EMBO/sd-character-level-ner huggingface dataset:
A. Size exclusion chromatography elution profile (1.6 cm × 50 cm Superdex S75) and SDS-PAGE of full-length N-terminally 7×His tagged yeast Oxr1. B. Inhibition of V1ΔH and V1Hchim's MgATPase activity by Oxr1 in absence and presence of subunit C. The data from one representative of two experiments using two different preparations are shown. Individual data points (n=2) and mean from one representative of two biological replicates are shown with error bars representing S.E.M. . C. Oxr1 binds wild type V1. Samples of V1, Oxr1, and mixtures of V1 with a 2-fold molar ratio of Oxr1 in absence or presence of a 3-fold molar ratio of subunit C were subjected to size exclusion chromatography on a 1 cm × 30 cm Superose 6 Increase column. SDS-PAGE is shown for all four samples and immunoblot analysis of column fractions using a penta-His antibody is shown for samples containing Oxr1 and Oxr1 plus C. Note that incubation of V1 with Oxr1 in presence of excess subunit C leads to partial release of subunit H (highlighted by the rectangular box in the V1 + Oxr1 + C gel). Also, some degradation of Oxr1's unstructured N-terminus is observed as indicated by the asterisk (only the full-length protein is detected by the αHis-tag antibody). The data from one representative of two experiments using two different preparations are shown.
(A) CD21 expression was evaluated by flow cytometry analysis on freshly isolated pDCs and B cells.
(F) Venn diagrams of proteins down-modulated by APBD and up-modulated by 144DG11 and vice versa under starvation (48) and glycogen burden (48+24) conditions.
Induction of Grp78 promoter activity by TMZ in RGD4C/AAVP-Grp78-Luc cells. LN229, U87 and SNB19 cells stably transduced with RGD4C/AAVP-Grp78-Luc or RGD4C/AAVP-CMV-Luc were grown in the presence of TMZ for the indicated times. Results represent the average RLU/1μg protein. Data shown are representative of two experiments, n=3. Two-way ANOVA with Bonferroni correction (GraphPad Prism 6) was used for data analysis.
(E) Plots of MHC II staining intensity in neutrophils (top) and in macrophages (bottom) from flow cytometry analysis of forepaws from 10-wk-old WT and RDEB mice.
Comparison of human mascRNA and tRNAGlnUUG secondary structures. The identical nucleotides were marked in red.
(A,A') Specific expression of FAM134B mRNA (green) in sensory neurons (red) of P4d vGlut2Cre;R26lsl-tdTommouse. Scale bars, 100μm. The white dotted line indicates the dorsal root ganglia (DRG) where sensory neurons are genetically labeled with Tomato. Insets of (a) and (a') are high magnifications of sensory neurons showing the co-localization of FAM134B mRNA and Tomato. Scale bars, 10 μm.
(F) Relative qRT-PCR analysis of IFNB mRNA in PBMCs treated with DMSO or Ac-YVAD-cmk (20μM) for 3hrs followed by ZIKV infection (MOI=1) for 36 hrs.
b, Reciprocal social interaction in juvenile miR379-410 wt- and ko mice pairs (P23). Aberrant time spending in social interaction activity in miR379-410 ko-pairs compared to their control wt littermate pairs. Left panel: wt-pairs male n=13, ko-pairs male n=10, t21=2.433, *p=0.0240, unpaired Student's t-test. Middle panel: wt-pairs female n=15, ko-pairs female n=13, t26=1.873, ns p=0.0723, unpaired Student's t-test. Right panel: pooled data of wt-pairs n=28 (male n=13, female n=15), ko-pairs n=23 (male n=10, female n=13), t49=2.969, **p=0.005; unpaired Student`s t-test.
B Analysis of NMJ and muscle morphologies were performed from ERp57WT (n=5), ERp57Nes+/- (n=5) and ERp57Nes-/- (n=4). Quantifications of endplate width, measuring the most ventral region of the diaphragms every 134 µm considering both sides of the innervation profile. Twenty to forty measurements per diaphragm were obtained per animal.
