EMBO/sd-character-level-ner huggingface dataset:
Flow cytometric analysis of peripheral blood showing B cells (CD19+ Thy1.2-) and T cells (Thy1.2+ CD19-) of wild-type (left) and B cell-deficient (right) mice. Cells were pre-gated on lymphocytes. Representative of three independent experiments (n=5/group).
16HBE cells were stably infected with pSUPER, pSUPER expressing shCdc42, shARHGEF18, shSOS1 hairpins 1-3, All data are representative of 3 independent experiments. (a) Cells were seeded sparsely on glass coverslips, incubated for 3 days, then fixed and stained for ZO-1 (tight junctions) and DNA (nuclei). Scale bar represents 20m.
(A&B) Stable cell lines for CP20 and OVCAR4 expressing GFP-miR-195 or non-target miR-GFP were generated using lentiviral mediated transduction and were selected using puromycin; representative images are shown. Scale bars, 50 µm.
(C) Cellular fractions were prepared from HEK293 cells that were transfected with a plasmid that encoded wildtype or mutant COA7. The fractions were analyzed by reducing SDS-PAGE and Western blot. T, total; C, cytosol; M, mitochondria.
(d,e) Transcript levels of HS memory genes HSP18.2 and APX2 in hsfa2 mutant. Data information: For transcript level analysis, the data were normalized to tubulin as reference gene and the respective 22°C NHS, NHS+187 control plants, that were harvested at the same time points. All treatments are compared with direct 44°C HS treatment for statistical significance. All plots represent the means of 3 biological replicates. Error bars indicate SE. Asterisks indicate a statistical difference based on the Student's t-test *P ≤ 0.05; **P ≤ 0.01; **P ≤ 0.001 for differences between NP in comparison to NP+187, P and P+187 treatments.
Regulation of 4E-BP1 expression and binding to eIF4E by TGF-β. TNBC cells were treated with TGF-β and equal amounts of proteins were subjected to immunoprecipitation and/or examined by immunoblotting analysis.
(b) Pgam5 WT and KO MEFs were transduced with either nonspecific (NS) or Parl shRNA and either treated (+) or not (−) with CCCP for 3 h. Mitochondria were then purified and analysed by immunoblot for the indicated proteins.
A Screening of the potential KDM6A-regulated transcriptional factors involved in repression of nephrin expression. After transduction with a control lentiviral vector or a lentiviral vector expressing KDM6A into primary podocytes for 48 hours, intracellular RNAs were isolated and used for RNA sequencing (RNA-Seq) analysis. The transcript expression patterns of 86 selected transcriptional factors from three independent RNA-Seq experiments are presented in a heat map. Notably, among these 86 selected genes, KLF10 is the most upregulated gene.
(C The effect of different amounts of EBV-LMP1 on the binding of ANT1-VDAC1 was detected by CO-IP.
(A) Western blotting for Islr in the supernatant from primary cultured intestinal epithelial cells (IECs) transfected with pcDNA3.1 or pcDNA3.1-mIslr-HA plasmids, and western blotting for pMst1/2, Mst1, pMob1 and Mob1, pYap1 and Yap1 in lysates from primary IECs cultured in the supernatants with or without mIslr-HA. β-actin was used as a loading control.
(F) COX and COX/SDH activity staining showed that KO-NDUFS3 quadriceps were reverted to levels found in wild-type, at 6 months. n-indicates the number of animals used per group, scale: 100 µm.
C. As in (B), except that cells were pre-treated with the proteasome inhibitor MG132 and/or SUMOi for 30 and 15 min, respectively, before exposure to 5-azadC (red bars, mean; >1900 cells analyzed per condition). Data are representative of three independent experiments.
Schematic model of the electron transport chain (ETC) and targets of the inhibitors used.
(A) Relation of chromatin state changes and gene expression changes. For 81% of differentially expressed genes, a change in a regulatory chromatin feature was observed.
a Immunoblot analysis of equal amounts of proteins from total lysates of Cas9-EGFP OT-I CD8+ T cells transfected with sgEGFP, sgITSN2-1 or sgITSN2-2 and left unstimulated (-) or stimulated for 2 or 5 min with N4 tetramers (20 nM). Upper panel: membrane probed with antibody to phosphorylated tyrosine (Anti-p-Tyr) or anti-LAT (loading control). Lower panel: membrane probed with antibodies to anti-CBL-pY774, anti-ZAP70-pY319/352, anti-AKT-pT308, anti-ERK1/2-pY204/T202 or anti-ERK1/2 (loading control).
