EMBO/sd-character-level-ner huggingface dataset:
EUC1 displays negative genetic interactions with genes involved in particular with members of the Rpd3L histone deacetylase complex For , serial dilutions of the indicated strains were spotted and grown on YPD control or selective media plates, or under conditions as indicated. Note that all strains used in (A-D) contained an extra copy of MED11,
RT-qPCR analysis of mRNAs for the indicated genes in 1205Lu cells treated or not with EV secreted by primary adipocytes from lean (ND) and obese (HFD) mice for 48 h. Results are expressed relative to the corresponding value for control cells (n=3).
(D) IFNγ-primed WT, Irgm2-/-, Gbpchr3-/- and Irgm2-/- Gbpchr3-/- BMMs were treated with LPS (1 µg/ml) for 24 hours and cell lysates and supernatants collected. Protein levels in cell lysates (Caspase-1, and actin) and supernatants (Caspase-1 p20) were visualized via immunoblotting.
B. Immunodetection of BES1-CFP from heat-stressed plants, treated with epiBL or BRZ. 35S:BES1-CFP plants were treated for 24 hours with DMSO (control), 1 μM 24-epiBL or 5 μM BRZ and then heat-stressed as follows: lane 1: untreated control; lane 2: 45°C for 30 minutes; lane 3: 45°C for 60 minutes; lane 4: 45°C for 60 minutes and recovery at 21°C for 180 minutes.
Proteins enriched in aggregates show a predicted higher molecular chaperone requirement for folding (top vs. bottom 20% p=0.0055, Kolmogorov-Smirnov test), and are richer in intrinsically disordered regions (s2D-derived scores, top vs. bottom 20% p=0.0019, Kolmogorov-Smirnov test). Violin plots: the solid line shows the median, the dotted lines the interquartile ranges. The same result was obtained with cleverSuite-derived scores (top vs. bottom 20% p=0.0201, Kolmogorov-Smirnov test) (Figure EV4C). ** p < 0.01, Kolmogorov-Smirnov test.
Skin infiltration of pDCs (BST-2+ B220+ CD11cint CD11b-) was analyzed by flow cytometry. Graph shows immune cells as % of live, single cells. (n= 2-15; 1-3 independent experiments). Data information: Data are shown as mean ± SEM. P‐values were calculated by multiple t-test with one-way ANOVA with Bonferroni (A), multiple comparison test. Statistical significance: ns > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001, **** P < 0.0001. See Appendix Table S3 for exact P‐values.
(A) Euc1 domain structure is reminiscent of transcription factors. Top: Schematic representation of Euc1, with a predicted coiled-coil domain (CC) and GCR1-domain indicated. Predicted DNA binding of the C-terminal part was confirmed in Y1H experiments (Appendix Fig. S3A-C). Bottom: Euc1-like protein sequences from closely related Saccharomyces species were aligned and a phylogenetic tree was generated using Clustal Omega. Jalview was used to graphically display the degree of sequence conservation (see also Appendix Fig. S4A).
B Body weight of Uqcrh -/- mice and wild-type littermates at 1-2 weeks (n = 5 to 10), during the post-weaning period from 5-6 weeks of age (n = 3 to 7) and weekly from 6 to 10 weeks (n = 13 to 66), data are shown as mean ± SD. **** p < 0.0001, 2-Way ANOVA, from 7.5wk of age for Uqcrh-/- males and females versus sex-matched controls. Data are shown as single data points and median, or categorical data, males and females pooled, since genotype-related effects were comparable for both sexes from different cohorts. * p < 0.05, *** p <0.001, Wilcoxon rank-sum test.
C. Representative 3 hour migration paths of either MDA-MB-231CFP;Cre;Control (Control, left) or MDA‑MB‑231CFP;Cre;HA-RASSF1C (RASSF1C, right) within a single intravital imaging field of tumors co‑injected with T47DDsRed reporter cells.
(E) Effects of starvation for 6 or 12 h on the degradation of Htt-552 in PC12 cells. The effects of these starvations on protein levels of Htt-552 protein were determined with Western blot analysis. Values are the mean±SE of three independent experiments. **P<0.01 (compared with Htt-552-18Q without treatment); ##P<0.01, #P<0.05 (compared with Htt-552-100Q without treatment).
