.39	0.29	0.95	0.93	24	20
4L5F	111	79	9	2	Y	3	Y	0.52	0.1	0.97	0.8	30	30
4LVH	223	184	13	5	Y	6	N	0.12	0.05	0.93	0.9	30	29
4M62	155	105	6	2	Y	2	N	0.12	0.11	0.92	0.81	24	24
4NP4	272	230	25	3	Y	5	Y	0.09	0.07	0.96	0.67	30	30
4RGO	226	187	17	3	N	6	Y	0.16	0.21	0.97	0.96	30	30
5D96	235	198	22	4	Y	4	Y	0.23	0.15	0.95	0.96	30	30
Average	162.88	122.52	16.48	3.30		3.18		0.33	0.24	0.95	0.82	27.12	27.67
STD	57.57	51.53	5.54	1.19		1.21		0.21	0.18	0.03	0.13	4.53	3.55

elife-29023-v2.xml

10.7554/eLife.29023.022

Table 4.Ab modeling quality.

Antibody structures were generally highly accurately predicted both overall (average TM-score: 0.95) and for CDRs (all-backbone-atom, including N, C, Cα and O, RMSDs reported). Overall, non-CDR-H3 loops were very well predicted based on the canonical rules, and even for CDR-H3 loops the average RMSDs was <2 Å.

10.7554/eLife.29023.023Table 4—source data 1.

Target	Species	CDR-L1	L2	L3	H1	H2	CDR-H3			TM-score
Target	Species	CDR-L1	L2	L3	H1	H2	RMSD	Sequence	Length	TM-score
1FE8	MOUSE	0.42	0.22	0.74	1.01	0.51	0.63	AGNYYGMDY	9	0.96
1FNS	MOUSE	0.54	0.18	0.93	0.27	0.60	2.10	VRDPADYGNYDYALDY	16	0.96
1H0D	MOUSE	1.43	0.57	0.42	0.44	1.11	0.66	TRLGDYGYAYTMDY	14	0.98
1LK3	RAT	0.41	0.43	0.52	0.57	1.51	1.00	TRGVPGNNWFPY	12	0.97
1OAZ	MOUSE	1.15	0.44	0.88	1.30	0.56	1.25	ARMWYYGTYYFDY	13	0.97
1OB1	MOUSE	0.58	0.31	0.63	0.42	0.63	1.97	ARNYYRFDGGMDF	13	0.97
1RJL	MOUSE	1.43	0.57	4.96	0.69	1.00	1.16	ARMRYGDYYAMDN	13	0.96
1V7M	MOUSE	0.70	0.26	0.83	0.65	1.10	0.59	SGWSFLY	7	0.96
1YJD	MOUSE	0.88	0.51	1.34	0.62	1.19	1.76	TRSHYGLDWNFDV	13	0.98
2ARJ	RAT	0.71	0.67	1.12	0.46	0.70	0.65	TPLIGSWYFDF	11	0.97
2VXQ	HUMAN	0.35	0.74	0.96	0.90	1.27	1.05	ARLDGYTLDI	10	0.89
2VXT	MOUSE	0.47	0.37	1.14	0.45	0.53	0.43	ARGLRF	6	0.95
2XQB	HUMAN	1.61	0.43	0.98	1.19	0.89	7.21	ARDPAAWPLQQSLAWFDP	18	0.92
3D9A	MOUSE	0.40	0.61	1.18	0.99	1.88	0.51	ANWDGDY	7	0.93
3HI1	HUMAN	0.80	0.86	0.83	0.61	0.44	1.25	ARGPVPAVFYGDYRLDP	17	0.97
3L5X	HUMAN	0.56	0.61	0.91	1.05	0.90	1.73	ARMGSDYDVWFDY	13	0.98
3MXW	HUMAN	0.58	0.71	0.71	1.09	0.82	0.96	ARDWERGDFFDY	12	0.96
3QWO	HUMANIZED	0.48	0.28	1.09	0.87	0.50	1.13	ARDMIFNFYFDV	12	0.96
3RKD	MOUSE	0.62	0.42	0.52	1.06	0.65	1.45	ARIKSVITTGDYALDY	16	0.97
4DN4	HUMAN	2.11	0.37	1.58	1.64	2.40	2.36	ARYDGIYGELDF	12	0.92
4DW2	MOUSE	1.20	0.43	4.12	0.85	1.14	3.18	ERGELTYAMDY	11	0.92
4ETQ	MOUSE	1.07	0.29	1.59	0.35	0.91	0.94	TRSNYRYDYFDV	12	0.96
4G3Y	CHIMERIC	0.68	0.71	0.57	0.90	0.98	1.22	SRNYYGSTYDY	11	0.94
4G6J	HUMAN	0.72	0.44	0.90	0.41	0.35	1.14	ARDLRTGPFDY	11	0.97
4I3S	HUMAN	1.34	0.46	0.64	4.33	1.08	3.49	ARQKFYTGGQGWYFDL	16	0.81
4JZJ	HUMAN	0.59	0.54	0.98	0.84	1.04	2.96	ARSHLLRASWFAY	13	0.95
4KI5	MOUSE	0.74	0.52	0.78	2.14	0.44	1.49	AREDDGLAS	9	0.95
4L5F	MOUSE	0.76	0.42	1.03	0.49	0.94	1.83	TKRINWALDY	10	0.97
4LVH	MOUSE	1.63	0.71	2.82	1.46	2.70	1.91	ARHGSPGYTLYAWDY	15	0.93
4M62	HUMAN	2.08	0.79	1.40	2.55	2.78	8.26	AREGTTGSGWLGKPIGAFAY	20	0.92
4NP4	HUMAN	2.21	0.87	2.84	0.88	0.55	1.53	ARRRNWGNAFDI	12	0.96
4RGO	MOUSE	0.53	1.01	0.75	0.71	0.31	2.20	VRDLYGDYVGRYAY	14	0.97
5D96	MOUSE	0.74	0.57	0.53	0.62	0.89	3.43	ASDSMDPGSFAY	12	0.95
Average		0.92	0.52	1.25	0.99	1.01	1.92			0.95
STD		0.53	0.20	1.01	0.78	0.62	1.71			0.03

elife-29023-v2.xml

10.7554/eLife.29023.025

Table 6.Success rates with epitopes defined according to IEDB or according to contacts in the binding interface.

Success is indicated as ‘T’ and failure as ‘F’. In test cases colored blue, EpiScope failed to find IEDB epitopes but did find binding interface residues.

Target	Crystal structure		Model structure		Target	Crystal structure		Model structure
Target	IEDB	Interface	IEDB	Interface	Target	IEDB	Interface	IEDB	Interface
1FE8	T	T	F	F	3QWO	T	T	T	T
1FNS	T	T	T	T	3RKD	T	T	T	T
1H0D	F	F	T	T	4DN4	T	T	T	T
1LK3	T	T	T	T	4DW2	T	T	T	T
1OAZ	F	F	F	F	4ETQ	T	T	T	T
1OB1	T	T	T	T	4G3Y	T	T	T	T
1RJL	T	T	T	T	4G6J	T	T	T	T
1V7M	T	T	T	T	4I3S	T	T	T	T
1YJD	T	T	T	T	4JZJ	T	T	T	T
2ARJ	T	T	T	T	4KI5	T	T	T	T
2VXQ	T	T	T	T	4L5F	T	T	T	T
2VXT	T	T	T	T	4LVH	T	T	F	T
2XQB	T	T	T	T	4M62	T	T	F	T
3D9A	T	T	T	T	4NP4	T	T	T	T
3HI1	F	F	F	F	4RGO	F	T	T	T
3L5X	T	T	T	T	5D96	T	T	T	T
3MXW	T	T	T	T	Total	29 (88%)	30 (91%)	28 (85%)

elife-29023-v2.xml

10.7554/eLife.29023.034

Table 8.Comparison of predictive components of PEASE and EpiScope on retrospective test set of 33 non-redundant Ab-Ag pairs.

The number of designs needed/considered indicates the number of designs generated by EpiScope to cover all ClusPro docking models. An equivalent number of the top ranked PEASE patch predictions are considered for each Ab. Coloring highlights the cases in which Episcope (green) or PEASE (red) succeeded where the other method failed. Grey coloring indicates cases in which both methods failed.

Target	Crystal structure of ag			Modeled structure of ag
Target	# of Designs Needed/Considered	# of EpiScopeDesigns Overlapping True Epitope	# of PEASE patches Overlapping True Epitope	# of Designs Needed/Considered	# of EpiScopeDesigns Overlapping True Epitope	# of PEASE patches Overlapping True Epitope
1FE8	4	2	4	3	0	0
1FNS	5	2	5	2	1	2
1H0D	3	0	0	2	1	0
1LK3	3	1	0	3	1	0
1OAZ	2	0	2	2	0	2
1OB1	3	1	0	4	2	4
1RJL	3	1	3	2	1	2
1 V7M	6	1	0	3	1	2
1YJD	2	1	0	3	1	0
2ARJ	3	1	3	3	1	3
2VXQ	3	1	3	3	1	3
2VXT	3	1	3	3	1	3
2XQB	2	1	2	3	1	3
3D9A	3	1	0	2	1	0
3HI1	4	0	0	3	0	0
3L5X	6	1	6	3	2	3
3MXW	2	1	2	2	1	2
3QWO	3	2	3	4	3	4
3RKD	5	2	3	3	1	2
4DN4	2	1	0	2	1	0
4DW2	4	1	2	3	1	1
4ETQ	4	1	1	3	1	1
4G3Y	3	1	0	4	2	3
4G6J	3	1	2	3	1	3
4I3S	4	2	3	4	1	2
4JZJ	4	1	0	6	4	0
4KI5	1	1	0	1	1	0
4 L5F	2	1	0	3	1	0
4LVH	5	1	0	6	0	2
4 M62	2	1	0	2	0	0
4 NP4	3	1	0	5	3	0
4RGO	3	0	2	6	1	3
5D96	4	1	0	4	1	0

elife-29088-v1.xml

10.7554/eLife.29088.003

Table 1.Neonatal, socio-demographic, cognitive and scanning measures.

	Very preterm-perinatal brain injury	Very preterm-no diagnosed injury	Controls	Test statistic	Significance
	(n = 16)	(n = 13)	(n = 14)	Test statistic	Significance
Gestational age in weeks Mean (SD)	28.44 (2.28)	30.46 (1.76)		U₂₇ = 47.00	p=0.011
Birth weight in grams Mean (SD)	1203.19 (304.95)	1557.15 (364.98)		U₂₇ = 46.50	p=0.012
Age in years Mean (SD)	30.21 (1.78)	30.85 (2.09)	29.81 (3.24)	F_2,40 = 1.50	p=0.236
Sex (female:male)	03:13	04:09	05:09	X ²₂ = 1.14	p=0.564
High SES (%)*	68.75	69.23	61.53	X ²₂ =0.22	p=0.894
IQ Mean (SD)	106.67 (14.52)	107.73 (10.07)	110.40 (10.52)	F_2,33 = 0.28	p=0.755
Alcohol consumption (Units/week)	7.40 (11.30)	12.50 (11.99)	5.50 (4.72)	X ²₂ =3.172	p=0.205
Injected dose (MBq) Mean (SD)	146.44 (2.15)	146.25 (2.52)	145.73 (2.38)	F_2,40 = 0.23	p=0.793

*SES was collapsed into two groups; the percent of participants belonging to the high SES (level 1–2) category is presented in the table.

elife-29275-v2.xml

10.7554/eLife.29275.021

Table 2.Parameters for the biophysical model capturing the release dynamics during forward-masking and repetitive tone burst experiments

	Forward masking		All tone bursts – global fit
	RBE^WT/WT	RBE^KO/KO	RBE^WT/WT	RBE^KO/KO
N_slots	8	6.5	15.6	13.7
k_{refill, stim}	29.5	18.2	18.4	19.9
k_{refill, spont}	13.3	7.1	5.59	2.71
k_{fusion, stim}	32.2	31	82.5	45.1
k_{fusion, spont}	0.6	0.9	0.63	0.54

elife-29365-v2.xml

10.7554/eLife.29365.013

Table 4.Subgroup analysis across sex of the effect of N + WSH intervention on telomere length (T/S ratio) after 1 and 2 years of intervention and on change in telomere length between Year 1 and Year 2

10.7554/eLife.29365.014Table 4—source data 1.Source data and code for <xref ref-type="table" rid="table4">Table 4</xref>.

Arm	Female children		Male children		Female children Unadjusted difference: Intervention vs. Control (95% CI)	Male children Unadjusted difference: Intervention vs. Control (95% CI)	Interaction term sex by treatment (95% CI)
Arm	N	Mean	N	Mean			Interaction term sex by treatment (95% CI)
After 1 year of intervention (age ~ 14 months)
Control	162	1.50	159	1.43
N + WSH	180	1.42	161	1.37	−0.08 (−0.13,–0.03) p=0.001*	−0.06 (−0.11,–0.00) p=0.040*	0.03 (−0.04,0.09) p=0.435
After 2 years of intervention (age ~ 28 months)
Control	167	1.50	163	1.42
N + WSH	202	1.45	181	1.42	−0.05 (−0.10,0.01) p=0.082	0.00 (−0.05,0.05) p=0.877	0.05 (−0.01,0.12) p=0.105
Change in telomere length between Year 1 and 2
Control	134	–0.01	126	−0.01
N + WSH	160	0.03	137	0.04	0.04 (−0.02,0.09) p=0.227	0.05 (0.00,0.09) p=0.048*	0.01 (−0.06,0.08) p=0.747

*P<0.05

Confidence intervals were adjusted for clustered observations using robust standard errors.

elife-29365-v3.xml

Table 4—source data 1.Source data and code for <xref ref-type="table" rid="table4">Table 4</xref>.

Arm	Female children		Male children		Female children Unadjusted difference: Intervention vs. Control (95% CI)	Male children Unadjusted difference: Intervention vs. Control (95% CI)	Interaction term sex by treatment (95% CI)
Arm	N	Mean	N	Mean			Interaction term sex by treatment (95% CI)
After 1 year of intervention (age ~ 14 months)
Control	162	1.50	159	1.43
N + WSH	180	1.42	161	1.37	−0.08 (−0.13,–0.03) p=0.001*	−0.06 (−0.11,–0.00) p=0.040*	0.03 (−0.04,0.09) p=0.435
After 2 years of intervention (age ~ 28 months)
Control	167	1.50	163	1.42
N + WSH	202	1.45	181	1.42	−0.05 (−0.10,0.01) p=0.082	0.00 (−0.05,0.05) p=0.877	0.05 (−0.01,0.12) p=0.105
Change in telomere length between Year 1 and 2
Control	134	–0.01	126	−0.01
N + WSH	160	0.03	137	0.04	0.04 (−0.02,0.09) p=0.227	0.05 (0.00,0.09) p=0.048*	0.01 (−0.06,0.08) p=0.747

*P<0.05

Confidence intervals were adjusted for clustered observations using robust standard errors.

elife-29742-v2.xml

10.7554/eLife.29742.012

Table 4.Connection probabilities for the random network model.

		From
		E	PV	SST	VIP
to	E	0.02	1	1	0
	PV	0.01	1	0.85	0
	SST	0.01	0	0	−0.55
	VIP	0.01	0	0.5	0

elife-29742-v3.xml

10.7554/eLife.29742.012

Table 4.Connection probabilities for the random network model.

		From
		E	PV	SST	VIP
to	E	0.02	1	1	0
	PV	0.01	1	0.85	0
	SST	0.01	0	0	−0.55
	VIP	0.01	0	0.5	0

elife-29742-v4.xml

Table 4.Connection probabilities for the random network model.

		From
		E	PV	SST	VIP
to	E	0.02	1	1	0
	PV	0.01	1	0.85	0
	SST	0.01	0	0	−0.55
	VIP	0.01	0	0.5	0

elife-29944-v1.xml

10.7554/eLife.29944.020

Appendix 1—table 1.Selected models of molecular evolution for partitions of the first five mtDNA genome alignment data sets.

All lengths are in base pairs. Reduced length excludes the Coding3 and CR partitions. For all RAxML analyses the GTR model was implemented. *The TrN model was selected, but this cannot be implemented in MrBayes and so the HKY model was used. EPA: evolutionary placement algorithm; CR: control region.

Data set		Partition						Total length
Data set		Coding1	Coding2	Coding3	rRNAs	tRNAs	CR	All	Reduced
1. White rhino outgroup	Length	3803	3803	3803	2579	1529	1066	16583	11714
1. White rhino outgroup	Model	GTR + I + G	HKY + I + G	GTR + I + G	GTR + I + G	HKY + I + G	HKY*+I + G
2. Malayan tapir outgroup	Length	3803	3803	3803	2585	1530	1065	16589	11721
2. Malayan tapir outgroup	Model	GTR + I + G	HKY + I + G	GTR + I + G	GTR + I + G	HKY + I + G	HKY*+G
3. Dog + ceratomorphs outgroups	Length	3803	3803	3803	2615	1540	N/A	15564	11761
3. Dog + ceratomorphs outgroups	Model	GTR + I + G	HKY + I + G	GTR + I + G	GTR + I + G	HKY + I + G	N/A
4. EPA	Length	3803	3803	3803	2601	1534	1118	16662	11741
4. EPA	Model	GTR + I + G	TrN + I + G	GTR + I + G	GTR + I + G	HKY + I + G	HKY + I + G
5. Equids only	Length	3802	3802	3802	2571	1528	971	16476	11703
5. Equids only	Model	TrN + I + G	TrN + I + G	GTR + G	TrN + I + G	HKY + I	HKY + G

elife-29944-v1.xml

10.7554/eLife.29944.028

Appendix 2—table 1.Topological shape and support values for the best supported trees.

These results are from the Bayesian and maximum likelihood (ML) analyses of mtDNA data sets 1–3, including either the all or reduced partition sets, and with Hippidion sequences either included or excluded. Topology numbers and node letters refer to those outlined in Appendix 2—figure 3. Bayesian posterior probability support of >0.99 and ML bootstrap support of >95% are in bold for nodes A and B. *support for nodes that are consistent with topology one in Appendix 2—figure 3. NCs: non-caballines.

Outgroup	Partitions	Hippidion?	Tips	Analysis method	Topology	Support
Outgroup	Partitions	Hippidion?	Tips	Analysis method	Topology	Node A	Node B	Hippidion	NWSL	NCs	Caballines
White rhino (Data set 1)	All	Excluded	63	Bayesian	1/2/3	0.996*	N/A	N/A	1.000	1.000	1.000
		Excluded	63	ML	1/2/3	71*	N/A	N/A	100	99	100
		Included	69	Bayesian	2	0.751	1.000*	1.000	1.000	1.000	1.000
		Included	69	ML	1	64*	96*	100	100	100	100
	Reduced	Excluded	63	Bayesian	1/2/3	1.000*	N/A	N/A	1.000	1.000	1.000
		Excluded	63	ML	1/2/3	100*	N/A	N/A	99	100	100
		Included	69	Bayesian	2	0.948	1.000*	1.000	1.000	1.000	1.000
		Included	69	ML	2	73	98*	100	99	100	100
Malayan tapir (Data set 2)	All	Excluded	63	Bayesian	5/7	0.971	N/A	N/A	1.000	1.000	1.000
		Excluded	63	ML	5/7	87	N/A	N/A	100	99	99
		Included	69	Bayesian	6	0.808	0.867	1.000	1.000	1.000	1.000
		Included	69	ML	6	55	63	100	100	100	100
	Reduced	Excluded	63	Bayesian	1/2/3	0.675*	N/A	N/A	1.000	1.000	1.000
		Excluded	63	ML	4/6	28	N/A	N/A	100	96	98
		Included	69	Bayesian	3	0.685	0.864*	1.000	1.000	1.000	1.000
		Included	69	ML	3	70	69	100	100	100	100
Dog + ceratomorphs (Data set 3)	All	Excluded	71	Bayesian	1/2/3	0.598*	N/A	N/A	1.000	1.000	1.000
		Excluded	71	ML	4/6	59	N/A	N/A	100	100	100
		Included	77	Bayesian	1	1.000*	1.000*	1.000	1.000	1.000	1.000
		Included	77	ML	1	94*	96*	100	100	100	100
	Reduced	Excluded	71	Bayesian	1/2/3	0.999*	N/A	N/A	1.000	1.000	1.000
		Excluded	71	ML	1/2/3	97*	N/A	N/A	100	100	100
		Included	77	Bayesian	1	1.000*	1.000*	1.000	1.000	1.000	1.000
		Included	77	ML	1	99*	100*	100	100	100	100

elife-29944-v1.xml

10.7554/eLife.29944.029

Appendix 2—table 2.The <italic>a posteriori</italic> phylogenetic placement likelihood for eight ceratomorph (rhino and tapir) outgroups.

These analyses used a ML evolutionary placement algorithm, whilst varying the partition set used (all or reduced), and either including or excluding Hippidion sequences. Likelihoods >0.95 are in bold. Topology numbers refer to those outlined in Appendix 2—figure 3. Genbank accession numbers are given in parentheses after outgroup names.

Partitions	Outgroup	Hippidion?	Included				Excluded
Partitions	Outgroup	Topology	1	2	3	6	1/2/3	4/6	5/7
All	Tapirus terrestris (AJ428947)		0.456	0.317	0.205	0.018	0.549	0.313	0.139
	Tapirus indicus (NC023838)		0.275	0.105	0.225	0.389	0.050	0.908	0.042
	Coelodonta antiquitatis (NC012681)		0.998				0.248	0.451	0.301
	Dicerorhinus sumatrensis (NC012684)		0.981		0.009		0.155	0.553	0.292
	Rhinoceros unicornis (NC001779)		0.998				0.529	0.334	0.137
	Rhinoceros sondaicus (NC012683)		0.989	0.006			0.732	0.196	0.072
	Ceratotherium simum (NC001808)		0.448	0.499	0.053		0.949	0.018	0.033
	Diceros bicornis (NC012682)		0.917	0.065	0.018		0.851	0.073	0.076
Reduced	Tapirus terrestris (AJ428947)		0.410	0.391	0.199		0.987		0.012
	Tapirus indicus (NC023838)		0.536	0.298	0.166		0.995
	Coelodonta antiquitatis (NC012681)		0.411	0.554	0.035		1.000
	Dicerorhinus sumatrensis (NC012684)		0.983	0.015			1.000
	Rhinoceros unicornis (NC001779)		0.998				1.000
	Rhinoceros sondaicus (NC012683)		0.895	0.102			1.000
	Ceratotherium simum (NC001808)		0.296	0.704			1.000
	Diceros bicornis (NC012682)		0.996				1.000

elife-29944-v1.xml

10.7554/eLife.29944.030

Appendix 2—table 3.The <italic>a posteriori</italic> phylogenetic placement likelihood for 21 published equid mitochondrial sequences.

These analyses used the ML evolutionary placement algorithm, whilst varying the partition set used (all or reduced), and either including or excluding Hippidion sequences. Sample names are given in parentheses after the species or group name. Localities are given for NWSL equids only. Likelihoods >0.95 are in bold. *Equus includes only caballines and non-caballine equids (NCE). **For EQ04 from Alberta, other placement likelihood values for the Hippidion included/excluded partitions were: Within caballines: 0.003/0.002, Sister to caballines: 0.002/0.002, Within NCE: 0.246/0.245, Sister to NCE: 0.004/0.003. No placements were returned for ‘within Hippidion’. bp: base pairs.

Hippidion?	Partition	Published sample	Sequence length (bp)	Locality	Placement
Hippidion?	Partition	Published sample	Sequence length (bp)	Locality	Sister to E. ovodovi	Sister to Hippidion	Within NWSL	Sister to NWSL	Sister to Equus*	Other**
Included	All	E. ovodovi (ACAD2305)	688		1.000
		E. ovodovi (ACAD2302)	688		1.000
		E. ovodovi (ACAD2303)	688		1.000
		H. devillei (ACAD3615)	476		N/A	1.000
		H. devillei (ACAD3625)	543		N/A	1.000
		H. devillei (ACAD3627)	543		N/A	1.000
		H. devillei (ACAD3628)	543		N/A	0.999
		H. devillei (ACAD3629)	476		N/A	0.999
		NWSL equid (JW125)	720	Klondike, YT	N/A		0.996
		NWSL equid (JW126)	720	Klondike, YT	N/A		0.999
Included	All	NWSL equid (EQ01)	620	Dry Cave, NM	N/A		0.735	0.256
		NWSL equid (EQ03)	117	Dry Cave, NM	N/A	0.002	0.974	0.011	0.003
		NWSL equid (EQ04)	117	Edmonton, AB	N/A	0.004	0.703	0.014	0.007	0.255
		NWSL equid (EQ09)	620	Natural Trap Cave, WY	N/A		0.981	0.014
		NWSL equid (EQ13)	620	Natural Trap Cave, WY	N/A		0.992
		NWSL equid (EQ16)	464	Dry Cave, NM	N/A		0.854	0.138
		NWSL equid (EQ22)	620	Natural Trap Cave, WY	N/A		0.999
		NWSL equid (EQ30)	393	San Josecito Cave, MX-NL	N/A		0.792	0.198
		NWSL equid (EQ41)	398	Natural Trap Cave, WY	N/A		0.997
		NWSL equid (JW328)	mitogenome	Mineral Hill Cave, NV	N/A		1.000
		NWSL equid (MS272)	mitogenome	Klondike, YT	N/A			1.000
	Reduced	NWSL equid (JW328)	mitogenome	Mineral Hill Cave, NV	N/A		0.996
	Reduced	NWSL equid (MS272)	mitogenome	Klondike, YT	N/A			1.000
Excluded	All	E. ovodovi (ACAD2305)	688		1.000	N/A			N/A
		E. ovodovi (ACAD2302)	688		1.000	N/A			N/A
		E. ovodovi (ACAD2303)	688		1.000	N/A			N/A
		NWSL equid (JW125)	720	Klondike, YT	N/A	N/A	0.996		N/A
		NWSL equid (JW126)	720	Klondike, YT	N/A	N/A	0.999		N/A
		NWSL equid (EQ01)	620	Dry Cave, NM	N/A	N/A	0.731	0.259	N/A
		NWSL equid (EQ03)	117	Dry Cave, NM	N/A	N/A	0.980	0.010	N/A
		NWSL equid (EQ04)	117	Edmonton, AB	N/A	N/A	0.721	0.013	N/A	0.252
		NWSL equid (EQ09)	620	Natural Trap Cave, WY	N/A	N/A	0.987	0.008	N/A
		NWSL equid (EQ13)	620	Natural Trap Cave, WY	N/A	N/A	0.993		N/A
		NWSL equid (EQ16)	464	Dry Cave, NM	N/A	N/A	0.844	0.148	N/A
		NWSL equid (EQ22)	620	Natural Trap Cave, WY	N/A	N/A	0.999		N/A
		NWSL equid (EQ30)	393	San Josecito Cave, MX-NL	N/A	N/A	0.788	0.203	N/A
		NWSL equid (EQ41)	398	Natural Trap Cave, WY	N/A	N/A	0.995		N/A
		NWSL equid (JW328)	mitogenome	Mineral Hill Cave, NV	N/A	N/A	1.000		N/A
		NWSL equid (MS272)	mitogenome	Klondike, YT	N/A	N/A		1.000	N/A
	Reduced	NWSL equid (JW328)	mitogenome	Mineral Hill Cave, NV	N/A	N/A	0.995		N/A
	Reduced	NWSL equid (MS272)	mitogenome	Klondike, YT	N/A	N/A		1.000	N/A

elife-30454-v1.xml

Allele	PCR conditions and comments						Genotping methods
Allele	Primer pair (ID#s)	Align (T^oC)	Extend (secs)	Cycles	Size in bp (WT/M)	Notes	AGE	HMA	Sequencing Primer ID#
gipc1^skt1	12891–12889	62	25	34	372/368	N-PCR (if fixed)	n/a	For hetz	12891
gipc1^skt1	13655–13653	64	19	40	300/296	N-PCR (if fixed)	n/a	For hetz	13653
gipc1 ^skt2	12891–12889	57	30	34	372/379	n/a	n/a	For hetz	12891
gipc2 ^skt3	13667–13422	60	14	35	218/216	n/a	n/a	n/a	13421
gipc2 ^skt4	13667–13422	60	14	35	218/172	n/a	Yes	n/a	13421
gipc3 ^skt5	13510–13512	67.7	25	38	377/337	n/a	Yes	n/a	13512
plxnd1^skt6	11844–11845	65.9	30	34	442/438	N-PCR	n/a	n/a	n/a
plxnd1^skt6	12532–11845	57.7	30	34	262/258	N-PCR	n/a	n/a	12532
plxnd1^fov01b	13498–10167	63	16	38	519/519	N-PCR	n/a	n/a	13646
plxnd1^fov01b	13646–13647	57.5	11	38	395/395	N-PCR	n/a	n/a	13646
Tg(fli1a: GAL4FF)^ubs4	11730–11731	57.5	45	35	402	Only Tg presence	Yes	n/a	n/a

elife-30483-v1.xml

10.7554/eLife.30483.013

Table 2.Statistics of PilQ domain fits.

