EMBO/sd-character-level-ner huggingface dataset:
HIV-mediated autophagy induction is dependent upon TFEB.Fig 5(A) Macrophages transduced with non-specific scrambled shRNA (shNS), or TFEB shRNA (shTFEB) were infected with HIV for 10 days. Cells were lysed and analyzed for TFEB and ACTB content by Western blotting. Left, a representative blot is shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4. (B) At 1, 3, 5, 7, and 10 days post-infection cells from (A) were harvested, lysed, and analyzed for endogenous LC3B and SQSTM1 by Western blotting. Left, representative blots are shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4. (C) Macrophages transduced with non-specific cDNA (Control), or TFEB cDNA (TFEB) then exposed to HIV. Cells were lysed and analyzed for TFEB and ACTB content by Western blotting. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4. (D) Transduced cells from (C) were exposed to purified HIV for the indicated time (minutes) harvested, lysed, and analyzed for endogenous LC3B and SQSTM1 by Western blotting. Left, representative blots are shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4.
Plcg1 deletion reduces the volume of the corpus callosum and causes abnormal axon projection into the olfactory tubercle.Figure 4(A) Schematic of the main phenotype (CC: corpus callosum, OT: olfactory tubercle, SI: substantia innominata) (B) Immunohistochemical staining of control and Plcg1 conditional knockout (cKO) sagittal brain sections. The deletion of Plcg1 caused structural changes in SI and OT projections in the Plcg1f/f;Nes-Cre (d) mice compared to the controls (a) (n = 4; scale bar = 1 mm). The areas delineated by the white boxes (insets) are magnified images of the OT (b and e), and the yellow boxes are magnified images of the SI (c and f). (C) Quantification of the axon bundle distribution. Green boxes in (b) and (e) were selected as tegions of interest (ROIs) using the ZEN software (n = 4) (one-way ANOVA, F-value: 118.5745, P**<0.005). (D) Representative images of tyrosine hydroxylase (TH)- positive neurons (scale bar = 1 mm). The areas delineated by the white boxes are magnified in the insets. The yellow arrow indicated misoriented TH-positive axons (magenta: TH). (E) Fluorescence intensities in the ROIs were measured according to distance (n = 4) (one-way ANOVA, F-value: 271.8, **P<0.005). Cumulative values of fluorescence intensities per section are shown in the lower graph (S: section). (F) In situ hybridization of PLCγ1 in mDA neurons (scale bar = 50 μm) (green: TH, violet: DIG-labeled probe). (G) Representative images of the CC axon bundles in control (left) and a Plcg1f/f;Nes-Cre (right) mice (n = 4). The tip of the CC was triangular in the control mouse, but oval in the Plcg1f/f;Nes-Cre mouse. The areas delineated by the white boxes are magnified in the insets (red: neurofilament, green: glial fibrillary acidic protein, blue: Hoechst; scale bar = 1 mm). (H) The area of the CC in the Plcg1f/f;Nes-Cre mouse was 36% smaller than that in the control mouse (scale bar = 500 μm) (I) Quantitative comparison of the CC areas in the control and Plcg1f/f;Nes-Cre mice (n = 4; t-test; **p < 0.005). Data are presented as the mean ± s.e.m.
Figure 1A WT MDFs were treated ± TSI individually or in combination for 3 hrs. Whole cell lysates (WCL) and UBA-pull down (UBA-PD) fractions were analysed by Western blot and probed with antibodies as indicated. Representative of three independent experiments. Samples of UBA-pull down in following figures were analysed in the same way unless otherwise indicated. B WT, Ripk3-/-, Mlkl-/-, Tnfr1-/- and Traf2-/- MDFs were untreated (UT) or treated with TSI for 3 hrs. Nec-1 and GSK872 were added to inhibit RIPK1 and RIPK3 kinase activities respectively. C WT and Tnf-/- BMDMs were treated ± death ligands including TNF (T), LPS (L), Fas ligand (F) and Poly I:C (P) in addition to S and I for 3 hrs. D WT HT29 cells were untreated (UT) or treated with TSI for 16 hrs. E RIPK3-gyrase were inducibly expressed in Ripk3-/- MDFs by doxycycline (dox) for 5 hrs, and cells were then treated ± combination of TSI, or coumermycin (coum) for 3 hrs.