C. ChIP-qPCR assays in LCLs showing decreased occupation of CHD7 on the PAQR3 proximal promoter in a CHD7-mutation positive patient (N=3) compared to parental controls (N=6); *p< 0.05; Student's t-test, All data were expressed as mean fold change ± SD, N is the number of experimental repeats.
(C) The levels of CRAMP in duodenum (n = 6). Data information: Data were representative and were the mean ± SD from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons.
B. Table showing location, number of inserted or deleted residues and motility phenotype of all 18 stalk mutants. Quantification and classification are based on three technical repetitions. C. Example kymographs for 'Directional - WT like', 'Diffusive like', 'No movement', and 'Transient binding'. Magnified area for 'Diffusive like' motion shows run of a single molecule.
Western blot analysis of cell lysates from albumin- and/or ALDH1A-transfected HSCs as in (B). **P = 0.002, paired t-test (n = 3) (albumin compared to control).
F-J Many Age-TFs function in a synergetic manner. Synergetic interactions networks were generated from top 30 Age-TFs by synergy analysis, filtered by P<0.001. The hub genes selected from the synergetic network using the MCC algorithm of CytoHubba plugin in Cytoscape. The Age-TFs are ranked by the P-values from MARINa. The Age-TFs in the synergetic network are coloured by their MCC values. proAge-TFs are defined as those promoting the transcriptomic changes (up- and down-regulation) during ageing, whereas antiAge-TFs are those inhibiting these changes. proAge-TFs promote whereas antiAge-TFs suppress the ageing-induced transcriptomic changes. Please note that these two classes of TFs are not necessarily pro- or anti-aging by their names. The transcriptomic changes triggered by a proAge-TF could be adaptive for ageing and induce longevity.
A BioLayer interferometry (BLI) derived association and dissociation traces of monomeric FICDL258D-H363A (mFICDH363A) or dimeric FICDH363A (dFICDH363A) from immobilised biotinylated BiPT229A-V461F in absence or presence of nucleotides. Unless indicated (*) BiP was saturated with ATP before exposure to FICD variants. A representative experiment of three independent repetitions is shown. B BLI dissociation traces of proteins as in (A). At t = 0 a pre-assembled complex of immobilised, ATP-saturated BiP and the indicated FICD proteins (associated without ATP) were transferred into a solution without or with ATP, as indicated. A representative experiment is shown and the biphasic dissociation kinetics are quantified in (C) and (D). C Graph of the slow dissociation rates (koff,slow) of monomeric FICD from BiP:ATP as shown in (B). Bars represent mean values ± SD of three independent experiments. D The ATP-induced fold change in the percentage of the dissociation phase attributed to a fast dissociation (%Fast), koff,fast, and koff,slow derived from the data represented in (B). Bars represent mean values ± SD of three independent experiments.
j, k, Similar experiments to those in c and i were performed by starvation. Red and blue lines in b, c, g and j indicate means and s.e.m., respectively. The dashed line in c, g and j indicates the autophagic cell border (6%). Black error bars indicate s.d.
(J) Crystal violet viability assay of M238R cells treated with BRAFi/MEKi (BRAFi, Vemurafenib and MEKi, Trametinib) (1 µM), BIBF (2 μM) or with BRAFi/MEKi (1 μM) plus BIBF (2 μM) for 72 h. Paired Student t-test was used for statistical analysis. ****P≤0.0001. Significance was calculated against the control group. Statistical significance of BIBF vs BIBF + BRAFi/MEKi was also calculated. Data is represented as mean ± SD from a triplicate representative of 3 independent experiments.
(C) A heatmap diagram shows the expression profile of genes involved in glycolysis, the TCA cycle, the pentose phosphate pathway, pyruvate oxidation, gluconeogenesis, and glycogen metabolism obtained from two sets of GFP and MIG-6 knockdown BT549 cells.
(F) Immunoassay of NFL level in cerebrospinal fluid. One-way ANOVA, Tukey's post hoc test, F(3,11)=1.911, p=0.1862. ** p<0.01. TG-Ova-(GA)10 vs. TG-PBS p=0.0081.
