EMBO/sd-character-level-ner huggingface dataset:
(A) HeLa cells pre-extracted for 1 min with 0.5% Triton X-100 in PHEM buffer and immunostained for CITK (green), γ-tubulin (red) and DNA (blue). Scale bars, 10μm
G-I Specific force (Po/CSA) (G), maximum shortening velocity (Vo) (H), and cross-sectional area (CSA) (I) of single fibres (n = 153) from artificial muscles and control (CTRL) muscles (n = 103).
Western blot analysis demonstrates a greater increase in phosphorylated p38 (p‐p38) from THP1 Siglec‐14 cells after exposure to Hsp70 in comparison with control THP1 EV cells in a time‐dependent manner. Graph below immunoblots indicates densitometric analysis of each band normalized to the respective cell line's unstimulated control group, divided by the respective loading control.
D Mean fluorescence intensity ratios evoked by 405 nm and 488 nm excitation wavelengths at individual mitochondria in mutant hAPP axons expressing Snapin or Snapin-L99K were quantified and normalized to those of mutant hAPP controls. Note that oxidatively stressed mitochondria are reduced within AD axons expressing Snapin after CCCP treatment.
I Gene set enrichment analysis (GSEA) plots displaying significant enrichment for inflammatory response and Tumor Necrosis Factor (TNF) signalling in mouse prostate organoids cultured without A83-01 (24 hours) versus complete medium (ENRAD).
G The period of DD locomotor rhythm of flies co-expressing Nipped-A RNAi and not RNAi. Digits on the bar are the number of flies tested. Percentage of rhythmicity is indicated above the bars. Statistical difference is measured using one-way ANOVA, P<0.001, Tukey's multiple comparison test, **P<0.01, ***/###/+++/$$$P<0.001, * compared with the G4 control, # compared with the UAS control, + compared with the Nipped-A RNAi flies, $ compared with the not overexpression flies. White bar indicates UAS or GAL4 controls. Dashed bar indicates flies with genetically manipulated not. Gray bar indicates flies with Nipped-A knocked down. Checked bar indicates flies with both genetically manipulated not and Nipped-A knocked down.
(E) Single confocal sections of HeLa cells at metaphase stained to visualize the mitotic spindle and DNA. (F) Averaged spindle pole length based on >20 cells with bipolar spindles/sample. The P value is obtained by two-tailed paired t-test.
F Western blot analysis of USP33 protein in p97-sufficient (WT) or p97-knockout (KO) 2fTGH cells transfected with Flag-USP33 (F-USP33) and then treated with additional NaCl (+34 mM) for 12 hrs. Data information: Data are representative of at least two biological replicates.
Micropeptide CIP2A-BP levels were detected by western blot with anti-CIP2A-BP antibody in the indicated non-metastatic TNBC tissues (non-metastasis) and metastatic TNBC tissues (metastasis). Micropeptide CIP2A-BP expression in MCF-10A cells was used as the positive control.
The relative abundance of individual GL and GPL classes in the wild-type fat body, as detected by mass spectrometry (MS). n=10 individual analyses.
C. HopAO1 dephosphorylates LORE Y600 in vitro. The recombinant GST-HopAO1/HopAO1CS and GST-LORE-CD were subjected to in vitro phosphatase assays. Phosphorylation level of Y600 was detected by anti-pY600 immunoblotting. The experiment was repeated three times with similar results.
A representative nuclease assay with MR, MBP-NBS1-his (denoted MBP-NBS1), MRN and pCtIP on 5'-end labeled 70-bp dsDNA with all ends blocked with streptavidin. Samples were separated on 15 % denaturing polyacrylamide gel. Quantitation of nuclease assays such as in (A). Averages shown; n ≥ 3; error bars, SEM.
K qPCR analysis of IFNβ mRNA in SIRT5-deficient H1299 cells (SIRT5-/-) transfected with the control plasmid (Myc empty) or the plasmid expressing Myc-SIRT5 (Myc-SIRT5) or its enzyme-deficient mutant H158Y (Myc-SIRT5-H158Y) for 24 h, followed by infection with (+) or without (-) SeV for 8 h. Data information: All data are presented as the mean values based on three independent experiments, and error bars indicate S.E.M. (unpaired two-tailed Student's t test).