Homology models of the different PilQ domains were fitted into the respective ring module maps. Each domain was initially placed within the density maps in multiple orientations (n = 10,000), spanning the entire Euler angular space, and subjected to steepest descent local optimization. The resulting fits were clustered and ranked by their CC-scores with the corresponding density maps fits. The table lists the top-5 fits for each domain in the Euler-angle search, along with their CC-scores and the number of independent optimization runs ending in this cluster. The top-ranked fits were assessed for compatibility of the N-to-C-terminal domain orientations (bottom-to-top). The compatible orientations with the highest CC-value was selected as initial fit. Subsequent refinement using MDFF flexible fitting (Trabuco et al., 2008) further improved the fits with minimal structural change.

PilQ domain fits	Total no. of fits	No. of unique fits	Top 5 solutions			Initial chosen protomer fit. CC (Cluster #)	Fit after MDFF. CC (RMSD, Å)	CC for C₁₃ oligomeric ring model	CC after MDFF run with masked density map
PilQ domain fits	Total no. of fits	No. of unique fits	Rank #	CC with map	Runs	Initial chosen protomer fit. CC (Cluster #)	Fit after MDFF. CC (RMSD, Å)	CC for C₁₃ oligomeric ring model	CC after MDFF run with masked density map
N0	10000	152	Rank 1 Rank 2 Rank 3 Rank 4 Rank 5	0.7028 0.6715 0.6696 0.6681 0.6670	576 327 167 33 174	0.7028 (Rank 1)	0.7863 (3.210)	0.70	0.85
N1	10000	115	Rank 1 Rank 2 Rank 3 Rank 4 Rank 5	0.6673 0.6639 0.6583 0.6570 0.6551	530 682 336 110 211	0.6673 (Rank 1)	0.7682 (4.044)	0.70	0.85
N2	10000	48	Rank 1 Rank 2 Rank 3 Rank 4 Rank 5	0.8381 0.8270 0.8270 0.8256 0.8248	784 815 364 475 953	0.8381 (Rank 1)	0.9139 (1.883)	0.84	0.91
N3	10000	32	Rank 1 Rank 2 Rank 3 Rank 4 Rank 5	0.8279 0.8253 0.8249 0.8237 0.8222	473 457 889 829 408	0.8249 (Rank 3)	0.9026 (3.376)	0.84	0.91
N4	10000	32	Rank 1 Rank 2 Rank 3 Rank 4 Rank 5	0.7982 0.7931 0.7793 0.7521 0.7479	1106 757 483 434 511	0.7982 (Rank 1)	0.8539 (2.166)	0.77	0.93
N5	10000	65	Rank 1 Rank 2 Rank 3 Rank 4 Rank 5	0.7394 0.7371 0.7274 0.7218 0.7203	206 292 364 559 329	0.7203 (Rank 5)	0.7562 (2.378)	0.77	0.82
Secretin	9527	86	Rank 1 Rank 2 Rank 3 Rank 4 Rank 5	0.7634 0.7063 0.7013 0.6958 0.6899	672 156 285 104 370	0.7634 (Rank 1)	0.8314 (1.872)	0.77	0.82

elife-30490-v2.xml

10.7554/eLife.30490.007

Table 4.Compilation of Whole-Exome-Sequencing data for the genes of the FANC pathway, excluding all the genes except FANCM as potentially harboring a causative variant.

Gene name	Alias	Mean depth in targeted exons (1)			Nb variants in	Htz variants	Mean ratio for htz allelic	Presence of htz variants (5)					Nbr of rare variants (6)
Gene name	Alias	mother	POI 1	POI 2	family (2)	in >= 1 sister (3)	reads in sisters (4)	upstream	5'UTR	deep intronic	3'UTR	downstream	correct segregation	and pathogenic
FANCA		87.9	94.9	90.3	29	yes	0.92	no	no	yes	yes	yes	0	0
FANCB		88.6	93.8	89.9	2	yes	1.14	no	no	no	no	no	0	0
FANCC		64.4	71.5	68.2	0 in this family
FANCD1	BRCA2	84.6	90.5	84.5	12	yes	1.01	yes	yes	no	no	no	0	0
FANCD2		76.1	82.1	75.0	2	yes	0.825	no	no	no	yes	yes	0	0
FANCE		89.5	100.2	99.0	2	yes	1.08	no	no	no	no	no	0	0
FANCF		143.0	150.2	139.7	0 in this family
FANCG		123.5	139.8	130.2	1	yes	1.22	no	no	no	no	no	0	0
FANCI		75.7	80.3	76.6	9	yes	0.89	no	no	no	no	yes	0	0
FANCJ	BRIP1	104.2	113.0	107.7	4	yes	0.76	no	no	yes	no	no	0	0
FANCL		80.2	88.5	80.7	3	yes	0.96	no	no	no	no	no	0	0
FANCM		86.9	91.3	87.8	1	no	/	no	no	no	no	no	1	1
FANCN	PALB2	97.0	106.9	101.1	0 in this family
FANCO	RAD51C	92.1	103.2	94.9	1	yes	0.77	no	yes	no	no	no	0	0
FANCP	SLX4	107.9	116.4	112.8	15	yes	0.88	no	no	no	yes	no	0	0
FANCQ	ERCC4	91.5	98.1	90.9	2	yes	1.21	no	no	yes	no	no	0	0
FANCR	RAD51	75.9	82.4	74.5	0 in this family
FANCS	BRCA1	87.6	94.3	86.8	1	yes	0.85	no	no	no	no	no	0	0
FANCT	UBE2T	53.9	63.2	52.6	2	yes	0.91	no	no	no	no	no	0	0
FANCU	XRCC2	104.3	116.1	113.1	0 in this family
FANCV	MAD2L2	72.6	85.4	74.3	0 in this family
FAAP100	C17orf70	69.0	66.8	69.1	7	yes	0.94	no	yes	yes	yes	no	0	0
FAAP24	C19orf40	58.3	64.6	59.2	2	yes	0.89	no	no	no	no	no	0	0
FAAP20	C1orf86	57.7	62.0	59.7	3	yes	1.20	yes	no	yes	yes	no	0	0
FAAP16	APITD1	37.7	44.2	40.7	4	yes	1.12	no	yes	yes	no	no	0	0
FAAP10	STRA13	57.3	62.1	57.8	4	yes	1.18	no	yes	no	no	yes	0	0
FAN1		101.8	112.9	102.6	4	yes	0.97	no	no	no	yes	no	0	0
	mean	84.0	91.7	85.9	110		0.99

(1) For each gene, the mean depth per exon was averaged over all exons of the gene. The high coverage for all genes excludes the possibility of not detecting a causative variant in other FANC genes.

(2) Total number of upstream, downstream, 5' and 3' UTRs, intronic, synonymous, splice site, missense, frameshift and stop variants in each gene.

(3) The presence of heterozygous variants in at least one of the patients excludes the possibility of hemizygosity for all genes (with the exception of the variant in FANCM that is homozygous)

(4) The ratio between the number of reads for each allele was averaged for all heterozygous variants in the two affected sisters. A ratio close to one for each gene indicates no bias and argues against a possible deletion for the gene.

(5) The presence of heterozygous variants in the various genic portions argues against the possibility of partial deletions.

(6) Among the 110 variants detected in the genes included in the FANC pathway, only the non-sense variant found in FANCM is homozygous in both patients, is rare (below 1% in ExAC database) and predicted as pathogenic.

elife-30637-v1.xml

10.7554/eLife.30637.002

Table 1.Distribution of infection types and relatedness of nose-colonizing and infecting <italic>S. aureus</italic> among 105 patients revealed by genomic comparison.

Infection sites	Relation of nose-colonizing to infecting bacteria
	Unrelated (≥1104 variants)	Closely related (≤66 variants)
	Unrelated (≥1104 variants)	Zero shared genotypes	One shared genotype
Bloodstream	4	43	8
Soft tissue	4	23	10
Bone and joint	2	8	3
Total	10	74	21

elife-30743-v2.xml

10.7554/eLife.30743.006

Table 1.Experimental data used to fit the model (training set).

Animals heterozygous for null mutations in lin-3 or lin-12 are described in the model by dividing the signal by two (‘half dose’). The EGF level for one overexpression line (JU1107) was set according to the measured lin-3 mRNA level. For other perturbations, the change in signal is included as a fitting parameter, cf. Table S2. * Notch null mutations result in the formation of two anchor cells, thus the effect of suppressing Notch signaling between VPCs it not obvious; however, several lines of evidence suggest that it yields the pattern 33133.

Experiment	VPC fates (fate or % 1°, 2°, 3°)					References
Experiment	P4.p	P5.p	P6.p	P7.p	P8.p	References
Wild type	3°	2°	1°	2°	3°
EGF/Notch mutants
let-23 mosaic (no EGF receptors in P5/7 .p)	wild type					(Koga and Ohshima, 1995; Simske et al., 1995)
Half dose of EGF (lin-3/+)	wild type					(Ferguson and Horvitz, 1985)
Half dose of Notch (lin-12/+)	wild type					(Greenwald et al., 1983)
No Notch signaling *	3°	3°	1°	3°	3°	(Sundaram and Greenwald, 1993; Shaye and Greenwald, 2002; Komatsu et al., 2008)
Notch null mutant, 2 ACs * (described as 2 × WT EGF)	3°	1°	1°	1°	3°	(Greenwald et al., 1983)
lin-15 mutant (ectopic EGF; fit to ~0.4 × WT)	alternating 1° and 2° fates (with or without AC)					(Sternberg, 1988)
EGF overexpression
JU1107 2.75 × WT EGF (based on measured mRNA level)	2, 16, 82	22, 78, 0	100, 0, 0	16, 84, 0	3, 13, 84	(Barkoulas et al., 2013)
JU1100 (mRNA level not determined; level fit)	24, 54, 21	54, 46, 0	96, 4, 0	37, 63, 0	12, 39, 49	(Hoyos et al., 2011)
AC ablation at successive developmental stages (mapped to evenly spaced time points in the model)						(Milloz et al., 2008)
L2 lethargus (t = 0.2)		3°	3°	3°
early L3 (t = 0.32)		3, 24, 74	18, 19, 64	0, 20, 80
DU divided (t = 0.44)		0, 59, 41	31, 37, 32	0, 53, 47
VU divided (t = 0.56)		0, 95, 5	53, 48, 0	8, 86, 6
3° divided (t = 0.68)		3, 98, 0	65, 35, 0	0, 100, 0
two-cell stage (t = 0.8)		1, 99, 0	93, 7, 0	1, 99, 0
Epistasis between EGF/Notch						(Barkoulas et al., 2013)
CB1417 (lin-3(e1417) EGF hypomorph; level fit)	0, 0, 100	0, 10, 90	54, 0, 46	0, 10, 90	0, 0, 100
JU2064 (mild ectopic Notch activity; level fit)	0, 1, 99	0, 100, 0	100, 0, 0	0, 100, 0	1, 2, 97
JU2095 (mild ectopic Notch activity in the lin-3(e1417) background)	0, 0, 100	1, 14, 86	72, 1, 28	0, 16, 84	0, 2, 98

elife-30743-v2.xml

10.7554/eLife.30743.016

Table 4.Comparison between model predictions and experimental outcomes from (<xref ref-type="bibr" rid="bib2">Barkoulas et al., 2013</xref>).

The model prediction (mean ±SD within the parameter ensemble) is displayed below the experimental outcome.

Experiment	VPC fates (% 1°, 2°, 3°)
Experiment	P4.p	P5.p	P6.p	P7.p	P8.p
Excess EGF × reduced Notch (Figure 3) The Notch level is our fit for Notch RNAi in the JU2039 line ~ 0.4 × WT. The EGF level is based on the mRNA level measured in the JU2036 EGF perturbation line (Barkoulas et al., 2013).
JU2039 (WT EGF)	1, 0, 99	1, 91, 8	100, 0, 0	1, 87, 11	0, 0, 100
	0 ± 0, 0 ± 0, 99 ± 0	3 ± 1, 88 ± 1, 8 ± 1	99 ± 0, 0 ± 0, 1 ± 0	3 ± 1, 89 ± 1, 8 ± 1	0 ± 0, 0 ± 0, 99 ± 0
JU2113 (1.25 × WT EGF)	7, 10, 83	32, 60, 8	100, 0, 0	4, 79, 17	0, 2, 98
	0 ± 0, 0 ± 0, 99 ± 0	16 ± 8, 76 ± 9, 9 ± 2	99 ± 0, 0 ± 0, 1 ± 0	16 ± 9, 75 ± 10, 9 ± 2	0 ± 0, 0 ± 0, 99 ± 0
Excess EGF × ectopic Notch activity (Figure 4) Increasing EGF levels in a background with mild ectopic Notch activity. The level of ectopic Notch activity is our fit for the JU2064 line ~ WT + 0.05. EGF levels are based on measured mRNA levels in the EGF perturbation lines JU2036, JU2035, and JU1107 (Barkoulas et al., 2013).
JU2091 (1.25 × WT EGF)	0, 0, 100	0, 100, 0	100, 0, 0	0, 100, 0	0, 1, 99
	0 ± 0, 1 ± 1, 99 ± 1	1 ± 0, 99 ± 1, 1 ± 0	98 ± 0, 1 ± 0, 1 ± 0	1 ± 0, 99 ± 1, 1 ± 0	0 ± 0, 1 ± 1, 99 ± 1
JU2089 (1.79 × WT EGF)	0, 5, 96	2, 98, 0	100, 0, 0	2, 99, 0	1, 7, 92
	0 ± 0, 6 ± 5, 93 ± 5	2 ± 1, 97 ± 2, 1 ± 1	99 ± 0, 1 ± 0, 1 ± 0	2 ± 1, 97 ± 2, 1 ± 1	1 ± 0, 6 ± 5, 93 ± 6
JU2092 (2.75 × WT EGF)	3, 24, 74	0, 100, 0	100, 0, 0	0, 100, 0	8, 24, 68
	1 ± 1, 38 ± 14, 61 ± 14	9 ± 4, 88 ± 5, 3 ± 1	99 ± 0, 1 ± 0, 1 ± 0	8 ± 4, 88 ± 5, 3 ± 1	1 ± 1, 38 ± 14, 61 ± 14

elife-30822-v2.xml

10.7554/eLife.30822.008

Table 1.Root-mean square deviation (RMSD) values (in Å) between subunit pairs within 80α, within SaPI1 and between 80α and SaPI1.

Values for ‘unpruned’ structures include all atoms when determining the best fit. Values for ‘pruned’ structures only include the best matching residue pairs. Pruning was done in UCSF Chimera using standard parameters. For 80α, pairs of subunits related across the quasi-twofold axis are highlighted in green. Comparison of subunits for which the E-loops are in the ‘UP’ conformation are highlighted in blue.

Root mean square deviation between CP subunits
		Pruned		Unpruned
		# res.	RMSD (Å)	# res.	RMSD (Å)
80α procapsid
subA	subB	215	0.986	284	2.927
subA	subC	250	0.897	284	1.521
subA	subD	239	0.943	284	2.902
subA	subE	218	0.989	284	2.900
subA	subF	252	0.899	284	1.533
subA	subG	239	1.024	284	2.878
subB	subC	224	0.881	284	3.072
subB	subD	229	0.955	284	1.901
subB	subE	251	0.727	284	1.506
subB	subF	219	0.907	284	3.244
subB	subG	232	0.909	284	1.686
subC	subD	241	0.853	284	3.002
subC	subE	225	0.923	284	3.108
subC	subF	271	0.764	284	0.987
subC	subG	237	0.860	284	2.974
subD	subE	231	1.001	284	1.715
subD	subF	246	0.781	284	3.195
subD	subG	262	0.704	284	1.302
subE	subF	220	0.979	284	3.257
subE	subG	236	0.981	284	1.654
subF	subG	242	0.847	284	3.104
SaPI1 procapsid
subA	subB	218	1.047	284	2.656
subA	subC	247	1.092	284	1.572
subA	subD	223	1.108	284	2.862
subB	subC	220	1.040	284	2.865
subB	subD	231	1.040	284	1.633
subC	subD	242	0.921	284	2.669
SaPI1 vs. 80α
SaPI1	80α
subA	subA	259	0.920	284	1.495
subB	subB	250	0.926	284	1.443
subB	subE	257	0.823	284	1.380
subC	subC	268	0.935	284	1.165
subC	subF	268	0.997	284	1.190
subD	subD	247	0.948	284	1.536
subD	subG	262	0.939	284	1.170

elife-31023-v1.xml

10.7554/eLife.31023.006

Table 1.Examples of proteins identified by enChIP-MS.

Gene name	Sample				Category
	gD4Z4		gMYOD1
	# peptides*	% coverage^†	# peptides*	% coverage^†
CBX3/HP1γ	4.7	15.7	0.0	0.0	Known D4Z4-associated proteins
NCL	47.4	22.3	34.0	14.2
PDS5B	2.0	11.2	0.0	0.0
RAD21	1.8	2.9	0.0	0.0
SMC1A	7.0	5.8	2.0	1.8
SMC3	17.0	6.7	1.0	1.0
SMCHD1	1.6	2.4	0.0	0.0
CHD4	8.3	3.1	0.0	0.0	NuRD complex components
HDAC2	2.5	5.6	3.0	6.8
MTA2	1.2	2.2	1.0	1.5
RBBP4	4.5	7.5	4.0	6.9

*Average number of peptides recovered from each sample type, combining like (gD4Z4 or gMYOD1) immunoprecipitations.

^†Average percentage of each protein covered by the identified peptides from each sample type, combining like (gD4Z4 or gMYOD1) immunoprecipitations.

elife-31126-v1.xml

10.7554/eLife.31126.005

Table 1.Summary of demographics for donors with and without dementia.

P-values for upper seven and lower two metrics are uncorrected significance values from T-tests and hypergeometric tests, respectively (*p<0.05 after Bonferroni correction for multiple comparisons). Demographic summary includes 106 donors used in analysis (Materials and methods).

Category	Non-demented		Demented
Category	Mean	SD	Mean	SD	P-value
Age at death (yrs)	89	7	90	6	2.8E-01
Education (yrs)	15	3	14	3	4.9E-02
Number of TBIs	0.6	0.7	0.7	0.7	8.0E-01
Age at first TBI	23	31	24	32	8.2E-01
Braak stage	2.8	1.5	4.1	1.7	8.9E-05*
NIA Reagan	1.4	0.7	1.9	0.9	1.8E-03*
CERAD score	1.2	0.9	1.8	1.2	1.4E-02
	Count		Count		P-value
Sex	20 F / 36 M		23 F / 27 M		1.0E-01
>0 APOE ɛ4 alleles	47 No/7 Yes		32 No/13 Yes		2.1E-02

elife-31225-v1.xml

10.7554/eLife.31225.004

Table 1.Parameters of analyses of variance for the effects of group (early-born, late-born) and diet (fed ad libitum or intermittently fasted) on the rate (‘slope’) of body mass gain and structural growth (assessed by body length), the maximal level (‘plateau’) at which BM and BL levelled off and the time (‘time of plateau’) at which the plateau of BM or BL occurred during the pre-hibernation period.

p-values shown in bold correspond to statistically significant and interpretable values.

Parameter	Term	Response variables
		Slope		Plateau		Time of plateau
		F-value	p-value	F-value	p-value	F-value	p-value
Body mass	Group Diet Group х Diet	70.93 1.00 3.58	<0.001 0.33 0.07	5.73 0.05 0.13	<0.05 0.83 0.72	368.71 0.07 0.44	<0.001 0.80 0.52
Body length	Group Diet Group х Diet	103.55 0.01 1.65	<0.001 0.92 0.21	1.46 0.01 0.12	0.24 0.97 0.73	190.11 0.43 0.29	<0.001 0.52 0.60

elife-31225-v1.xml

10.7554/eLife.31225.009

Table 4.Parameters of analyses of variance for the effects of group and diet on the time (‘starting time’) and the rate (‘slope’) of torpor increase or decrease of activity time.

Mean torpor duration was also added as a predictor variable in the model for activity time and mean ambient temperature was included as a random effect in all models. p-values shown in bold correspond to statistically significant and interpretable values.

Response variable	Term	Parameters
		Starting time		Slope
		χ²	p-value	χ ²	p-value
Torpor frequency	Group Diet Group х Diet	46.47 8.64 1.82	<0.001 <0.01 0.18	3.16 1.18 7.02	0.08 0.28 <0.01
Mean torpor duration	Group Diet Group х Diet	43.49 8.84 0.50	<0.001 <0.01 0.48	38.26 0.35 16.64	<0.001 0.55 <0.001
Total torpor duration	Group Diet Group х Diet	43.49 8.84 0.50	<0.001 <0.01 0.48	77.86 0.55 9.66	<0.001 0.46 <0.01
Activity time	Group Diet Group х Diet Mean torpor duration	0.09 14.06 6.96 7.61	0.76 <0.001 <0.01 <0.01	6.45 2.64 0.22 2.68	<0.05 0.10 0.64 0.10

elife-31469-v2.xml

10.7554/eLife.31469.016

Table 2.Disassembly rates <italic>k0</italic> (min−1) and dispersion of F-actin length distributions.

	UtrCH-stabilized				Lat A-treated*		SMIFH2-treated
	Control	Low	Medium	High	Control	Lat A	Control	SMIFH2
k₀	0.162	0.126	0.073	0.048	0.0819	0.5106	0.1995	0.1650
λ’	0.677	0.889	6.946	709.4	0.0671	14.66	1.555	1.540

*The solvent, DMSO had an effect on the viscolelastic parameters even in controls (Supplementary file 3).

elife-31486-v2.xml

10.7554/eLife.31486.040

Appendix 1—table 7.Sequence similarity comparison.

Frequencies of dipeptides (pairs of neighboring amino residues) were computed for phase-separating proteins and the human proteome, and enrichment was measured by the percentage of human proteins with lower frequency than found in a given sequence. The fifteen dipeptides enriched (≥99%) in the most sequences within the phase separation test sets are shown in the table vs. enrichment values obtained for the phase separation training set and three experimentally verified proteins. Values in the top fifth percentile are shown in bold.

Protein Name	Dipeptide enrichment (Percentage of human proteome with lower frequency)
Protein Name	GV	VG	VP	PG	FG	RG	GR	GG	YG	GS	SG	GA	GF	GD	DS
Training Set Proteins
Elastin	100	100	100	100	97	31	32	99	99	20	20	100	89	38	30
Nsp1	30	34	31	26	100	31	30	75	52	90	38	99	60	66	68
TIA1	73	75	46	26	86	31	86	77	99	29	53	26	84	54	30
LAF1	30	78	65	29	67	99	99	100	77	88	97	65	78	97	32
EIF4H	30	65	31	52	98	99	95	99	52	99	42	79	99	98	89
Ddx3x	51	70	34	43	89	98	97	96	93	93	95	68	96	59	78
hnRNPA1	30	55	31	44	100	99	99	100	99	99	98	44	99	60	79
DDX4	33	77	48	53	98	96	91	89	59	87	96	29	98	96	45
FUS	30	31	31	83	78	100	99	100	100	98	99	33	93	91	57
EWS	52	31	35	97	51	100	99	100	100	72	61	30	97	91	48
TAF15	36	38	31	30	53	100	99	100	100	92	99	26	71	100	94
Experimentally Verified Proteins
FMR1	69	89	93	44	43	96	94	83	62	62	34	70	48	41	67
SCAF pAP	75	50	89	91	43	49	73	97	75	92	96	96	40	36	44
Engrailed-2	30	31	31	97	70	78	90	100	52	99	91	99	40	95	97

elife-31511-v2.xml

10.7554/eLife.31511.016

Table 1.<italic>SLC7A8</italic> Humans mutations found in ARHL and controls individuals.

Phenotype	Age	Sex	Chr. 14	Variant	Consequence	Code	Frequency
Phenotype	Age	Sex	Chr. 14	Variant	Consequence	Code	Esp6500siv2	1000 g	Campion	ExAC	Studied cohort
ARHL	75	Female	23597290	14:23597291 C / T	p.Val460Glu	V460E	NA	NA	0.0013	0.00002475	0.015
ARHL	57	Male	23598917	14:23598917 G / A	p.Thr402Met	T402M	NA	NA	0.0047	0.00002471	0.015
ARHL	75	Male	23608641	14:23608641 C / T (rs142951280)	p.Val302Ile	V302I	0.0005	NA	0.0047	0.0004613	0.015
ARHL	86	Female	23598870	14:23598869 C / T	p.Arg418His	R418C	0.0005	NA	0.002	0.00002477	0.015
control	50	Male	23652101	14:23652101 C / G (rs141772308)	p.Arg8Pro	R8P	0.0008	NA	0.0013	0.0008156	0.012
control	50	Male	23635621	14:23635621 C / T (rs139927895)	p.Ala94Thr	A94T	0.0012	0.002	0.0013	0.00202	0.012
control	90	Female	23612368	14:23612368 C / T (rs149245114)	p.Arg185Gln	R185L	NA	NA	0.002	0.00002471	0.012

ARHL (age-related hearing loss). The age (years) of the subject when the Audiogram was performed is indicated. Variant [CHR: position reference/alternate (dbSNP135rsID)]. Consequence [HGUS annotation (protein change)]. Code [short description of the alternate variant]. Frequency of the mutations: Esp6500siv2 (NHLBI Exome Sequencing Project), 1000 g (1000 Genomes Project), Campion (The Allele Frequency Net Database) and ExAC (The Exome Aggregation Consortium).

elife-31511-v3.xml

10.7554/eLife.31511.016

Table 1.<italic>SLC7A8</italic> Humans mutations found in ARHL and controls individuals.

Phenotype	Age	Sex	Chr. 14	Variant	Consequence	Code	Frequency
Phenotype	Age	Sex	Chr. 14	Variant	Consequence	Code	Esp6500siv2	1000 g	Campion	ExAC	Studied cohort
ARHL	75	Female	23597290	14:23597290 A / T	p.Val460Glu	V460E	NA	NA	0.0013	0.00002475	0.015
ARHL	57	Male	23598917	14:23598917 G / A	p.Thr402Met	T402M	NA	NA	0.0047	0.00002471	0.015
ARHL	75	Male	23608641	14:23608641 C / T (rs142951280)	p.Val302Ile	V302I	0.0005	NA	0.0047	0.0004613	0.015
ARHL	86	Female	23598870	14:23598870 G / A (rs146946494)	p.Arg418His	R418C	0.0005	NA	0.002	0.00002477	0.015
control	50	Male	23652101	14:23652101 C / G (rs141772308)	p.Arg8Pro	R8P	0.0008	NA	0.0013	0.0008156	0.012
control	50	Male	23635621	14:23635621 C / T (rs139927895)	p.Ala94Thr	A94T	0.0012	0.002	0.0013	0.00202	0.012
control	90	Female	23612368	14:23612368 C / A (rs149245114)	p.Arg185Gln	R185L	NA	NA	0.002	0.00002471	0.012

elife-31511-v4.xml

10.7554/eLife.31511.016

Table 1.<italic>SLC7A8</italic> Humans mutations found in ARHL and controls individuals.

Phenotype	Age	Sex	Chr. 14	Variant	Consequence	Code	Frequency
Phenotype	Age	Sex	Chr. 14	Variant	Consequence	Code	Esp6500siv2	1000 g	Campion	ExAC	Studied cohort
ARHL	75	Female	23597290	14:23597290 A / T	p.Val460Glu	V460E	NA	NA	0.0013	0.00002475	0.015
ARHL	57	Male	23598917	14:23598917 G / A	p.Thr402Met	T402M	NA	NA	0.0047	0.00002471	0.015
ARHL	75	Male	23608641	14:23608641 C / T (rs142951280)	p.Val302Ile	V302I	0.0005	NA	0.0047	0.0004613	0.015
ARHL	86	Female	23598870	14:23598870 G / A (rs146946494)	p.Arg418Cys	R418C	0.0005	NA	0.002	0.00002477	0.015
control	50	Male	23652101	14:23652101 C / G (rs141772308)	p.Arg8Pro	R8P	0.0008	NA	0.0013	0.0008156	0.012
control	50	Male	23635621	14:23635621 C / T (rs139927895)	p.Ala94Thr	A94T	0.0012	0.002	0.0013	0.00202	0.012
control	90	Female	23612368	14:23612368 C / A (rs149245114)	p.Arg185Gln	R185L	NA	NA	0.002	0.00002471	0.012

elife-31543-v2.xml

10.7554/eLife.31543.009

Table 1.Bursting characteristics of CA1 place cells during exploration and rest.

10.7554/eLife.31543.010Table 1—source data 1.CA1 bursting analysis - full data set.

	Linear track								Rest
	WT			Dp16				p-value	WT			Dp16				p-value
Bursts per min	7.901	±	0.532	5.777	±	0.383	***	0.0007	7.152	±	0.685	5.741	±	0.468	*	0.0315
Mean Inter-burst Interval (s)	18.940	±	1.692	25.145	±	1.907	***	0.0002	30.061	±	2.141	56.144	±	6.640	*	0.0320
Mean burst duration (ms)	7.720	±	0.186	8.435	±	0.318	***	2.67E-07	12.718	±	4.251	8.281	±	0.072		0.1305
% of spikes in burst	33.1%	±	0.8%	24.4%	±	0.7%	***	2.17E-13	29.7%	±	0.8%	22.3%	±	0.7%	***	9.58E-12
Nb. Spikes per burst	2.264	±	0.008	2.243	±	0.009	*	0.0110	2.374	±	0.010	2.264	±	0.009	***	1.59E-14

elife-31596-v1.xml

10.7554/eLife.31596.007

Table 1.Assignments of Ile δ1 methyl groups of full-length MgtE.