(E) The transcriptional activity of β-catenin in 22Rv1-P cells with different patterns of ESM1 overexpression. Bars are the mean ± SD of three independent experiments.
a. A flow-chart showing the sample preparation for the SILAC-based relative quantification of K48/K63-branched ubiquitin chains from yeast by mass spectrometry. 10xHis-Ub(R54A) was overexpressed in wildtype cells (wt) and either in cells deleted for UBC1 (Δubc1) or cells expressing ubiquitin-binding-deficient Ubc1-EA. The R54A substitution in ubiquitin enables the production of a marker peptide for K48/K63-branched ubiquitin by trypsin digest, which can be detected by targeted proteomics (PRM).
Oocyst counts in the mosquitoes at day 7 post blood-feeding. x/y on the top is the number of mosquitoes containing oocyst/the number of mosquitoes dissected; the percentage number is the mosquito infection prevalence. Right panels are the stained midgut oocysts.
D. Western blot of Atg13 in Ofd1fl/y;creKsp and control kidneys at pre-cystic (P8, left) and cystic (P22, right) stages. Gapdh was used as loading control. Atg13 protein levels are expressed as fold change compared with control mice; n=7 mutant/5 control mice at P8, n= 4mice/group at P22.
(a-c) HeLa cells transfected with ARL8B or KIF2 siRNA, or with ARL8B overexpression construct (non-targeting siRNA and empty pcDNA vector used as transfection controls), were either left untreated, serum/amino-acid starved for 5 h, or starved and then recovered in amino-acid- and FBS-containing medium for 30 min. Cells were immunostained using LAMP1 antibody (a) and the percentage of cells with predominantly peripheral localization of LAMP1-positive vesicles was quantified (b) or subjected to immunoblotting (c) using antibodies as shown. Quantification of phospho-S6K levels relative to the total S6K is shown in (c). Values are means ± s.e.m. of three independent experiments carried out in triplicate. All comparisons are with the control within each treatment condition, *P0.05, **P0.01, ***P0.005 Student's t-test; n.s. not significant. Uncropped images of blots are shown in Supplementary Fig. S7.
Total protein lysates (input) from GSC#9 treated with vehicle (-, DMSO) or MPZ (+, 20 μM, 1 hour) or with vehicle (-, H2O) or Z-VRPR-FMK (+, 75 μM, 4 hours), were processed for control immunoglobulins (Ig) or anti-QKI antibodies immunoprecipitation (IP). Western-blots were performed with indicated antibodies. Western-blots were performed with indicated antibodies.
B, C. Expression analysis of miR-34/449 by in situ hybridization using locked nucleic acid (LNA) probes in wild type cortices at E14. Mature miR-449, miR-34b and miR-34c are preferentially expressed in the subventricular (SVZ) and ventricular (VZ) zones of the neocortex. Scale bar, 50 μm (B), 10 μm (C).
G. Newly synthesised R-loops in BU-1 during S phase in wild type (black) and primpol (red). Error bars represent 1SD of three biological repeats of the experiment. *** p ≤ 0.001, * p ≤ 0.05; unpaired t-test
A. HeLa cells treated with non-targeting (Ctrl) or C9orf72 siRNA were immunostained for endogenous p62. Accumulation of p62 was quantified by counting p62 positive puncta per cell from 3 independent experiments (Mean ± SEM; unpaired t-test, **** P ≤ 0.0001); N (cells) = Ctrl: 74, C9orf72: 55). C9orf72 knockdown was confirmed by RT-qPCR (Appendix Fig S2). Scale bar = 10 µm.
F. Quantification of rescued ovaries harboring at least one stage 9 egg chamber in genotypes numbered from 1 to 11 after one day or several days on yeast. Grey bars (1-4) are control flies. n= number of ovaries.
B. Top panel; depiction of amino acid sequence corresponding to the SIMs in the indicated proteins used in this study. Hydrophobic residues involved in SUMO binding are indicated in red. Bottom panel; constructs expressing GFP-control or GFP-fused SIMs of indicated proteins were co-transfected with HA-AGO2 in HEK293T cells and IP and WB were performed to determine the extent of interaction.
(E) Images were captured of the hair coats of Sirt7+/+ and Sirt7-/- mice at 15 months. The yellow dashed lines indicate hair thinning or hair loss.