Yap regulates hepatoblast formation and expansion.Figure 2Whole-mount in situ hybridization (WISH) analysis of progenitor marker prox1, hhex, and foxa3 expression in WT and yap-/- mutant embryos at 36 hpf. Arrow and bracket highlight the hepatic bud. Scale bar: 200μm qPCR analysis of hhex and prox1 gene expression in WT and yap-/- mutant embryos at 48 hpf. n>3, *p<0.05, two-sided Student's t-test; values represent the mean ± s.e.m WISH analysis of prox1, hhex and foxa3 expression in WT, hs:dnYap and hs:Yap transgenic embryos heat shocked at 24 hpf and fixed at 36 hpf. Arrow and bracket highlight the hepatic bud. Scale bar: 200μm Quantitative analysis of hepatic bud area (prox1 staining) in WT, hs:dnYap and hs:Yap transgenic embryos heat shocked at 24 hpf and fixed at 36 hpf. n>10, *p<0.05, two-sided Student's t-test; values represent the mean ± s.e.m
Figure 3(A). Representative flow cytometric analysis of human neutrophils cultured alone (Control), incubated with late-stage NF54 parasites (wild type) or PfEMP1 Knock out (PfEMP1 KO) GFP+ iRBC. (B). Flow cytometric quantification of the effect of trypsin treatment on neutrophil interaction with wild type and PfEMP1 KO GFP+ iRBC. (C). Luciferase-based killing assay and neutrophil elimination of late-stage wild type (wt) and PfEMP1ko iRBC.
Na+ and transmitter bindingA.Figure 1A. Tryptophan-fluorescence time course associated to Na+ (blue) and K+ (black) binding, respectively, to detergent-purified apo EAAT1CRYST at pH 7.4. Horizontal and vertical scale bars represent time and ∆F/F0, respectively. B. Tryptophan-fluorescence time course associated to L-asp binding in presence of 1 mM (blue) and absence (black) of Na+, respectively, at pH 9. C C. Na+ binding isotherms of EAAT1CRYST at pH 7.4 in the presence (pink) and absence (blue) of UPCH101. Mutation D400380N at Na3 strongly impairs Na+ binding (green). Solid lines represent fits of Hill equation. D. Log-log plot of L-asp KD as a function of Na+ concentration. Empty circles are KD values (n=20) at pH=9.0 in the absence of UCPH101 (blue), and solid line is the fit of a straight line. For comparison, average L-asp KD at 1 mM Na+ in the presence pf of UPCH101 is also shown (n=3; red).
PYCR1 knockout results in reduced invasion of MCF7 cells.Figure 6A) Representative pictures of transwell migration and invasion after PYCR1 knockout. Scale bar :100 μm. B) Bar plot represents mean ± SD of three biological replicates for transwell migration and invasion. Samples were compared using Kruskal Wallis test followed by Dunnett's test for multiple pairwise comparisons. Corrected p-values are reported as follows *** p < 0.001. C) Representative images of colony formation in soft agar upon PYCR1 KO. Scale bar: 100 μm. D) Growth measurements of MCF7 wild type and PYCR1 KO cells over 96 hours. Data represents mean ± SE of three biological experiments. Samples were compared using paired Student's t-test. E-H) Bar plots show percentage of viable cells after treatment with 0.75 mM H2O2 (E), 0.06 µM paclitaxel (F), 0.15 µM doxorubicin (G), 2.5 mM cyclophosphamide (H). Data represent mean ± SE of three biological experiments. Samples are compared using Kruskal Wallis test followed by Dunnett's test for multiple pairwise comparisons. Corrected p values are indicated as follows *p < 0.05. I) Tumor volume measurements for 26 days in MCF7 injected NSG mice. CRISPR control and PYCR1 KO tumors with (n=8) and without treatment (n=5) are shown. Data represents mean ± SE. Pax: Paclitaxel, Dox: Doxorubicin. Groups were compared by one way ANOVA followed by Tukey's multiple comparisons test for pairwise group comparisons. Corrected p-values are reported as follows *p < 0.05, ** p < 0.01. Shapiro Wilk test was used to check data normality and Bartlett test was used to examine homogeneity of variances. J) Bar plot indicates mean ± SE of tumor volume measurements for day 26. CRISPR control and PYCR1 KO tumors with (n=8) and without treatment (n=5) were compared by one way ANOVA followed by Tukey's multiple comparisons test for pairwise group comparisons. Corrected p-values are reported as follows *** p < 0.001. Shapiro Wilk test was used to check data normality and Bartlett test was used to examine homogeneity of variances.