(F) Copy number analysis of the Pax5Jak2 allele by quantitative PCR analysis with primers amplifying unique sequences across the Pax5 exon 5-Jak2 exon 19 junction of the Pax5Jak2 allele. The PCR analysis was performed with genomic DNA isolated from lymph node (LN) Pax5Jak2/+ B-ALL cells (3 experiments), from flow cytometry-sorted CD19+B220+ and CD19+B220low B cells from the bone marrow (BM) of 6-week-old Pax5Jak2/+ mice (2 experiments each) and from CD19+B220+ B cells from Pax5+/+ bone marrow (2 experiments). The PCR data were normalized to the product amplified from a control region located 35 Mb upstream of Pax5, and the ratio obtained for B220+ B cells from Pax5Jak2/+ bone marrow was set to 1 copy number of the Pax5Jak2 allele.
N-O, Flow cytometric analysis of macrophages (N) and CD8 T cells (O) in primary and secondary MC38 tumours. Data presented as mean SEM and analysed by Kruskal-Wallis test with Dunn's multiple comparison (n=5 mice/group). *P <0.05 **P <0.01 ***P <0.001.
A, B Laggard chromosomes were observed in the metaphase I of 6-month-old Usp26-/Y spermatocytes. Immunofluorescence analysis of tubulin (green) was performed in 6-month-old Usp26+/Y and Usp26-/Y spermatocytes. Nuclei were stained with DAPI (blue). The arrowheads indicate the laggard chromosomes.
(d) Model depicting the possible impact of an acetylation of SUMO2 at K11 on formation of SUMO signaling. SUMO2/3K11Ac can restrict chain length by acting as a K11 chain terminator (A), SUMO2/3K11Ac can function as a binding platform for acetyllysine binding proteins (B), SUMO2/3K11Ac can trigger the formation of alternatively linked SUMO2/3 chains (C).
E. Cdk can promote Apc1-loop500 and B56 interaction. MBP fused WT or 3A Apc1-loop500 fragment was incubated in the presence or absence of Cdk2-cyclin A at 30˚C for 60 min. MBP-fused peptides (-/+ kinase) were isolated and incubated with purified Flag-B56γ at 23˚C for 30 min. The bound proteins were recovered by amylose beads and analysed by SDS-PAGE and immunoblotting with indicated antibodies. F. Quantification of E. Bound B56γ to WT Apc1-loop500 control (-Cdk) was arbitrarily set to 1.0. Error bars, s.e.m. from three independent experiments.
A Impact of Stat1 deficiency or of STAT1Y701F mutation on the growth of Listeria monocytogenes in macrophages. Bone marrow derived macrophages (BMDMs) of wild type (WT), Stat1Y701F and Stat1-/- mice were infected with L. monocytogenes (LO28, MOI 10). Colony forming unit (CFU) numbers were determined 1, 2, 4, 6 or 8 h after infection by plating on brain-heart-infusion (BHI) agar plates. The graph represents biological triplicates and the data are represented as mean values. Error bars represent standard deviation (SD) and asterisks denote statistically significant differences (ns, p>0.05; **, p≤0.01; ***, p≤ 0.001); p-values were calculated using unpaired t-test.
Light-induced optoDroplet formation of Cry2-mCherry-53BP1, Cry2-mCherry-53BP1 W1495A, and Cry2-mCherry-MDC1. Cells were imaged at 15 seconds intervals. Representative images of optoDroplet formation before and 6 minutes after light induction are shown. Quantifications from single-cell QIBC analysis of 2-3 independent experiments are shown with mean (solid line) and standard deviation from the mean (dashed lines) indicated.
(B) Oxygen consumption rate (OCR) of WT cells and MICOS mutants as analyzed by Seahorse Analyzer. Basal and maximal OCR are shown relative to the WT. Error bars: SEM, n=6.