Chemical shifts for δ1 methyl groups in Ile residues in the Mg²⁺-free and bound states are shown. Labels a and b are used to discriminate two signals from a single Ile residue. ¹H chemical shifts were referenced to external sodium 2,2-dimethyl-2-silapentane-5-sulfonate (0 ppm), and ¹³C chemical shifts were referenced indirectly. Spectral width (eight ppm) in the ¹³C dimension was subtracted from the ¹³C chemical shift of I338 owing to spectral aliasing.

Methyl group	Mg²⁺-free state (0 mM Mg²⁺)		Mg²⁺-bound state (5.0 mM Mg²⁺)
Methyl group	¹H (ppm)	¹³C (ppm)	¹H (ppm)	¹³C (ppm)
I28	0.729	14.16	0.714	14.13
I84	0.559	13.63	0.526	13.62
I168a	0.539	14.12	0.526	14.14
I168b	–	–	0.606	14.62
I171a	0.651	13.99	0.644	13.98
I171b	–	–	0.606	14.62
I190a	0.627	13.77	0.621	13.77
I190b	–	–	0.641	12.83
I201	0.606	14.62	0.599	14.33
I242	–	–	0.85	14.13
I260	0.771	13.13	0.762	13.15
I291	–	–	−0.171	11.63
I293	0.773	12.66	0.858	15.45
I302	–	–	0.872	14.68
I338	0.145	8.67	0.264	10.16
I339	0.799	12.66	0.798	12.65
I397	0.771	14.59	0.728	14.92
I438	0.674	13.54	0.693	13.58

elife-31596-v2.xml

10.7554/eLife.31596.007

Table 1.Assignments of Ile δ1 methyl groups of full-length MgtE.

Methyl group	Mg²⁺-free state (0 mM Mg²⁺)		Mg²⁺-bound state (5.0 mM Mg²⁺)
Methyl group	¹H (ppm)	¹³C (ppm)	¹H (ppm)	¹³C (ppm)
I28	0.729	14.16	0.714	14.13
I84	0.559	13.63	0.526	13.62
I168a	0.539	14.12	0.526	14.14
I168b	–	–	0.606	14.62
I171a	0.651	13.99	0.644	13.98
I171b	–	–	0.606	14.62
I190a	0.627	13.77	0.621	13.77
I190b	–	–	0.641	12.83
I201	0.606	14.62	0.599	14.33
I242	–	–	0.85	14.13
I260	0.771	13.13	0.762	13.15
I291	–	–	−0.171	11.63
I293	0.773	12.66	0.858	15.45
I302	–	–	0.872	14.68
I338	0.145	8.67	0.264	10.16
I339	0.799	12.66	0.798	12.65
I397	0.771	14.59	0.728	14.92
I438	0.674	13.54	0.693	13.58

elife-31677-v1.xml

10.7554/eLife.31677.014

Table 1.Mating procedure results for the six proof-of-principle AGOC sublines from the F3 to the F7 generation.

Bold entries mark progeny that were used in the subsequent cross. F6-S, F7-O and F7-C are control crosses. No significant differences between the arithmetic means and the theoretical Mendelian ratios were found. See Source Data 1 for raw scores ordered by transgenic sublines.

10.7554/eLife.31677.015Table 1—source data 1.Raw scores for all mating procedure result tables ordered by transgenic sublines.

Gen	Cross	Subline	Progeny
Gen	Cross	Subline									Total
F3		Theoretical	-	50.0%	-	-	-	-	-	50.0%	-
		AGOC #1	-	47.9% (46)	-	-	-	-	-	52.1% (50)	96
		AGOC #2	-	52.4% (44)	-	-	-	-	-	47.6% (40)	84
		AGOC #3	-	55.1% (49)	-	-	-	-	-	44.9% (40)	89
		AGOC #4	-	44.1% (41)	-	-	-	-	-	55.9% (52)	93
		AGOC #5	-	47.6% (39)	-	-	-	-	-	52.4% (43)	82
		AGOC #6	-	48.2% (27)	-	-	-	-	-	51.8% (29)	56
		Mean	-	49.2 ± 3.9%	-	-	-	-	-	50.8 ± 3.9%	83.3
F4		Theoretical	25.0%	25.0%	12.5%	12.5%	12.5%	12.5%	-	-	-
		AGOC #1	25.6% (30)	34.2% (40)	4.3% (5)	10.2% (12)	6.0% (7)	19.7% (23)	-	-	117
		AGOC #2	27.3% (36)	28.9% (38)	15.1% (20)	8.3% (11)	9.8% (13)	10.6% (14)	-	-	132
		AGOC #3	25.8% (33)	32.8% (42)	13.3% (17)	10.1% (13)	5.5% (7)	12.5% (16)	-	-	128
		AGOC #4*	14.0% (14)	15.0% (15)	20.0% (20)	13.0% (13)	22.0% (22)	9.0% (9)	3.0% (3)	4.0% (4)	100
		AGOC #5	17.1% (20)	40.2% (47)	16.2% (19)	8.5% (10)	10.3% (12)	7.7% (9)	-	-	117
		AGOC #6	33.6% (39)	33.6% (39)	8.6% (10)	6.9% (8)	6.1% (7)	11.2% (13)	-	-	116
		Mean	23.9 ± 7.2%	30.8 ± 8.5%	12.9 ± 5.6%	9.5 ± 2.1%	9.9 ± 6.3%	11.8 ± 4.2%	0.5%	0.7%	118.3
F5		Theoretical	25.0%	-	25.0%	25.0%	-	-	25.0%	-	-
		AGOC #1	27.2% (31)	-	26.3% (30)	23.7% (27)	-	-	22.8% (26)	-	114
		AGOC #2	28.9% (26)	-	33.3% (30)	17.8% (16)	-	-	20.0% (18)	-	90
		AGOC #3	24.8% (30)	-	27.3% (33)	24.8% (30)	-	-	23.1% (28)	-	121
		AGOC #4	19.3% (21)	-	22.9% (25)	37.6% (41)	-	-	20.2% (22)	-	109
		AGOC #5	28.2% (31)	-	29.1% (32)	12.7% (14)	-	-	30.0% (33)	-	110
		AGOC #6	26.2% (22)	-	29.7% (25)	16.7% (14)	-	-	27.4% (23)	-	84
		Mean	25.8 ± 3.5%	-	28.1 ± 3.5%	22.2 ± 8.8%	-	-	23.9 ± 4.0%	-	104.7
F6-S		Theoretical	-	-	50.0%	50.0%	-	-	-	-
		AGOC #1	-	-	46.4% (39)	53.6% (44)	-	-	-	-	84
		AGOC #2	-	-	50.0% (49)	50.0% (49)	-	-	-	-	98
		AGOC #3	-	-	54.0% (68)	46.0% (58)	-	-	-	-	126
		AGOC #4	-	-	53.8% (50)	46.2% (43)	-	-	-	-	93
		AGOC #5	-	-	51.3% (59)	48.7% (56)	-	-	-	-	115
		AGOC #6	-	-	57.0% (49)	43.0% (37)	-	-	-	-	86
		Mean	-	-	52.1 ± 3.7%	47.9 ± 3.7%	-	-	-	-	100.3
F6		Theoretical	-	-	25.0%	25.0%	-	-	50.0%	-	-
		AGOC #1	-	-	20.3% (23)	24.8% (28)	-	-	54.9% (62)	-	113
		AGOC #2	-	-	21.5% (23)	35.5% (38)	-	-	43.0% (46)	-	117
		AGOC #3	-	-	22.9% (27)	22.9% (27)	-	-	54.2% (64)	-	118
		AGOC #4	-	-	22.0% (29)	22.7% (30)	-	-	55.3% (73)	-	132
		AGOC #5	-	-	17.5% (18)	31.1% (32)	-	-	51.4% (53)	-	103
		AGOC #6	-	-	19.8% (22)	24.3% (27)	-	-	55.9% (62)	-	111
		Mean	-	-	20.7 ± 1.9%	26.9 ± 5.2%	-	-	52.4 ± 4.9%	-	115.7
F7-O		Theoretical	-	-	100%	-	-	-	-	-	-
		AGOC #1	-	-	100% (94)	-	-	-	-	-	94
		AGOC #2	-	-	100% (50)	-	-	-	-	-	50
		AGOC #3	-	-	100% (49)	-	-	-	-	-	49
		AGOC #4	-	-	100% (79)	-	-	-	-	-	79
		AGOC #5	-	-	100% (79)	-	-	-	-	-	79
		AGOC #6	-	-	100% (63)	-	-	-	-	-	63
		Mean	-	-	100 ± 0%	-	-	-	-	-	69.0
F7-C		Theoretical	-	-	-	100%	-	-	-	-	-
		AGOC #1	-	-	-	100% (101)	-	-	-	-	101
		AGOC #2	-	-	-	100% (105)	-	-	-	-	105
		AGOC #3	-	-	-	100% (89)	-	-	-	-	89
		AGOC #4	-	-	-	100% (54)	-	-	-	-	54
		AGOC #5	-	-	-	100% (74)	-	-	-	-	74
		AGOC #6	-	-	-	100% (64)	-	-	-	-	64
		Mean	-	-	-	100 ± 0%	-	-	-	-	81.2

*In the AGOC #4 subline, incomplete recombination occurred in the F4 (mCe; mO-mC) double hemizygous generation, as we obtained several F5 individuals that still carried both transformation markers (7.0% in total). We continued the mating procedure with the F5 (mO) and (mC) post-recombination hemizygous progeny.

elife-31677-v2.xml

10.7554/eLife.31677.014

Table 1.Mating procedure results for the six proof-of-principle AGOC sublines from the F3 to the F7 generation.

10.7554/eLife.31677.015Table 1—source data 1.Raw scores for all mating procedure result tables ordered by transgenic sublines.

Gen	Cross	Subline	Progeny
Gen	Cross	Subline									Total
F3		Theoretical	-	50.0%	-	-	-	-	-	50.0%	-
		AGOC #1	-	47.9% (46)	-	-	-	-	-	52.1% (50)	96
		AGOC #2	-	52.4% (44)	-	-	-	-	-	47.6% (40)	84
		AGOC #3	-	55.1% (49)	-	-	-	-	-	44.9% (40)	89
		AGOC #4	-	44.1% (41)	-	-	-	-	-	55.9% (52)	93
		AGOC #5	-	47.6% (39)	-	-	-	-	-	52.4% (43)	82
		AGOC #6	-	48.2% (27)	-	-	-	-	-	51.8% (29)	56
		Mean	-	49.2 ± 3.9%	-	-	-	-	-	50.8 ± 3.9%	83.3
F4		Theoretical	25.0%	25.0%	12.5%	12.5%	12.5%	12.5%	-	-	-
		AGOC #1	25.6% (30)	34.2% (40)	4.3% (5)	10.2% (12)	6.0% (7)	19.7% (23)	-	-	117
		AGOC #2	27.3% (36)	28.9% (38)	15.1% (20)	8.3% (11)	9.8% (13)	10.6% (14)	-	-	132
		AGOC #3	25.8% (33)	32.8% (42)	13.3% (17)	10.1% (13)	5.5% (7)	12.5% (16)	-	-	128
		AGOC #4*	14.0% (14)	15.0% (15)	20.0% (20)	13.0% (13)	22.0% (22)	9.0% (9)	3.0% (3)	4.0% (4)	100
		AGOC #5	17.1% (20)	40.2% (47)	16.2% (19)	8.5% (10)	10.3% (12)	7.7% (9)	-	-	117
		AGOC #6	33.6% (39)	33.6% (39)	8.6% (10)	6.9% (8)	6.1% (7)	11.2% (13)	-	-	116
		Mean	23.9 ± 7.2%	30.8 ± 8.5%	12.9 ± 5.6%	9.5 ± 2.1%	9.9 ± 6.3%	11.8 ± 4.2%	0.5%	0.7%	118.3
F5		Theoretical	25.0%	-	25.0%	25.0%	-	-	25.0%	-	-
		AGOC #1	27.2% (31)	-	26.3% (30)	23.7% (27)	-	-	22.8% (26)	-	114
		AGOC #2	28.9% (26)	-	33.3% (30)	17.8% (16)	-	-	20.0% (18)	-	90
		AGOC #3	24.8% (30)	-	27.3% (33)	24.8% (30)	-	-	23.1% (28)	-	121
		AGOC #4	19.3% (21)	-	22.9% (25)	37.6% (41)	-	-	20.2% (22)	-	109
		AGOC #5	28.2% (31)	-	29.1% (32)	12.7% (14)	-	-	30.0% (33)	-	110
		AGOC #6	26.2% (22)	-	29.7% (25)	16.7% (14)	-	-	27.4% (23)	-	84
		Mean	25.8 ± 3.5%	-	28.1 ± 3.5%	22.2 ± 8.8%	-	-	23.9 ± 4.0%	-	104.7
F6-S		Theoretical	-	-	50.0%	50.0%	-	-	-	-
		AGOC #1	-	-	46.4% (39)	53.6% (44)	-	-	-	-	84
		AGOC #2	-	-	50.0% (49)	50.0% (49)	-	-	-	-	98
		AGOC #3	-	-	54.0% (68)	46.0% (58)	-	-	-	-	126
		AGOC #4	-	-	53.8% (50)	46.2% (43)	-	-	-	-	93
		AGOC #5	-	-	51.3% (59)	48.7% (56)	-	-	-	-	115
		AGOC #6	-	-	57.0% (49)	43.0% (37)	-	-	-	-	86
		Mean	-	-	52.1 ± 3.7%	47.9 ± 3.7%	-	-	-	-	100.3
F6		Theoretical	-	-	25.0%	25.0%	-	-	50.0%	-	-
		AGOC #1	-	-	20.3% (23)	24.8% (28)	-	-	54.9% (62)	-	113
		AGOC #2	-	-	21.5% (23)	35.5% (38)	-	-	43.0% (46)	-	117
		AGOC #3	-	-	22.9% (27)	22.9% (27)	-	-	54.2% (64)	-	118
		AGOC #4	-	-	22.0% (29)	22.7% (30)	-	-	55.3% (73)	-	132
		AGOC #5	-	-	17.5% (18)	31.1% (32)	-	-	51.4% (53)	-	103
		AGOC #6	-	-	19.8% (22)	24.3% (27)	-	-	55.9% (62)	-	111
		Mean	-	-	20.7 ± 1.9%	26.9 ± 5.2%	-	-	52.4 ± 4.9%	-	115.7
F7-O		Theoretical	-	-	100%	-	-	-	-	-	-
		AGOC #1	-	-	100% (94)	-	-	-	-	-	94
		AGOC #2	-	-	100% (50)	-	-	-	-	-	50
		AGOC #3	-	-	100% (49)	-	-	-	-	-	49
		AGOC #4	-	-	100% (79)	-	-	-	-	-	79
		AGOC #5	-	-	100% (79)	-	-	-	-	-	79
		AGOC #6	-	-	100% (63)	-	-	-	-	-	63
		Mean	-	-	100 ± 0%	-	-	-	-	-	69.0
F7-C		Theoretical	-	-	-	100%	-	-	-	-	-
		AGOC #1	-	-	-	100% (101)	-	-	-	-	101
		AGOC #2	-	-	-	100% (105)	-	-	-	-	105
		AGOC #3	-	-	-	100% (89)	-	-	-	-	89
		AGOC #4	-	-	-	100% (54)	-	-	-	-	54
		AGOC #5	-	-	-	100% (74)	-	-	-	-	74
		AGOC #6	-	-	-	100% (64)	-	-	-	-	64
		Mean	-	-	-	100 ± 0%	-	-	-	-	81.2

elife-31724-v2.xml

10.7554/eLife.31724.037

Table 1.Summary of topo VI functional activities and mutant effects.

Assay	Wildtype activity	Effect of mutation to:
Assay	Wildtype activity	KGRR loop	Stalk/WKxY	H2TH
Supercoil relaxation	distributive strand passage activity	kills strand passage	kills strand passage	greatly impairs strand passage
ATPase activity
-on linear DNA	stimulates above basal activity	no activity	no activity	~wildtype activity
-on supercoiled DNA	stimulates more than linear DNA	increased activity, futile cycling	no activity	~wildtype activity, futile cycling
DNA binding
-short duplexes	affinity increases from 20 bp to 40 bp in length	moderately impairs binding for longer duplexes	greatly impairs binding	slightly impairs binding for longer duplexes
-sheared salmon-sperm DNA	similar affinity as for 40–70 bp duplexes	moderately impairs binding	N.D.	slightly impairs binding
-supercoiled DNA	increased affinity compared to linear DNA	moderately impairs binding	N.D.	moderately impairs binding
-stacked junction	tighter binding than to duplex	greatly impairs binding	N.D.	~wildtype affinity
Top6B dimerization
-on short DNA duplexes	DNA promotes closure AMPPNP promotes further closure	loss of substrate promoted closure AMPPNP promotes some closure	N.D.	N.D.
-on supercoiled DNA	promotes greater closure than linear DNA AMPPNP promotes further closure	supercoiled DNA promotes closure loss of AMPPNP promoted closure	N.D.	weaker substrate dependent closure than wildtype AMPPNP promotes further closure
Short duplex cleavage	AMPPNP promotes cleavage on 60 and 70 bp duplexes	similar to wildtype	greatly impairs cleavage	no cleavage
Short duplex bending	AMPPNP promotes bending	similar to wildtype	greatly slows bending	no bending

elife-31724-v3.xml

10.7554/eLife.31724.037

Table 1.Summary of topo VI functional activities and mutant effects.

Assay	Wildtype activity	Effect of mutation to:
Assay	Wildtype activity	KGRR loop	Stalk/WKxY	H2TH
Supercoil relaxation	distributive strand passage activity	kills strand passage	kills strand passage	greatly impairs strand passage
ATPase activity
-on linear DNA	stimulates above basal activity	no activity	no activity	~wildtype activity
-on supercoiled DNA	stimulates more than linear DNA	increased activity, futile cycling	no activity	~wildtype activity, futile cycling
DNA binding
-short duplexes	affinity increases from 20 bp to 40 bp in length	moderately impairs binding for longer duplexes	greatly impairs binding	slightly impairs binding for longer duplexes
-sheared salmon-sperm DNA	similar affinity as for 40–70 bp duplexes	moderately impairs binding	N.D.	slightly impairs binding
-supercoiled DNA	increased affinity compared to linear DNA	moderately impairs binding	N.D.	moderately impairs binding
-stacked junction	tighter binding than to duplex	greatly impairs binding	N.D.	~wildtype affinity
Top6B dimerization
-on short DNA duplexes	DNA promotes closure AMPPNP promotes further closure	loss of substrate promoted closure AMPPNP promotes some closure	N.D.	N.D.
-on supercoiled DNA	promotes greater closure than linear DNA AMPPNP promotes further closure	supercoiled DNA promotes closure loss of AMPPNP promoted closure	N.D.	weaker substrate dependent closure than wildtype AMPPNP promotes further closure
Short duplex cleavage	AMPPNP promotes cleavage on 60 and 70 bp duplexes	similar to wildtype	greatly impairs cleavage	no cleavage
Short duplex bending	AMPPNP promotes bending	similar to wildtype	greatly slows bending	no bending

elife-32110-v2.xml

10.7554/eLife.32110.022

Table 1.Predicted gene function: Mutants with increased lipid accumulation.

Predicted functions for genes for which mutants were high-confidence candidates for increased lipid accumulation (enrichment scores clustered in LA1, Figure 5).

	Gene ID	Short name	Annotation from	Description	Enrichment
	Gene ID	Short name	Annotation from	Description	BD	FACS
G Protein Switches
*	RTO4_15883	RAS1	S. cerevisiae	GTPase	2.0	2.3
	RTO4_14088	RAC1	H. sapiens	GTPase	2.0	0.9
*	RTO4_16215	GNAI1-like	H. sapiens	GTPase	1.6	1.0
	RTO4_11402	gapA	A. nidulans	GTPase-activating protein	0.6	1.4
	RTO4_13336	RIC8A	H. sapiens	Guanine nucleotide exchange factor	1.3	1.4
	RTO4_16170	sif-like	D. melanogaster	Guanine nucleotide exchange factor	1.5	0.9
	RTO4_16644	BMH1	S. cerevisiae	14-3-3 protein	1.3	2.2
	RTO4_16068	BMH1	S. cerevisiae	14-3-3 protein	0.7	1.2

Kinases and Phosphatases
	RTO4_13246	CNA1	S. cerevisiae	Phosphatase (Calcineurin catalytic subunit)	0.8	1.2
	RTO4_11675	CNB1	S. cerevisiae	Phosphatase (Calcineurin regulatory subunit)	1.1	1.2
	RTO4_11667	PTC1	S. cerevisiae	Phosphatase	0.9	1.2
	RTO4_10638	CLA4	S. cerevisiae	Kinase	3.4	4.5
*	RTO4_16605	TPK1	S. cerevisiae	Kinase	1.1	0.5

Gene Expresssion
	RTO4_10333	SET1	S. cerevisiae	Chromatin modifying	3.0	1.1
	RTO4_10279	BRE2	S. cerevisiae	Chromatin modifying	2.5	1.0
	RTO4_12689	SPP1	S. cerevisiae	Chromatin modifying	2.0	1.3
	RTO4_15412	RCO1	S. cerevisiae	Chromatin modifying	3.5	1.6
	RTO4_10209	MIT1-like	S. cerevisiae	Transcripition factor	1.4	0.3
	RTO4_14550	CYC8	S. cerevisiae	Transcription factor	3.7	3.8
	RTO4_10274	SKN7-like	S. cerevisiae	Transcription factor	2.2	1.5
	RTO4_13346	CBC2	S. cerevisiae	RNA splicing factor	1.6	1.2

Protein Modification
	RTO4_11272	ALG12	S. cerevisiae	Alpha-1,6-mannosyltransferase	3.5	1.7
	RTO4_14881	CAP10-like	C. neoformans	Xylosyltransferase	1.5	2.0
	RTO4_16598	LARGE1	H. sapiens	N-acetylglucosaminyltransferase-like protein	1.8	1.3

Protein Trafficking
	RTO4_12145	ERP1	S. cerevisiae	COPII cargo adapter protein (p24 family)	2.4	2.7
	RTO4_16731	ERP2	S. cerevisiae	COPII cargo adapter protein (p24 family)	1.7	2.0
	RTO4_12521	EMP24	S. cerevisiae	COPII cargo adapter protein (p24 family)	1.9	2.4
	RTO4_14054	BST1	S. cerevisiae	GPI inositol-deacylase	1.5	0.2
*	RTO4_15883	RAS1	S. cerevisiae	GTPase	2.0	2.3

Other ER/Golgi Proteins
	RTO4_10371	KDELC1-like	H. sapiens	Endoplasmic reticulum protein EP58	3.1	6.0
	RTO4_15763			SH3 Domain-containing ER Protein	1.0	1.5

Amino Acid Biosynthesis
	RTO4_11050	MET1	S. cerevisiae	Uroporphyrinogen III transmethylase	3.8	2.0
	RTO4_8744	MET5	S. cerevisiae	Sulfite reductase	4.4	2.1
§	RTO4_10374	MET10	S. cerevisiae	Sulfite reductase	2.5	1.3
	RTO4_8709	MET14	S. cerevisiae	Adenylylsulfate kinase	4.1	1.1
	RTO4_11741	MET16	S. cerevisiae	Phosphoadenosine phosphosulfate reductase	1.7	1.1
	RTO4_12031	cysB	A. nidulans	Cysteine synthase A	3.3	2.1
*	RTO4_16196	ARG1	S. cerevisiae	Argininosuccinate synthase	1.3	1.8

Translation
	RTO4_12273	MRN1	S. cerevisiae	RNA-binding protein	2.5	1.6
	RTO4_8595	EIF4E2	H. sapiens	Translation initiation factor	2.0	0.5

Ubiquitination and Proteolysis
	RTO4_11150	Mub1-like	S. cerevisiae	Ubiquitin ligase complex member	3.8	2.0
	RTO4_15576	CDC4	S. cerevisiae	Ubiquitin ligase complex member	1.7	1.8

Triacylglyceride Synthesis
†	RTO4_8972	NDE1	S. cerevisiae	NADH dehydrogenase	1.6	1.9

Lipid Droplet Associated
	RTO4_14088	RAC1	H. sapiens	GTPase	2.0	0.9

Mitochondrial Beta-oxidation
	RTO4_16284	HSD17B10	H. sapiens	3-hydroxyacyl-CoA dehydrogenase	1.6	0.5

Other
	RTO4_12175	mesA	A. nidulans	Myosin binding protein	1.3	1.8
	RTO4_8401	SHE4	S. cerevisiae	Transmembrane protein involved in cell polarity	1.0	1.3

Unknown Function
	RTO4_16524			Protein of unknown function	3.1	1.9
	RTO4_11613			Protein of unknown function	2.5	1.7
	RTO4_12505			Protein of unknown function	2.1	2.1
	RTO4_13512			Protein of unknown function	1.5	1.9
	RTO4_10805			Protein of unknown function	1.2	1.8
	RTO4_15251			Protein of unknown function	1.6	1.3
	RTO4_15358			Protein of unknown function	2.0	0.5
	RTO4_13513			Protein of unknown function	1.3	1.2
	RTO4_12461			Protein of unknown function	1.5	0.8
	RTO4_13351			Protein of unknown function	1.2	1.0

Cellular processes grouped as in Figure 6. BD: Enrichment score from buoyant density separation. FACS: Enrichment score from fluorescence activated cell sorting.

Protein abundance under nitrogen limitation: * increased; † increased 10-fold or more; ‡ decreased; § decreased 10-fold or more (Zhu et al., 2012).

elife-32110-v2.xml

10.7554/eLife.32110.023

Table 2.Predicted gene function: Mutants with decreased lipid accumulation.

Predicted functions for genes for which mutants were high-confidence candidates for decreased lipid accumulation (enrichment scores clustered in LA6 - LA8, Figure 5).