Plasma levels of IFNα were measured in a cohort of 36 patients with chronic HBV.
H - Schematic drawing of conclusions from this study. Let-7 expressed in the early telencephalic neuroepithelium represses the expression of p53 and Irs2, which maintains the cellular homeostasis and epithelial integrity. Loss of let-7, as in Dicer1 mutants, de-represses expression of Irs2 and of p53 pathway components, which further increase Irs2 levels. High Irs2 enhances progenitor cell proliferation and loss of apical adhesion, altering neuroepithelial homeostasis and integrity, and leading to the formation of hyperproliferative rosettes.
G, H. The number of tumors of different sizes (diameter) in each mouse (G) and the distribution of different tumor sizes (H) were shown (WT n=11 biological replicates, and OMA1-/- n=12 biological replicates). Results are shown as mean ± SEM. p-values were calculated by unpaired student's t-test, **p < 0.01, ***p < 0.001.
G. METTL5 localized to the nucleoli in U-2 OS cells (HPA038223). Data information: Protein of interest is shown in green, nuclear marker DAPI in blue and the reference marker of microtubules in red. Scale bar 10 µm.
Various GFP-tagged DIA1 plasmids were transfected into HeLa cells, and fixed 24 h after transfection. Fixed cells were stained with Alexa568-conjugated phalloidin and DAPI (A, B: representative of 5 experiments).(A) Stress fiber formation was observed with a confocal laser microscope. Note the induction of stress fibers by GFP-DIA1(M1190D) (asterisks). Arrow and arrowheads indicate a plasma membrane (PM) localization of GFP-DIA1(M1190D) and a dot-like localization of GFP-DIA1(R1204X) adjacent to the PM, respectively. Inset in the top panel of DIA1 (R1204X) shows the magnified image of the region indicated by rectangle. Scale bars: 10 μm..
E. Representative immunoblot (top) and densitometry quantification (bottom) of hMENA∆v6 expression level in P-NFs grown in RPMI control medium (-) or PANC-1-CM for 24 h (n = 3). Data are represented as fold increase with respect to control medium ± SD (set as 1). Data were analyzed using two‐sided Student's t‐test. *P < 0.05.
Quantification of cardiomyocyte area (B), N=6 to 8 samples/group in NRCM transduced with Ad.Con or Ad.TIP30 and stimulated as indicated. ET-1: endothelin-1, FBS: fetal bovine serum, PE: phenylephrine.
A Population doublings (PDs) determined in BJ cells cultured at the indicated folate concentrations for 48 days.
A) Western blot detection of LC3 in MoDCs infected with Pg381 and mutant strains for 12 hours. B) The mean ±standard deviation of LC3-II intensity represents three different experiments and the values were analyzed using Kruskal-Wallis test analysis of different groups and Dunn's test for multiple comparisons.
Scatter plots comparing the estimated logFCs across mice groups. ++. Panel I: mdx vs mdx+-. Panel J: mdx++ vs mdx+-.
A In vivo bioluminescent imaging analysis of intracranial tumor growth in mice bearing GBM xenografts derived from the T387 GSCs expressing shUSP33 or shNT. Two thousand GSCs transduced with luciferase and shUSP33 or shNT were implanted into mouse brains through intracranial injection. Representative bioluminescent images on day 7, day 15 and day 30 post-transplantation of GSCs were shown. Disruption of USP33 delayed tumor growth of intracranial GBM xenografts.