Figure 3A. DIC images of abnormal embryo sacs in cycb1 mutant combinations. Red arrowheads indicate the visible nuclei in Col-0 embryo sacs (central and egg cells) and the corresponding structures in the quadruple cycb1;1-/- cycb1;2+/- cycb1;3+/- cyb1;4- mutant. Scale bars: 20 μm. B. Quantification of the different abnormal embryo sac structures in cycb1 mutant combinations (n = 202-459 embryo sacs per genotype). Different letters indicate significant differences in the proportion of abnormal embryo sacs in a Chi-squared test followed by the Marascuilo procedure to identify significant pairwise comparisons. WT = wildtype. C. DIC images of embryo sacs 3 DAP with wildtype pollen (female x male). Red arrowheads indicate the visible embryo sac nuclei in the crosses with the quadruple cycb1;1-/- cycb1;2+/- cycb1;3+/- cyb1;4- mutant as a female donor, while the control Col-0 x Col-0 cross exhibits a developing embryo. Scale bars: 20 μm. D. Quantification of seed abortion in different cycb1 mutant combinations. Graph represents the average seed abortion rate per plant ± SD of three biological replicates, n = 463-579 seeds analyzed per genotype. Asterisks indicate significant differences in seed abortion rate in an ordinary one-way ANOVA test, followed by a Dunnett's multiple comparisons test (**** P < 0.0001). E. Silique pictures of cycb1 triple and quadruple mutants. White arrowheads indicate early aborted ovules. Scale bars: 500 μm.
The accumulation of S7P in carbon starvation facilitates survival of subsequent oxidative stress.Figure 8(A) Experimental design. Yeast cells growing on glucose were switched to no carbon media for 30 min. Thereafter, 20 mM H2O2 was added and metabolome analyzed by LC‐MS. (B) Diagram of proposed reactions and their regulation. S7P accumulates during carbon starvation due to low level of glyceraldehyde‐3‐phosphate (GAP). Oxidative stress blocks GAP consumption via glycolysis by inhibiting GAPDH. This provides sufficient GAP to react with S7P, producing F6P via transaldolase. F6P is further converted to G6P which enters the oxidative PPP. The resulting NADPH is utilized for regeneration of reduced glutathione. 1,3‐DPG, 1,3‐diphosphoglycerate; GSSG, glutathione disulfide; GSH, reduced glutathione. (C and D) DHAP, S7P, G6P, and glutathione levels and NADPH/NADP+ ratio in wild type, phm8 and pnp1/urh1 strains in the experiment shown in (A) The x axis represents minutes after oxidative stress, and the y axis represents absolute intracellular concentration or ratio of intracellular concentration (mean±range of N=2 biological replicates). (E) Viability of wild type, phm8 and pnp1/urh1 strains in oxidative stress. The y axis represents percentage of survived cells calculated by dividing the number of colonies formed after oxidative stress by the number of colonies formed under the same starvation condition but without H2O2 treatment (mean±range of N=2 biological replicates).
Figure 2(A) Immunoblotting against the HA tag or the GAPDH of proteins extracted from HEK293 cells transfected for 24 hours with 100 C4G2 repeats embedded in the human antisense C9ORF72 and fused in all three possible frames with a HA tag. (B) LC-MS/MS spectra of the N-terminal part of the HA-immunoprecipitated and LysC digested polyPG protein expressed as in (A). (C, D) Immunoblotting against the GFP (C) or the HA tag (D) or the GAPDH of proteins extracted from HEK293 cells transfected for 24 hours with 3, 10 or 100 C4G2 repeats embedded in the human antisense C9ORF72 sequence fused to the GFP in the PG frame. (E) Scheme of human antisense C9ORF72 transcript. Expanded C4G2 repeats, AUG initiation codon and polyPG ORF are indicated in red.
MBP-CoV-2 N and cleaved CoV-2 N elute larger than their predicted molecular weights.Figure 2A) Superdex 200 26/600 gel filtration chromatogram of ~7ml of ~500 μM MBP tagged SARS-CoV-2 N (top) and ~300μl ~50 μM SARS-CoV-2 N (previously cleaved from MBP) (bottom). Vertical lines represent peak elution volumes of gel filtration protein calibration standards. Brackets represent range of gels lanes. Predicted molecular weight of the tagged and untagged N are 90 kDa and 46 kDa respectively, much smaller than their corresponding calibrated peak elution volumes, consistent with oligomerization. B) SDS-PAGE showing the peak fractions of the MBP-SARS-CoV-2 N chromatogram showing expected 90 kDa molecular weight. Circular feature in SDS-PAGE gels is a divet in plastic on which pictures were taken. C) SDS-PAGE showing the peak fractions of the cleaved SARS-CoV-2 N chromatogram showing expected 46 kDa molecular weight. Circular feature in SDS-PAGE gels is a divet in plastic on which pictures were taken.