	Gene ID	Short name	Annotation from	Description	Cluster	Enrichment
	Gene ID	Short name	Annotation from	Description	Cluster	BD	FACS
tRNA thiolation
	RTO4_10764	NCS2	S. cerevisiae	tRNA 2-thiolation protein	LA7	0.5	−2.3
	RTO4_12817	NCS6	S. cerevisiae	tRNA 2-thiolation protein	LA7	0.7	−2.6
	RTO4_14918	ELP2	S. cerevisiae	Elongator complex protein	LA7	0.7	−1.2
	RTO4_14716	IKI3	S. cerevisiae	Elongator complex protein	LA7	0.4	−1.1
	RTO4_11341	UBA4	S. cerevisiae	Adenylyltransferase and sulfurtransferase	LA7	0.6	−2.6

G Protein Switches
†	RTO4_15198	Rab6	H. sapiens	GTPase	LA6	−1.3	−1.6
	RTO4_14622	RGP1	H. sapiens	Guanine nucleotide exchange factor	LA6	−1.4	−1.5

Kinases and Phosphatases
	RTO4_10698	VHS1	S. cerevisiae	Kinase	LA6	0.8	−3.7
	RTO4_16375	HRK1	S. cerevisiae	Kinase	LA6	0.4	−2.2
*	RTO4_11453	GLC7	S. cerevisiae	Kinase	LA8	−1.2	−0.9
	RTO4_16810	KIN1	S. cerevisiae	Kinase	LA6	0.1	−1.1
	RTO4_10025	SAT4	S. cerevisiae	Kinase	LA7	1.6	−3.6
	RTO4_13327	ATG1	S. cerevisiae	Kinase	LA6	0.1	−2.5
	RTO4_14907	SCH9	S. cerevisiae	Kinase	LA6	−0.6	−2.0
	RTO4_14906	kinase-like	S. cerevisiae	Kinase	LA6	−0.3	−1.8
	RTO4_13290	YAK1	S. cerevisiae	Kinase	LA8	−1.1	−0.9
	RTO4_11732	PPH3	S. cerevisiae	Phosphatase 4 catalytic subunit	LA6	0.9	−3.6
	RTO4_12586	PSY2	S. cerevisiae	Phosphatase 4 regulatory subunit	LA6	0.2	−1.2
	RTO4_16463	PTC7-like	S. cerevisiae	Phosphatase	LA6	0.1	−2.0

Autophagy
	RTO4_13327	ATG1	S. cerevisiae	Kinase	LA6	0.1	−2.5
	RTO4_13598	ATG2	S. cerevisiae	Membrane protein	LA6	−0.6	−3.4
	RTO4_12968	ATG3	S. cerevisiae	Ubiquitin-like-conjugating enzyme	LA6	−0.8	−4.5
	RTO4_13496	ATG4	S. cerevisiae	Cysteine protease	LA6	−0.1	−2.3
	RTO4_11901	ATG7	S. cerevisiae	Ubiquitin-like modifier-activating enzyme	LA6	−0.8	−4.2
	RTO4_13543	ATG8	S. cerevisiae	Ubiquitin-like protein	LA6	−1.0	−4.2
	RTO4_11326	ATG9	S. cerevisiae	Membrane protein	LA6	0.0	−1.3
	RTO4_9008	ATG14	S. cerevisiae	Autophagy-specific subunit of PtdIns3P-kinase complex	LA6	0.0	−5.0
	RTO4_16723	ATG18	S. cerevisiae	Phosphoinositide binding protein	LA6	−0.9	−5.8

Ubiquitination and Proteolysis
†	RTO4_16672	PRB1	S. cerevisiae	Vacuolar proteinase	LA6	−0.2	−1.7
	RTO4_15345	SIS1	S. cerevisiae	Protein chaperone	LA6	−0.4	−1.2
	RTO4_10423	RMD5	S. cerevisiae	GID complex E3 ubiquitin ligase	LA6	−0.4	−2.0
	RTO4_11737	GID8	H. sapiens	GID complex member	LA6	−0.1	−1.5
	RTO4_9816	LONRF1	H. sapiens	E3 ubiquitin ligase	LA6	−0.5	−4.5
	RTO4_15320	USP48	H. sapiens	Ubiquitin carboxyl-terminal hydrolase	LA6	0.0	−1.2
	RTO4_9600	COPS3	H. sapiens	COP9 signalosome complex subunit	LA1	1.4	0.6
	RTO4_11569	GPS1	H. sapiens	COP9 signalosome complex subunit	LA6	0.7	−2.1
Triacylglyceride Synthesis
†	RTO4_12154	GPD1	S. cerevisiae	Glycerol-3-phosphate dehydrogenase	LA6	−1.7	−4.0
	RTO4_11043	BCSL2-like	H. sapiens	Seipin	LA6	−0.8	−2.9
	RTO4_16460	DGA1	H. sapiens	Diacylglycerol acyltransferase	LA6	−0.7	−4.0
	RTO4_14597	ACS1	S. cerevisiae	Acetyl-CoA synthetase	LA8	−1.7	−1.0
	RTO4_10182	YEF1	S. cerevisiae	NAD+/NADH kinase	LA6	−0.1	−1.6
‡	RTO4_11039	GUT2	S. cerevisiae	Glycerol-3-phosphate dehydrogenase	LA6	−0.2	−1.1

Lipid Droplet Associated
	RTO4_16381	PLIN1-like	S. cerevisiae	Perilipin	LA6	−1.7	−4.3
‡	RTO4_11039	GUT2	S. cerevisiae	Glycerol-3-phosphate dehydrogenase	LA6	−0.2	−1.1
	RTO4_15372	EGH1	S. cerevisiae	Steryl-beta-glucosidase	LA6	0.7	−2.5
	RTO4_13614	RIP1	S. cerevisiae	Mitochondrial complex III iron-sulfur protein	LA6	−0.5	−2.8
	RTO4_11043	BCSL2-like	H. sapiens	Seipin	LA6	−0.8	−2.9
	RTO4_16460	DGA1	H. sapiens	Diacylglycerol acyltransferase	LA6	−0.7	−4.0

Protein Modification
	RTO4_12670	B3GALT1-like	H. sapiens	Beta-1,3-Galactosyltransferase	LA6	−0.9	−3.1

Protein Trafficking
†	RTO4_15198	Rab6	H. sapiens	GTPase	LA6	−1.3	−1.6

Other ER/Golgi Proteins
	RTO4_8838	DNAJC4	H. sapiens	DnaJ family chaperone	LA6	−0.8	−1.3
	RTO4_13971	DNAJC3	H. sapiens	DnaJ family chaperone	LA6	−1.1	−2.2

Gene Expression
	RTO4_11333	KLF18-like	H. sapiens	Transcription factor	LA6	−0.2	−1.1
	RTO4_15641	SKN7	S. cerevisiae	Transcription factor	LA6	0.9	−2.9
	RTO4_14676	LHX5-like	H. sapiens	Transcription factor	LA6	−0.2	−2.8
	RTO4_11891	HAP2	S. cerevisiae	Transcription factor	LA6	−0.8	−2.4
	RTO4_12420	OPI1-like	S. cerevisiae	Transcription factor	LA6	0.0	−3.7
	RTO4_14100	HAPX	C. neoformans	Transcription factor	LA8	−1.2	−1.7
	RTO4_13255	SGF73	S. cerevisiae	SAGA-associated factor	LA6	0.4	−1.5

Methylcitrate Cycle
	RTO4_14162	ICL2	S. cerevisiae	2-methylisocitrate lyase	LA6	−0.3	−1.8
	RTO4_12642	PDH1	S. cerevisiae	2-methylcitrate dehydratase	LA6	−0.1	−1.7

Electron Transport and Redox Balancing
	RTO4_11165	CBP4	S. cerevisiae	Mitochondrial complex III assembly factor	LA6	−0.4	−2.5
	RTO4_13614	RIP1	S. cerevisiae	Mitochondrial complex III iron-sulfur protein	LA6	−0.5	−2.8
	RTO4_13902	AFG1	S. cerevisiae	Mitochondrial complex IV assembly factor	LA6	−0.3	−1.3
‡	RTO4_10010	NDUFS4	H. sapiens	Mitochondrial complex I accessory factor	LA8	−1.3	−0.1
	RTO4_13925	NDUFAF3	H. sapiens	Mitochondrial complex I assembly factor	LA8	−1.0	−1.6

Amino Acid Biosynthesis
†	RTO4_12302	CPA2	S. cerevisiae	Large subunit of carbamoyl phosphate synthetase	LA6	−0.4	−2.4

Glucose and Energy Metabolism
	RTO4_10423	RMD5	S. cerevisiae	GID complex E3 ubiquitin ligase	LA6	−0.4	−2.0
	RTO4_11737	GID8	H. sapiens	GID complex member	LA6	−0.1	−1.5
	RTO4_12034	TPS2	S. cerevisiae	Trehalose 6-phosphate synthase	LA6	0.0	−3.8
*	RTO4_10264	GLK1	S. cerevisiae	Hexokinase	LA7	2.1	−2.0
Transporters
†	RTO4_12909	OAT1	C. neoformans	Nucleobase transporter	LA6	−0.2	−1.1
	RTO4_11397	COT1	S. cerevisiae	Vacuolar zinc transporter	LA6	−0.2	−1.1
	RTO4_11924	SNF3	S. cerevisiae	Plasma membrane low glucose sensor	LA6	0.0	−2.8

Other
	RTO4_12512	cry	N. crassa	Blue-light photoreceptor cryptochrome	LA7	0.6	−1.6
	RTO4_14974			Steroidogenesis/phosphatidylcholine transfer domain	LA6	−0.3	−1.2
	RTO4_15889	MAEA	H. sapiens	EMP macrophage erythroblast attacher	LA6	−0.1	−1.7
	RTO4_16287	CDD1	S. cerevisiae	Cytidine deaminase	LA6	0.3	−2.3
	RTO4_15247	WDR26	H. sapiens	WD repeat protein	LA6	−0.9	−1.3
	RTO4_8764	MGS1	S. cerevisiae	DNA-dependent ATPase and ssDNA annealing protein	LA6	0.2	−1.2

Unknown
	RTO4_10431			Protein of unknown function	LA6	0.7	−1.6
	RTO4_8973			Protein of unknown function	LA8	−0.2	−1.1
	RTO4_13195			Protein of unknown function	LA6	−0.2	−1.1
	RTO4_10367			Protein of unknown function	LA6	−0.1	−1.3
	RTO4_10102			Protein of unknown function	LA6	−0.3	−1.2
	RTO4_14926			Protein of unknown function	LA6	0.2	−1.7
	RTO4_12045			Protein of unknown function	LA6	0.0	−1.5
	RTO4_13600			Protein of unknown function	LA6	−0.3	−1.3
	RTO4_10976			Protein of unknown function	LA6	−0.2	−1.5
	RTO4_9970	LDB17	S. cerevisiae	Protein of unknown function	LA8	−1.3	−0.5
	RTO4_13435			Protein of unknown function	LA7	0.2	−2.0
	RTO4_9692			Protein of unknown function	LA6	−0.5	−1.4
	RTO4_15521			Protein of unknown function	LA6	0.2	−2.2
	RTO4_8769			Protein of unknown function	LA6	−0.5	−1.6
	RTO4_8770			Protein of unknown function	LA6	−0.5	−1.9
	RTO4_11259			Protein of unknown function	LA7	0.7	−3.3
	RTO4_9490			Protein of unknown function	LA6	−0.6	−2.4
	RTO4_15520			Protein of unknown function	LA6	−0.5	−2.5
	RTO4_8771			Protein of unknown function	LA6	−0.6	−2.5
	RTO4_13452			Protein of unknown function	LA6	−1.3	−4.0
	RTO4_15211			Protein of unknown function	LA8	−1.1	−1.5

Cellular processes grouped as in Figure 6. BD: Enrichment score from buoyant density separation. FACS: Enrichment score from fluorescence activated cell sorting.

Protein abundance under nitrogen limitation: * increased; † increased 10-fold or more; ‡ decreased; § decreased 10-fold or more (Zhu et al., 2012).

elife-32208-v2.xml

10.7554/eLife.32208.004

Table 1.Associations with death in 817 subjects with admission retinal exam and retinopathy-positive paediatric cerebral malaria, 137 of whom died and 680 survived.

Retinal features are presented for the worse eye. Estimates are from unadjusted logistic regression. p≤0.01 is bold.

Variable name	Units	Died			Survived			Association with death
Variable name	Units	Numerical characteristics			Numerical characteristics			OR	95% CI	p
Demographics
Age (median, IQR)	months	35	23–59	136	39	27–58.75	680	0.99	0.00–1.00	0.43
Weight (median, IQR)	kg	11	9–15	137	12	10–15	680	0.97	0.93–1.02	0.22
Height (median, IQR)	cm	89	79–103	135	92	83–103	671	0.99	0.98–1.00	0.15
Sex (%)	boy	48.9		66	50.29		680	1.06	0.73–1.53	0.77
Sex (%)	girl	51.1		69	49.71
Clinical
Coma score (%)	0	23.3		32	9.85		67	3.57	2.13–5.88	<0.001
	1	41.6		57	37.7		256	2.13	1.28–3.57	0.003
	2	35.0		48	52.5		357	reference
Respiratory distress (%)	Present	48.9		67	39.0		265	1.5	1.04–2.17	0.03
Respiratory distress (%)	Absent	51.1		70	61.0		415	1.5	1.04–2.17	0.03
Convulsions at admission (%)	Present	12.4		17	14.9		98	0.83	0.45–1.44	0.51
Convulsions at admission (%)	Absent	87.6		120	85.4		574	0.83	0.45–1.44	0.51
Temperature (median, IQR)	degrees C	38.7	37.8–39.5	137	38.9	38–39.7	680	0.89	0.77–1.03	0.12
Systolic BP (median, IQR)	mmHg	100	90–110	127	100	90–110	652	0.99	0.99–1.01	0.63
Pulse (median, IQR)	beats/min	156	136.5–170.5	137	152	136.75–169	678	1.0	0.99–1.01	0.98
Duration of coma (median, IQR)	Hours	7	4–18	110	7	4–17	558	0.99	0.98–1.01	0.29
Duration of fever (median, IQR)	Hours	48	33.25–72	130	60	43.25–72	652	0.99	0.99–1.00	0.09
Hypoglycaemia on ward (%)	Present	14.6		20	7.81		53	2.02	1.16–3.5	0.012
Hypoglycaemia on ward (%)	Absent	85.4		117	92.1		626	2.02	1.16–3.5	0.012
Laboratory
Parasitaemia (median, IQR)	#cells	79052	16695–357000	134	68076	11700–298000	649	1.0	0.99–1.00	0.27
White cell count (median, IQR)	#cells	11300	6925–18225	120	9200	6600–13725	630	1.0	1.00–1.00	0.004
Haematocrit (median, IQR)	%	19.5	15–24.75	136	20	15.8–25	673	0.99	0.97–1.02	0.69
Lactate (median, IQR)	mmol/L	8.75	5.38–12.78	92	5.3	3.2–9.9	519	1.11	1.06–1.16	<0.001
HRP2 (median, IQR)	ng/ml	8838.5	4435.5–15102.3	120	5765	2471.5–10031	609	1.0	1.00–1.00	0.004
HIV (%)	Positive	22.5		29	14.9		88	1.66	1.03–2.66	0.036
HIV (%)	Negative	77.5		100	85.1		503	1.66	1.03–2.66	0.036
Ophthalmoscopy
Retinal haemorrhage (%)	>50	16.0		22	4.7		32	3.4	1.78–6.5	<0.001
	21 to 50	11.0		15	6.50		44	1.69	0.85–3.34	0.14
	6 to 20	13.1		18	19.0		129	0.69	0.38–1.27	0.23
	1 to 5	32.9		45	42.9		291	0.76	0.48–1.23	0.27
	None	27.0		37	27.0		183	reference
Macular whitening (%)	>1	23.9		32	14.8		100	2.31	1.16–4.59	0.017
	1/3 to 1	28.4		38	25.1		170	1.61	0.83–3.12	0.16
	<1/3	37.3		50	45.2		306	1.18	0.63–2.22	0.61
	None	10.5		14	14.9		101	reference
Foveal whitening (% of foveal zone)	>2/3	23.3		31	11.5		78	3.39	1.83–6.26	<0.001
	1/3 to 2/3	18.1		24	15.2		103	1.99	1.05–3.74	0.03
	<1/3	42.8		57	46.8		316	1.54	0.90–2.62	0.11
	none	15.8		21	26.5		179	reference
Temporal whitening (%)	3	10.0		13	12.9		87	0.83	0.41–1.66	0.60
	2	24.6		32	18.4		124	1.43	0.83–2.47	0.20
	1	41.5		54	43.1		290	1.03	0.64–1.67	0.89
	none	23.9		31	25.6		172	reference
Orange vessels, temporal quadrant (%)	present	44.6		58	21.7		145	2.9	1.96–4.3	<0.001
Orange vessels, temporal quadrant (%)	absent	55.4		72	78.3		523	2.9	1.96–4.3	<0.001
White vessels, temporal quadrant (%)	present	25.4		33	24.3		162	1.06	0.69–1.64	0.78
White vessels, temporal quadrant (%)	absent	74.6		97	75.8		506	1.06	0.69–1.64	0.78
White capillaries (%)	present	26.9		35	33.1		221	0.75	0.49–1.13	0.17
White capillaries (%)	absent	73.1		95	66.9		447	0.75	0.49–1.13	0.17
Papilloedema (%)	present	39.0		53	21.8		148	2.29	1.55–3.38	<0.001
Papilloedema (%)	absent	61.0		83	78.2		530	2.29	1.55–3.38	<0.001
Disc hyperaemia (%)	present	48.7		54	35.3		212	1.73	1.15–2.61	0.008
Disc hyperaemia (%)	absent	51.4		57	64.7		388	1.73	1.15–2.61	0.008

elife-32208-v2.xml

10.7554/eLife.32208.010

Table 4.Relationship between severe sequestration (pigmented/late parasitised RBCs sequestered around 360<bold>° </bold>of the lumen circumference) and orange discoloration visible clinically and on gross pathology in 412 venules (diameter 10–50 μm) from nine cases

		Orange discolouration
		+	-
Severe sequestration	+	188	5
Severe sequestration	-	24	195

elife-32208-v2.xml

10.7554/eLife.32208.023

Table 5.Frequency of intravascular filling defects (worse eye) on fluorescein angiography manual grading by involvement of retinal vessel in 259 children with MR-positive disease and FA within 24 hr of admission and unadjusted association with death (n = 35) and coma recovery of consciousness (BCS ≥3; n = 225)

Retinal vessel	Sequestration	Died*			Survived*			Association with death
Retinal vessel	Sequestration	N	%	Total	N	%	Total	OR	95% CI	p

large venules	present	26	86.7	30	172	79.3	217	1.70	0.56–5.12	0.35
large venules	absent	4	13.3	30	45	20.7	217	1.70	0.56–5.12	0.35
small venules	present	29	96.7	30	211	98.1	215	0.88	0.71–1.09	0.23
small venules	absent	1	3.33	30	4	1.86	215	0.88	0.71–1.09	0.23
post-capillary venules	present	25	96.2	26	201	98.5	204	0.37	0.04–3.70	0.4
post-capillary venules	absent	1	3.85	26	3	1.47	204	0.37	0.04–3.70	0.4
pre-capillary arterioles	present	19	76.0	25	109	56.2	194	2.47	0.94–6.45	0.065
pre-capillary arterioles	absent	6	24.0	25	85	43.8	194	2.47	0.94–6.45	0.065
small arterioles	present	15	51.7	29	93	42.9	217	1.43	0.66–3.11	0.37
small arterioles	absent	14	48.3	29	124	57.1	217	1.43	0.66–3.11	0.37
large arterioles	present	9	30.0	30	29	13.2	219	2.81	1.17–6.72	0.02
large arterioles	absent	21	70.0	30	190	86.8	219	2.81	1.17–6.72	0.02

elife-32213-v3.xml

10.7554/eLife.32213.030

Table 1.Histopathologic analysis relative to <xref ref-type="fig" rid="fig3">Figure 3</xref>.

	Grade
	No PIN	Low grade PIN	High grade PIN	Microinvasive carcinoma	Invasive carcinoma
Pbsn-Cre4;Pten^f/f*			66%	33%
Pbsn-Cre4;Pten^f/f R + P^†	33%	16%	33%	16%
Pbsn-Cre4;Pten^f/f + NAC^‡				25%	75%

*The anterior lobes of prostates from untreated mice were analyzed by histopathology at 8 months (percentage of mice with highest grade is indicated).

†The anterior lobes of prostates from mice treated at 4 months with rapamycin and PEITC (R + P) were analyzed by histopathology at 8 months (percentage of mice with highest grade is indicated).

‡The anterior lobes of prostates from mice treated at 4 months with NAC were analyzed by histopathology at 8 months (percentage of mice with highest grade is indicated).

elife-32353-v2.xml

10.7554/eLife.32353.004

Table 1.Overlap of striosomes outlined using tdTomato and MOR1.

		MOR1
		Positive	Negative
tdTomato	Positive	14.2%±1.3%	2.0%±0.3%
tdTomato	Negative	3.7%±0.6%	80.2%±1.9%

MOR1 test-retest error rate = 2.4%

tdTomato test-retest error rate = 2.3%

elife-32353-v2.xml

10.7554/eLife.32353.008

Table 3.Baseline fluorescence and ΔF/F values for striosomal and matrix neurons.

	Cell type
	Striosomal	In striosomal neuropil	tdTomato labeled	Matrix
Baseline fluorescence	290.0 (8.5) ***	274.9 (8.1) ***	337.2 (27.9)	364.5 (6.8)
ΔF/F baseline mean	11.3 (0.7)	11.9 (0.7)	9.3 (1.9)	11.9 (0.4)
ΔF/F baseline standard deviation	37.2 (1.3)	38.2 (1.4)	33.5 (3.5)	38.5 (0.7)
ΔF/F baseline maximum	250.6 (9.9)	259.3 (11.2)	216.2 (22.8)	255.2 (6.0)

***p<0.001.

elife-32506-v1.xml

10.7554/eLife.32506.022

Table 1.Frequency of cell-intercalation events.

10.7554/eLife.32506.023Table 1-source data 1Source data for <xref ref-type="supplementary-material" rid="table1sdata1">Table 1</xref>.

Genotype	Frequency of intercalation (%)			n
Genotype	Leftward	Rightward	Total	n
+/+	4.0	4.8	9.2*	250
Myo31DF	2.2	3.3	6.0*	182

Frequency is defined as the number of intercalation events divided by the total number of examined cells, in 30 min.

When two cells in a column had initial contact and were subsequently separated by another intervening cell, cell intercalation was said to occur, and the direction from which the intervening cell came was determined.

*includes one event that was not distinguished as leftward or rightward.

elife-32605-v2.xml

10.7554/eLife.32605.017

Table 1.SVM statistics. AUC: area under curve; Acc: accuracy; Prc: precision; Rec: recall.

Behavior	Train						Withheld						Test
Behavior	AUC	AUC chance	Acc	Acc chance	Prc	Rec	AUC	AUC chance	Acc	Acc chance	Prc	Rec	AUC	AUC chance	Acc	Acc chance	Prc	Rec
Silent	1	0.5	100%	9.6%	100%	100%	0.98	0.5	95.6%	9.6%	75.6%	97.4%	0.95	0.5	90.3%	1.9%	18.4%	90.3%
Elongation	1	0.5	100%	14.2%	100%	100%	0.96	0.5	93.4%	13.6%	76.4%	95.9%	0.91	0.5	87.9%	22.2%	71.4%	92.6%
Tentacle sway	1	0.5	100%	25.1%	100%	100%	0.95	0.5	89.6%	25.0%	77.5%	92.4%	0.76	0.5	71.9%	30.2%	47.9%	76.7%
Body sway	1	0.5	100%	10.0%	100%	100%	0.92	0.5	92.9%	9.3%	65.7%	97.0%	0.75	0.5	83.4%	17.7%	52.8%	95.4%
Bending	1	0.5	100%	5.2%	100%	100%	0.98	0.5	97.3%	6.1%	74.4%	98.4%	0.81	0.5	93.9%	6.1%	38.9%	96.5%
Contraction	1	0.5	100%	6.6%	100%	100%	0.97	0.5	95.7%	6.9%	70.4%	97.7%	0.92	0.5	92.8%	11.7%	63.2%	95.5%
Feeding	1	0.5	100%	29.2%	100%	100%	1	0.5	98.8%	29.6%	98.5%	99.4%	0.83	0.5	81.0%	10.2%	39.6%	94.1%

elife-32638-v2.xml

10.7554/eLife.32638.013

Table 2.Pharmacological alterations of NAD+ and NADPH/NADP + in U2OS cells measured by flow cytometry.

	Normalized FRET ratio (TMR/FRET)
Treatment	NAD-Snifit		NADP-Snifit
Treatment	Cytosol	Mitochondria	Cytosol	Mitochondria
Control	1.00 (±0.03)	1.00 (±0.02)	1.00 (±0.01)	1.00 (±0.01)
1 mM NA	0.91 (±0.01)	n.d.	0.92 (±0.01)	1.00 (±0.01)*
10 mM NAM	0.92 (±0.02)	n.d.	1.05 (±0.01)	n.d.
1 mM NMN	0.82 (±0.01)	n.d.	0.95 (±0.01)	0.99 (±0.01)*
1 mM NR	0.80 (±0.02)	n.d.	0.96 (±0.01)	1.00 (±0.01)*
100 nM FK866	1.61 (±0.06)	1.48 (±0.04)	1.05 (±0.01)	0.99 (±0.01)*
1 mM 6-AN	n.d.	n.d.	0.80 (±0.02)	n.d.
1 mM Metformin	0.89 (±0.04)	1.09 (±0.03)	0.90 (±0.01)	0.95 (±0.01)
1 mM Phenformin	0.79 (±0.05)	1.13 (±0.06)	0.88 (±0.01)	0.83 (±0.01)
10 µM Rotenone	0.67 (±0.03)	1.08 (±0.02)	0.75 (±0.02)	0.80 (±0.02)
25 µM Oligomycin A	1.14 (±0.03)	1.63 (±0.01)	1.12 (±0.03)	1.36 (±0.07)

Values represent the average of medians (±s.d.) TMR/FRET ratios of three independent measurements normalized to control condition (n = 3). Control: untreated cells (full growth medium with 25 mM glucose), NA: nicotinic acid, NAM: nicotinamide, NMN: nicotinamide mononucleotide, NR: nicotinamide riboside, FK866: (E)-N-[4-(1-benzoylpiperidin-4-yl)butyl]−3-(pyridin-3-yl)acrylamide, 6-AN: 6-aminonicotinamide.

*The effect of the treatment is not statistically significant compared to the control condition (Kruskal-Wallis with Dunn’s post-hoc multiple comparison test, α = 0.05). n.d., not determined. All compounds were also tested for interactions with the sensor in vitro (Appendix 1—figures 5, 6).

elife-32638-v2.xml

10.7554/eLife.32638.043

Appendix 1—table 6.Determination of FRET efficiency in U2OS cells.

Sensors	Localization	<τ> (ns) ± SD			E (%) ± SD (Basal)	E_min (%) ± SD (2 mM SPY)
Sensors	Localization	Donor only	FRET, basal	FRET, 2 mM SPY	E (%) ± SD (Basal)	E_min (%) ± SD (2 mM SPY)
NADP-Snifit	Cytosol	2.80 ± 0.02	2.12 ± 0.06	2.35 ± 0.04	24.2 ± 0.7	16.0 ± 0.3
	Nucleus	2.69 ± 0.03	1.98 ± 0.04	2.28 ± 0.04	26.3 ± 0.6	15.5 ± 0.4
	Mitochondria	2.55 ± 0.05	2.08 ± 0.03	2.16 ± 0.02	18.2 ± 0.4	15.2 ± 0.3
NAD-Snifit	Cytosol	2.89 ± 0.04	2.19 ± 0.02	2.42 ± 0.02	24.3 ± 0.4	16.3 ± 0.3
	Nucleus	2.66 ± 0.03	2.11 ± 0.04	2.49 ± 0.06	20.6 ± 0.4	6.5 ± 0.2
	Mitochondria	2.63 ± 0.03	2.02 ± 0.02	2.30 ± 0.06	23.0 ± 0.3	12.2 ± 0.3

The data represent the amplitude-weighted average lifetime <τ> as mean ± SD (N = 10) measured in living U2OS cells in full growth medium (DMEM +10% FBS) at 37 °C. The ‘donor-only’ sample was obtained by single labeling of the sensor constructs with CP-TMR-SMX. The FRET samples are labeled with both CP-TMR-SMX and SiR-Halo. The cells labeled with both fluorophores were first measured without treatment to obtain their basal fluorescence lifetime, then the same cells were measured again after the treatment with 2 mM sulfapyridine (SPY) to obtain the fully sensor open state. The correlated FRET efficiencies (E) were calculated for each conditions.

elife-32740-v2.xml

10.7554/eLife.32740.014

Table 2.Number of videos for each intensity presented as InputMovie in the EEG and TMS experiment.

The last line shows the average movie intensities and their standard deviation presented for each condition and experiment.

Perceived intensity	EEG experiment		TMS experiment per session
Perceived intensity	Hand	Face	Hand	Face
2	13	23	4	10
3	2	3	10	4
4	0	4	4	4
5	27	10	10	6
6	1	11	2	6
7		1
Average intensity	4 ± 1.4	3.7 ± 1.7	3.9 ± 1.2	3.8 ± 1.6

elife-33105-v1.xml

10.7554/eLife.33105.004

Table 1.Reagents permuted during optimisation of the single cell RNAseq protocol and stats of each treatment condition after sequencing.

Different combinations of the protocol were tested by sequencing. Initial trials were performed with 2 µl of lysis buffer, this was increased to 4 µl to augment capture efficiency. Permutations of the protocol that were tested were a terminal anchoring base (A,G,C; V) or not (T), two reverse transcriptase enzymes (Smartscribe (SmSc); Superscript II (SII)) and 25 or 30 cycles of preamplification. Both sexual and asexual cells of P. berghei and P. falciparum were tested. For each sequenced dataset, we calculated the mean percentages of rRNA, mRNA and other reads across the cells. For some samples we also downsampled the data to 50,000 reads per cell to allow comparison of the number of genes detected. This was done to determine differences in the complexity of each library. For the three larger datasets produced (P. falciparum gametocytes, P. berghei mixed blood stages, and P. falciparum asexual stages), we provide the numbers of pre- and post-filtered cells and median number of genes in those filtered cells.

Conditions tested	Protocol	SSII, V30, 30 cycles	SSII, T30, 30 cycles	SmSc, T30, 30 cycles	SSII, T30, 25 cycles	SmSc, T30, 25 cycles	SmSc, T30, 25 cycles	SmSc, T30, 25 cycles	SmSc, T30, 25 cycles
	Cells	Sexual	Asexual	Asexual	Asexual	Asexual	Sexual	Mixed blood	Asexual
	Species	Pf	Pf	Pf	Pf	Pf	Pf	Pb	Pf
Lysis buffer volume	2 µl	✓
Lysis buffer volume	4 µl		✓	✓	✓	✓	✓	✓	✓
Oligo Dt (IDT)	Anchored 30 bp	✓
Oligo Dt (IDT)	Non-Anchored 30 bp		✓	✓	✓	✓	✓	✓	✓
Reverse transcriptase	Superscript II (Life Technologies) 10U	✓	✓		✓
Reverse transcriptase	Smartscribe (Clontech) 5U			✓		✓	✓	✓	✓
Cycle number	25				✓	✓	✓	✓	✓
Cycle number	30	✓	✓	✓
Sequencing machine	HiSeq						✓	✓	✓
Sequencing machine	MiSeq	✓	✓	✓	✓	✓
Sequencing results summary	% rRNA	5.7	33.5	36.2	6.4	18.4	17.8	16.7	34.8
	% coding genes	4.4	11.3	39.3	10.5	33	51.7	49	40.5
	% other	90	55.2	24.4	83.1	48.6	30.5	34.2	24.6
	Median genes detected for 50k reads	25	84	145	174	181	502.5	NA	NA
	Total cells	5	6	6	6	6	237	182	174
	Cells passing filters	NA	NA	NA	NA	NA	191	144	161
	Median gene count	NA	NA	NA	NA	NA	2011	1922.5	1793

elife-33125-v2.xml

10.7554/eLife.33125.019

Table 1.Summary of simulation results and comparison of methods.