G In the cup model, the mandible slice was simplified as a cup according to its dimensions (unit, mm). Red arrows indicate the uniform force (stress) exerted on the inner wall of the mandible. The bottom of the cup was fixed to avoid rigid body motions.
E) Representative western blot analysis of PARP1 cleavage upon tBID-GFP expression in HCT AKO cells. n=3 independent experiments.
E-H. Expression of Rab25 decreases glucose and serum deprivation induced signalling activation. Protein expression was measured by RPPA or WB analysis.E. RPPA detection of time-dependent activation of AMPK after nutrient withdrawal.
D and E. Average traces of changes in iBAT temperature (D) or rectal body temperature (E) from WT and TRPV2KO mice after BRL37344 (600 µg/kg body weight) administration (i.p., arrows). Mean ± SEM, n = 5. * P < 0.05 vs. WT group. Unpaired Student's t-test.
(B) Pancreata of the same batch of mice as in (A), at the age of 14 weeks, were stained with anti-insulin (αIns) antibody and DHE (left). Islet area (μm2) and relative fluorescence intensity (RFI) were quantified (right). Scale bar = 100 μm. The dash circles indicate islet regions. Data information: Data from 3 experiments more are presented as the mean ± SD. One-way ANOVA test was used for statistical analysis of differences between groups, and P (*) < 0.05; P (**) < 0.01 and P (***) < 0.001 are considered statistically significant.
DU145 cells were transfected with the indicated siRNA (control, siCTRL; UBTD1: siUBTD1pool or siUBTD1single1 or single2) for 24 h and plated on fibronectin-coated glass coverslips. (A) The scatter plot shows the apparent Young's moduli obtained by AFM analysis. Bars represent the median values of the distributions. The immunoblot shows UBTD1 siRNA knock-down efficiency.
(K) Phagocytosis of fAβ42 by primary microglia from wt and Trem2 ko animals in the presence or absence of mAb11, or an isotype control antibody (IC). (n = 5, +/- SEM; 2 way ANOVA, interaction P=0.4797, genotype P<0.0001, treatment P<0.0001; post hoc tests wt vs. ko for the following conditions: fAβ42-mAb11 5 µg/ml P=0.0449, fAβ42-mAb11 10 µg/ml P=0.0370, fAβ42-mAb11 20 µg/ml P=0.0299, fAβ42-mAb11 50 µg/ml P=0.0120).(L) Quantification of relative fAβ42uptake to lowest antibody concentration used.
(A, B) Pharmacological targeting of SPRK1 with (A) 40 μM SRPIN340 or (B) 8 μM SPHINX31 reduced the cumulative risk of death in +1(CGG) 100-EGFP (encoding FMRpolyG) expressing neurons. n= # of neurons quantified for each condition; Cox proportional hazard analysis, ∗∗∗p < 0.001.
G) Representative western blot analysis of BAK activation in Nalm6 and Nalm6 199R cells at different time points after treatment.
I. CTRL#1 or BRD9-KO#1 cells were stably-transduced with BRD9-expressing, or control (EV, empty vector), lentiviruses and treated with 1000 IU/mL of IFN-α2 for 16h prior to infection with IAV (WSN/33) at an MOI of 0.01 PFU/cell. Viral titers were determined after 24h by plaque assay. Data information: data represent means and standard deviations from n=3 biological experiments (individual data points shown). Statistical significance was determined by 1-way ANOVA on log-transformed plaque counts (**p-value < 0.001; ****p-value < 0.0001). Dotted lines are a visual guide for maximum and minimum virus replication in control cells in the absence and presence of IFN-α2, respectively. Numbers above IFN-α2-treated bars indicate their approximate difference to the respective untreated conditions.
A U2OS cells were subjected to immunofluorescence staining. Example images of mitotic cells at various stages are shown. Data information: Scale bars, 10 μm.