Figure 2(A)-(C) Upper panels: Scatter plots associating the expression of the GCD (CFTR) vs. identified PMs (A) EHF, (B) SLC6A14, and (C) SFTPA2 in healthy lung tissues from GTEx. Bottom Panels: Boxplots associating the expression of the identified DPMs in case-control studies; the expression of (A) EHF, (B) SLC6A14, and (C) SFTPA2 in severe and mild CF and in healthy controls. For all boxplots, center lines indicate medians, box edges represent the interquartile range, whiskers extend to the most extreme data points not considered outliers, and the outliers are plotted individually. Points are defined as outliers if they are greater than q3 + w × (q3-q1) or 1-w × (q3 − q1), where w is the maximum whisker length, and q1 and q3 are the 25th and 75th percentiles of the sample data, respectively. There are five severe (red), four mild (orange) and eleven control (blue) biological replicates. Data information: ** is P-value<0.01 and *** is P-value<0.001, using the permutation test The P-values in panels A, B, C are for the hyper-geometric enrichment test. (D) Map of coincidence of the low expression (lowest 10% of expression levels) of the 7 top DPMs with the low expression of CFTR in GTEx lung samples (lowest 10% of expression levels, when symptoms would be present in CF patients (Ramalho et al, 2002; Kerem et al, 1997); each small rectangle inside the big rectangle represents one individual; all presented samples are those with low CFTR expression. Dark blue rectangles indicate samples with low expression of the listed DPM). (E), (F) Upper panels: scatter plot associating the expression of the GCD (CFTR) vs. identified PMs in healthy colon GTEx tissue; the expression of CFTR (X-axis) vs. that of (E) CLCA1 and (F) SLC4A4, respectively, in healthy colon tissues. Bottom panels: Boxplots associating the expression of the identified DPMs in case-control studies; the expression of (E) CLCA1 and (F) SLC4A4 in colon tissues from CF and healthy controls. Empirical P-value significance is indicated qualitatively for two thresholds. There are sixteen CF (red) and thirteen control (blue) biological replicates. Data information: ** is P-value<0.01 and *** is P-value<0.001, using the permutation test The P-values in panels , E, F are for the hyper-geometric enrichment test. (G) The p-values assigned by GENDULF to genes within chr11p12-p13, chr6p21.3, chr3q29 and chrXq22-q23 chromosomal segments, ordered by their location. The lower dashed line represents a significance threshold corrected for the number of genes evaluated and the upper dashed line represents a significance threshold corrected for all genes and transcripts in GTEx, with alpha = 0.05. Data information: ** is P-value<0.01 and *** is P-value<0.001, using the permutation test The P-values in panels G are for the hyper-geometric enrichment test.
Figure 2A,B Expression of pHERK1::H2B-TdTomato in mature ovules. White dotted lines delineate the egg cell and synergid cells. Data information : Scale bars = 50 µm. M, micropyle. CC, central cell. EC, egg cell. SC, synergid cell. C,D Expression of pANJ::H2B-TdTomato in mature ovules. White dotted lines delineate the egg cell and synergid cells. Data information : Scale bars = 50 µm. M, micropyle. CC, central cell. EC, egg cell. SC, synergid cell. E,F Localisation of HERK1-GFP in the synergid cell from the pFER::HERK1-GFP construct in (F) and corresponding differential interference contrast (DIC) image in (E). White and red dotted lines delineate the egg cell and synergid cells, respectively. Data information : Scale bars = 50 µm. M, micropyle. Arrows, filiform apparatus. G,H Localisation of ANJ-GFP in the synergid cell from the pANJ::ANJ-GFP construct in (H) and corresponding DIC image in (G). White and red dotted lines delineate the egg cell and synergid cells, respectively. Data information : Scale bars = 50 µm. M, micropyle. Arrows, filiform apparatus.
Figure 4(A) PCA plot showing the clustering of stiff, soft cells and cancer stem cells (CSC). cells. The variance is the smallest between stiff and soft on PC2. (B) Venn diagram comparing the hits from stiff, soft or CSC MCF-7 cells. (C) Heatmap of differentially mRNA-seq expressed genes in stiff, soft or ALDH+ cells (CSC) MCF-7 cells. The unit for the color scale was z-score of log2 expression data shown. (D) ATAC-seq tracks of BCL9L and WNT3A in stiff or soft cells. (E) Heatmap of stemness association genes expression determined by mRNA sequencing comparing stiff and soft MCF-7 cells. n = 3. The unit for the color scale was z-score of log2 expression data shown.