(g) Immunohistochemical analysis of cellular localization of p62 and Keap1. Paraffin sections of the liver from 9-week-old mice of the indicated genotypes were immunolabelled with anti-p62 (left) and anti-Keap1 (right) antibodies. Scale bars, 20 μm.
A, B) Time course analysis and severity of the symptoms in wt and Sfrp1-/- mice after EAE induction. In A means are depicted with black (wt, n=19) and cyan (Sfrp1-/-, n=19) lines. In B data are expressed as % of the total number of analysed animals (n=19 per genotype).In A, Error bars represent Standard Error.
(E) Trans-SNARE Formation Assay: t- and v-SNARE SUVs were incubated in the presence or absence of different Munc18-1 constructs for 30min at 4°C. After solubilization and precipitation of the t-SNAREs using nickel beads, presence of full-length VAMP2 in the precipitates was probed by immunoblotting, which was used as an indicator for trans-SNARE assembly between SUVs.
A Macroscopic appearance of livers in 120-day-old (P120) wild-type (WT) and PR-SET7loxp/Alb-Cre (KO) mice. Note, small adenomatous foci in KO livers.
Representative images showing Ki67-labeling in xenografts generated from implantation of HN31 cells stably expressing control shRNA (left) or MCOLN1 shRNA (right). Pseudocolored panels show the representative distribution Ki67 positive or negative nuclei. Scale bars shown (0.5 mm) apply to all panels.
(E-F) Immunoblotting of indicated proteins in the lysates of mouse peritoneal macrophages (E) and THP1 cells (F) stimulated with 2'3' cGAMP (0.1 μg/mL) in the presence of DMSO or Palbociclib (10 μM) for indicated times. The data shown are representative of n=3 biological replicates.
A Thermodynamic characterization of the RBPJ/L3MBTL3 interaction. Representative thermograms (raw heat signal and nonlinear least squares fit to the integrated data) for L3MBTL3-(31-70) binding to RBPJ-(53-474).
Synaptic transmission in autaptic excitatory munc18-1 neurons expressing M18WT or a non-phosphorylatable Munc18-1 variant, M18Y473F, was tested with whole-cell patch clamp electrophysiology.(E) EPSC amplitude recovery two seconds after an RRP depleting 40 Hz train. Average EPSC recovery (M18WT: 82.2 ± 6.7 %, n=17; M18Y473F: 65.5 ± 11.0 %, n=12, t-test, p = 0.1805).
B. Proteomic/phospo-proteomic signaling network modulated by FGF18 in chondrocytes. Red= activating phosphorylation; blue= inhibitory phosphorylation. Cubes dimensions and colors are relative to level of protein regulations.
(F) The Slx5 middle domain (Slx5-Md) is required for interaction with Euc1. Y2H assays with AD-Euc181-183 and BD-Slx5 constructs. Slx5-Md: aa 201-335, Slx5-Md∆: ∆aa 201-338. Serial dilutions were spotted and cells were grown at 30°C for 4 days. See also Fig. EV3C.
E Molecular dynamics snapshot of homodimer formation by human MITF and MITF mutants. K243 and K248 in the bHLH-Zip domain of human MITF correspond to K274 and K279 in human TFEB respectively. Steric interference is shown by yellow lines. Images were created using Chimera and Protein Data Bank (PDB) accession 4ATH.
Experimental outline. IL-7 was injected intravenously into HSC-humanized NSG mice before 2x106 t.u. of CD8-LVCD19CAR (CAR), or PBS as control (PBS), were administered. Distinct symbols for each individual animal are used throughout B-F (M16: lilac triangle; M19: blue triangle). Open symbols indicate animals from the vector-injected group devoid of PCR-detectable CAR T cells.
(E) Quantification of Alizarin Red staining at 570 nm (A570). n=3, one‐way ANOVA, Bonferroni post hoc.
pros clones (green) generated in myc hypomorphic background did not significantly alter pros nucleolus/nuclear ratio (E-F), nucleolus labelled with Fib (red) [quantified in G (n=44,43)], clone size [quantified in H (n=41,34)], or the proportion of Dpn+ NBs and Elav+ neurons per clone [quantified in I (n=15,15,15,15)].
G. Representative images of Sec24C localization at SGs (stained for G3BP) in TRAPPC2-KO cells treated with SA. Data information: Scale bars, 10 µm.