A Bacterial sodium pumping A/V-type ATPase from E. hirae (subunit nomenclature of the eukaryotic V-ATPase). Note that the bacterial A/V-type enzyme has only two peripheral stalks (EG1 and EG2) and no equivalents for the C and H subunits found exclusively in eukaryotic V-ATPase (see next panel).B Eukaryotic proton pumping V-ATPase. The eukaryotic V-ATPase is dedicated proton pump composed of a soluble catalytic sector (V1) and a membrane integral proton translocating sector (Vo). The two functional sectors are linked via a peripheral stator that is formed from the N-terminal extension of the 100 kDa membrane integral subunit (aNT), three peripheral stalks (EG1-3; shown in blue/orange) and subunits C (red) and H (yellow) that are unique to the eukaryotic enzyme.C Reversible disassembly of eukaryotic V-ATPase. Cellular signals, such as starvation, lead to a dramatic structural rearrangement wherein the V1 sector dissociates from Vo and subunit C is released from the enzyme. While dissociated, both the V1-ATPase and Vo proton translocation domain are functionally silenced. This process is fully reversible and upon reassembly, enzymatic activity is restored.
Relative expression levels of total PPARδ protein in HSPCs (K) Data shown in bar graphs are mean fluorescence intensity of indicated protein expression in PKCδ cKO HSPCs subsets relative to WT controls (n=4-6 mice per genotype per target). Data information: The statistical significance of difference was assessed using Two-tailed Student's unpaired t-test analysis for comparison of control and PKCδ cKO HSPCs. All data are presented as mean± SEM., *p<0.05, **p<0.001.
C Quantification of testis weight in 6-month-old Usp26+/Y and Usp26-/Y mice (n=6 independent experiments). Red dots indicate Usp26+/Y mice and green dots indicate Usp26-/Y mice.
(F) SHP2 depletion in BMEC and B16F10 by 6 distinct shRNAs (#1-#6); pLKO: vector; none: no infection. Immunoblotting with SHP2 antibody followed by reblotting for β-actin.
Spine density in apical dendrites of CA1 pyramidal neurons of Tardbpfx/fx and CamKIIaCRE;Tardbpfx/fx mice after injection of EGFP-expressing lentivirus or Sortilin rescue virus. Results are presented as average ± SEM (N=3 mice per condition, 15 sections per mouse). **, p<0.01. Data information: Results are presented as average ± standard error of the mean (SEM). All statistical tests were performed using 2-way ANOVA with Sidak post hoc analysis.
Mice were analysed 2 days after TAC (a-c). c, Immunohistochemical analysis using antibodies to CD45, CD68, Ly6G and CD3. Scale bar, 100 µm.
(g) NRK cells were starved for 0 or 4 h and stained with antibody against PI(4) P. Scale bar, 5 μm.
A-C The cation concentrations used are indicated for each experiment; AU, arbitrary units.
(J) The response of a mitochondrial matrix-localized roGFP2-Tsa2ΔCR probe, expressed in wild-type and Δpor1 cells to the addition of 10 µM antimycin A. Cells were grown to exponential phase in SGal (-Leu) medium. Lighter colored curves are controls showing the probe response upon the addition of 0.1% (v/v) ethanol.
(j,k) Negative shRNA (j) and MCUR1-overexpressing (k) HEK293T cells were permeabilized with digitonin in intracellular-like medium containing thapsigargin and bath [Ca2+] indicator Fura2FF, and then pulsed with 10 μM Ca2+. After mitochondrial clearance of bath Ca2+, Ru360 caused an elevation of bath [Ca2+], indicating that steady-state bath [Ca2+] after the pulse was maintained by a balance of MCU-mediated Ca2+ uptake and CGP37157 (10 μM)-sensitive Na+-Ca2+ exchanger-mediated extrusion. CCCP was added as indicated. The solid line is the mean; shaded areas are ±s.e.m. (n = 3).
G) Quantification of the number of (G) cells with TP53 activation within a 250 μm-width column of E14.5 cortices. WT N = 5, Smc5cKO N = 4; two-tailed Mann-Whitney t-test. WT data are from Figures 4E and 4G and shown alongside for comparison.
F) insulin in supernatants of the mouse islets (F) in GSIS assays. High glucose (HG, 16.7 mM) or low glucose (LG, 3.3) were used in GSIS assays. Data information: Data from over 3 experiments are presented as the mean ± SD. one-way ANOVA test were used for statistical analysis of differences between groups, and P (*) < 0.05; P (**) < 0.01 and P (***) < 0.001 are considered statistically significant.