Figure 6: Model. In absence of HH, Smaug is associated, likely as S-bodies (in red) to inactive SMO present on intracellular vesicles and leads to the repression (blue line) of its target mRNA(s) (called here xmRNA) via the recruitement of proteins (not represented here) that promotes their decay. Upon HH reception, activated and phosphorylated (yellow P circles) SMO accumulates at the plasma membrane where it relocates both the kinase FU and Smaug. This lead to FU activation which in turn phosphorylates (green full circle) SMO and Smaug. This phosphorylation of Smaug would reduce its negative effect (dashed blue line) favoring the release of its target mRNAs - possibly via the dissolution of the S-foci - and leading to their accumulation. Finally, when the highest levels of SMO phosphorylation are reached (red P circle), phosphorylated Smaug is released, leading to attenuation of the effects of HH/SMO/FU on Smaug. EV Figure Legends
D-E Western blot analysis of UCP1 and CDK4 protein expression (D) and quantified protein levels of UCP1 (E) (n=4 biological replicates) in iBAT. HSP90 was used as loading control.
(A) Autophagosome-lysosome fusion is analysed in wild‐type and HDAC6 KO MEFs with or without starvation (6 h) using mCherry‐GFP‐LC3 as described in Figure 2A.
C Lysates from Hela cells transfected as described in B were immunoprecipitated with anti-Flag or control IgG antibodies and probed with Flag and GFP antibodies.
(D) Cell morphology of B-RafAVKA expressing MEFs are enlarged and present with abnormal nuclei
C-F. TEM images of 4 week old retinas: (C, D) wildtype, or (E, F) ADAM17-/- flies reared from first larval instar either in total light (C, E) or total dark (D, F). Scale bars: 10μm.
(C) Cell‐cycle progression of HCT116 (left panel) and HCT116 5/4 (right panel) after release from thymidine block, analyzed by flow cytometry. The major delay occurs in the G1 and the S phase. The length of each cell‐cycle phase is indicated above the graph. Population was considered to enter a specific phase of cell cycle if at least 50% of cells showed corresponding DNA content. See also Supplementary Figure S1. Source data is available for this figure in the Supplementary Information.
A Individual frames from time-lapse imaging of a cell expressing GAL promoter-driven GFP-Pho8 and stained with the vacuole membrane dye FM4-64. Numbers indicate the time in minutes after the start of the image sequence. Scale bar: 2 µm.
(D) Recombinant Flag-GP130-his (Flag-GP130) proteins were mixed with HA-GFP-his (HA-GFP) or HA-NEDD4L-his (HA-NEDD4L) proteins, and then, the proteins were pulled down with ANTI-HA agarose beads and detected using anti-Flag and anti-HA antibodies.
MISTRG and MISTRG6 mice were intravenously injected with 10x106 U-2932 or RC-K8 cells at six weeks of age and monitored weekly by IVIS until the study endpoint (A).
Immunoblot analyses of TDG and TDG-SUMO in whole cell extracts of mESCs and MEFs. TDG and TDG-SUMO conjugates before (2i, 0 h) and during differentiation of TDG wildtype (TDGwt) and TDG deficient (TDGnull) mESC and MEFs (5 µM all-trans retinoic acid (RA, 24 h, 48 h). Percentages of TDG-SUMO relative to total TDG signal are indicated.
(F) EGFR is required for STING Tyr phosphorylation. STING-GFP was expressed in 293XL cells in which EGFR expression had been knocked down. STING phosphorylation was analyzed by LC-MS/MS
E. Co-localization of SARS-CoV-2 (AB4, green) and phosphorylated Tau protein (magenta) at somas of cortical neurons revealed by high-resolution imaging and de-convolution. Representative images from at least 300 cells examined. Figures display scale bars. F. The bar diagram quantifies the fraction of Tau AT180-positive neurons that co-localize with SARS-CoV-2-positive neurons. For statistics, at least 250 cells from four organoids and two independent batches (n=2) were examined. Unpaired t test with Welch's correction. Data presented as mean + SEM.
E, Viability test in starved (-AA) CTNSWT, CTNS‑/-, and CTNSPatient cells in the presence or absence of DMKG (2 mM) for 24 hrs. Results are shown relative to the fed condition (n = 3).
H Immunofluorescence staining of HEK293T cells transfected with GFP-TLR7 and TLR7 mutant vectors, prior to treatment of R848 (10 µg/ml) for 30 min and labelled with specific antibodies. Scale bar: 50 μm.