The table shows the bias (mean error), ‘std’ (standard deviation) and ‘iqr’ (inter-quartile range: difference between the 75th and 25th percentile) for each method for all 3480 simulations. The left column shows the relative bias/std/iqr for the D_FREE-estimate and the right column shows the absolute bias/std/iqr for the F_BOUND-estimate.

Analysis method	D_FREE			F_BOUND
Analysis method	bias	std	iqr	bias	std	iqr
Spot-On (all)	−4.8%	3.3%	3.5%	−1.7%	1.2%	1.8%
vbSPT (2-state)	0.8%	12.5%	6.8%	5.0%	4.6%	6.1%
MSD_i (R² > 0.8)	8.0%	28.5%	4.9%	−20.6%	26.4%	32.1%
MSD_i (all)	−39.6%	41.8%	19.0%	22.0%	15.8%	17.8%

elife-33126-v1.xml

10.7554/eLife.33126.002

Table 1.Relative gene expression level in HAP1 cells of selected genes discussed in this work.

RPKM (Reads Per Kilobase of transcript per Million mapped reads) values from duplicate RNAseq datasets described previously (NCBI GEO accession number GSE75515, https://www.ncbi.nlm.nih.gov/geo/), obtained from two different passages of WT HAP1 cells (Dubey et al., 2016). Groups of paralogues or genes with redundant function are shaded in alternating colors to facilitate comparisons.

Gene	RPKM
Gene	Replicate 1	Replicate 2	Average
LGR4	160.61	174.69	167.65
LGR5	0.02	0.00	0.01
LGR6	0.02	0.00	0.01
ZNRF3	30.9	33.3	32.1
RNF43	0.12	0.08	0.1
GPC1	49.55	47.53	48.54
GPC2	4.17	4.79	4.48
GPC3	170.22	144.37	157.29
GPC4	209.39	229.86	219.63
GPC5	0.1	0.1	0.1
GPC6	13.88	14.90	14.39
SDC1	51.37	47.88	49.63
SDC2	11.42	9.2	10.31
SDC3	43.58	50.64	47.11
SDC4	8.16	8.21	8.18

elife-33126-v2.xml

10.7554/eLife.33126.004

Table 1.Relative gene expression level in HAP1 cells of selected genes discussed in this work.

Gene	RPKM
Gene	Replicate 1	Replicate 2	Average
LGR4	160.61	174.69	167.65
LGR5	0.02	0.00	0.01
LGR6	0.02	0.00	0.01
ZNRF3	30.9	33.3	32.1
RNF43	0.12	0.08	0.1
GPC1	49.55	47.53	48.54
GPC2	4.17	4.79	4.48
GPC3	170.22	144.37	157.29
GPC4	209.39	229.86	219.63
GPC5	0.1	0.1	0.1
GPC6	13.88	14.90	14.39
SDC1	51.37	47.88	49.63
SDC2	11.42	9.2	10.31
SDC3	43.58	50.64	47.11
SDC4	8.16	8.21	8.18

elife-33126-v3.xml

10.7554/eLife.33126.004

Table 1.Relative gene expression level in HAP1 cells of selected genes discussed in this work.

Gene	RPKM
Gene	Replicate 1	Replicate 2	Average
LGR4	160.61	174.69	167.65
LGR5	0.02	0.00	0.01
LGR6	0.02	0.00	0.01
ZNRF3	30.9	33.3	32.1
RNF43	0.12	0.08	0.1
GPC1	49.55	47.53	48.54
GPC2	4.17	4.79	4.48
GPC3	170.22	144.37	157.29
GPC4	209.39	229.86	219.63
GPC5	0.1	0.1	0.1
GPC6	13.88	14.90	14.39
SDC1	51.37	47.88	49.63
SDC2	11.42	9.2	10.31
SDC3	43.58	50.64	47.11
SDC4	8.16	8.21	8.18

elife-33183-v1.xml

10.7554/eLife.33183.012

Table 2.Transmembrane reversal potentials (<italic>E</italic>rev) measured from pIMCD and HEK-293 PKD2-GFP cilia.

External solution	pIMCD, whole-cilium		HEK-293 PKD2-GFP, whole-cilium
External solution	ΔE_rev (mean ± S.D.)	P_x/P_Na (mean ± S.D.)	ΔE_rev (mean ± S.D.)	P_x/P_Na (mean ± S.D.)
NaCl	0	1	0	1
NaMES	−2 ± 3 mV	0.96	Not tested	-
KCl	26 ± 3 mV	2.4 ± 0.3	23 ± 4 mV	2.4 ± 0.4
CaCl₂	−49 ± 4 mV	0.06 ± 0.04	−48 ± 3 mV	0.09 ± 0.04
NMDG	−57 ± 4 mV	0.04 ± 0.02	−58 ± 4 mV	0.04 ± 0.02

elife-33321-v2.xml

10.7554/eLife.33321.004

Table 1.Description of the 12 nodes showing larger-than-chance gastric-BOLD phase coupling.

AAL: Automated Anatomical labeling (Tzourio-Mazoyer et al., 2002). MNI: Montreal Neurological Institute.

Node name	Monte-Carlo p	Sum (t)	Cluster volume in mm³	Label AAL	mm³	% Area in Cluster	Max t	MNI of max t			EGG-BOLD shared Variance ± sem
Node name	Monte-Carlo p	Sum (t)	Cluster volume in mm³	Label AAL	mm³	% Area in Cluster	Max t	X	Y	Z	EGG-BOLD shared Variance ± sem
Primary Somatosensory Right (SIr)	0.0049	216.5	180	Postcentral R	171	8.8	4.8	45	−28	46	12.5% ± 2.0
Secondary Somatosensory Right (SIIr)	0.0131	146.1	120	Rolandic Oper R	12	1.8	4.2	54	−22	13	15.7% ± 2.2
				Heschl R	6	4.7	3.9	51	−19	10
				Temporal Sup R	99	6	5.3	57	−25	13
Secondary Somatosensory Left (SIIl)	0.0094	167.0	138	Postcentral L	39	2.0	4.5	−66	−22	22	16.6% ± 2.2
				SupraMarginal L	21	3.3	3.8	−60	−25	16
				Heschl L	15	13.1	3.9	−54	−16	7
				Temporal Sup L	60	5	5.2	−54	−19	7
Medial Wall Motor Regions (MWM)	0.0036	269.5	228	Supp Motor Area L	30	2.7	3.8	0	−13	49	15.8% ± 2.1
				Supp Motor Area R	54	4.5	4.8	9	-4	52
				Cingulum Mid L	66	6.7	4.9	0	−22	43
				Cingulum Mid R	75	6.7	4.7	6	−10	43
Posterior Cingulate Sulcus (pCS)	0.0061	196.7	171	Cingulum Mid L	39	3.9	4.2	-9	−37	52	16.9% ± 2.3
				Cingulum Mid R	24	2.1	4.5	6	−37	49
				Precuneus L	21	1.2	3.9	0	−37	55
				Precuneus R	39	2.3	3.8	6	−40	52
				Paracentral Lobule R	39	9.1	4.1	15	−40	55
Dorsal Precuneus (dPrec)	0.0071	186.6	156	Precuneus L	42	2.3	4.9	-3	−67	61	12.7% ± 1.9
Dorsal Precuneus (dPrec)	0.0071	186.6	156	Precuneus R	87	5.2	4.4	3	−64	64	12.7% ± 1.9
Dorsal Precuneus Left Anterior (ladPrec)	0.0178	125.5	108	Precuneus L	57	3.2	4.1	-6	−55	73	12.0% ± 2.0
Dorsal Precuneus Left Anterior (ladPrec)	0.0178	125.5	108	Paracentral Lobule L	48	7.0	4.3	-6	−34	76	12.0% ± 2.0
Occipital Ventral (vOcc)	0.0017	374.2	321	Calcarine L	18	1.6	4.1	0	−64	10	16.6% ± 2.6
				Lingual L	66	6	4.4	0	−67	7
				Lingual R	108	9	4.4	6	−70	-5
				Cerebellum 6 R	21	2.3	4.3	12	−70	−14
				Vermis 4 5	51	15.0	4.6	0	−61	-2
				Vermis 6	9	4.8	3.7	3	−70	-8
Occipital Dorsal (dOcc)	0.0034	285.1	243	Calcarine L	21	1.8	4	3	−76	16	16.7% ± 2.7
				Cuneus L	138	17.7	4.5	-3	−85	31
				Cuneus R	72	9.9	4.9	6	−76	28
Extrastriate Body Area Right (EBA)	0.0103	163.3	138	Occipital Inf R	45	8.9	4.5	48	−76	−14	14.3% ± 2.0
				Temporal Inf R	27	1.5	4.4	57	−70	−11
				Cerebellum Crus1 R	33	2.4	4.8	45	−82	−26
Superior Parieto-Occipital Sulcus (sPOS)	0.0245	107.1	87	Cuneus R	21	2.9	4.6	21	−76	43	12.5% ± 1.8
Superior Parieto-Occipital Sulcus (sPOS)	0.0245	107.1	87	Occipital Sup R	54	7.5	5.1	24	−79	43	12.5% ± 1.8
Retrosplenial Cortex (RSC)	0.0084	175.6	147	Cingulum Post L	3	1.3	3.5	-6	−43	10	15.4% ±2.1
				Cingulum Post R	9	5.3	3.7	6	−40	7
				Lingual R	18	1.5	4.1	9	−37	-2
				Precuneus L	36	2.0	4.4	-6	−49	7

elife-33420-v2.xml

10.7554/eLife.33420.003

Table 1.Candidate plasticity proteins (CPPs) include FMRP targets and autism spectrum disorder (ASD) genes.

CPPs were compared to FMRP targets identified by CLIP (Darnell et al., 2011) and genes from the Simons Foundation and Autism Research Initiative (SFARI) database (gene.sfari.org) for potential activity-regulated FMRP targets and ASD genes. The final fold changes in AHA labeling is from the average of two independent experiments (Supplementary file 2). The 83 CPPs shown here are AHA-labeled newly synthesized proteins (NSPs) that showed consistent increases or decreases in synthesis in response to visual experience with at least 20% change in one of the experiments.

	Gene names	Human Uniprot ID	Final Fold Change	FMRP targets and ASD genes			Gene names	Human Uniprot ID	Final Fold Change	FMRP targets and ASD genes
	Gene names	Human Uniprot ID	Final Fold Change	FMRP targets	SFARI database		Gene names	Human Uniprot ID	Final Fold Change	FMRP targets	SFARI database
Up in two experiments	capza1	P52907	1.36			Down in two experiments	cct7	Q99832	0.40
	capza2	P47755	1.33				clasp1	Q7Z460	0.74	V
	cbx1	P83916	1.36				col18a1	P39060	0.71
	cbx3	Q13185	1.36				ctnnb1	P35222	0.63	V	V
	fus	P35637	1.36				papss1	O43252	0.67
	hdlbp	Q00341	1.26	V			psmc6	P62333	0.75
	rps17	P08708	1.71				tln1	Q9Y490	0.71
	tuba1b	P68363	1.95				atp2a2	P16615	0.66	V
	lonp1	P36776	1.31				pmp2	P02689	0.55
	sfpq	P23246	1.54				acta1	P68133	0.73
	ttpal	Q9BTX7	1.42				atp2a1	O14983	0.66
	tuba1a	Q71U36	1.95				kif1a	Q12756	0.65	V
Up in one experiment	cox5a	P20674	1.30			Down in one experiment	actb	P60709	0.78	V
	eif3a	Q14152	1.16				aplp2	Q06481	0.74
	krt75	O95678	1.17				cand1	Q86VP6	0.83	V
	metap2	P50579	1.22				dnm1l	O00429	0.78		V
	naca	Q13765	1.38				hist1h4a	P62805	0.61
	nono	Q15233	1.15				hnrnpa1	P09651	0.81
	psmd2	Q13200	1.40				hnrnpc	P07910	0.76
	rab5a	P20339	1.14				hsp90ab1	P08238	0.79	V
	rab5c	P51148	1.14				hspa5	P11021	0.68
	eif4a1	P60842	1.18				mdh2	P40926	0.75
	hnrnpab	Q99729	1.21				ncl	P19338	0.81
	pbrm1	Q86U86	1.36				pcbp3	P57721	0.60
	rab5b	P61020	1.20				snw1	Q13573	0.75
	skiv2l2	P42285	1.25				actg1	P63261	0.79
	ap2a2	O94973	1.15	V			hn1	Q9UK76	0.82
	iws1	Q96ST2	1.25				kif1b	O60333	0.81	V
	vim	P08670	1.19				pcbp2	Q15366	0.60
	nsrp1	Q9H0G5	1.36				smc1a	Q14683	0.80
	syp	P08247	1.17				sptan1	Q13813	0.84	V
	cxxc4	Q9H2H0	1.47				stip1	P31948	0.74
	dpysl3	Q14195	1.19				trim69	Q86WT6	0.71
	fasn	P49327	1.23	V			arnt2	Q9HBZ2	0.78	V	V
	kiaa1598	A0MZ66	1.16				cdh11	P55287	0.80		V
Up in one experiment	krt7	P08729	1.17			Down in one experiment	hk1	P19367	0.80	V
	lgmn	Q99538	1.55				mcm4	P33991	0.76		V
	sptbn1	Q01082	1.18	V			smarcd2	Q92925	0.84
							stmn2	Q93045	0.70
							acta2	P62736	0.80
							actc1	P68032	0.80
							kif1c	O43896	0.81
							kif5c	O60282	0.80	V	V
							smarcd1	Q96GM5	0.84
							smarcd3	Q6STE5	0.84

elife-33465-v2.xml

10.7554/eLife.33465.007

Table 1.Data for selected proteins from mass spectrometry comparison of GFP-Mto1[9A1-NE]-HTB and GFP-Mto1[9A1-bonsai]-HTB interactomes.

Peptide counts and label-free quantification (LFQ) values for selected proteins shown in Figure 1F. Data from two independent biological replicates are shown. Nsp1 and Nup82 are included as likely representative Nup146 interactors, based on homology to budding yeast (Belgareh et al., 1998). See also Supplementary file 3.

Protein	Replicate 1 (E160307)					Replicate 2 (E161126)
Protein	Peptides from strain KS7611	Peptides from strain KS8371	LFQ intensity from strain KS7611	LFQ intensity from strain KS8371	LFQ ratio	Peptides from strain KS7611	Peptides from strain KS8371	LFQ intensity from strain KS7611	LFQ intensity from strain KS8371	LFQ ratio
Alp7	17	3	2.3e8	7.5e6	30.5	14	5	1.9e8	3.7e7	5.2
Crm1	20	5	2.7e8	1.7e7	15.6	18	5	2.7e8	2.0e7	13.7
Mto1	59	46	2.8e11	2.3e11	1.2	52	43	2.8e11	2.5e11	1.1
Mto2	14	20	6.6e9	5.1e9	1.3	16	22	6.7e9	5.8e9	1.2
Nsp1	14	11	2.5e8	1.8e8	1.4	14	12	2.2e8	1.3e8	1.7
Nup146	20	2	2.1e8	7.7e6	27.3	20	1	2.1e8	NQ	NQ
Nup82	13	9	1.5e8	7.3e7	2.1	9	4	7.4e7	2.2e7	3.4
Plo1	28	13	4.9e8	1.1e8	4.6	20	9	3.3e8	6.3e7	5.3

NQ = not quantified, because peptide count in the relevant sample was below threshold for quantification.

elife-33465-v2.xml

10.7554/eLife.33465.013

Table 2.Data for selected proteins from mass spectrometry comparison of GFP-Mto1[9A1-NE]-HTB interactomes from control cells and after treatment with leptomycin B.

Peptide counts and label-free quantification (LFQ) values for selected proteins from the two replicate experiments contributing to the graph in Figure 3C. See also Supplementary file 4.

Protein	Replicate 1 (E150924)					Replicate 2 (E151106)
Protein	Peptides from strain KS7669 -LMB	Peptides from strain KS7669 +LMB	LFQ intensity from strain KS7669 -LMB	LFQ intensity from strain KS7669 + LMB	LFQ ratio	Peptides from strain KS7669-LMB	Peptides from strain KS7669 +LMB	LFQ intensity from strain KS7669 -LMB	LFQ intensity from strain KS7669 + LMB	LFQ ratio
Alp7	20	13	2.5e8	1.4e8	1.7	14	15	6.3e8	4.4e8	1.4
Crm1	17	4	1.1e8	1.3e7	9.0	19	3	2.9e8	6.8e6	43.3
Mto1	59	58	2.6e11	2.9e11	0.9	58	59	6.1e11	6.7e11	0.9
Mto2	7	7	2.0e8	2.2e8	0.9	5	5	6.5e8	8.4e8	0.8
Nsp1	7	7	6.9e7	6.0e7	1.2	11	11	3.7e8	3.7e8	1.0
Nup146	14	8	7.4e7	3.3e7	2.3	12	5	1.9e8	5.6e7	3.4
Nup82	9	10	4.5e7	7.6e7	0.6	9	9	1.7e8	2.9e8	0.6
Plo1	26	26	2.4e8	2.4e8	1.0	25	27	8.5e8	7.7e8	1.1

elife-33465-v2.xml

10.7554/eLife.33465.015

Table 3.Data for selected proteins from mass spectrometry comparison of GFP-Mto1[9A1-NE]-HTB and GFP-Mto1[∆NES-9A1-NE]-HTB interactomes.

Peptide counts and label-free quantification (LFQ) values for selected proteins shown in Figure 4D. Data from two independent biological replicates are shown. See also Supplementary file 5.

Protein	Replicate 1 (E160419)					Replicate 2 ((E161127)
Protein	Peptides from strain KS7611	Peptides from strain KS8573	LFQ intensity from strain KS7611	LFQ intensity from strain KS8573	LFQ ratio	Peptides from strain KS7611	Peptides from strain KS8573	LFQ intensity from strain KS7611	LFQ intensity from strain KS8573	LFQ ratio
Alp7	15	14	2.2e8	1.4e8	1.5	12	9	2.1e8	1.4e8	1.5
Crm1	21	2	2.9e8	3.4e6	85.2	20	2	3.5e8	5.5e6	63.4
Mto1	47	47	3.1e11	3.2e11	1.0	40	40	3.1e11	3.2e11	1.0
Mto2	10	10	4.8e9	4.1e9	1.2	8	8	6.3e9	5.9e9	1.1
Nsp1	10	9	2.2e8	1.2e8	1.8	10	9	2.4e8	1.0e8	2.4
Nup146	15	3	2.0e8	9.5e6	20.7	19	0	1.5e8	NQ	NQ
Nup82	10	7	8.1e7	2.2e7	3.7	6	2	5.1e7	NQ	NQ
Plo1	17	15	2.5e8	1.6e8	1.5	17	10	2.2e8	1.8e8	1.2

NQ = not quantified, because peptide count and/or LFQ intensity in the relevant samples was below threshold for quantification.

elife-33465-v2.xml

10.7554/eLife.33465.023

Table 4.Data for selected proteins from mass spectrometry comparison of GFP-Mto1[9A1-NE]-HTB interactomes in wild-type (<italic>nup146+</italic>) and <italic>nup146[∆FG5-12]</italic> cells.

Peptide counts and label-free quantification (LFQ) values for selected proteins from the two replicate experiments contributing to the graph in Figure 6F. Complete datasets are in Supplementary file 6.

Protein	Replicate 1 (E170214)					Replicate 2 (E170306)
Protein	Peptides from strain KS9021	Peptides from strain KS9077	LFQ intensity from strain KS9021	LFQ intensity from strain KS9077	LFQ ratio	Peptides from strain KS9021	Peptides from strain KS9077	LFQ intensity from strain KS9021	LFQ intensity from strain KS9077	LFQ ratio
Alp7	17	15	1.4e8	1.4e8	1.0	16	16	1.0e8	8.2e7	1.3
Crm1	31	17	3.4e8	9.2e7	3.6	27	18	1.7e8	6.1e7	2.9
Mto1	62	61	2.7e11	2.6e11	1.0	55	54	1.7e11	1.8e11	0.9
Mto2	12	12	6.0e9	5.0e9	1.2	13	13	3.8e9	3.1e9	1.2
Nsp1	11	3	8.3e7	2.7e7	3.0	9	4	3.5e7	1.7e7	2.1
Nup146	29	6	2.1e8	1.5e7	13.9	31	10	1.4e8	1.5e7	9.2
Nup82	13	10	1.1e8	4.0e7	2.8	12	11	4.9e7	2.5e7	2.0
Plo1	17	17	1.5e8	1.3e8	1.1	17	17	1.1e8	8.1e7	1.3

elife-33953-v1.xml

10.7554/eLife.33953.036

Table 1.Primers and constructs for heterologous expression of Cgr proteins in <italic>R. erythropolis</italic>.

Restriction sites are bolded.

Construct	For/	Sequence	Restriction sites	Vector	Anneal temp (°C)	Extend time (s)
Construct	Rev	Sequence	Restriction sites	Vector	Anneal temp (°C)	Extend time (s)
cgr operon	For	ACTGACCCATGGATGGAATACGGAAAGTGCC	n/a	n/a	71	75
cgr operon	Rev	GTTTTACTGCAGTTACGCCGCCGTCGAA	n/a	n/a	71	75
Cgr1 + Cgr2	For	TGACGAATTCTAATGGAATACGGAAAGTGCCG	EcoRI,	pTipQT2	70	90
Cgr1 + Cgr2	Rev	TTATAAGATCTCGCCGCCGTCGAAAG	BglII	pTipQT2	70	90
Cgr1	For	TCGAACATATGATGGCTGAGGAACCTGTGG	NdeI,	pTipQT1	65	60
Cgr1	Rev	ATAACTCGAGTCACGCCGCCGTCGAAA	XhoI	pTipQT1	65	60
Cgr2 (native)	For	ACTGACCCATGGGCATGGAATACGGAAAGTGCC	NcoI, HindIII	pTipQC2	65	60
Cgr2 (native)	Rev	ATTAGAAGCTTTCACTCCCACGGCTCGAG	NcoI, HindIII	pTipQC2	65	60
Cgr2-CHis₆ (native)	For	ACTGACCCATGGGCATGGAATACGGAAAGTGCC	NcoI, HindIII	pTipQC1	65	60
Cgr2-CHis₆ (native)	Rev	GTTAGAAGCTTCTCCCACGGCTCGAG	NcoI, HindIII	pTipQC1	65	60
Cgr2(−48aa)-NHis₆	For	TATTACCATGGATCAGACCGCGCCTGC	NcoI, HindIII	pTipQC2	65	60
Cgr2(−48aa)-NHis₆	Rev	ATACTAAGCTTCTCCCACGGCTCGA	NcoI, HindIII	pTipQC2	65	60
Cgr2(−48aa)-CHis₆	For	TATTACCATGGATCAGACCGCGCCTGC	NcoI, HindIII	pTipQC1	65	60
Cgr2(−48aa)-CHis₆	Rev	ATACTAAGCTTTTACTCCCACGGCTCGA	NcoI, HindIII	pTipQC1	65	60
Sequencing primers	For	CGTGGCACGCGGAAC	n/a	All pTip vectors	n/a	n/a
Sequencing primers	Rev	GTGCAGGTTTCGCGTG	n/a	All pTip vectors	n/a	n/a

elife-34286-v1.xml

10.7554/eLife.34286.016

Table 1.Salivary secretion and the transgene enzyme activities from the unilateral parotid gland of transgenic (TG) pigs (Line2) during the grower (92–96 days old; estimated body weight: 42–45 kg) and finisher (159–191 days old; estimated body weight: 100–115 kg) phases of growth.

10.7554/eLife.34286.017Table 1–Source data 1.Salivary secretion from the unilateral parotid gland in the growing transgenic (TG) pigs and wild type (WT) pigs during the grower phase (92–96 days old; estimated body weight of 42–45 kg).

10.7554/eLife.34286.018Table 1–Source data 2.Salivary secretion from the unilateral parotid gland in the transgenic (TG) pigs during the finisher phase (159–191 days old; estimated body weight of 100–115 kg).

10.7554/eLife.34286.019Table 1–Source data 3.The transgene enzyme activities from the unilateral parotid gland in the transgenic (TG) pigs during the grower (92–96 days old; estimated body weight of 42–45 kg) and the finisher phases (159–191 days old; estimated body weight of 100–115 kg).

Item	Growth stages			Pooled SEM	P values
Item	Grower	Finisher		Pooled SEM	P values
Saliva secreted ^* Saliva secretion rate (mL/min·pig)
Saliva secreted ^* Saliva secretion rate (mL/min·pig)	8.48	16.97^**		0.25	<0.0001
Saliva secretion volume (mL/kg diet consumed)	407.66^**	151.70		5.33	<0.0001
Enzymes activity secreted (U/mL saliva)^†
β-glucanase	5.72		6.07^**	0.05	<0.0001
Xylanase	5.92		6.19^**	0.05	0.0005
Phytase	7.2		6.87	0.14	0.1033
Enzyme activity secreted (U/kg diet consumed)^†
β-glucanase	2,331.84^**		920.82	30.7	<0.0001
Xylanase	2,413.38^**		939.03	31.73	<0.0001
Phytase	2,935.19^**		1,042.19	38.29	<0.0001

*Saliva samples were collected daily from two transgenic growing pigs and two transgenic finishing pigs at 9:00 and 16:00, respectively, over the four-day period. Values are expressed as the mean and pooled SEM (n = 16 repeated sampling and measurements).

†Means and pooled SEM (n = 16) repeated sampling and measurements). Asterisks indicate significant differences between the grower and the finisher phases within the same row (Unpaired t-test, **p<0.01).

elife-34801-v2.xml

10.7554/eLife.34801.004

Table 3.Sample milestones for one of the subcompetencies within Critical Thinking Skills. Verbs in bold font indicate observable behaviors representing each stage of skill acquisition.