C HeLa cells stably expressing SEPT6-GFP were harvested, and then tested with Co-IP. HeLa cells expressing GFP were used in parallel as control. GFP-trap magnetic agarose beads were used to isolate SEPT6-GFP from cells, and extracts were immunoblotted for Drp1, SEPT2, SEPT7, or GFP. The lysates were immunoblotted for GAPDH as control for cellular protein levels.
A Schematic representation of the exon/intron organization of Celf2 genomic locus. Arrows indicate TSS sites.
(C) Immunofluorescent microscopy staining of Fstl1 (green) and S100a4 (red) in the ischemic area. Arrows indicate Fstl1 and S100a4 double positive cells. Scale bar indicates 20μm.
Control and si-IRGM transfected HT-29 cells uninfected or infected with CHIKV and qRT-PCR analysis were performed with (E) SAMHD1
(B-C'') Immunostaining of mosaic germaria with anti-GFP (green), to identify clonal cells by the lack of GFP, and either 8C4 (B-B'') or 10F1 (C-C'') monoclonal anti-Cbl (red). DAPI was used to visualize DNA. White arrowheads indicate aubHN2/+ control GSCs; yellow arrowheads indicate clonal mutant aubHN2 GSCs. Scale bar: 10 μm.
(F) In vitro kinase assay of RSK3 with N-terminal (F1), middle (F2), and C-terminal fragment (F3) of ATXN1.
I-J, Kaplan-Meier recurrence-free (I) and overall (J) survival analysis of PCa patients stratified according to median THEM6 expression. Data information: Statistical analysis: logrank test. Data reproducibility: n = 35 tumours for THEM6 low and n = 34 tumours for THEM6 high.
(B) Two-colour SIM images in control and myosin VI-depleted cells illustrating the localisation and distribution of the distal appendage markers Cep164 and ODF2 at the centrioles, stained with anti-acetylated tubulin antibody. Representative images are shown; scale bar, 500 nm.
(G) IDH1 K224 deacetylation regulated cellular NADPH/NADP+ redox in cells. In HCT116 stable cells with IDH1 knockout and re-expressing the indicated proteins, the ratio of NADPH/NADP+ in cells was measured as followed by manufacture's instruction. Data information: All results were expressed as mean ± SD of three independent experiments (n ≥ 3 per experimental condition). For , G statistical significance was assessed with the one-way ANOVA with Newman-Keuls post hoc test. *P<0.05 and **P<0.01. n.s. = not significant.
Heat map diagram of DEGs in LV during late Telogen compared to mid Telogen, relative to biological processes, analyzed using the Enrichr platform (Chen et al., 2013; Kuleshov et al., 2016). Data shown represent the log2 (FPKM+1).
(B) Immunoprecipitates of anti‐Beclin antibodies prepared as described in (A) were assayed for PI 3‐kinase activity in the presence of wortmannin at concentrations of 0 nM (lane 1), 1 nM (lane 2), 10 nM (lane 3), 100 nM (lane 4). The labeled lipids were extracted and separated by thin layer chromatography, followed by detection by autoradiography using a bioimaging analyzer BAS2000 (Fuji Film).
C. Phosphorylation status of Ser127 or Ser128 determines interaction between 14-3-3 and YAP. Lysates from HEK293T cells transfected with plasmids indicated in the figure were immunoprecipitated with anti-Flag antibody and immunoblotted with anti-HA antibodies (top two panels). Lysates were immunoblotted with anti-HA or anti-Flag antibodies (bottom two panels). "n.s." arrow indicates a non-specific band also visible in the non-transfected lane.
A) Schematic illustration of Suv39h1 protein. ΔN-Suv39h1 lacks the 41 N-terminal amino acids but contains a chromodomain.
Membrane lipid class composition of classes contributing at least 1% of total membrane lipids, the inset shows CDP-DAG and the separate lyso(L)-phospholipids (lyso-PL); Data information: All data were obtained by mass spectrometry and are presented as mean ±SD (n=3 biological replicates); * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001, unpaired two-tailed t-test of the indicated bar compared to the cho2opi3 parent unless indicated otherwise.
D) Trajectory plots comparing the trajectories of Chordc1 and Psat1 in WT and mdx mice.