(E-F) Serum antibodies collected pre-immunization and 7- or 14-days post NP-CGG immunization, detected by NP7-BSA ELISA using isotype-specific secondary antibodies. Data show mean ± SEM from N = 3 experiments with statistical significance from 2-way ANOVA with multiple comparisons.
A. Pre-mRNA processing of the serotonin 2C receptor. Exons are shown as boxes, introns are lines. Due to the use of two alternative splice sites (PS, DS: proximal and distal splice site) exon Vb is alternatively used, resulting in two RNAs: RNA1 lacking and RNA2 including exon Vb. Alternative splicing patterns are indicated by dashed and dotted lines; constitutive splicing patterns are indicated by solid lines. The start codon is indicated using a line with circle. Alternative usage of exon Vb introduces a frameshift, leading to different stop codons being used (lines with rectangles in exon VI, red box in exon VI indicates a different reading frame). The proteins formed by RNA1 (truncated 5HT2C) and RNA2 (full-length 5HT2C) are indicated. Circles in the second intracellular loop of RNA2-protein depict three amino acids changed by RNA editing. The location of the epitope against the truncated 5HT2C is indicated with a Y.
b, olfactory performance in infected hamsters. The olfaction test is based on the hidden (buried) food finding test. Curves represent the percentage of animals that did not find the buried food. Food finding assays were performed at 3 days post-infection. Data were obtained from three independent experiments for males and two independent experiments for females. Data information: Horizontal lines indicate medians. The p value is indicated in bold when significant at a 0.05 threshold. Log-rank (Mantel-Cox) test M: male hamsters; F: female hamsters. Data were obtained from two independent experiments for each sex.
A-D. Response of HyPer7 probes targeted to indicated compartments to reoxygenation after hypoxia (red curve and data points) or to continued hypoxia (black line and data points). HEK293 cells were grown either with glucose or galactose as carbon source. Solid line represents mean, points colored in the lighter version of the respective color are the corresponding ratios measured in individual cells. E. Model. Cells grown on galactose-containing medium exhibit increased production of H2O2 and thus also increased detection of cytosolic H2O2 indicating H2O2 gradients of different steepness around mitochondria. Data information: As most of the data were not normal distributed, instead of a t-test, a Wilcoxon/Mann-Whitney-U-test was performed and samples were compared in pairs.***, p ≤ 0.001
C. Bar plots of selected ERK7-regulated pathways with overrepresentation of significantly changing genes (adj.p.val <0.05, LFC <-0.5 or LFC >0.5). The bar plot shows enrichment (-log 10 adj.p.val, generated by piano package). Blue color denotes downregulated in mutants and red denotes upregulated in mutants. G - Gene Ontology (GO), K - KEGG Pathway, R - Reactome Pathway Database.
D HeLa cells were transfected with control or TIAR si-RNAs, alone or together with Cdc25B siRNA. 72 hours after transfection, p(S10)-H3-positive cells were quantified by flow cytometry (mean ± SD; n = 3). Data information: Statistical significance was determined by unpaired Student's t-test; *, p < 0.05; **, p < 0.01; ***, p < 0.001.
C Transactivation analysis of BIC1 using a yeast assays. The GAL4 DNA-binding domain (BD) alone was used as the negative control. SD-W, synthetic dextrose medium lacking Trp; SD-WH, synthetic dextrose medium lacking both Trp and His.
D) Western blot analysis of Ste-1 parental and isogenic Alectinib resistant cell lines for the indicated proteins.
(D) Model for the role of the PEAT complexes in chromatin regulation. In heterochromatin regions, the PEAT complexes either directly mediate heterochromatin condensation or interact with the histone deacetylases HDA6 and HDA9 and thereby mediate heterochromatin condensation by histone deacetylation. Thus, the PEAT complexes repress transcription mediated by both Pol II and Pol IV. The repression of Pol II transcription is required for transcriptional silencing in heterochromatin regions. Moreover, the repression of Pol II and Pol IV transcription prevents overproduction of siRNAs that are responsible for DNA methylation. In euchromatin regions, we predict that the PEAT complexes may regulate histone acetylation by interaction with the histone acetyltransferases HAM1 and HAM2. However, further studies are required to elucidate how the molecular mechanisms of the regulation.