(A) Tumor volume of MDA-MB-468 mammary fat-pad xenografts treated with vehicle, AZD8186 (50 mg/kg, og twice/day), erlotinib (50 mg/kg IP once/day) alone or in combination (5-6 mice per group, mean±SEM). Statistical significance of two-way ANOVA statistical test **P=0.0028 and ***P<0.0001. (B) Tumor volume of HCC-70 mammary fat-pad xenografts treated with vehicle, AZD8186 (150 mg/kg, og once/day), erlotinib (50 mg/kg IP once/day) alone or in combination (6-7 mice per group, mean±SEM). Growth curves were compared using two-way ANOVA statistical test. Statistical significance of two-way ANOVA statistical test ***P=0.0006 and ****P<0.0001.
B-C. Fluorescent images of retinas from 1 day old flies grown on either DMSO or TAPI-1, stained with BODIPY (green) and FM-dye (red) to mark lipid droplets and photoreceptor membranes respectively. Scale bars: 10μm.
H. Mock-, SCAI-, REV1- or SCAI/REV1-depleted egg extracts were analyzed by immunoblotting with indicated antibodies. Asterisks denote antibody cross-reactivity.
Measurement of euploid control (Ctrl) and ArCK cell proliferation without NK cells. Live cell imaging of target cells without NK cells was performed using the same condition as described in the method section. For each condition, 50 cells were randomly chosen at the beginning of the movie as the initial population (indicated by the dashline, ninitial = 50). The cumulative cell number was recorded. Dot plot of individual data points and mean were presented; n=2 biological replicates.
Representation of labeling with nucleotide analogues CldU (red) and IdU (green) and photographs of DNA fibers from sorted B220+GFP+ B lymphocytes activated for 48 h. Scale bar, 10 µm.
B PRK5‐CFP localized to the cell periphery in Col‐0mesophyll protoplasts.C-F Co‐localization of PRK5‐CFP and PM localized CAAX‐YFP in Col‐0mesophyll protoplasts. (C) overlay; (D) PRK5‐CFP (465-510 nm); (E) CAAX‐YFP (521-587 nm); (F) chloroplast (636-711 nm).
(B) Whole mount immunofluorescence of 9.5hpf pax2amKO2 embryos stained with anti-mKO2 antibody (red) and anti-PAX2A antibody (green). Anterior is to the left, and dorsal side is to the top. Scale bar: 0.1 mm.
M-O (M) Oxygen consumption rates (N) energy expenditure (daily: P=0.0357, dark phase: P=0.030), and (O) respiratory exchange ratio (daily: P=0.0424, dark phase: P=0.0016) measured by continuous high-resolution indirect calorimetry after 3-weeks of CTRL or BAM15 treatment (N=8 per group).
TEM cross sections of WT and α1-tubulin(-) parasites showing the aberrant structure of the latter. Subpellicular and centriolar plaque (spindle pole body) associated (hemispindle) microtubules are readily recognizable in the WT sporozoites (green arrowheads in insert) but absent in the mutant, while the inner membrane complex is formed below the plasma membrane of both parasites (white arrowheads). Note the different scale chosen to highlight the malformed shapes in the mutant. N: nucleus; scale bars: 0.2 µm, magnification boxes: 0.1 µm,.
RNA-seq revealed 1067 DEGs between young HO-1-/- and HO-1+/+ LT-HSCs. RNA-seq revealed 595 DEGs between old HO-1-/- and HO-1+/+ LT-HSCs.
Micrographs of maximum intensity projections of forebrain sections from 3 mo old GLASTCreERT2/eGFP mice 21 days after tamoxifen treatment Double-positive cells are indicated by arrowheads. CTX: cerebral cortex; DIE: diencephalon; HC: hippocampus. Scale bars: 300 µm (A), 20 µm (B), 75 µm (C), 30 µm (D), Histograms showing quantifications (B, n = 6 animals; 5 region of interest (ROI) covering the diencephalon on a total of 3 slides analyzed per animal Data information: data are presented as mean ± SEM. Each data point represents one animal.
Tomographic 3D reconstructions of the RA-SV pool at wild-type (B-D) and OtofPga/Pga (E-G) in inhibitory (inhib, B,E), resting (rest, C,F) and stimulatory (stim, D,G) conditions (color codes see A). MP-SVs, PD and AZ-membrane in transparent. Scale bar, 100 nm.