A. Ectopic expression of NLK attenuates interaction between YAP and 14-3-3. Lysates from HEK293T cells transfected with plasmids indicated in the figure were immunoprecipitated with anti-HA antibody and immunoblotted with anti-GFP antibody (top two panels). Whole cell lysates (WCL) were immunoblotted with antibodies shown in the figure (bottom three panels).
Overview of all identified vemurafenib resistance mechanisms in patient and PDX samplesResistance mechanisms discovered in each of the lesions have been identified: a) in patients samples by WES (BRAFV600E amplification in M032R1, R2 and R5; MEK1T55delinsRT in M032R4 and M032) and immunoblotting (of alternative form of BRAF in M032R3); and b) in PDX by IHC and qPCR (BRAFV600E amplification in M032R2 and R5) and PCR analysis (MEK1T55delinsRT in M032R1 and R4). Gray arrows indicate that the lesion was at the back side. ampl., amplification; alt., alternative.
b, Analysis of HeLa cells treated with the indicated siRNAs and stained with NDP52 antiserum. NDP52-positive bacteria were counted by microscopy 1 h after infection with S. Typhimurium. siRNAs are further characterized in Supplementary Fig. 2.
Mice were analysed 2 days after TAC (a-e). a, Electron microscopic analysis. Images of mitochondria at higher magnification are shown in subsets. Scale bar, 1 µm. b, Autolysosome after incubation with anti-DNA antibody and 10 nm gold staining. Scale bar, 200 nm. Arrows indicate labelled DNA.
Gene ontology enrichment analysis of the upregulated genes indicates male-specific or preferential biological processes.
Erlotinib IC50 values were quantified in RHOB-overexpressing or RHOB-depleted (D) HCC827 cells, (E) HCC2935 cells and (F) H3255 cells, as determined by an MTS assay after 72 h treatment. RHOB overexpression or inhibition was monitored by western blotting for each condition.
Sublingual C. albicans infection of WT and Stim1fl/flCd4Cre mice as described in Figure 5. (C) Macroscopic images of the C. albicans-infected tongues of mice at day 7 p.i.
Intracellular un-esterified cholesterol distribution as detected by filipin staining in Npc2+/hypo IMCs cultured with or without 50 μg/ml bNPC2 for 48 h. Scale bars, 25 μm. Quantitative data in the bar graph were obtained by analysing 265 bNPC2-untreated (-bNPC2) and 252 bNPC2-treated (+bNPC2) cells from three independent cultures using the method described in (A).
A. The interaction partners of YTHDF1 were identified by pull-down assays and mass spectrometry. The Flag-YTHDF1 pull-down assay was performed in CNE2EBV cells transfected with a plasmid encoding Flag-tagged YTHDF1. The proteins in the differentially abundant bands were identified by mass spectrometry.
ciPSCs have developmental potentials to form teratomas containing tissues from all three germ layers. Scale bar, 100 μm. Chimeric mice were generated from ciPSCs.
D: GST-tagged full length ORF (aa 1-132) and deletion constructs (aa 1-64, aa 65-132 and aa 31-132) of p14ARF as well as GST alone were subjected to in vitro-MT assays in the presence of GST-PRMT1 as described in (B). Methylation activities were detected by autoradiography (upper panel). Asterisks indicate methylated p14ARF proteins, whereas the arrowhead marks p14ARF-unrelated background signals (likely deriving from PRMT1 automethylation). Amounts of p14ARF proteins and GST alone were visualized by immunoblotting using α-GST antibody (lower panel). Asterisks highlight the expected size and location of the different proteins. Size markers (in kDa) are shown on the left.
(E) Immunohistochemistry (IHC) of pS6 (Ser235/236) on skin sections from HS and Rosacea. Higher magnified images of boxed areas are shown at the bottom right of lower magnified images for each group. Epi, epidermis; Der, dermis. Scale bar: 50 μm.
Quantitation of cells shown in A-C. Number of cells counted/condition: 712 - 1343 in three independent experiments; statistical significance via One-way ANOVA; p < 10-5, ± s.e.m.
RT-PCR analysis validation of selected alternatively spliced exons. RT-PCR was performed on total RNA from WT or slow/slow ESCs, NPCs or neurons. PCR products were visualized and quantified by Bioanalyzer (Agilent). Images are representative of experiments performed in triplicate. Themean ± SEMis plotted with *p-value<0.05, **p<0.005, ***<0.0001 as determined by t-test.