CRITICAL THINKING SKILLS	MILESTONES
CRITICAL THINKING SKILLS	Beginning PhD Student	Advanced PhD Student	PhD Graduate	Early-Career Scientist	Science Professional
B. Design a single experiment (answer questions, controls, etc.)	Follow experimental protocols, seek help as needed, describe critical role of controls	Plan experimental protocol; include relevant controls; choose appropriate methods; troubleshoot experimental problems	Design and execute hypothesis- based experiments independently; evaluate protocols of others; predict range of experimental outcomes	Consistently design and execute experiments with appropriate controls; assess next steps; critique experiments of others	Teach experimental design; guide others doing experiments

elife-35122-v2.xml

10.7554/eLife.35122.008

Table 1.List of differentially expressed genes between Hv_Sym and Hv_Apo, which are likely to be involved in symbiotic relationship

Probename	Fold change			Human_BestHit		blast2GO_Description
Probename	Hv_Sym /Hv_Apo	Hv_Sym_sexy /Hv_Apo	Hv_NC64A /Hv_Sym	Human_BestHit		blast2GO_Description
Localization and Transport
Hv_Sym > Hv_Apo
rc_6788	9.87	8.00	1.01			helicase conserved c-terminal domain containing protein
rc_10246	8.26	5.15	1.82			protein
rc_6298	7.10	4.73	0.99	hypothetical protein LOC220081		protein fam194b
2268	6.96	3.58	1.26	protein Daple		viral a-type inclusion protein
10548	6.74	6.89	0.73	transient receptor potential cation channel subfamily M member three isoform d		transient receptor potential cation channel subfamily m member 3-like
rc_1290	6.44	7.18	0.99	tetratricopeptide repeat protein eight isoform B		tetratricopeptide repeat protein 8
18736	6.04	6.34	1.03	BTB/POZ domain-containing protein KCTD9		btb poz domain-containing protein kctd9-like; unnamed protein product
rc_9270	5.96	10.03	1.37	PREDICTED: hypothetical protein LOC100131693		eukaryotic translation initiation factor 4e
NPNHRC_15697	3.85	2.74	0.62			major facilitator superfamily domain- containing protein 1
290	3.68	3.73	1.32	splicing factor, arginine/ serine-rich 6		splicing arginine serine-rich 4
rc_9596	3.56	4.19	1.62	BTB/POZ domain-containing protein KCTD10		btb poz domain-containing adapter for cul3-mediated degradation protein 3
rc_6774	3.34	3.32	1.31	solute carrier family 43, member 2		large neutral amino acids transporter small subunit 4
rc_26218	3.29	2.91	0.41	sodium-dependent phosphate transport protein 2A isoform 1		sodium-dependent phosphate transport protein 2b
NPNHRC_26094	3.20	3.98	1.31	SPE-39 proteinid="T5"		spe-39 protein
9096	3.10	2.20	0.69	otoferlin isoform d		otoferlin
rc_21349	2.89	4.25	0.78	5'-AMP-activated protein kinase catalytic subunit alpha-2		5 -amp-activated protein kinase catalytic subunit alpha-2
npRC_14488	2.88	2.65	0.71	solute carrier family 2, facilitated glucose transporter member 8		solute carrier family facilitated glucose transporter member 8-like
8863	2.75	2.70	0.81	ATP-binding cassette, sub-family B, member 10 precursor		abc transporter b family protein
rc_11896	2.49	2.56	1.52	ATP-binding cassette, sub-family B, member 10 precursor		abc transporter b family member 25-like
rc_6842	2.41	3.35	1.59	hypothetical protein LOC112752 isoform 2		intraflagellar transport protein 43 homolog
5242	2.36	3.35	1.22	growth arrest-specific protein 8		growth arrest-specific protein 8
5815	2.23	2.47	0.78	plasma membrane calcium- transporting ATPase 4 isoform 4a		plasma membrane calcium atpase
8765	2.22	3.25	0.91	growth arrest-specific protein 8		growth arrest-specific protein 8
NPNH_14052	2.19	2.17	0.79	V-type proton ATPase 21 kDa proteolipid subunit isoform 2		v-type proton atpase 21 kda proteolipid subunit-like
rc_2499	2.18	2.03	1.47	endoplasmic reticulum-Golgi intermediate compartment protein three isoform a		endoplasmic reticulum-golgi intermediate compartment protein 3 isoform 2
rc_13969	2.08	3.09	0.97			major facilitator superfamily
(IPR023561) Carbonic anhydrase, alpha-class
rc_24825	2.49	2.38	0.83		protein tyrosine phosphatase, receptor type, G precursor	receptor-type tyrosine-protein phosphatase gamma
Cell Adhesion and extracelluar matrix
Hv_Sym > Hv_Apo
7915	4.01	5.09	0.94	fibrillin-2 precursor		fibrillin-1- partial
npRC_24163	glutamate3.69	3.59	1.32	semaphorin 5A precursor		rhamnospondin 1
Immunity, apoptosis and recognition
Hv_Sym > Hv_Apo
(IPR000157) Toll/interleukin-1 receptor homology (TIR) domain
5168	9.28	4.92	0.61			protein; PREDICTED: uncharacterized protein LOC100893943
12749	5.13	3.35	1.26			PREDICTED: uncharacterized protein LOC100893943 [Strongylocentrotus purpuratus]
(IPR011029) DEATH-like
6508	6.70	5.10	0.64			PREDICTED: hypothetical protein [Hydra magnipapillata]
rc_2417	5.39	2.70	1.01			nod3 partial; PREDICTED: uncharacterized protein LOC100206003
(IPR002398) Peptidase C14, caspase precursor p45
NPNH_21275	2.36	3.53	1.18	caspase seven isoform alpha precursor		caspase d
(IPR016187) C-type lectin fold
11411	2.93	2.98	0.75	C-type mannose receptor 2		PREDICTED: similar to predicted protein, partial [Hydra magnipapillata]
Hv_Sym < Hv_Apo
(IPR000488) Death
7319	0.45	0.31	1.10	probable ubiquitin carboxyl- terminal hydrolase CYLD isoform 2		ubiquitin carboxyl-terminal hydrolase cyld
(IPR001875) Death effector domain
RC_FV81RT001CSTY	0.31	0.39	0.93	astrocytic phosphoprotein PEA-15		fadd
Chitinase
Hv_Sym > Hv_Apo
(IPR001223) Glycoside hydrolase, family 18, catalytic domain
rc_4450	2.78	3.83	0.66			chitinase 2
Hv_Sym < Hv_Apo
(IPR000726) Glycoside hydrolase, family 19, catalytic
FPVQZVL01EAWBY	0.21	0.16	1.78			endochitinase 1-like
1028	0.23	0.18	1.47			endochitinase 1-like
Oxidative Stress Response
Hv_Sym > Hv_Apo
np_1276	5.99	7.16	0.78	glutaredoxin-2, mitochondrial isoform 2		cpyc type
10926	3.9	2.3	0.8	hydroxysteroid dehydrogenase- like protein 2		hydroxysteroid dehydrogenase-like protein 2
469	2.97	3.53	0.76	cytochrome P450 3A7		cytochrome p450
FV81RT001DCTAQ	2.69	2.50	0.75	oxidoreductase NAD-binding domain-containing protein one precursor		oxidoreductase nad-binding domain- containing protein 1
696	2.30	3.24	0.69	methionine-R-sulfoxide reductase B1		selenoprotein 1; methionine-r-sulfoxide reductase b1-a-like
6572	2.23	2.15	1.06	L-xylulose reductase		l-xylulose reductase
13298	2.10	3.49	0.64	eosinophil peroxidase preproprotein		peroxidase
npRC_6975	2.04	2.77	1.42	methionine-R-sulfoxide reductase B1		selenoprotein 1; methionine-r-sulfoxide reductase b1-a-like
(IPR024079) Metallopeptidase, catalytic domain
Hv_array_4952	4.77	13.31	0.72	meprin A subunit beta precursor		zinc metalloproteinase nas-4-like
Hv_array_rc_3992	2.66	2.23	1.27	matrix metalloproteinase seven preproprotein		matrix metalloproteinase-24-like
Hv_Sym < Hv_Apo
RC_FWZAEML02HKSC	0.255	0.153	1.444			ascorbate peroxidase
np_14962	0.293	0.455	1.390	tryptophan 5-hydroxylase 2		phenylalanine hydroxylase
rc_4151	0.318	0.463	1.693	phenylalanine-4-hydroxylase		phenylalanine hydroxylase
2835	0.384	0.344	1.787			u1 small nuclear ribonucleoprotein 70 kda
rc_11426	0.413	0.458	1.591	short-chain dehydrogenase/ reductase family 9C member 7		uncharacterized oxidoreductase -like
FWZAEML02IC34R	0.427	0.448	1.159	aldehyde dehydrogenase 5A1 isoform two precursor		succinate-semialdehyde mitochondrial-like
FWZAEML02HKSCO	0.454	0.307	0.833			ascorbate peroxidase
(IPR004045) Glutathione S-transferase, N-terminal
RC_FWZAEML02GGHN	0.09	0.07	1.81	hematopoietic prostaglandin D synthase		glutathione s-transferase family member (gst-7)
(IPR024079) Metallopeptidase, catalytic domain
rc_11270	0.14	0.20	1.33	meprin A subunit beta precursor		protein; zinc metalloproteinase nas-4-like
rc_RSASM_15059	0.22	0.29	1.42			---NA---
2111	0.37	0.43	1.74	meprin A subunit beta precursor		zinc metalloproteinase nas-4-like
12451	0.50	0.39	0.78	meprin A subunit alpha precursor		zinc metalloproteinase nas-13- partial
(IPR013122) Polycystin cation channel, PKD1/PKD2
28854	0.37	0.28	0.94	polycystin-2		receptor for egg jelly partial
15774	0.40	0.26	0.76	polycystic kidney disease protein 1-like two isoform a		protein

elife-35122-v2.xml

10.7554/eLife.35122.009

Table 2.List of genes differentially expressed in Hv_Sym compared to both Hv_Apo and Hv_NC64A (‘A99-specific’)

Fold change of expression level determined by microarray analysis and qPCR analysis

10.7554/eLife.35122.010Table 2—source data 1.Expression level of ‘A99-specific’ genes and ‘Symbiosis related’ genes examined by microarray and qPCR.

Hv_Sym > Hv_Apo, Hv_NC64A
Probe name (gene ID)	Microarray		qPCR		Gene annotation	InterProScan
Probe name (gene ID)	Sym/Apo	Sym/NC64A	Sym/Apo	Sym/NC64A	Gene annotation	InterProScan
rc_13579	12.8	4.0	11.2	4.0	(Hydra specific)
rc_12891	9.0	2.9	14.6	6.9	(Hydra viridis specific)
27417	4.5	4.8	3.0	3.0		IPR009786 Spot_14
rc_26218	3.3	2.4	2.5	2.3	sodium-dependent phosphate transport protein	PTHR10010 Sodium-dependent phosphate transport protein 2C
1046	3.1	2.1	2.2	1.6	glutamine synthetase
Hv_Sym < Hv_Apo, Hv_NC64A
Probe name (gene ID)	Microarray		qPCR		Gene Annotation	InterProScan
Probe name (gene ID)	Apo/Sym	NC64A/Sym	Apo/Sym	NC64A/Sym	Gene Annotation	InterProScan
NPNHRC_26859	83.2	9.7	∞	∞	(Hydra viridis specific)
RC_FVQRUGK01AXSJ	13.7	2.6	2.1	1.5	acetoacetyl-CoA synthetase
rc_14793	7.2	4.1	9.4	4.8	2-isopropylmalate synthase	IPR013785 Aldolase_TIM,
FV81RT002HT2FL	2.8	2.0	3.1	1.8	histidine ammonia-lyase	IPR001106 Aromatic_Lyase IPR008948 L-Aspartase-like
NPNHRC_12201	2.7glutamate	2.3	2.6	2.5	(Hydra viridis specific)

elife-35122-v2.xml

10.7554/eLife.35122.015

Table 4.List of the genes differentially expressed between Hv_Sym and Hv_Apo

Fold change of expression level determined by microarray analysis and qPCR

10.7554/eLife.35122.016Table 4—source data 1.Expression level of 'Symbiosis related' genes examined by microarray and qPCR.

Hv_Sym > Hv_Apo
Probe name (gene ID)	Microarray	qPCR	Gene annotation	InterProScan
Probe name (gene ID)	Sym/Apo	Sym/Apo	Gene annotation	InterProScan
5168	9.3	7.4		IPR000157 TIR_dom PTHR23097 Tumor necrosis factor receptor superfamily member
6508	6.7	2.9		IPR011029:DEATH-like_dom
11411	2.9	2.0	C-type mannose receptor 2	IPR000742 EG-like_dom IPR001304 C-type_lectin
26108	7.2	7.2	ephrin type-A receptor six isoform a
rc_2417	5.4	3.5		IPR000488 Death_domain
rc_24563	6.1	6.7	Proline-rich transmembrane protein 1	IPR007593 CD225/Dispanin_fam PTHR14948 NG5
rc_9398	6.2	5.4	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	PTHR11697 general transcription factor 2-related zinc finger protein
Hv_Sym < Hv_Apo
Probe name (gene ID)	Microarray	qPCR	Gene Annotation	InterProScan
Probe name (gene ID)	Apo/Sym	Apo/Sym	Gene Annotation	InterProScan
rc_10789	2.5	3.7	endoribonuclease Dicer	IPR000999 RNase_III_dom PTHR1495 helicase-related
rc_12826	3.0	2.3	interferon regulatory factor 1	IPR001346 Interferon_reg_fact_DNA-bd_dom; IPR011991 WHTH_DNA-bd_dom PTHR11949 interferon regulatory factor
rc_8898	6.1	4.1	leucine-rich repeat-containing protein 15 isoform b	IPR001611 Leu-rich_rp PTHR24373 Toll-like receptor 9
FV81RT001CSTY	3.2	2.0	astrocytic phosphoprotein PEA-15	IPR001875 DED, IPR011029 DEATH-like_dom
RSASM_17752	4.0	2.1	CD97 antigen isoform two precursor	IPR000832 GPCR_2_secretin-like PTHR12011 vasoactive intestinal polypeptide receptor 2

elife-35468-v1.xml

10.7554/eLife.35468.034

Appendix 1—table 1<italic>G</italic>min and power to detect simulated introgression on the X chromosome and autosomes.

Numbers in parentheses indicate the standard deviation from 100 replicate simulations

	400 ybp		4000 ybp		40,000 ybp
	A	X	A	X	A	X
Windows with migration (#)	202.12 (18)	31.06 (7.2)	250.65 (16)	66.48 (10)	281.15 (20)	65.22 (8.7)
Windows with migration (%)	2.4% (0.21)	1.7% (0.4)	3% (0.19)	3.7% (0.56)	3.4% (0.24)	3.6% (0.48)
Significant G_min windows (#)	179.08 (17)	28.5 (6.4)	111.44 (9.8)	27.02 (4.7)	15.87 (4.4)	2.4 (1.3)
Significant G_min windows (%)	2.2% (0.2)	1.6% (0.35)	1.3% (0.12)	1.5% (0.26)	0.19% (0.052)	0.13% (0.07)
True positive rate	96% (1.5)	95% (3.9)	94% (2.4)	93% (5.1)	45% (11)	30% (34)
False postive rate	3.7% (1.5)	4.8% (3.9)	5.7% (2.4)	6.8% (5.1)	55% (11)	70% (34)
Migration Events Detected	85% (3.2)	88% (7.5)	42% (2.9)	38% (5.1)	2.6% (1)	1.2% (1.4)

elife-35684-v2.xml

10.7554/eLife.35684.008

Table 1.Number of orthologs assigned as Z-linked and autosomal in <italic>S. mansoni</italic>, <italic>S. haematobium</italic> and <italic>S. japonicum</italic>, based on the female:male (or female for <italic>S. haematobium</italic>) coverage patterns.

	Categories		Schistosoma japonicum				Schistosoma haematobium
	Categories		Z-specific	Autosomal	Ambiguous	Not covered	Z-specific	Autosomal	Ambiguous	Not covered
Schistosoma mansoni	Z-specific	476 (S0)		306 (S1mans)	20	3	847	36	23	10
	Autosomal	137 (S1jap)		7062	91	13	216	7462	262	105
	Excluded	57		383	4	3	105	411	20	7
	Orthologs total	8555					9504

elife-35856-v2.xml

10.7554/eLife.35856.021

Table 4.Analysis of selected predictors for age-5 wheeze within each CAS cluster, with demographic covariates (sex, BMI, parental history of asthma)

Selected predictors for age-5 wheeze
Selected predictors for age-5 wheeze		Cas1 (N = 88) Or (95% CI)	P-value	Cas2 (N = 107) Or (95% CI)	P-value	Cas3 (N = 22) Or (95% CI)	P-value	Or (95% CI)	P-value
LRI (events per y)	1	0.97 (0.71–1.3)	0.84	1 (0.61–1.5)	0.99	0.48 (0.13–1.1)	0.16	1 (0.81–1.2)	0.92
	2	1.2 (0.88–1.6)	0.26	1.5 (0.97–2.5)	0.069	0.99 (0.34–2.6)	0.98	1.4 (1.1–1.7)	5.3E-03
	3	2 (1.3–3.2)	2.3E-03	2.6 (1.5–5.3)	2.7E-03	0.98 (0.4–2.6)	0.96	2 (1.5–2.7)	3.8E-06
	4	2 (1.4–3.4)	2.0E-03	3.6 (1.8–8.3)	6.5E-04	1.9 (0.57–8.4)	0.32	2.5 (1.8–3.6)	1.5E-07
Wheezy LRI (events per y)	1	1.3 (0.68–2.4)	0.43	1.1 (0.35–3)	0.83	2.6 (0.62–58)	0.34	1.5 (0.98–2.3)	0.06
	2	1.2 (0.8–2)	0.33	1.6 (0.89–2.9)	0.12	2.4 (0.67–16)	0.24	1.6 (1.2–2.2)	5.6E-03
	3	2.8 (1.6–5.6)	1.3E-03	3 (1.4–8)	0.016	1.2 (0.43–4.6)	0.76	2.7 (1.8–4.2)	4.1E-06
	4	2.5 (1.5–5)	4.0E-03	6.3 (2.5–21)	6.8E-04	7.1 (1.2–169)	0.1	3.9 (2.5–6.7)	5.4E-08
Febrile LRI (events per y)	1	1.6 (0.77–3.6)	0.21	0.84 (0.28–1.9)	0.71	7.3 (0.78–178)	0.12	1.5 (0.93–2.4)	0.098
	2	1 (0.44–2.2)	1	4.8 (1.8–15)	3.9E-03	1.6 (0.48–10)	0.5	2.3 (1.4–3.9)	1.2E-03
	3	2 (1–4.8)	0.08	4.3 (1.2–15)	0.02	4.2 (0.55–519)	0.37	2.4 (1.4–4.3)	2.3E-03
	4	1.8 (0.97–4.1)	0.092	2.6 (0.88–8.3)	0.082	1.1 (0.11–18)	0.93	2.2 (1.3–4)	5.9E-03
Quartile of % healthy NPAs with infection-associated MPGs	0–2	1 (0.54–1.8)	0.98	1.3 (0.72–2.4)	0.36	NA	NA	1.3 (0.89–1.8)	0.19
	2–4	0.45 (0.19–0.88)	0.035	1 (0.51–2.1)	0.9	NA	NA	0.8 (0.53–1.2)	0.24
HDM IgE (kU/L)*	6m	8 (0.85–94)	0.074	0.93 (0.14–3.6)	0.92	3.4 (0.26–180)	0.4	2.3 (0.99–5.8)	0.054
	1	1.5 (0.22–7.8)	0.65	0.54 (0.039–2.3)	0.51	39 (2.5–22000)	0.082	2.7 (1.5–5)	0.00089
	2	0.93 (0.28–2.5)	0.89	2 (1.2–3.7)	0.016	1.4 (0.38–4.8)	0.62	2 (1.5–2.8)	2.80E-05
	3	1.4 (0.68–2.9)	0.32	1.5 (0.9–2.4)	0.12	1.5 (0.4–5.2)	0.55	1.7 (1.3–2.2)	1.00E-04
	4	1.9 (0.94–4.1)	0.086	1.9 (1.2–3.1)	0.011	1.4 (0.31–5.5)	0.64	1.9 (1.5–2.5)	3.70E-06
HDM IgG4 (μg/L)*	6m	NA (NA-NA)	0.55	0.053 (NA-6.5e + 24)	0.99	28 (1.7e-34-NA)	0.99	1.4 (0.88–2.6)	0.17
	1	NA (NA-NA)	0.61	1.1 (0.8–1.5)	0.5	0.9 (0.58–1.3)	0.6	1.2 (1–1.4)	0.053
	2	1.1 (0.71–1.6)	0.67	1.1 (0.85–1.4)	0.61	0.4 (0.038–1.2)	0.26	1.1 (1–1.3)	0.056
	3	1.1 (0.85–1.5)	0.35	1.1 (0.77–2)	0.64	0.94 (0.19–2.3)	0.9	1.1 (0.98–1.2)	0.1
	4	1.2 (0.98–1.5)	0.082	0.89 (0.7–1.1)	0.33	0.46 (0.031–5.4)	0.53	1.1 (1–1.3)	0.034
HDM IgG (mg/L)*	1	25 (0.32–1.6E + 04)	0.19	3.3 (0.16–46)	0.38	5.6E-03 (8.4E-06–0.57)	0.058	2 (0.31–11)	0.44
	2	0.8 (0.15–3.5)	0.78	0.97 (0.24–3.7)	0.96	0.79 (0.031–18)	0.88	1.3 (0.6–2.9)	0.48
	3	2.3 (0.14–35)	0.54	0.48 (0.057–2.5)	0.43	3.9 (0.26–96)	0.34	2.1 (0.89–5)	0.089

BMI = body mass index; HDM = house dust mite; LRI = lower respiratory infection. Association analyses performed via generalised linear models (GLM) with demographic covariates: age-5 wheeze ~predictor + sex (male) +BMI at age 3 + paternal history of asthma +maternal history of asthma. Bold text indicates statistical significance (p<0.05); italics indicate near-significance (p<0.10). *Odds ratio (OR) is for every 10-fold increase in IgE, IgG4 or IgG.

elife-35898-v2.xml

10.7554/eLife.35898.019

Table 3.Identified cross-linked peptides of Commd9 and NN-CH domain of CCDC93.

Predicted mass (Da)	Observed mass (Da)	Error (ppm)	xQuest score
Predicted mass (Da)	Observed mass (Da)	Error (ppm)	xQuest score	Cross-linked peptides
Sample 1:				Commd9 - Commd9
2751.419	2751.407	2.3	21.10	VDIK(133)TSSDSISR-VDIK(133)TSSDSISR
2305.209	2305.206	3.0	20.35	ASSK(21)DVVR-VDIK(133)TSSDSISR
4316.319	4316.306	3.2	18.78	DLSSAEAILALFPENFHQNLK(95)NLLTK(100)IILEHVSTWR
3266.789	3266.782	1.8	18.67	NLLTK(100)IILEHVSTWR-VDIK(133)TSSDSISR
2820.589	2820.579	2.4	17.28	ASSK(21)DVVR-NLLTK(100)IILEHVSTWR
3648.889	3648.881	1.0	15.22	LVDLDWRVDIK()TSSDSISR-VDIK(133)TSSDSISR
3202.679	3202.677	2.0	14.22	ASSK(21)DVVR-LVDLDWRVDIK(133)TSSDSISR
2571.299	2571.288	4.1	12.78	IQEDPSLCGDK(163)PSISAVTVELSK(175)
1859.009	1859.006	2.7	12.40	ASSK(21)DVVR-ASSK(21)DVVR
Sample 2:				Commd9 - CCDC93
2998.479	2998.476	1.5	16.86	VDIK(133)TSSDSISR	AIETK(131)EEMGDYIR
3513.859	3513.842	1.4	14.74	NLLTK(100)IILEHVSTWR	AIETK(131)EEMGDYIR
4772.479	4772.501	5.1	7.11	MAVPTCLLQMK(152)IQEDPSLCGDKPSISAVTVELSK	IK(45)GLSPFDK
				Commd9 - Commd9
2820.589	2820.583	1.1	18.60	ASSK(21)DVVR-NLLTK(100)IILEHVSTWR
				CCDC93 - CCDC93
3569.679	3569.675	0.3	14.92	AIETK(131)EEMGDYIR-SYSVSQFQK(148)TYSLPED
Sample 3:				Commd9 - Commd9
2820.589	2820.599	4.6	20.02	ASSK(21)DVVR-NLLTK(100)IILEHVSTWR
2305.209	2305.226	5.8	19.51	ASSK(21)DVVR-VDIK(133)TSSDSISR

elife-35898-v2.xml

10.7554/eLife.35898.020

Table 4.Identified cross-linked peptides of zfRetromer.

Predicted mass (Da)	Observed mass (Da)	Error (ppm)	xQuest score
Intermolecular cross-linked peptides				zfVPS26	zfVPS29	zfVPS35
2929.569	2929.550	8.0	13.20	APEK(301)MR		K(90)VADLYELVQYAGNIIPR
1844.019	1844.040	9.4	10.12	SKYHLK(188)		NK(38)LMDALK
1342.809	1342.805	4.9	9.99	MRK(304)R		K(127)DILK
1756.069	1756.070	2.8	9.83		FK(23)KLLVPGK	WEKK(556)
3809.959	3809.982	7.1	8.01		GDFDENLNYPEQK(73)VVTVGQFK	TQCALAASK(659)LLK
Intramolecular cross-linked peptides				zfVPS26 – zfVPS26
1441.829	1441.819	3.3	28.12	VNINVK(57)QTSK(61)R
1630.869	1630.863	4.6	26.54	TAELK(30)TEEGK(35)LEK
1247.689	1247.679	2.1	26.15	DVNK(266)K(267)FSVR
2571.239	2571.229	4.3	22.06	TEEGK(35)LEK(38)HYLFYDGESVSGK
3241.639	3241.662	7.0	20.14	K(25)TAELKTEEGK(35)LEKHYLFYDGESVSGK
3626.859	3626.875	5.8	19.78	K(214)EMTGIGPSTTTETETVAK-YFK(288)QQEIVLWR
844.489	844.487	4.4	18.66	K(25)TAELK(30)
1014.549	1014.544	1.4	12.32	K(297)APEK(301)MR
Intramolecular cross-linked peptides				zfVPS29 - zfVPS29
1184.749	1184.736	5.9	18.59	FK(23)KLLVPGK(30)
Intramolecular cross-linked peptides				zfVPS35 – zfVPS35
1607.729	1607.726	3.3	22.38	ENSSSDDK(552)WEKK(556)
844.469	844.449	6.9	19.26	EK(208)REK(211)
2245.219	2245.215	5.1	18.55	LLDEAVQAVK(24)VQSFQMK(31)R
1255.699	1255.688	2.5	17.69	LLK(662)K(663)PDQCR

elife-35957-v1.xml

10.7554/eLife.35957.022

Table 10.Analyses of selection on Characiphysi rhodopsin (<italic>rh1</italic>) using PAML random sites models.

Model	lnL	Parameters1			Null	P [df]2	Δ AIC^§
Model	lnL	ω₀/p	ω₁/q	ω₂/ω_p	Null	P [df]2	Δ AIC^§
M0	−10819.13	0.06	-	-	N/A	-	842.6
M1a	−10586.68	0.03 (91%)	1.00 (9%)	-	M0	0.000 [1]	379.73
M2a	−10586.68	0.03 (91%)	1.00 (9%)	9.07 (0%)	M1a	1 [(2	383.7
M3	−10403.20	0.00 (60%)	0.08 (29%)	0.40 (11%)	M0	0.000 4)	18.8
M7	−10401.45	0.17	1.77	-	N/A	-	9.27
M8a	−10395.82	0.18	2.27	1.00	N/A	-	0.23
M8	−10394.82	0.18	2.22	1.50	M7	0.000 (2]	0*
M8	−10394.82	0.18	2.22	1.50	M8a	0.136 [1]	0*

^∗†ω values of each site class are shown are shown for model M0-M3 (ω₀– ω₂) with the proportion of each site class in parentheses. For M7 and M8, the shape parameters, p and q, which describe the beta distribution are listed instead. In addition, the ω value for the positively selected site class (ω_p, with the proportion of sites in parentheses) is shown for M8.

^‡Significant p-values (α ≤0.05) are bolded. Degrees of freedom are given in square brackets after the p-values.

Model fits were assessed by Akaike information criterion differences to the best fitting model (asterisk).

Abbreviations—lnL, ln Likelihood; p, p-value; N/A, not applicable.

elife-35957-v1.xml

10.7554/eLife.35957.010

Table 3.Results of Clade Model C (CmC) analyses of vertebrate <italic>rh1</italic> under various partitions.

Model and Foreground^†	ΔAIC^‡	lnL	Parameters			Null	P [df]
Model and Foreground^†	ΔAIC^‡	lnL	ω₀	ω₁	ω₂/ω_d	Null	P [df]
M2a_rel	225.5	−47185.37	0.02 (69%)	1 (3%)	0.20 (28%)	N/A	-
CmC_Tetrapod Branch	97.44	−47119.33	0.20 (28%)	1 (3%)	0.02 (69%) Tetra Br: 0.00	M2a_rel	0.000 [1]
CmC_Tetrapod	4.92	−47073.06	0.02 (67%)	1 (3%)	0.24 (30%) Tetra: 0.13	M2a_rel	0.000 [1]
CmC_Teleost	1.88	−47071.54	0.02 (67%)	1 (3%)	0.14 (30%) Teleost: 0.24	M2a_rel	0.000 [1]
CmC_Teleost vs Tetrapod	0*	−47069.60	0.02 (67%)	1 (3%)	0.17 (30%) Tetra: 0.13 Teleost: 0.24	M2a_rel	0.000 [2]

^†The foreground partition is listed after the underscore for the clade models and consists of either: the clade of Teleost fishes (Teleost); the clade Tetrapods (Tetrapod;Tetra) or branch leading to tetrapods (Tetrapod branch; Tetra Br); or the clades of both the teleost fishes and tetrapods as two separate foregrounds (Teleost vs Tetrapods). In any partitioning scheme, the entire clade was tested, and all non-foreground data are present in the background partition.

^‡All ΔAIC values are calculated from the lowest AIC model. The best fit is shown with an asterisk (*).

ω_d is the divergent site class, which has a separate value for the foreground and background partitions.

^¶Significant p-values (α ≤0.05) are bolded. Degrees of freedom are given in square brackets after the p-values.

Abbreviations—lnL, ln Likelihood; p, p-value; AIC, Akaike information criterion.

elife-35957-v1.xml

10.7554/eLife.35957.012

Table 5.Results of Clade Model C (CmC) analyses of teleost <italic>rh1</italic> under various partitions.

Model and Foreground^†	ΔAIC^‡	lnL	Parameters			Null	P [df]
Model and Foreground^†	ΔAIC^‡	lnL	ω₀	ω₁	ω₂/ω_d	Null	P [df]
M2a_rel	17.1	−30987.99	0.01 (60%)	1 (5%)	0.19 (35%)	N/A	-
CmC_Characi branch	19.05	−30986.96	0.01 (60%)	1 (5%)	0.19 (35%) Char Br: 0.20	M2a_rel	0.794 [1]
CmC_Characi clade	0*	−30977.43	0.00 (60%)	1 (5%)	0.20 (20%) Char Cl: 0.10	M2a_rel	0.000 [1]

The foreground partition is listed after the underscore for the clade models and consists of either: the ancestral branch leading to the Characiphysi (Characi branch; Char Br) or the entire Characiphysi clade (Characi clade; Char Cl). In any partitioning scheme, the entire clade was tested, and all non-foreground data are present in the background partition.

^‡All ΔAIC values are calculated from the lowest AIC model. The best fit is bolded with an asterisk (*).

^§ω_d is the divergent site class, which has a separate value for the foreground and background partitions.

Significant p-values (α ≤0.05) are bolded. Degrees of freedom are given in square brackets after the p-values.