Intrinsic disorder level for mitotic chromosome and nucleolar proteins as predicted by IUPRED2A.Figure 5A. The fraction of disordered residues per protein for the nucleolar proteins is significantly higher (*, adjusted P < 1x10-4, Dunn's test with Bonferroni correction. n = 848) compared to the cytosolic proteome as defined in the HPA Cell Atlas (n = 2,054). Additionally, the disorder levels for the nucleoli rim proteins (**, adjusted P = 4x10-4, n = 153) and the mitotic chromosome proteins (***, adjusted P < 1x10-4, n = 65) are significantly higher compared to the other nucleolar proteins. Box limits mark 1st and 3rd quantile, whiskers the 1.5x interquartile range and center line the median. Outliers are shown as dots. B. Fraction of proteins (in percent) having at least one functional disordered domain (>30 consecutive amino acids) for the mitotic chromosome proteins compared to the cytosolic proteome. More than 81% of the mitotic chromosome proteins have at least one long disordered domain. C-E. IF stainings of previously uncharacterized mitotic chromosome proteins predicted to be highly disordered. Protein of interest shown in green and DAPI in blue. Scale bar 10 µm. C. CCDC86 (HPA041117), 100% predicted disorder level. D. RRP15 (HPA024639), 87% predicted disorder level. E. PRR19 (HPA070350), 67% predicted disorder level.
Loss‐of‐function screen using haploid KBM7 cells identifies LRCC8A and LRRC8D as determinants of carboplatin resistance.Figure 1Outline of the loss‐of‐function screen. Genes enriched for gene‐trap insertions in a carboplatin‐selected cell population compared to unselected control cells. Circles represent genes and their size corresponds to the number of independent insertions identified in the carboplatin‐selected population. Genes are ranked on the x‐axis based on chromosomal position.Location of gene‐trap insertion sites (red arrowheads). White boxes indicate the 5′‐ and 3′‐untranslated regions, and the black boxes show the coding sequence in exons 3 and 4 (LRRC8A) and exon 3 (LRRC8D). Loss of LRRC8D causes resistance to carboplatin and cisplatin, but not to oxaliplatin. Survival of parental, vector‐transduced, or LRRC8D‐deficient GT1 and GT2 KBM7 cells exposed for 96 h to increasing concentrations of cisplatin, carboplatin, and oxaliplatin. The corresponding IC50 values and 95% confidence interval (CI) are given in Appendix Table S2. Data are presented as mean ± SEM.
Weight progression and neurological evaluation.Fig 2A) Evolution of rat weight of different treatment groups (12 animals in each group): control, L-BMAA (300 mg/kg/day during 5 consecutive days treated at weaning), VP2.51 (2,5 mg/kg during 15 days) with a group treated at PT1 and another at PT30, L-BMAA (with the same treatment as the group of L-BMAA) + VP2.51 (with the same treatment groups VP2.51) with a group treated at PT1 and another at PT30. B). Evolution of neurological evaluation in the treatment assay with VP2.51 (12 animals in each group). The control group and the groups treated exclusively with VP2.51 (at PT1 and PT30) are not shown because its assessment coincides with the horizontal axis. The time when the inhibitor is added is indicated with arrows.
Figure 2A, Outline of live-cell BODIPY-cholesteryl linoleate/LDL labeling and chase combined with AF680-integrin β1 antibody labeling. Cells were pre-treated for 1 day in 5 % LPDS. B, Quantification of the fraction of BODIPY-cholesterol (BC) fluorescence in integrin β1 positive organelles at the indicated chase times. Examplary images are shown in Fig. EV2B. Mean ± SEM, n = 8 (0 min); 6 (15 min); 5 (30 min); 6 (45 min); 7 (60 min) cells from 3 independent experiments. C, Schematic outline of intracellular D4H labeling. D, After 1 day LDL depletion in 5 % LPDS, cells were loaded with 50 μg/ml LDL for the indicated times and intracellular cholesterol was detected with D4H as in C by confocal microscopy. CM, complete medium. Dashed lines indicate cell outlines. E, Quantification of D. Mean ± SD, n = 25-26 cells pooled from 2 independent experiments. F, Cells were treated for 1 day in 5 % LPDS followed by 50 μg/ml LDL loading for the indicated times. Representative confocal images of cells triple labeled with intracellular accessible cholesterol (D4H), NPC1-GFP and internalized integrin β1. Dashed lines indicate cell outlines. G, Quantification of D4H area positive for NPC1 or internalized integrin β1 as in F. H, Fraction of D4H area overlapping with NPC1 or internalized integrin β1 in a peripheral region toward the leading edge (exemplary box shown as inset in F). Mean ± SD, n = 27-30 cells pooled from 2 independent experiments. Student's t-test.