E, F Force-dependent bond lifetimes of NKG2D and various ligands at 5 pN, 10 pN and 15 pN (E) and full force spectrum (F). Data information: Bond lifetimes in (E) and (F) (in which n = 1505 for MICA, n = 1852 for MICB, n = 531 for ULBP1, n = 1241 for ULBP3) of all ligands with NKG2D came from at least 19 NK cell-bead pairs of at least four independent biological experiments. bars in (E), and data points in (F) represent mean values. Error bars represent mean ± SEM.
(A)Knockdown of SIRT5 inhibits NADPH production in HEK293T cells. The ratio of [NADPH/NADP+] was determined in cell extracts as described in 'Materials and Methods'. The results are average ± SD of 3 independent experiments **p<0.01, ***p<0.001 (two-tailed unpaired t-test).
(H) G6PD and IDH2 are activated by SIRT5 in vitro. Upon pre-incubation with SIRT5 in vitro, the activities of the indicated ectopically expressed proteins were determined as described in 'Materials and Methods'. The results are average ± SD of 3 independent experiments **p<0.01, n.s.: not significant (two-tailed unpaired t-test).
D Quantification of PDH E2/E3 bp‐positive/TOM20‐negative vesicles from HeLa cells transfected with the indicated siRNA; both the total number (white bars) and the number colocalizing with GFP‐parkin (gray bars) are indicated. Error bars represent the mean ± s.e.m. P‐values are given for the total vesicle number (n = 42-64 cells in 2-3 experiments); ns, not significant.
(Top) The Cripavirus family of type IV IRESs is able to capture free 40S sub- units and engage them on a pre-translocation complex by recruiting 60S. This complex is extremely dynamic, with the 40S alternating between non-rotated and rotated configurations with respect to the 60S subunit. IRESs belonging to this family, exemplified by the CrPV-IRES, recruit elongation factors by mimicking a rotated stated of the ribosome with tRNAS. (Bottom), The Aparavirus family of IRESs follows a similar pathway in order to assemble a pre-translocation complex, however, specific structural components of this family allow for additional contacts with the 60S, limiting the rotational freedom of the 40S. Elongation factors engagement and thus effective ribosome hijacking is accomplished by mimicking a ribosome state with tRNAs in hybrid configurations.
CSF extract was treated with DMSO, CsA, buffer or His-CnA420-508 at the indicated concentrations. Meiotic exit was induced by calcium addition and samples were taken at the indicated time points. Samples were immunoblotted for cyclin B2. The cyclin B2 membrane was stripped and reprobed for α-tubulin.
HEK293 cells were transfected with siCTL, siDDX5 or siXRN2. The cells were subjected to Western blotting, RNA Pol II ChIP and DRIP analysis of β-actin gene. The graphs show the average and S.E.M. from at least three independent experiments. Statistical significance was assessed using Student's t-test. *: p < 0.05; **: p < 0.01 and ****: p < 0.0001.
D. Quantification of EVs isolated from MDA-MB-231 cells transfected with Control (pcDNA3), RhoA‑CA, RhoA‑DN, FLAG‑RASSF1C, FLAG-RASSF1C‑R199F, or FLAG‑RASSF1C + RhoA‑DN using Nanoparticle Tracking Analysis. Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, **** p ≤ 0.0001.
a, GFP-LC3-positive dots in tissues of 6-week-old GFP-LC3 mice treated with the indicated peptide (20 mg kg−1 i.p., 6 h). A minimum of ten fields was counted per tissue section. Bars represent mean ± s.e.m. for three mice. Similar results were observed in three independent experiments.
B, Hypocotyl lengths in free-running period of Col-0, toc1-101 and two independent native or 35S promoter lines of wild-type TOC1 and each phosphosite mutants. The middle line of the box represents the median, the x in the box represents the mean. The bottom line and the top line of the box represent 1st and 3rd quartile, respectively. The whiskers extend from the ends of the box to the minimum value and maximum value.