Abbreviations—lnL, ln Likelihood; p, p-value; AIC, Akaike information criterion.

elife-35957-v1.xml

10.7554/eLife.35957.019

Table 7.Analyses of selection on Vertebrate rhodopsin (<italic>rh1</italic>) using PAML random sites models.

Model	lnL	Parameters1			Null	P [df]2	Δ AIC^§
Model	lnL	ω₀/p	ω₁/q	ω₂/ω_p	Null	P [df]2	Δ AIC^§
M0	−49624.89	0.08	-	-	N/A	-	5516.80
M1a	−48355.44	0.05 (89%)	1.00 (11%)	-	M0	0.000 [1]	2979.91
M2a	−48355.44	0.05 (89%)	1.00 (3%)	1.00 (8%)	M1a	1 [2]	2983.91
M3	−47104.84	0.01 (58%)	0.11 (30%)	0.44 (12%)	M0	0.000 [4]	484.71
M7	−46906.24	0.24	1.19	-	N/A	-	81.51
M8a	−46864.60	0.32	3.10	1.00	N/A	-	0.230
M8	−46863.49	0.32	2.94	1.14	M7	0.000 [2]	0*
M8	−46863.49	0.32	2.94	1.14	M8a	0.135 [1]	0*

1ω values of each site class are shown are shown for model M0-M3 (ω₀– ω₂) with the proportion of each site class in parentheses. For M7 and M8, the shape parameters, p and q, which describe the beta distribution are listed instead. In addition, the ω value for the positively selected site class (ω_p, with the proportion of sites in parentheses) is shown for M8.

2Significant p-values (α ≤0.05) are bolded. Degrees of freedom are given in square brackets after the p-values.

^3#Model fits were assessed by Akaike information criterion differences to the best fitting model (asterisk).

Abbreviations—lnL, ln Likelihood; p, p-value; N/A, not applicable.

elife-35957-v1.xml

10.7554/eLife.35957.020

Table 8.Analyses of selection on Teleost rhodopsin (<italic>rh1</italic>) using PAML random sites models.

Model	lnL	Parameters1^†			Null	P [df]^†	Δ AIC^§
Model	lnL	ω₀/p	ω₁/q	ω₂/ω_p	Null	P [df]^†	Δ AIC^§
M0	−32949.46	0.10	-	-	N/A	-	4489.79
M1a	−31605.10	0.05 (86%)	1.00 (14%)	-	M0	0.000 [1]	1803.10
M2a	−31605.10	0.05 (86%)	1.00 (10%)	1.00 (4%)	M1a	1 [2]	1807.10
M3	−30887.40	0.01 (58%)	0.13 (29%)	0.57 (13%)	M0	0.000 [4]	373.67
M8a	−30790.44	0.28	3.05	1.00	N/A	-	173.76
M7	−30767.11	0.19	0.68	-	N/A	-	127.10
M8	−30702.57	0.25	1.62	1.92	M7	0.000 [2]	0*
M8	−30702.57	0.25	1.62	1.92	M8a	0.000 [1]	0*

2Significant p-values (α ≤0.05) are bolded. Degrees of freedom are given in square brackets after the p-values.

^3#§Model fits were assessed by Akaike information criterion differences to the best fitting model (asterisk).

Abbreviations—lnL, ln Likelihood; p, p-value; N/A, not applicable.

elife-35957-v1.xml

10.7554/eLife.35957.021

Table 9.Analyses of selection on Tetrapod rhodopsin (<italic>rh1</italic>) using PAML random sites models.

Model	lnL	Parameters^†			Null	P [df]^‡	Δ AIC^§
Model	lnL	ω₀/p	ω₁/q	ω₂/ω_p	Null	P [df]^‡	Δ AIC^§
M0	−15541.64	0.05	-	-	N/A	-	1154.78
M1a	−15345.33	0.03 (93%)	1.00 (7%)	-	M0	[1]	764.17
M2a	−15345.33	0.03 (93%)	1.00 (0%)	1.00 (7%)	M1a	1 [2]	768.17
M3	−14981.40	0.00 (61%)	0.06 (28%)	0.29 (11%)	M0	0.000 [4]	42.31
M7	−14971.78	0.19	2.76	-	N/A	-	17.10
M8	−14961.25	0.20	3.55	1.00	M7	0.000 [2]	0*

2Significant p-values (α ≤0.05) are bolded. Degrees of freedom are given in square brackets after the p-values.

^3#Model fits were assessed by Akaike information criterion differences to the best fitting model (bolded asterisk).

Abbreviations—lnL, ln Likelihood; p, p-value; N/A, not applicable.

elife-36018-v2.xml

10.7554/eLife.36018.012

Table 1.Best-fitting parameters of HDDM.

10.7554/eLife.36018.013Table 1—source data 1.HDDM model fitting parameters for each session.

The same data are also used in Figures 3, 4, 5, Figure 5—figure supplement 1, Figure 6, Figure 6—figure supplements 1, 2, 3, Figure 8 and Figure 8—figure supplement 1)

	Monkey F (26079 trials)				Monkey C (37161 trials)				Monkey A (21089 trials)
	LR-Left		LR-Right		LR-Left		LR-Right		LR-Left		LR-Right
	Mean	Std	Mean	Std	Mean	Std	Mean	Std	Mean	Std	Mean	Std
a	1.67	0.16	1.43	0.12	1.77	0.09	1.53	0.13	1.33	0.13	1.36	0.09
k	10.22	1.87	9.91	2.11	6.58	0.51	5.08	0.92	4.04	0.33	3.45	0.46
t₁	0.31	0.03	0.29	0.03	0.35	0.04	0.33	0.05	0.29	0.04	0.27	0.04
t₀	0.28	0.04	0.31	0.05	0.33	0.04	0.31	0.03	0.21	0.08	0.26	0.04
z	0.60	0.03	0.57	0.04	0.62	0.03	0.40	0.04	0.57	0.06	0.39	0.04
me	−0.06	0.04	0.08	0.05	−0.14	0.04	0.21	0.06	−0.22	0.05	0.27	0.09

elife-36018-v2.xml

10.7554/eLife.36018.014

Table 2.The difference in deviance information criterion (ΔDIC) between the full model (i.e., the model that includes both <italic>me</italic> and <italic>z</italic>) and either reduced model (<italic>me-</italic>only or <italic>z-</italic>only), for experimental data and data simulated using each reduced model.

Negative/positive values favor the full/reduced model. Note that the ΔDIC values for the experimental data were all strongly negative, favoring the full model. In contrast, the ΔDIC values for the simulated data were all positive, implying that this procedure did not simply prefer the more complex model.

10.7554/eLife.36018.015Table 2—source data 1.DIC for model fitting to the monkeys’ data and to the simulated data.

	Experimental data				Simu: me model		Simu: z model
	∆DIC: full - me		∆DIC: full - z		∆DIC: full - me		∆DIC: full - z
	Mean	Std	Mean	Std	Mean	Std	Mean	Std
Monkey F	−124.6	2.3	−2560.4	5.2	3.1	9.8	0.2	11.8
Monkey C	−1700.4	2.1	−6937.9	1.3	17.5	11.3	1.8	1.3
Monkey A	−793.6	3.4	−2225.7	4.0	25.4	9.0	1.2	3.4

elife-36234-v2.xml

10.7554/eLife.36234.021

Table 3.Reproduction data and pup weight after in utero WIN exposure.

Dam weight gain was calculated from GD 1 to GD 21 for n = 10 dams per treatment group. Pup weight at different postnatal days (PND) was calculated for n = 9–10 male and female pups from different litters. Data represent mean values ± SEM. Statistical significance was determined using the one-way ANOVA test.

					p-Value (ANOVA)
		Naive	SHAM	WIN
		mean ± SEM	mean ± SEM	mean ± SEM
	Dam weight gain (%)
	Dam weight gain (%)	33.8 ± 0.93	34.3 ± 1.91	33.1 ± 1.42	0.745
	Pregnancy length (days)
Reproduction data	Pregnancy length (days)	22.4 ± 0.14	22.6 ± 0.29	22.6 ± 0.17	0.923

	Litter size	13 ± 0.82	12.9 ± 0.78	12.7 ± 0.67	0.854
	PND 1	6.8 ± 0.2	6.7 ± 0.1	6.8 ± 0.2	0.965
	PND 10	23.5 ± 0.89	24.6 ± 0.65	22.6 ± 0.72	0.207
Pup weight (grams)	PND 13	31.8 ± 0.62	30.3 ± 0.82	30.5 ± 0.75	0.339
	PND 25	64.5 ± 2.24	65.6 ± 0.77	66.7 ± 1.55	0.647
	PND 90	452.7 ± 12.28	484.2 ± 12.52	481.7 ± 17.33	0.261

elife-36326-v2.xml

10.7554/eLife.36326.020

Table 1.<italic>Lonset</italic>, <italic>Lmax</italic>, and <italic>Lend</italic> values calculated from the <italic>fFL</italic> profiles in <xref ref-type="fig" rid="fig3">Figure 3</xref>.

		ADR1a			R16			I27
	WT	uL23 Δloop	uL24 Δloop	WT	uL23 Δloop	uL24 Δloop	WT	uL23 Δloop	uL24 Δloop
L_onset	21	17	20	31	31	29	32	33	28
L_max	25	22	25	35	35	33	35	35	35
L_end	27	26	27	42	39	40	38	38	41

elife-36340-v2.xml

10.7554/eLife.36340.009

Table 2.In vitro inhibition of HIV-1 reverse transcriptase by 25a and RPV.

RT variants	25a			RPV
RT variants	IC₅₀ (nM)	Fold R^*	Curve slope	IC₅₀ (nM)	Fold R	Curve slope
WT	4.3 ± 0.080^†	–	3.8 ± 0.70	3.5 ± 0.052	–	3.1 ± 0.17
K103N/Y181C	31 ± 0.83	7.2	1.9 ± 0.092	51 ± 1.5	15	1.4 ± 0.047
Y188L	3.0 ± 0.15	0.70	1.9 ± 0.16	7.6 ± 0.22	2.2	1.7 ± 0.069
V106A/F227L	7.3 ± 0.23	1.7	3.1 ± 0.17	14 ± 0.27	4.0	2.1 ± 0.083
K101P	5.4 ± 0.16	1.3	2.9 ± 0.21	71 ± 3.0	20	1.2 ± 0.056
Y181I	38 ± 1.1	8.8	2.3 ± 0.16	315 ± 15	90	1.4 ± 0.081
K103N/Y181I	412 ± 13	96	1.8 ± 0.094	6317 ± 339	1805	1.4 ± 0.10
P225H	2.5 ± 0.059	0.58	3.5 ± 0.15	3.7 ± 0.070	1.1	3.4 ± 0.34
P236L	2.6 ± 0.13	0.60	4.3 ± 0.43	3.7 ± 0.085	1.1	3.6 ± 0.47

* Mean fold change in the IC₅₀ values of mutant RT versus WT RT.

† Data reported as mean ±standard error.

elife-36340-v2.xml

10.7554/eLife.36340.013

Table 4.Buried area (Å2) between HIV-1 RT and each NNRTI*.

	Total	Individual residue
	Total	101	103	106	181	183	188	227	236	138
WT RT/K-5a2	584.1	46.5	81.2	91.1	63.9	0	75.4	89.3	69.6	54.6
K103N RT/K-5a2	579.4	44.3	73.4	85.5	59.6	0	71.2	92.9	71.2	52.6
E138K RT/K-5a2	587.9	44.3	83.5	89.6	63.0	0	72.9	86.4	69.9	54.3
Y188L RT/K-5a2	571.3	44.3	83.0	93.9	57.9	0	70.0	73.2	74.0	51.5
WT RT/25a	620.5	51.9	88.2	91.7	68.5	19.6	84.8	96.9	68.4	54.8
K103N RT/25a	626.8	47.9	74.7	86.4	67.8	15.6	84.3	106	72.0	53.7
E138K RT/25a	621.4	45.5	87.1	92.5	66.4	14.0	86.6	98.4	69.1	54.1
K103N/Y181C RT/25a	624.7	51.9	76.1	86.8	56.5	33.5	83.2	106	73.3	54.1
V106A/F227L RT/25a	614.9	47.6	87.1	79.2	58.1	0	79.2	91.8	62.8	52.0
K101P RT/25a	613.6	62.6	93.9	90.7	66.6	21.1	85.6	89.9	70.5	53.5
Y181I RT/25a	618.5	62.9	90.9	90.8	58.9	31.5	84.6	99.8	71.7	52.4

* The buried area between HIV-1 RT and each NNRTI was calculated using UCSF ChimeraX.

elife-36340-v2.xml

10.7554/eLife.36340.014

Table 5.Torsion angles and energies of K-5a2 and 25a in different binding poses.

	Torsion angles (°)								NNRTI energy^* (kcal/mol)
	τ1	τ2	τ3	τ4	τ5	τ6	τ7	τ8	NNRTI energy^* (kcal/mol)
WT RT/K-5a2	14	−17	−84	−71	2	−8	−97	—	−161.4
K103N RT/K-5a2	11	−23	−83	−73	6	−11	−102	—	−162.4
E138K RT/K-5a2	9	−19	−87	−68	2	−9	−97	—	−162.7
Y188L RT/K-5a2	3	−49	−66	−70	4	−2	−94	—	−160.9
WT RT/ETR^†	—	—	—	16	−2	−13	−95	—	N/A
WT RT/25a	23	−26	−79	−79	1	0	−109	−40	−191.1
K103N RT/25a	7	−22	−81	−74	3	0	−110	−53	−187.7
E138K RT/25a	19	−29	−76	−77	0	3	−108	−53	−188.5
K103N/Y181C RT/25a	−4	−26	−76	−77	4	−1	−107	−54	−186.2
V106A/F227L RT/25a	14	−24	−72	−82	4	−4	−103	−163	−187.3
K101P RT/25a	5	−24	−84	−81	5	6	−112	−44	−190.1
Y181I RT/25a	−2	−15	−87	−72	6	4	−107	−57	−189.2
WT RT/RPV^‡	—	—	—	10	−7	−13	−103	−28	N/A

* The NNRTI energy refers to the energy of K-5a2 or 25a itself at the specific conformations in different RT complexes. It was calculated using the MacroModel program in the Schrödinger software suite.

† Torsion angles of ETR were measured using the structure from PDB ID: 3MEC.

‡ Torsion angles of RPV were measured using the structure from PDB ID: 4G1Q.

elife-36401-v3.xml

10.7554/eLife.36401.005

Table 1.Summary of all mice.

Experimental group	Injection site	Behavioral assays
Experimental group	Injection site	Grooming	Social chamber	Y-maze	Elevated Plus Maze	Gait	Eyeblink
Adult	Lobule VI	12	12	12	12	12	8
	Lobule VII	10	10	7*	10	10	-
	Crus I	10	10	10	10	10	8
	Crus II	11	11	11	11	11	6
	Eyeblink	-	-	-	-	-	9
*not counting three mice excluded from group comparison during habituation phase
Developmental	Lobule VI	13	13	13	13	13	6**
	Lobule VII	8	8	8	8	8	-
	Crus I	7	7	7	7	7	6**
	Crus II	12	12	12	12	12	3
**not counting four mice (1 crus I, 3 lobule VI) excluded due to eyeblink-zone spillover expression
Controls	Type
Adult	DREADDs (eyeblink zone)+saline injections	-	-	-	-	-	5
	Saline i.p.	9	9	9	9	9	-
	CNO alone	10	10	10	10	10	9
	No treatment	8	8	17	18	18	16
	GCaMP6f injections + CNO	-	-	8	-	-	-
Developmental	CNO alone	10	10	10	10	10	-

elife-36401-v3.xml

10.7554/eLife.36401.023

Table 3.Cohen’s d effect size of motor and non-motor metrics.

10.7554/eLife.36401.024Table 3—source data 1.Extended <xref ref-type="table" rid="table3">Table 3</xref>.

Flexible/Social/Learning metrics
		Y-maze reversal		Three-chamber		Elevated plus-maze		Grooming	Eyeblink conditioning
		Learning(Finallearning)	Persistive behavior (Multisession reversal1)	Social preference	Novelty-seeking	Open-arm preference	Exploratory behavior	Grooming ratio	% Conditional responses session 11
Lobule VI	Developmental	0.1	1.1	−0.1	0.7	0.3	0.4	−0.6	−0.3
Lobule VI	Acute	0.5	0.9	0.2	0.0	0.3	0.6	0.1	0.1

Lobule VII	Developmental	0.6	−0.3	−0.3	1.1	0.9	1.7	1.2	nd
Lobule VII	Acute	−0.6	0.3	0.9	−0.4	−0.9	0.5	0.2	nd

Crus I	Developmental	0.4	0.6	1.2	−0.8	0.1	0.3	0.0	1.6
Crus I	Acute	0.0	0.3	0.0	0.3	−0.6	−0.1	0.9	1.0

Crus II	Developmental	0.1	−0.5	1.2	0.0	0.6	−0.3	−0.5	−0.5
Crus II	Acute	−0.6	−0.6	0.0	0.2	−0.8	−0.2	0.9	0.3

Movement metrics
		Gait	Y-maze reversal	Three-chamber	EPM
		Stance	Distance	Distance Baseline	Distance
Lobule VI	Developmental	0.1	−0.1	0.1	0.7
Lobule VI	Acute	−0.3	−0.7	−0.4	0.7

Lobule VII	Developmental	0.2	−0.2	−0.3	1.2
Lobule VII	Acute	0.5	0.1	−0.1	0.3

Crus I	Developmental	−0.3	−0.4	−1.1	0.7
Crus I	Acute	0.7	0.2	0.2	0.0

Crus II	Developmental	0.1	−0.3	−0.2	1.2
Crus II	Acute	0.3	0.2	−0.2	−0.3

Effect size, calculated in units (Cohen, 1988) of the two-sample pooled standard deviation, of perturbations on key behavioral parameters. Values in Bold indicate statistical significance. Colored fields indicate large effect sizes (d≥0.8); Blue for improvement of function and red for impairment as defined in Table 2.

elife-36401-v3.xml

10.7554/eLife.36401.032

Table 4.Relative neocortical expression resulting from long-distance tracing.

	Injection site
	Lobule VI	Crus I
Target Region	Relative expression	Relative expression
Motor cortex	1.00	1.00
Somatosensory	0.66	1.23
Prelimbic	0.71	0.32
Orbitofrontal	0.72	0.22
Anterior cingulate	0.42	0.59
Infralimbic	0.28	0.28
Visual cortex	0.25	0.27
Parietal association	0.21	0.02
Retrosplenial	0.11	0.17
Agranular insular	0.03	0.00

elife-36405-v2.xml

10.7554/eLife.36405.013

Table 2.Sample composition by genotype and period.

Fgfr2^+/+: unaffected littermates; Fgfr2^+/P253R: Apert syndrome mutant littermates. Developmental periods were defined according to limb staging, as shown in Figure 4. Hindlimbs and forelimbs were analyzed separately because, in the same embryo, hindlimbs are delayed in development in comparison to forelimbs by about 6–8 hr. We thus presented in the main text the results from groupings highlighted in color, including those for the hindlimbs from the early and mid groups, as well as those for the forelimbs from the mid and the late groups. This represents a continuous time span of limb development, from E10 to E11.5, divided into four periods of 12 hr each. Results from the complete dataset that considers hindlimbs and forelimbs from each litter separately are available in Figures 5 and 6 (Figure 5—figure supplement 2, Figure 5—figure supplement 3, Figure 6—figure supplement 1 and Figure 6—figure supplement 2).

Genotype	Period	N limb	N gene	LIMB
Genotype	Period	N limb	N gene	Hindlimb (N = 34)		Forelimb (N = 46)
				Early (~E10)
				Limb	Gene	Limb	Gene
Fgfr2^+/+	EARLY: E10-E10.5	30	24	13	9	17	15
Fgfr2^+/P253R		16	15	11	9	5	6
Subtotal		46	39	24	18	22	21
				Mid early (~E10.5)		Mid late (~E11)
				Limb	Gene	Limb	Gene
Fgfr2^+/+	MID: E10.5-E11	15	10	7	3	8	7
Fgfr2^+/P253R		16	9	8	3	8	6
Subtotal		31	19	15	6	16	13
						Late (~E11.5)
				Limb	Gene	Limb	Gene
Fgfr2^+/+	LATE: E11-E11.5	8	8	4	4	4	4
Fgfr2^+/P253R		15	14	7	6	8	8
Subtotal		23	22	11	10	12	12
Total		100	80

elife-36422-v1.xml

10.7554/eLife.36422.008

Table 1.Crystallographic and structural features of RNA-ligand complexes.

	RNA- dGMP	RNA- Gp-AI-pG	Time-resolved structures (RNA-2-AIpG)
	RNA- dGMP	RNA- Gp-AI-pG	Stage 1 (5 min)	Stage 2 (15 min)	Stage 3 (30 min)	Stage 4 (1 h)	Stage 5 (1.5 h)	Stage 6 (2 h)	Stage 7 (3 h)
PDB code	6C8D	6C8E	6C8I	6C8J	6C8K	6C8L	6C8M	6C8N	6C8O
Ligand binding modes	Watson-Crick	Watson-Crick	mixed	Watson-Crick	Watson-Crick	Watson-Crick	Watson-Crick	Watson-Crick	Watson-Crick
N7 interaction	Mg²⁺	N.D.	H₂O	H₂O	N.D.	N.D.	N.D.	N.D.	N.D.
3ʹ-O-P distance, Å	~6.1	4.6	3.7–4.1	~5.0	~4.3	4.1–5.0	1.6–4.2	1.6–4.1	1.6
P-P distance between monomers, Å	N.D.	~5.1	N.D.	6.2	5.2	5.2–5.4	5.5–7.1	5.0–7.3	~6.2
N7-N7 distance between primer and + 1 monomer, Å	4.2	3.7–4.0	3.9–4.1	4.0	3.7–4.0	3.7–4.2	3.7–4.3	3.7–4.1	4.1

N.D.: not detectable

elife-36426-v2.xml

10.7554/eLife.36426.022

Table 1.GO term enrichment on chromosome four

GO	Corrected P-value	Number on Chr_04		Percent of Chr_04 genes	GO term
GO	Corrected P-value	Observed	Expected	Percent of Chr_04 genes	GO term
0043531	5.61×10−79	140	9	7.57	ADP binding
0016705	4.40×10−48	179	39	9.68	Oxidoreductase activity, actingon paired donors, withincorporation or reduction of molecular oxygen
0004497	7.19×10−46	158	32	8.55	Monooxygenase activity
0005506	2.73×10−41	181	46	9.79	Iron ion binding
0020037	2.57×10−37	186	53	10.06	Heme binding
0010333	1.72×10−15	39	4	2.11	Terpene synthase activity
0016829	2.08×10−13	39	5	2.11	Lyase activity
0055114	9.53×10−10	247	149	13.36	Oxidation-reduction process
0016747	6.66×10−5	44	16	2.38	Transferase activity,transferring acyl groups other than amino-acyl groups
0000287	1.23×10−4	42	15	2.27	Magnesium ion binding
0008152	2.56×10−4	137	83	7.41	Metabolic process
0006952	3.60×10−4	32	10	1.73	Defense response
0004674	4.52×10−4	23	5	1.24	Protein serine/threoninekinase activity
0016758	1.35×10−3	44	18	2.38	Transferase activity, transferringhexosyl groups
0005622	4.14×10−3	14	42	0.76	Intracellular
0008146	2.68×10−2	9	1	0.49	Sulfotransferase activity
0016760	3.72×10−2	12	2	0.65	Cellulose synthase(UDP-forming) activity

elife-36426-v2.xml

10.7554/eLife.36426.023

Table 2.Content of the <italic>A. coerulea</italic> v3.1 reference by chromosome

	Chromosome							Genome
	1	2	3	4	5	6	7	Genome
Number of genes	5041	4390	4449	3149	4786	3292	4443	29550
Genes per Mb	112	102	104	69	107	108	102	100
Mean gene length (bp)	3629	3641	3689	3020	3712	3620	3708	3580
Percent repetitive	38.9	41.1	39.1	54.2	39.4	39.3	40.6	42.0
Percent genes withHIGH effect variant	25.3	23.8	23.6	32.3	24.1	22.1	23.6	24.7
Percent GC	36.8	37.0	36.9	37.0	37.1	36.8	36.8	37.0

elife-36426-v2.xml

10.7554/eLife.36426.024

Table 3.Population genetics parameters for <italic>Semiaquilegia</italic> by chromosome

	Percent pairwise differences
	Chromosome							Genome
	1	2	3	4	5	6	7	Genome
Polymorphism within Semiaquilegia	0.079	0.085	0.081	0.162	0.076	0.078	0.071	0.082
Divergence between Aquilegia and Semiaquilegia	2.46	2.47	2.47	2.77	2.48	2.47	2.47	2.48

elife-36435-v1.xml

10.7554/eLife.36435.042

Table 1.The number of hyper- and hypomethylated DMRs overlapping with ChIP-seq peaks.

Relation between DMRs and Fam60a binding site for E9.5 embryos. Methyl-seq data were obtained for three Fam60a^–/– and three WT embryos, and ChIP-seq data were obtained for ChIP-seq1 and ChIP-seq2 experiments. The number of ChIP-seq peaks that overlap with all or the top 500 hyper- and hypomethylated DMRs are shown.

Data set	Total DMRs	Direction	DMRs	Overlap with ChIP-seq peaks
Data set	Total DMRs	Direction	DMRs	vs. all DMRs (%)	vs. top 500 (%)
3 embryos (triplicates) (mean Diff >= 0.05)	7245	Hyper	3049	388 (12.7)	83 (16.6)
3 embryos (triplicates) (mean Diff >= 0.05)	7245	Hypo	4196	1257 (30.0)	254 (50.8)

elife-36607-v2.xml

10.7554/eLife.36607.006

Table 1.Response types latencies and durations

Response type		Phase 1		Phase 2		Phase 3
Response type		Latency	Duration	Latency	Duration	Latency	Duration
I.	1.	37,80 ± 3,15 ms	338.40 ± 49.79 ms	—	—	—	—
I.	2.	20.18 ± 3.15 ms	34.47 ± 3.92 ms	—	—	—	—
II.		20.00 ± 3.02 ms	35.00 ± 3.86 ms	97.00 ± 6.97 ms	269.00 ± 40.05 ms	—	—
III.		23.00 ± 4.61 ms	69.00 ± 19.59 ms	133.70 ± 32.76 ms	176.70 ± 3.83 ms	—	—
IV.		16.4 ± 4.57 ms	46.4 ± 7.90 ms	101.2 ± 18.56 ms	28.2 ± 5.27 ms	227.6 ± 43.53 ms	216.8 ± 69.3 ms

elife-36607-v2.xml

10.7554/eLife.36607.008

Table 2.Nociceptive responses in the subthalmic nucleus, superior colliculus and parabrachial nucleus.

	Microinjection of muscimol in the superior colliculus
	Superior colliculus		Subthalamic nucleus
	Pre muscimol	Post muscimol	Pre muscimol	Post muscimol
Latency	9 ± 0.8 ms	7.60 ± 0.68 ms	25.33 ± 5.27 ms	28.38 ± 7.75 ms
Duration	19.62 ± 5.00 ms	14 ± 3.03 ms	176.13 ± 60.37 ms	135.74 ± 50.19 ms *
Amplitude	322.29 ± 58.16 Hz	125.00 ± 26.22 Hz *	15.61 ± 3.29 Hz	14.4 ± 2.44 Hz
Magnitude	140.20 ± 28.01 Hz	45.01 ± 9.16 Hz *	10.21 ± 1.99 Hz	7.24 ± 1.41 Hz
Baseline FR no footshock	18.27 ± 2.19 Hz	—	4.37 ± 0.8 Hz	-
Baseline FR footshock	20.79 ± 2.66 Hz	7.69 ± 3.00 Hz *	6.06 ± 1.48 Hz	6.45 ± 1.38 Hz

	Microinjection of muscimol in the parabrachial nucleus
	Parabrachial nucleus		Subthalamic nucleus
	Pre muscimol	Post muscimol	Pre muscimol	Post muscimol
Latency	11.55 ± 1.35 ms	19.00 ± 2.48 ms *	24.54 ± 3.13 ms	18.43 ± 1.73 ms
Duration	26.45.12 ± 3.85 ms	14 ± 3.49 ms *	98.00 ± 27.35 ms	45.75 ± 12.04 ms *
Amplitude	146.97.42 ± 23.66 Hz	83.26 ± 17.02 Hz *	26.98 ± 5.72 Hz	17.18 ± 3.26 Hz *
Magnitude	45.16 ± 7.45 Hz	23.70 ± 4.57 Hz *	10.31 ± 2 Hz	6.65 ± 1.44 Hz *
Baseline FR no footshock	24.25 ± 1.97 Hz	—	5.89 ± 0.49 Hz	—
Baseline FR footshock	20.55 ± 2.42 Hz	14.15 ± 2.76 Hz	5.50 ± 0.71 Hz	5.39 ± 0.57 Hz

Mean ± SEM - * statistically different from pre-muscimol measure.

Abbreviations: cp, cerebral peduncle; IS, injection site; lPBN, lateral parabrachial nucleus; mPBN, medial parabrachial nucleus; scp, superior cerebral peduncle; STN, subthalamic nucleus.