(B) The cell lysates from HeLa cells were collected and analyzed after GS for indicated time (lane 1~5), or GS for 2 h followed by 2 h chase in NM (lane 6). The cell lysates were subjected to Phos-tag gel and regular SDS PAGE respectively.
C. Representative western blot showing changes in various ER stress markers and O-GlcNAcylation-related protein expression in THP-1 cells treated with Stx2a (10 ng/mL) for 3 h in the presence or absence of O-linked N-acetylglucosamine transferase (OGT) inhibitor OSMI-1 (10 µM final) or serine/threonine-protein kinase/endoribonuclease inositol-requiring enzyme 1 a (IRE1a) inhibitor MKC-3946 (10 µM final). D. Quantification of the band intensities in (C). Data are presented as mean ± S.E.M. (n = 3 biological replicates) normalized against β-actin, which was used as a loading control. Data information: Statistical analysis was performed using two-tailed Student's t-test. *P < 0.05; **P < 0.01; and ***P < 0.001.
(A) Scheme of individual actin filaments polymerizing on functionalized glass surfaces from profilin-actin in solution. (B) Time-lapse TIRF microscopy of single filament growth from Alexa488phalloidin-stabilized seeds (green) in the presence of 5μM profilin-actin.
(d) Immunoblots for indicated proteins in isolated fractions from starved mouse liver. Hom, homogenate; LE, late endosomes; Cyt, cytosol; APG, autophagosomes; APL, autophagolysosomes.
(E) Representative pictures of ZEB1 and MITF immunostainings, before and after vemurafenib treatment, in the tumor from patient 1, exhibiting primary resistance to BRAFi. Scale bar = 80 µm. Right: Magnification of MITFhigh and MITFlow clones in the resistant tumor under treatment. Arrows indicate endothelial and stromal cells that also show positive staining for ZEB1, besides tumor cells.
ELISA analysis of IL-1β secretion from HMDMs transduced with lentiviruses expressing shCon or shABRO1 prior to stimulation with control medium (Con), LPS or LPS plus ATP. Cell lysates were immunoblotted with anti-ABRO1 and anti-GAPDH antibodies.
E, Time lapse video-microscopy snapshot on HeLa cells transfected with NAF-1-mRFP (red) and treated with fluoMito-C (green). The distance/intensity fluorescence quantification graph illustrates the codistribution of fluoMito-C and NAF-1-mRFP.
(C, D) THP1 cells were infected with HSV-1 KOS, ΔICP27 or HSV-1 ΔNLS. The localization of the major NLS is illustrated in panel C. Supernatants were harvested 18 hpi for measurement of type I IFN bioactivity.
Western blot analysis performed with lysates of (N) Irgm1+/+ and Irgm1-/- mouse brain to determine levels of STAT proteins (n=3 mice).
(d) The effects of induction of wild-type CerS1 and C18-ceramide and catalytically inactive mutant CerS1 (+ tet) in the regulation of mitochondrial function were assessed by measuring OCR using the SeaHorse and compared to roles of noninduced controls (− tet).
B. Representative traces of the forward DNA unzipping in the presence of dSaCas9/sgRNA showing the force versus the number of unzipped base pairs. The naked DNA unzipping signatures are also presented for comparison (gray). Insets: zoomed-in view of the regions with increases in force. The dashed lines illustrate the interaction sites between dSaCas9 and the DNA. Black arrows indicate the force peaks of the pre-PAM interaction.
(A) Schematic diagram of affected proteins and the locations of the point mutations identified in: EARS2 p.Gly110Ser, p.Gly224Ser, p.Arg516Gln, p.Arg120Trp, p.Gln199Arg and p.Ala88Glu mutations-catalytic and anticodon binding domain of the protein; TRMU p.Tyr301Cys and p.Ala10Ser- amino terminal catalytic and carboxy terminal β-barrel domain; QRSL1 p.Val229Gly -amidase signature domain; GOT2 p.Gly188Ser and p.Lys364Glu located in the large catalytic and small catalytic domains and GLS p.Ala432Ser found in the central glutaminase domain. Multiple sequence alignment of the above mentioned proteins shows the conservation of the affected amino acids across species using Jalview software. Analysis was performed using protein sequences from human (Q5JPH6, O75648, Q9H0R6, P00505, O94925), mouse (Q9CXJ1, Q9DAR5, Q9CZN8, P05202, D3Z7P3), zebrafish (Q0P499, Q503J2, F1QAJ4, Q7SYK7, Q8JFS4), frog (Q66JG3, F6TJB0, Q0VFI5, Q28F67, F7B417) and chicken (Q5ZJ66, Q5ZKW0, F1NLA0, P00508, A0A1D5PNV1).