F Water-soluble and water-insoluble cell wall precursors (UMP, Lipid I and Lipid II). In the pentapeptide (L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala), Ala, Glu and Lys residues are denoted by a dot in green, red and blue, respectively. The γ-D-glutamic acid and the pyrophosphate group pointed by two arrows are the target sites of defensins in UMP or Lipid II, and the C-terminal D-Ala-D-Ala residues marked by a single square bracket are the target sites of vancomycin in UMP or Lipid II.
C) Mean interaction frequencies centered on all TAD boundaries +/- 1Mb for each dataset at 40kb resolution, as well as the log2 ratios. The inter-TAD interactions are increased upon transcriptional inhibition.
(c) Formation of double-membrane autophagosomal vesicles (black arrows) in the absence (control) or presence of C18PC was visualized by TEM (left and right, respectively). Higher magnification of TEM visualization is shown in lower panels. Scale bars, 10 μm (top) and 500 nm (bottom).
(a) Giant unilamellar vesicles (GUVs) incubated with mCherry-Atg19. The membrane was marked by incorporation of an Oregon Green labelled lipid. (b) GUV coated with GFP-Atg8 incubated with mCherry-Atg19. (c) Schematic representation showing the proteins and reaction resulting in GFP-Atg8 conjugation to the GUV shown in b. (d) GUVs containing nickellipids incubated with GFP-Atg8-6×His and wild-type mCherry-Atg19.
E. Effect of Nox4 on GADD34/PP1-mediated eIF2 dephosphorylation in transfected HEK293 cells. Nox4 increased eIF2 phosphorylation in cells transfected with GADD34 and WT PP1, and resulted in even higher phospho-eIF2α levels in cells transfected with N124D or D64N PP1 variants.
(I-M) Quantification of β cells with or without β-cell ablation and igfbp1a overexpression by confocal microscopy, which detects even weakly insulin-expressing β cells. Scale bars: 15 μm. See also Figure EV1.
Mbd2 binding sites on Myc promoter in ESCs. Arrow denotes the position of ChIP-qPCR primers.
MITOL KO enhanced ER stress-induced Bax translocation and cytochrome c release. Mitochondria or cytosol fraction was isolated from MEFs treated with Tu for 18 hours, followed by immunoblotting with indicated antibodies.
Mean number of total γH2A.X foci in α-actinin positive CMs from C57BL/6 mice. Data are mean ± SEM of n=4-7 mice per age group. 100 α-actinin positive CMs were quantified per mouse.
(D) qPCR analysis of Ago2 RIPs in TREx cells transfected with scr, miR-29b or miR-30c showing circHIPK3 enrichment over GAPDH, with each repeat normalised to an IgG scr RIP (n=3). Data information: data are presented as mean ± SD. *P<0.05, **P<0.01, ***P<0.001 (Unpaired Student's t-test). All repeats are biological.
(A) HEK GFP-LC3 cells transfected with control (siCtrl) or two different SNX18 siRNA oligos (siSNX18-3 and siSNX18-5) were starved or not starved for 2 h in the presence or absence of BafA1. GFP-LC3 lipidation and SNX18 protein knockdown were monitored by immunoblotting. The graph shows the average GFP-LC3-II relative to actin normalized to siCtrl-1 fed ± SEM (error bars), n = 4.
(K) Quantification of Bak, Bax and Fas gene transcripts in lung resident fibroblasts isolated from TGFα mice and treated with either control or AURKB siRNA for 72hrs. *P < 0.005, **P < 0.005, unpaired t-test, (n=3).
Figure 7b. Genes with differentially used exons tend to be longer. Box plots show length of genes with no differentially used exons, or at least one exon differentially up-regulated (DEXSeq log2 fold-change≥0, p<0.01) or down-regulated (log2 fold-change ≤0, p<0.01). P-value from a two-sided Wilcoxon rank sum test comparing median lengths between genes with either up- or down-regulated exons is indicated on top. n=3 replicates.
Effects of BBR overexpression on KYA1797K-induced RAS degradation. I analyses to detect levels of RAS in MT-HCT116 cells transfected with GFP-Mock or -BBR for 24 hr and then treated with 20 µM of KYA1797K for 24 hr
(P) Fecal energy density (% recovered in feces) after 3-weeks of CTRL or BAM15 treatment (N=8 per group).