Quantification of embryo morphology at LB stage in C57BL/6J wild-type (white boxes/ black dots, n=22 including 16 in which allantois could be measured), and KtyII-/- embryos (grey boxes/ black triangles, n=9 including 8 in which allantois could be measured). (D) Embryonic region length. Ratios of whole embryo and ExE cavity lengths (E) , over embryonic region length.
Western blot of WNT8B and ACTIN in PAX6D KO cells with treatment of untreat, control shRNA lentivirus, WNT8B shRNA lentivirus.
(f) Western blot analysis of GST-RILP pull down showing direct interaction between RILP and GTP hydrolysis deficient (Q111L) Rab34 (at 200nM, in the presence of 1mM GTPγS) and FLCN-DENN domain (1μM), but not low nucleotide affinity (T66N) Rab34. FLCN-DENN enhances association of RILP with Q111L Rab34. Graph shows quantification of relative RILP / Rab34 Q111L binding. Error bars show SEM. ** = p<0.01.
GSEA of consensus squamous cancer marker genes (se Appendix Table S2) in A-431 cells stably transduced with sh-∆Np63#2 or sh-NTC. (N) ES: (normalised) enrichment score GSEA of consensus squamous cancer marker genes in A-431 cells stably transduced with sh-USP28#1 or sh-NTC. (N) ES: (normalised) enrichment score
(c) The production of acetate is shown over time for E. coli MG1655∆glnL∆pta poxB::E170 (black) as compared to the same strain containing the complete circuit (green). A version of the circuit in which the sgRNA is targeted to rfp (not present in the system) and is tested in MG1655∆glnL∆pta containing an untagged poxB as a control (red). Empty circles connected by the dashed line represent MG1655∆glnL∆pta∆poxB
(D) Cortices from E14.5 embryos stained with antibodies against Cleaved-Caspase 3 (CC3, white), TP53 (red) and DAPI. Scale bar = 50 μm. (E and F) Quantification of the number of CC3+ apoptotic cells (E) and cells with TP53 activation (F) within a 250 μm-width column of E14.5 cortices. WT N = 5, Cep63T/T N = 3, Cep63T/T;Usp28-/- N = 3, Sas4cKO N = 4, Sas4cKO;Usp28cKO N = 4; one-way ANOVA with post-hoc analysis.
(A) The overall structure of N-glycan on N58 of PD-1 is presented with N-glycans on N58 of PD-1 highlighted in sticks in green. The 2 Fo-Fc electron density map of the N58 N-glycans contoured at 1.0 sigma is represented in orange on the right. The β strands were labeled according to canonical IgV-strand designations.
E-F: Endogenous MOSPD2 (green) staining in HeLa cells expressin Flag-STARD3NL ∆FFAT (F) (anti-Flag; magenta) Data information: (A, D-F): The subpanels on the right are higher magnification (3.5x) images of the area outlined in white. The Overlay panel shows merged green and magenta images. The Coloc panel displays a colocalization mask on which pixels where the green and the magenta channels co-localize are shown in white. Right: Linescan analyses with fluorescence intensities of the green and magenta channels along the white arrow shown on the subpanel Overlay Scale bars: 10 µm
(B) Density of PRBS, defined as the total number of PR-peaks associated to each gene category (up-, down-, and non-regulated genes). PR-peaks were assigned to a gene when located from −5 Kb upstream of the TSS to the TTS (left panel) or to a window of -/+5Kb around the TSS (right panel). Peak density in the genome was calculated by considering random distribution of all PRBS in the whole genome. Data obtained after exposure to hormone for 5 and 30 minutes is shown. The p-values in comparison with the corresponding non-regulated genes are indicated. Left panel: for PRBs 5 min: *** P=1,04E-035 (UP), *** 2,40E-023 (DOWN); Right panel: PRBs 5 min: ** P=4,64E-008 (UP), * P=0.026 (DOWN).