K, L. mRNA expression relative to LysM-Cre/Nrp1+/+ of inflammation markers in mouse BMDMs for Il1b (K); n = 4 (LysM-Cre/Nrp1+/+), n = 5 (LysM-Cre/Nrp1fl/fl) and Il6 (L); n = 3 (LysM-Cre/Nrp1+/+), n = 2 (LysM-Cre/Nrp1fl/fl)
D. Cartoon illustration of the modes of WT or NN binding to MT lattice, based on cryo-EM results. WT decorates the GTP/GDP.Pi lattice predominantly via CDC ('C') or via both DC domains ('N-C') and the GDP lattice predominantly via NDC ('N') or via both DC domains ('N-C'). NN can decorate the GDP lattice via its N-terminal NDC ('N'), C-terminal NDC ('C') or both ('N-C'). Modes 'N' and 'C' are compatible with MT cross-linking (bundling) by NN.
(C) Brucella replication in BMMs expressing either GFP or GFP-BspF and infected with either wild type (2308), ΔbspF, or complemented ∆bspF (ΔbspF::bspF) bacteria, measured as number of bacteria per cell at 24 h pi. Data are means ± SD of n=3 independent experiments. Grey dots represent values from individual cells analyzed (n>300); black dots indicate means of individual experiments. Asterisks indicate statistically significant differences (P<0.05, two-way ANOVA followed by Dunnett's multiple comparisons test) compared to controls.
B Immunoblot showing LC3-II formation in WT, GCN5 KO and GCN5/TFEB DKO HeLa cells in the presence or absence of Baf.
Immuno-FISH for huTau mRNA (green) and phospho-tau (PHF1, red) shows obvious differences in the distribution of neurons in cortex layer II/III: 9-month-old rTg4510 mice had more neurons filled with NFT-like phosphorylated tau (PHF1+, red), and rTg4510-Mapt0/0 mice had significantly more huTau mRNA positive neurons (FISH+). rTg4510-Mapt0/0 mice had also more neurons still expressing both PHF1 and huTau mRNA (PHF1+ FISH+), suggesting a reduced neurotoxicity of P301Ltau expression in rTg4510-Mapt0/0 mice. Mean±SEM, n=3 sections per mouse, 3 mice/group. For all panels: two-tailed Student's T-test and one-way ANOVA with Bonferroni for multiple comparison, ns not significant, scale bars 100 μm.
B Fluorescence-activated cell sorting analysis of WT and GCN5 KO HEK293 cells stained with LysoTracker. Fluorescence intensity of 10,000 cells per sample was measured.
F. Recombinant fragments of CDKL5 fused to GST (1.2, 2.5, 5, 10 µg), or GST, were dot-blotted on nitrocellulose membrane and then incubated with synthetic PAR. PAR binding was detected by far western blotting. APLF was used as positive control. One of three independent experiments is shown
(B) Quantification of the apparent synaptic area (in pixels) of gephyrin clusters (KS test p < 0.0001).
C Quantification of ATG9 vesicular structures in cells from (B) under non‐stimulated conditions.
Resting CD4+ T cells purified from patient samples (n= 18, Appendix Table S3) were treated with 30 µM of each PH compound for 24 hours, and HIV-1 RNA was measured in culture supernatants. Results are presented as HIV virions/mL.
SQR activity (G, H) in kidneys (B, E, G) and muscle (C, F, H) of Coq9+/+, Coq9R239X and Coq9Q95X mice.
Representative FACS plots of retinas and sclera-choroid-RPE cell complexes from naïve and burned mice 3 days (D3) after laser-burn.
Bar plots depicting the quantification of chymotrypsin-like (CT-L) activity from native gels calculated for doubly capped (30S) or singly capped (26S) proteasomes. n >=5 per sample group; error bars indicate standard error of the mean. * p < 0.05, ** p < 0.005, *** p=0.0001, **** p < 0.001, one-way ANOVA, Holm-Sidak's multiple comparison test. For each sample group, the mean value of activity in young samples (5 wph) was set to 100%.
I. Illustration of the spatial relationship between the sites of RAB13 mRNA localisation, local translation and RAB13 protein-mediated filopodia distribution.
(D) Time course western blotting of endogenous SOX9 and apoptotic markers including cleaved PARP and caspase 3 following MB002 treatment with cisplatin, AZD2014, or their combination. β-actin were used as a loading control. The set of blots shown is representative from 3 independent experiments.