F,G, Western blots of lysates from HEK293T cells transfected with the indicated constructs. The asterisk marks an unspecific band. Representative blots from at least three independent experiments are shown.
A Differences in sensitivity to increasing IMT1 doses between RKO cells and resistant RKO cells. The graph shows mean values ± SEM of n=3 independent experiments.
(A) Superimposition of camrelizumab/PD-1 with PD-1/PD-L1 complex structure (PDB code: 4ZQK). PD-1 is shown as surface format in light blue, while PD-L1 is shown as deep teal cartoon and camrelizumab-scFv is depicted as cartoon. VL of camrelizumab-scFv is colored in yellow and VH in deep salmon.
(C) Dose-response curves of two drugs for which high MERTK (left panels) or ACVR2A (right panels) expression was predicted to confer drug resistance. For each drug, three cell lines predicted to be sensitive (dark blue) and three cell lines predicted to be resistant (yellow) were assayed for viability. The experimental data validated that cell lines predicted to be more sensitive to a drug indeed showed this phenotype (data represents the average of three technical replicates; see Appendix for details).
S100A9 expression was analysed by (A) immunoblotting or (B) flow cytometry in stably transduced HEK293T cells using anti-myc and anti-S100A9 as indicated. Immunoblot loading controls were done with anti-actin. Flow cytometry negative and positive controls were done with non-transduced parental cells (in grey) and HEK293T cells stably expressing the red emitting fluorescent protein E2C (E2C-Far Red), respectively. Experiments shown are representative of three (n=3).
H) Larval brains at various time points from grh-Gal4; UAS-CD8-GFP were labeled with Msps, Dpn, and GFP.
(C) Close-up of OTULINC129A and its interaction with the proximal ubiquitin (Ub). M86, Y91, E95, and R122 of OTULIN and their interaction with each other and with the F4 patch of the proximal Ub are depicted. Interactions (dotted red lines) and water molecules (light blue) < 5 Å are shown. Residues of the catalytic triad (A129, H339, N341) in pale cyan.
E. Jurkat cells were transfected with mtYFP and treated as indicated. 32h after AICD induction cells were fixed and immunostained with an anti-cytochrome c antibody. Cytochrome c localization index was calculated from 30 randomly selected images per condition. Data represent mean ± SE of four independent experiments.
Successful injections represented as a percentage of total for a novice user on the manual microinjection system, an experienced user on the manual microinjection system, and the Autoinjector.
MCF10A WT or two independent clones for MDA5 KO cells were pretreated with DMSO or AZD6738 (250 nM) for 2 hours, and then irradiated with 20 Gy, 3 days later E) cells were harvested for real-time quantitative PCR instead of immunoblotting. IFNB1 mRNA level was measured by real-time quantitative PCR. Data are presented as mean + standard error of the mean of three biological replicates.
H. Same as (E) except images are TIRF footprints of tsA201 cells treated either with vehicle (control) or with U18.
(D, E) Inhibition of the interaction between endogenous BCN1, TAB2 and TAB3 by a BCN1 fragment corresponding to the TBD. HeLa cells were transfected with pcDNA3.1 (empty vector) or with plasmids encoding the TBD or a His-tagged Beclin 1 variant lacking the TBD (His-BCN1ΔTBD), followed by co‐immunoprecipitation of endogenous TAB2 (D) or TAB3 (E) and detection of BCN1.
(A) Principal component analysis (PCA) plot of the first two components of the analyzed samples showing separation between the three treatments: far-red illuminated wild-type, far-red illuminated pXccBphP (XccBphP overexpressing) and dark wild-type Xcc treatments.
G. IHC for expression of active β-catenin in colon or wild-type and Angptl2-/- mice. Scale bar = 50 μm.