(L) SureQuant-based quantitative mass spectrometry analysis of CEST-2.2 protein levels. Light/heavy ratios (L/H) of the two unique CEST-2.2 peptides (LSTGTIEGR and HGEDFAYAFGTNR) used for quantitation are represented as violin plots (n=3 for wt and gas-1; cest-2.2 O/E, n=2 for gas-1; the n of analyzed samples per group refers to biological replicates of pooled nematodes from a single plate; the median is indicated with a dashed line). Statistical analysis was performed using the nonparametric t-test. Data information: , middle lines represents the median, and the upper and lower lines represent the upper and lower quartiles, respectively Across experiments, p value summary is ns= not significant, *p<0.05, **p < 0.01; ***p < 0.001, ****p<0.0001.
E: Additionally, PaTu8988t cell lysates were analyzed by immunoblotting using the indicated antibodies. A representative result is displayed in (E). The p14ARF signals were densitometrically quantified and normalized to the respective GAPDH signal, as specified by the numbers below the blots, with the untreated condition (- GEM, -MS013) set to 1. The percentage of PARP cleavage was also densitometrically quantified and is indicated below the blot.
E, Representative images cells labeled with γ-H2AX (green), 53BP1 (red) and DAPI (blue). Scale bars correspond to 10 μm
Zoom in to high MW peak shoulder of holo-COP9 Signalosome (compare Figure 5), where defined co-elution signals of CSN substrate components CUL4A and DDB2 suggest the partial resolution of substrate-bound and free pools of CSN holo-complex.
(C) Quantification of the radiolabeled mitochondrial polypeptides in panel (B) and similar gels, expressed relative to protein synthesis of the NT. Data represent the mean ± standard error (SEM) of n=6 independent experiments; 1 or 2 rounds of transfection for siR1 and siR3, but exclusively 2 rounds in the case of siR2
C HOPS and p53 binding in cytoplasm following apoptosis induction. RKO cells untreated or treated with etoposide as above were used to isolate cytoplasmic fractions. WCL and cytoplasmic fractions were immunoprecipitated with anti-HOPS antibody and subsequently immunoblotted using anti-p53 antibody.
E) NK cell-mediated cytotoxicity of K562 cells by 4-hour chromium-release assay of two-day cytokine activated NK cells in the presence or absence of Torin-1 (1µM) and PGE2 (1µM) (n=6, biological replicates). E:T ratio=5:1.
(C) CSR complementation assay using siRNA-resistant Phf5a with Myc and Flag (MF) epitopes tagged at the C-terminus.
E HeLa cells were transfected with control or TIAR siRNAs were treated with ATRi for 48 hours, and the sub-G1 population was quantified by flow cytometry following propidium iodide staining (mean ± SD, n = 3). Data information: statistical significance was determined by unpaired Student's t-test; *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001.
Quantification of the proportion of residual ALDHbr cells in treated PDX normalized to the proportion of ALDHbr cells in the vehicle-treated tumors, measured by flow cytometry. Statistical test used is a student t-test. Data represent mean ±SD (n=10).
D, Clonogenic assay with METhigh and METneg subpopulations sorted from BT308NS and irradiated (1-10 Gy, fold vs. non-irradiated cells, ctrl). *: t-test, p<0.05.
B) Schematic representation of the genomic background and the approximation used to measure DSB-SPB tethering. Wild-type Spc110 and spc110S36-91D were labelled with the RFP. Ddc2 was tagged with the GFP to be used as DSB reporter. D1: inter-SPB distance; D2: DSB distance to proximal SPB; D3: DSB distance to distal SPB. At least 100 cells from three independent experiments were scored using the maximum projection of nine z-planes. Graph shows the mean ± S.D. P values were calculated using a 2-tailed unpaired Student t test.
(E, F) Steady-state analysis of the FFAT peptide / MSP domain of VAP-A (E interaction: equilibrium responses (Req) extracted from panel A were plotted as a function of dimeric VAP concentration and fitted with a 1:1 binding model