Scatter plot elucidating fold change (FC) in gene expression between samples treated with JNKi compared to vehicle (Y-axis) and expression of constitutively active JNK (MKK7-JNK) versus vector control (X-axis) from biological triplicates. Representative examples of genes that are specifically induced by JNK in metastatic breast cancer cells are highlighted in red.
F. Representative images (high magnification; 60x) showing mTFP (cyan), Venus (yellow) and VECAD (purple) fluorescence from BMECs and laconic-infected HBVPs on a 2 well chamber. The upper panel shows HBVPs with endothelial contact and the lower panel shows HBVPs without endothelial contact. G. Quantification of the mTFP/Venus fluorescence ratio of laconic in HBVPs with endothelial contact (EC-PC contact) or HBVPs alone (PC only). (n=16 from independent experiments. Error bars indicate the standard error of the mean (SEM) from unpaired Student's t test.)
Percentage of females that became pregnant after mating with WT (white bar), Spatc1l+/- (gray bar), and Spatc1l-/- (black bar) male mice. Male mice used: WT, n = 5; Spatc1l+/-, n = 6; Spatc1l-/-, n = 7. WT female mice used for mating with the indicated genotype: WT, n = 30; Spatc1l+/-, n = 36; Spatc1l-/-, n = 42. Vaginal plugs were observed in all mated females.
(A) Immunoblots of protein lysates from Null- or TFEB/3 knockout-MEF cells incubated in the presence of DMSO (Control) or Tunicamycin (Tun.) (0.1 µg/ml) for the indicated times. Data are representative of three independent experiments.(B) Quantification of ATF4 protein levels in Null- or TFEB/3 knockout-MEF cells treated as indicated in (A) (mean ± SD of the ATF4 to actin protein ratio from three independent experiments, student's t-test versus the corresponding time point in Null-MEF cells, ns= not significant, **p < 0.01).
(B) Cell lysates from Δapg10 cells (TFD10‐L1) harboring empty vector, pRS316 (lane 1), wild‐type HAAPG10 (lane 2), HAAPG10C26S (lane 3), HAAPG10C133S (lane 4) or HAAPG10C137S (lane 5) on CEN plasmids were subjected to Western blotting analysis with anti‐API antiserum.
F. (top) Representative model of Fam134b∆LIR protein. LIR= LC3-Interacting-Region. (bottom) Western blot analysis of Fam134b in chondrocytes with indicated genotypes (ctrl=wild type) treated with FGF18 (50 ng/mL) for 16 hours. Representative images of N=3 biological replicates/treatment. β-actin was used as loading control. Bar graph showed quantification of Fam134b band intensity normalized to β-actin. Mean +/- standard error of the mean (sem). Student's paired T-test, *p<0.05.
(A) Substrate used for crystallization of the DNA binding complex. The oligo contains a templating 8-oxo-dG shown in green.
Regional plot of p values for SNP association with hearing difficulty around the CLRN2 gene locus. The genes within the region are annotated, and the direction of the transcripts is shown by arrows. Colouring is based on linkage disequilibrium (LD) across the region with the most associated SNP, rs35414371, shown in purple.
A. Uniform manifold approximation and projection (UMAP) embedding of single-cell RNA-Seq data from human ileum biopsies colored by the cell type (n=8,800 cells).
Developmental expression pattern of SPATC1L in testis, examined by immunoblotting using total lysates obtained from prepubertal and adult male mice (days 7, 14-21, 28, 35, 42, 49, and 56). An anti-α-tubulin antibody was used as a control.
(A) Representative confocal micrograph of HeLa cells transfected to produce either mCherry (red), GFP-ACAP1 (green) and Arf6-HA (blue; left hand panels) or mCherry-BspF (red), GFP-ACAP1 (green) and HA-Arf6 (blue; right hand panels) and treated with Cytochalasin D (200 nM) for 30 min prior to fixation. Scale bars: 10 µm and 2 µm (insets).
B, Surface representation of OmpF subunit 1 (grey) and ColE9 residues 3-24 (gold) containing OBS1 sequence. ColE9 OBS1 binds the inner vestibule of OmpF subunit 1 such that it runs along the edge of the vestibule, stopping at the eyelet.