Note: the amplitude of the response is the maximum amplitude during the response and the magnitude of the response is the mean number of single multi-unit events between response onset and offset minus the baseline mean.

elife-36745-v1.xml

10.7554/eLife.36745.012

Table 1.Viability of <italic>scs2/22∆</italic> mutant in combination with <italic>kar9∆</italic>, <italic>dyn1</italic>∆, or <italic>cin8∆</italic> mutant.

Mutant combination	Number of tetrads analyzed	Number of predicted double or triple mutants	Viability of mutants
Mutant combination	Number of tetrads analyzed	Number of predicted double or triple mutants	Viable	Microcolony
scs2/22∆	22	16	16	0
scs2/22∆ kar9∆	13	5	5	0
scs2/22∆ dyn1∆	22	9	9	0
scs2/22∆ cin8∆	29	17	17	0
dyn1∆ cin8∆	10	7	0	7

For scs2/22∆ and scs2/22∆ dyn1∆ combinations, YWL4865 was crossed with YWL521. For scs2/22∆ kar9∆ combination, YWL4865 was crossed with YWL4949. For scs2/22∆ cin8∆ and dyn1∆ cin8∆ combinations, YWL3955 was crossed with YWL4866 and YWL504, respectively. The resulting diploid strains were sporulated and tetrads were dissected.

elife-36979-v2.xml

10.7554/eLife.36979.028

Table 1.Correspondence of DNAH genes/proteins among zebrafish, human, and <italic>Chlamydomonas</italic>.

	Gene/protein names
	Zebrafish	Human	Chlamydomonas
OAD HCs			OAD α (DHC13)
	Dnah9	DNAH9	OAD β (DHC14)
	Dnah11	DNAH11
	Dnah9l
		DNAH17
	Dnah5	DNAH5	OAD γ (DHC15)
	Dnah8 (Dnah5l)
		DNAH8
IAD f HCs	Dnah10	DNAH10	IAD fα (DHC1)
IAD f HCs	Dnah2	DNAH2	IAD fβ (DHC10)
IAD HCs	Dnah3	DNAH3	IAD a (DHC6) IAD b (DHC5) IAD c (DHC9) IAD e (DHC8) minor var. DHC11 minor var. DHC4
	Dnah7	DNAH7
	Dnah12	DNAH12
	Dnah1	DNAH1	IAD d (DHC2)
	Dnah7l (Dnah6)	DNAH6	IAD g (DHC7) minor var. DHC3
	Dnah7l (Dnah6)	DNAH14	IAD g (DHC7) minor var. DHC3

elife-37090-v2.xml

10.7554/eLife.37090.005

Table 1.Overview of fermentation experiments and model fitting results (RMSE: root mean square error).

Means and standard deviations are reported across biological replicates.

Strains	Number of biological replicates	Added energy source and/or co-substrate	Consumption (-)/production (+) of metabolites in mM							Carbon recovery (%)	O/R balance	Selected for parame-terization 1	RMSE parame-terization 1	Selected for parame-terization 2	RMSE parame-terization 2
Strains	Number of biological replicates	Added energy source and/or co-substrate	Fructose	Acetate	Butyrate	Formate	Lactate	H₂	CO₂	Carbon recovery (%)	O/R balance	Selected for parame-terization 1	RMSE parame-terization 1	Selected for parame-terization 2	RMSE parame-terization 2
Monoculture fermentations
R. intestinalis L1-82	4	Fructose/acetate	−48.8 ± 0.9	−20.6 ± 2.4	58.5 ± 3.9	6.8 ± 1.2	3.9 ± 1.1	72.2 ± 4.9	84.0 ± 0.8	105 ± 14.3	0.86 ± 0.2	Yes	0.17 ± 0.04	No	0.83 ± 0.13
F. prausnitzii A2-165	3	Fructose/acetate	−23.1 ± 1.1	−13.5 ± 0.8	29.8 ± 0.2	22.7 ± 0.9	1.8 ± 0.2	0.2 ± 0.2	19.3 ± 1.6	100.9 ± 3.4	1.05 ± 0.09	Yes	0.15 ± 0.08	Yes	0.15 ± 0.08
B. hydrogenotrophica S5a33	3	Fructose/formate	−19.0 ± 5.6	23.0 ± 6.6	0.0 ± 0.0	−36.1 ± 1.8	6.0 ± 1.2	31.5 ± 7.7	26.0 ± 5.3	60.0 ± 2.1	0.76 ± 0.07	Yes	1.43 ± 0.27	No	3.53 ± 1.04
Bi-culture fermentations
R. intestinalis L1−82/F. prausnitzii A2-165	2	Fructose/acetate	−47.7 ± 2.2	−18.1 ± 2.7	56.3 ± 4.5	7.6 ± 2.7	4.3 ± 3.3	114 ± 16	85.7 ± 4.1	102.8 ± 0.3	0.79 ± 0	No	0.77 ± 0.06	No	0.68 ± 0.03
R. intestinalis L1−82/B. hydrogenotrophica S5a33	2	Fructose/acetate	−46.5 ± 1.5	−7.5 ± 1.9	53.5 ± 4.7	−0.5 ± 0.8	2.2 ± 0.3	53.0 ± 3.0	74.9 ± 4.1	100.2 ± 0.6	0.94 ± 0.12	No	0.78 ± 0.36	Yes	0.3 ± 0.04
R. intestinalis L1−82/B. hydrogenotrophica S5a33	2	Fructose	−48.0 ± 0.2	44.9 ± 5.4	27.9 ± 3.0	−1.0 ± 0.0	5.4 ± 2.4	33.1 ± 3.2	47.4 ± 3.9	91.6 ± 1.1	1.05 ± 0.06	No	0.9 ± 0.17	No	0.32 ± 0.04
F. prausnitzii A2−165/B. hydrogenotrophica S5a33	2	Fructose/acetate	−49.3 ± 1.0	41.4 ± 11.7	30.7 ± 1.8	−1.2 ± 0.0	3.9 ± 1.6	56.2 ± 37.1	54.8 ± 33.3	91.6 ± 9.4	0.88 ± 0.25	No	0.6 ± 0.14	Yes	0.26 ± 0.13
F. prausnitzii A2−165/B. hydrogenotrophica S5a33	1	Fructose	−47.0	62.5	25.5	−1.1	4.5	62.9	63.6	107.4	1.11	No	0.63	No	0.46
Tri-culture fermentations
R. intestinalis L1−82/F. prausnitzii A2−165/B. hydrogenotrophica S5a33	6	Fructose	−48.9 ± 1.3	38.4 ± 16.9	32.5 ± 5.5	−1.2 ± 0.1	7.4 ± 1.7	61.9 ± 3.2	57.1 ± 9.2	97.0 ± 3.1	0.84 ± 0.09	No	0.78 ± 0.27	No	0.58 ± 0.11

elife-37090-v3.xml

10.7554/eLife.37090.005

Table 1.Overview of fermentation experiments and model fitting results (RMSE: root mean square error).

Means and standard deviations are reported across biological replicates.

Strains	Number of biological replicates	Added energy source and/or co-substrate	Consumption (-)/production (+) of metabolites in mM							Carbon recovery (%)	O/R balance	Selected for parame-terization 1	RMSE parame-terization 1	Selected for parame-terization 2	RMSE parame-terization 2
Strains	Number of biological replicates	Added energy source and/or co-substrate	Fructose	Acetate	Butyrate	Formate	Lactate	H₂	CO₂	Carbon recovery (%)	O/R balance	Selected for parame-terization 1	RMSE parame-terization 1	Selected for parame-terization 2	RMSE parame-terization 2
Monoculture fermentations
R. intestinalis L1-82	4	Fructose/acetate	−48.8 ± 0.9	−20.6 ± 2.4	58.5 ± 3.9	6.8 ± 1.2	3.9 ± 1.1	72.2 ± 4.9	84.0 ± 0.8	105 ± 14.3	0.86 ± 0.2	Yes	0.17 ± 0.04	No	0.83 ± 0.13
F. prausnitzii A2-165	3	Fructose/acetate	−23.1 ± 1.1	−13.5 ± 0.8	29.8 ± 0.2	22.7 ± 0.9	1.8 ± 0.2	0.2 ± 0.2	19.3 ± 1.6	100.9 ± 3.4	1.05 ± 0.09	Yes	0.15 ± 0.08	Yes	0.15 ± 0.08
B. hydrogenotrophica S5a33	3	Fructose/formate	−19.0 ± 5.6	23.0 ± 6.6	0.0 ± 0.0	−36.1 ± 1.8	6.0 ± 1.2	31.5 ± 7.7	26.0 ± 5.3	60.0 ± 2.1	0.76 ± 0.07	Yes	1.43 ± 0.27	No	3.53 ± 1.04
Bi-culture fermentations
R. intestinalis L1−82/F. prausnitzii A2-165	2	Fructose/acetate	−47.7 ± 2.2	−18.1 ± 2.7	56.3 ± 4.5	7.6 ± 2.7	4.3 ± 3.3	114 ± 16	85.7 ± 4.1	102.8 ± 0.3	0.79 ± 0	No	0.77 ± 0.06	No	0.68 ± 0.03
R. intestinalis L1−82/B. hydrogenotrophica S5a33	2	Fructose/acetate	−46.5 ± 1.5	−7.5 ± 1.9	53.5 ± 4.7	−0.5 ± 0.8	2.2 ± 0.3	53.0 ± 3.0	74.9 ± 4.1	100.2 ± 0.6	0.94 ± 0.12	No	0.78 ± 0.36	Yes	0.3 ± 0.04
R. intestinalis L1−82/B. hydrogenotrophica S5a33	2	Fructose	−48.0 ± 0.2	44.9 ± 5.4	27.9 ± 3.0	−1.0 ± 0.0	5.4 ± 2.4	33.1 ± 3.2	47.4 ± 3.9	91.6 ± 1.1	1.05 ± 0.06	No	0.9 ± 0.17	No	0.32 ± 0.04
F. prausnitzii A2−165/B. hydrogenotrophica S5a33	2	Fructose/acetate	−49.3 ± 1.0	41.4 ± 11.7	30.7 ± 1.8	−1.2 ± 0.0	3.9 ± 1.6	56.2 ± 37.1	54.8 ± 33.3	91.6 ± 9.4	0.88 ± 0.25	No	0.6 ± 0.14	Yes	0.26 ± 0.13
F. prausnitzii A2−165/B. hydrogenotrophica S5a33	1	Fructose	−47.0	62.5	25.5	−1.1	4.5	62.9	63.6	107.4	1.11	No	0.63	No	0.46
Tri-culture fermentations
R. intestinalis L1−82/F. prausnitzii A2−165/B. hydrogenotrophica S5a33	6	Fructose	−48.9 ± 1.3	38.4 ± 16.9	32.5 ± 5.5	−1.2 ± 0.1	7.4 ± 1.7	61.9 ± 3.2	57.1 ± 9.2	97.0 ± 3.1	0.84 ± 0.09	No	0.78 ± 0.27	No	0.58 ± 0.11

elife-37125-v1.xml

10.7554/eLife.37125.009

Table 1.Significant positive clusters of noxious-evoked brain activity, observed across the whole group (n = 13, cluster forming threshold: z = 3.1, cluster significance threshold, p = 0.05).

This table provides an anatomical description and the location of the peak z-statistic within each active brain region. The group activity reported consisted of 14 distinct clusters, some of which spanned multiple brain regions.

Anatomical description of location of activity		Maximum z-statistic within cluster	Coordinates of maximum z-statistic in infant template space
Anatomical description of location of activity		Maximum z-statistic within cluster	X	Y	Z
Post-central gyrus	Contra	4.8	7.7	−27.5	50.7
Post-central gyrus	Ipsi	4.7	−23.2	−27.5	43.8
Posterior cingulate sulcus	Contra	4.8	6.9	−23.2	36.0
Posterior cingulate sulcus	Ipsi	3.8	−6.0	−20.6	34.3
Superior parietal lobule	Contra	4.8	12.9	−44.6	47.2
Superior parietal lobule	Ipsi	4.7	−14.6	−43.8	43.8
Thalamus	Contra	4.7	16.3	−19.7	12.0
Thalamus	Ipsi	4.6	−13.8	−24.0	16.3
Supra-marginal gyrus	Ipsi	4.7	−25.8	−29.2	37.8
Supra-marginal gyrus	Contra	4.6	30.1	−24.9	28.3
Superior frontal sulcus	Contra	4.7	16.3	−4.3	44.6
Middle frontal gyrus	Ipsi	4.7	−27.5	0.9	30.0
Middle frontal gyrus	Contra	4.0	24.1	5.2	33.5
Cuneus	Contra	4.7	7.7	−53.2	26.6
Cuneus	Ipsi	4.2	−5.1	−50.7	23.2
Superior parietal lobe / Precuneus	Contra	4.7	5.2	−35.2	39.5
Superior parietal lobe / Precuneus	Ipsi	4.0	−0.9	−43.8	41.2
Pre-central gyrus / Central sulcus	Contra	4.6	24.1	−14.6	45.5
Pre-central gyrus / Central sulcus	Ipsi	3.9	−8.6	−23.2	53.2
Posterior insula	Contra	4.6	19.0	−19.7	24.0
Parietal operculum	Ipsi	4.6	−34.4	−21.4	18.0
Superior temporal gyrus / Posterior operculum	Contra	4.6	31.0	−27.5	22.3
Occipital gyrus	Ipsi	4.6	−12.0	−63.5	21.4
Anterior cingulate cortex	Ipsi	4.2	−1.7	14.7	24.0
Anterior cingulate cortex	Contra	3.9	4.3	12.1	25.7
Superior temporal gyrus	Ipsi	4.2	−27.5	−28.3	12.8

elife-37161-v2.xml

10.7554/eLife.37161.018

Table 2.Ligand-binding affinities for WT, Y537S, and D538G mutant ERα LBD.

Ligand/Mutant	K_d (nM)^*
Ligand/Mutant	WT	Y537S	D538G
E₂^‡	0.22 ± 0.11	1.40 ± 0.54	1.77 ± 0.66
	K_i (nM)^†
4-OHT^‡	0.12 ± 0.003	2.64 ± 0.4	3.28 ± 0.7
RAL	0.30 ± 0.05	3.59 ± 1.0	3.77 ± 1.0
BZA	0.37 ± 0.01	3.50 ± 0.6	5.53 ± 0.7
Fulvestrant^‡	0.13 ± 0.03	3.68 ± 0.8	5.06 ± 1.2

* Measured directly by Scatchard Analysis using [³H]E2.

† Calculated using the Cheng-Prusoff equation from the IC₅₀ values determined in a competitive radiometric binding analysis using [³H]E2 as a tracer.

^‡Indicates previously published data (Fanning et al., 2016; Zhao et al., 2017).

elife-37227-v1.xml

10.7554/eLife.37227.006

Table 1.Summary demographic details and phantom sensations.

Data is shown for amputees (AMP), controls (CTR) and congenital one-handers (1H). Congenital one-handers did not feel any phantom limb sensations. All controls have full kinaesthetic sensations. F: female, M: male. Side: side of missing hand; L: left, R: right. Amputation level: 1: shoulder, 2: above elbow; 3: at elbow; 4: below elbow; 5: at wrist. Kin: Phantom limb kinaesthesia (number of independent controllable parts of the hand), Viv: Chronic phantom limb vividness (0: no sensation, 100: intact hand’s vividness), Pain: Chronic phantom limb pain (0: no pain, 100: worst pain imaginable), AViv/APain: Acute Viv/Pain (on the scanning day), Std: standard deviation, ND: nondominant.

AMP	Age (years)	Sex	Amputation				Phantom sensations
AMP	Age (years)	Sex	Side	Years since	Age at (years)	Level	Kin (0-5)	Viv (0-100)	Pain (0-100)	AViv (0-100)	APain (0-100)
Mean	50.4			17.6	32.9		3	58	46	65	21
St. dev.	12.1			10.4	11.8		2	38	37	30	23
A01	44	M	R	15	29	2	5	100	100	100	50
A02	53	M	L	32	21	2	5	50	100	60	70
A03	40	M	L	11	29	2	4	100	50	100	20
A04	51	M	L	32	19	2	5	100	0	100	0
A05	27	F	R	7	20	4	2	50	40	60	0
A06	71	M	R	16	55	2	1	20	85	60	20
A07	46	M	R	18	28	2	3	70	90	70	50
A08	56	M	L	26	30	4	5	6	40	10	0
A09	64	M	L	31	33	2	4	100	40	100	10
A10	58	M	L	2	56	2	3	90	0	80	0
A11	28	M	L	8	20	5	4	40	40	20	0
A12	57	M	R	29	28	2	1	80	90	80	40
A13	50	F	L	1	49	4	0	0	0	0	0
A14	52	M	R	27	25	2	5	100	80	80	50
A15	68	M	R	26	42	4	1	16	0	80	0
A16	39	F	R	9	30	3	4	35	40	50	30
A17	58	M	L	12	46	4	5	2	0	65	0
A18	46	F	L	14	32	4	3	80	30	50	30
CTR	Age (years)	Sex	ND hand		1H	Age (years)	Sex	Missing hand
CTR	Age (years)	Sex	Side		1H	Age (years)	Sex	Side	Level
Mean	45.3				Mean	45.7
St. dev.	14.9				St. dev.	10.4
C01	29	M	R		H01	41	M	L	4
C02	24	F	L		H02	37	M	R	4
C03	47	F	L		H03	31	F	L	4
C04	39	M	L		H04	60	M	L	4
C05	32	M	R		H05	39	F	L	4
C06	53	F	R		H06	54	F	L	4
C07	38	F	R		H07	34	M	L	4
C08	67	M	R		H08	63	M	L	4
C09	42	M	R		H09	44	F	R	4
C10	41	M	R		H10	55	F	L	4
C11	69	M	L		H11	46	M	R	4
C12	63	F	L		H12	37	M	R	4
					H13	53	F	L	4

elife-37231-v2.xml

10.7554/eLife.37231.019

Table 1.Summary of the deacetylation turnover (V/[E]) from data in <xref ref-type="fig" rid="fig6">Figure 6</xref> and <xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref> (p<0.001 for V/[E] of K9ac nucleosome vs. K14ac nucleosome substrates in both the monoacetylated and triacetylated assays); (n = 3 for all measurements except n = 2 for LHC on H3 and HDAC1 on nucleosomes; kinetic values shown are ± S.E.M.

	Substrate	V/[E] (min⁻¹)
	Substrate	K9ac	K14ac	K18ac
LHC	Kac Nucleosome	0.10 ± 0.0084	0.014 ± 0.0073	0.048 ± 0.011
	Kac H3	31 ± 3.9	35 ± 8.5	-
	3Kac Nucleosome	0.11 ± 0.0071	0.019 ± 0.0033	0.058 ± 0.0022
	3Kac H3	31 ± 4.3	35 ± 2.7	-
HDAC1	Kac Nucleosome	<0.005	<0.005	-
HDAC1	Kac H3	10 ± 0.89	12 ± 0.26	-

elife-37294-v2.xml

10.7554/eLife.37294.011

Table 2.Tumor CNA burden is associated with recurrence and overall survival independent of disease stage in multiple cancer types

Cohort	Model	Disease free Time				Overall Survival
Cohort	Model	Cases	HR	95% CI	P	Cases	HR	95% CI	P
Prostate cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	280	1.27	1.13, 1.42	<0.0001	Insufficient events
Prostate cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, adjusted for Gleason grade and mutation burden	279	1.18	1.03, 1.35	0.015
	Tumor CNA burden, per 5% tumor CNA burden, adjusted for purity (ABSOLUTE)*	243	1.22	1.07, 1.40	0.003
	Tumor CNA burden, per 5% tumor CNA burden, adjusted for ploidy	243	1.32	1.11, 1.56	0.002
Breast cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	709	1.07	1.01, 1.14	0.028	794	1.08	1.03, 1.13	0.0005
Breast cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, Multivariable, adjusted for disease stage	695	1.07	1.00, 1.14	0.049	777	1.08	1.03, 1.13	0.002
Endometrial Cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	496	1.10	1.06, 1.14	<0.0001	536	1.13	1.08, 1.17	<0.0001
Endometrial Cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for disease stage	496	1.08	1.04, 1.13	<0.0001	536	1.10	1.05, 1.15	<0.0001
Renal clear cell cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	425	1.05	1.01, 1.09	0.028	525	1.02	0.98, 1.06	NS (0.4)
Renal clear cell cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for disease stage	423	1.05	1.00, 1.11	0.035	522	1.01	0.97, 1.06	NS (0.7)
Thyroid cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	483	1.17	1.01, 1.35	0.033	497	1.30	1.04, 1.63	0.021
Thyroid cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for disease stage	481	1.18	1.00, 1.39	0.048	Insufficient events
Colorectal cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	512	1.05	1.00, 1.11	0.037	587	1.06	1.01, 1.12	0.012
Colorectal cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for disease stage	496	1.03	0.98, 1.09	NS (0.3)	567	1.03	0.97, 1.09	NS (0.3)
	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for tumor stage	511	1.06	1.01, 1.12	0.028	585	1.07	1.02, 1.13	0.009

*Result differed with similar adjustment in IMPACT prostate cancer cohort utilizing FACETS, see Supplementary file 3.

elife-37294-v2.xml

10.7554/eLife.37294.012

Table 3.Tumor CNA burden determined by clinically approved sequencing panel is associated with overall survival in primary and metastatic tumors

Model	Overall Survival
	Primary tumors				Metastatic tumors
	HR	95%		P	HR		95%		P
Prostate Cancer^*,†
Univariate, tumor CNA burden, per 5%	1.17		1.04, 1.31	0.007	1.07	1.01, 1.14		0.020
Multivariable Tumor CNA burden, per 5% Mutation burden (per mutation)	1.11 1.22		0.98, 1.26 1.12, 1.33	0.10 <0.0001	1.08 1.05	1.02, 1.15 1.02, 1.08		0.011 0.001
Multivariable Tumor CNA burden, per 5% TP53 CN loss or mutation	1.17 4.12		1.04, 1.31 2.02, 8.41	0.007 <0.0001	1.06 1.24	1.00, 1.13 0.76, 2.02		NS (0.069) NS (0.4)
Multivariable Tumor CNA burden, per 5% RB1 CN loss or mutation	1.15 3.24		1.02, 1.30 0.70, 14.98	0.026 NS (0.13)	1.06 1.68	0.99, 1.13 0.94, 2.99		NS (0.091) NS (0.080)
Multivariable Tumor CNA burden, per 5% PTEN CN loss or mutation	1.17 2.38		1.04, 1.32 1.03, 5.51	0.008 0.042	1.07 1.15	1.01, 1.14 0.70, 1.89		0.023 NS (0.6)
Pan- Cancer
Univariate, tumor CNA burden, per 5%^‡§	1.04		1.02, 1.05	<0.0001	1.02	1.01, 1.03				0.005
Univariate, mutation burden (per five units)^‡§	0.98		0.97, 1.00	NS (0.072)	0.99	0.97, 1.01				NS (0.4)
Meta-analysis, tumor CNA burden (per 5%)^#	1.04		1.02, 1.05	<0.0001**	1.02	1.01, 1.04				0.005^††
Meta-analysis, tumor CNA burden (per 5%), excluding outlier cancer types^‡‡	1.05		1.03, 1.07	<0.0001^§§	1.03	1.01, 1.04				0.002^##

*Prostate primary tumors: patient n = 261 for all models except multivariable model with mutation burden, where n = 227; event n = 33; median follow-up time for survivors 40 (IQR 25,81) months.

†Prostate metastatic tumors: patient n = 216 for all models except multivariable model with mutation burden, where n = 205; event n = 80; median follow-up time for survivors 59.5 (IQR 32, 129) months.

‡Pan-cancer primary tumors, univariate models: patient n = 6610, event n = 1535, median follow-up time for survivors 24 (IQR 11, 61) months

§Pan-cancer metastatic tumors, univariate models: patient n = 4864, event n = 1467, median follow-up time for survivors 51 (IQR 23, 109) months.

#Pan-cancer meta-analysis, among ten most prevalent cancer types: primary tumor patient n = 4863, metastatic tumor patient n = 3676. Estimates are based on overall fixed effects.

**p-value corresponds with test of effects size. Chi-square test for heterogeneity p-value=0.003.

††p-value corresponds with test of effects size. Chi-square test for heterogeneity p-value=0.024.

‡‡Exclusion of cancer types to reduce heterogeneity: primary tumor patient n = 3887, metastatic tumor patient n = 3098. Estimates are based on overall fixed effects.

§§Excluding pancreatic and colorectal cancer, test of effects size p-value. Chi-square test for heterogeneity p-value=0.3.

##Excluding pancreatic and prostate cancer, test of effects size p-value. Chi-square test for heterogeneity p-value=0.8.

elife-37294-v3.xml

10.7554/eLife.37294.011

Table 2.Tumor CNA burden is associated with recurrence and overall survival independent of disease stage in multiple cancer types

Cohort	Model	Disease free Time				Overall Survival
Cohort	Model	Cases	HR	95% CI	P	Cases	HR	95% CI	P
Prostate cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	280	1.27	1.13, 1.42	<0.0001	Insufficient events
Prostate cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, adjusted for Gleason grade and mutation burden	279	1.18	1.03, 1.35	0.015
	Tumor CNA burden, per 5% tumor CNA burden, adjusted for purity (ABSOLUTE)*	243	1.22	1.07, 1.40	0.003
	Tumor CNA burden, per 5% tumor CNA burden, adjusted for ploidy	243	1.32	1.11, 1.56	0.002
Breast cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	709	1.07	1.01, 1.14	0.028	794	1.08	1.03, 1.13	0.0005
Breast cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, Multivariable, adjusted for disease stage	695	1.07	1.00, 1.14	0.049	777	1.08	1.03, 1.13	0.002
Endometrial Cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	496	1.10	1.06, 1.14	<0.0001	536	1.13	1.08, 1.17	<0.0001
Endometrial Cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for disease stage	496	1.08	1.04, 1.13	<0.0001	536	1.10	1.05, 1.15	<0.0001
Renal clear cell cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	425	1.05	1.01, 1.09	0.028	525	1.02	0.98, 1.06	NS (0.4)
Renal clear cell cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for disease stage	423	1.05	1.00, 1.11	0.035	522	1.01	0.97, 1.06	NS (0.7)
Thyroid cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	483	1.17	1.01, 1.35	0.033	497	1.30	1.04, 1.63	0.021
Thyroid cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for disease stage	481	1.18	1.00, 1.39	0.048	Insufficient events
Colorectal cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, univariate	512	1.05	1.00, 1.11	0.037	587	1.06	1.01, 1.12	0.012
Colorectal cancer TCGA	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for disease stage	496	1.03	0.98, 1.09	NS (0.3)	567	1.03	0.97, 1.09	NS (0.3)
	Tumor CNA burden, per 5% tumor CNA burden, multivariable, adjusted for tumor stage	511	1.06	1.01, 1.12	0.028	585	1.07	1.02, 1.13	0.009

*Result differed with similar adjustment in IMPACT prostate cancer cohort utilizing FACETS, see Supplementary file 3.

elife-37294-v3.xml

10.7554/eLife.37294.012

Table 3.Tumor CNA burden determined by clinically approved sequencing panel is associated with overall survival in primary and metastatic tumors

Model	Overall Survival
	Primary tumors				Metastatic tumors
	HR	95%		P	HR		95%		P
Prostate Cancer^*,†
Univariate, tumor CNA burden, per 5%	1.17		1.04, 1.31	0.007	1.07	1.01, 1.14		0.020
Multivariable Tumor CNA burden, per 5% Mutation burden (per mutation)	1.11 1.22		0.98, 1.26 1.12, 1.33	0.10 <0.0001	1.08 1.05	1.02, 1.15 1.02, 1.08		0.011 0.001
Multivariable Tumor CNA burden, per 5% TP53 CN loss or mutation	1.17 4.12		1.04, 1.31 2.02, 8.41	0.007 <0.0001	1.06 1.24	1.00, 1.13 0.76, 2.02		NS (0.069) NS (0.4)
Multivariable Tumor CNA burden, per 5% RB1 CN loss or mutation	1.15 3.24		1.02, 1.30 0.70, 14.98	0.026 NS (0.13)	1.06 1.68	0.99, 1.13 0.94, 2.99		NS (0.091) NS (0.080)
Multivariable Tumor CNA burden, per 5% PTEN CN loss or mutation	1.17 2.38		1.04, 1.32 1.03, 5.51	0.008 0.042	1.07 1.15	1.01, 1.14 0.70, 1.89		0.023 NS (0.6)
Pan- Cancer
Univariate, tumor CNA burden, per 5%^‡§	1.04		1.02, 1.05	<0.0001	1.02	1.01, 1.03				0.005
Univariate, mutation burden (per five units)^‡§	0.98		0.97, 1.00	NS (0.072)	0.99	0.97, 1.01				NS (0.4)
Meta-analysis, tumor CNA burden (per 5%)^#	1.04		1.02, 1.05	<0.0001**	1.02	1.01, 1.04				0.005^††
Meta-analysis, tumor CNA burden (per 5%), excluding outlier cancer types^‡‡	1.05		1.03, 1.07	<0.0001^§§	1.03	1.01, 1.04				0.002^##