EMBO/sd-character-level-ner huggingface dataset:
(D) Bar graph shows enrichment of genes bound by SOX3 in NPCs within the differentially expressed gene sets. Yellow bar represents enrichment within NPC/GPC genes, green bar within neuronal genes, blue bar within astrocytic genes and red bar within oligodendrocytic genes. (E) Bar graph shows enrichment of genes bound by SOX2 in mouse E11 spinal cord within the different gene sets. SOX2 data from [21]
(B) UMAP representation of 487 individual choroid plexus cells from lateral and fourth ventricles of SPF (green dots) and GF (yellow dots) mice.
HCT-116 or HT-29 cells were treated with 5mM 3-MA or 5μM chloroquine (CQ) for 30 min, and then with 2mM sodium butyrate (NaB) for 24 h. Representative Western blots of LC3-I and LC3-II expression were quantified by densitometry and normalized to GAPDH (ratio of LC3:GAPDH). The fold change from control is indicated as the mean ± SD of three independent experiments. One-way ANOVA was used for statistical analysis. ** p<0.01, compared to the respective control group.(D) HT-20 cells treated with CQ and NaB.
F. Heat stress resistance of bes1-1, bes1-2 and bes1-D as compared to wild-type. For basal resistance assays (top charts) plants were directly exposed to 45°C for the indicated time. For acquired resistance (bottom charts), plants were primed with the respective temperatures for 120 minutes before transfer to 45°C for 150 minutes. Data show the mean ±SE. n=7. The asterisks indicate significant differences compared to wild-type by Student's t-test (*P≤0.05; **P≤0.01; ***P≤0.001).
E. Our data supports Rpn1 being translated and rotated to be positioned closer to the AAA-ATPase.
A-C, PIL1, AT5G02580 and CDF5 expression pattern in 3-d-old SD-grown seedlings from indicated plant lines at night. Data is representative of 3 biological trials.
Scatter plots of mean frequency of each shRNA per gene. Average of v HOXA4 is indicated as a red dot.
Representative images showing the morphology of ME180 cells with or without TGF-α (10 ng/ml) treatment for 24 h (scale bar: 50 μm) or 108 h (scale bar: 25 μm). Please note the elongation of ME180 cells after TGF-α treatment for 24 h (TGF-α, 24 h) and the formation of multiple layers in ME180 cells after TGF-α treatment for 108 h (TGF-α, 108 h).
Venn diagram representing intersections of active enhancer regions in Epi cells.
H: Representative images of embryos collected from the oviducts or uteri of WT and Cnot6l-/- female at indicated time points after hCG administration. Scale bar, 100 μm. Data information: Error bars, s.e.m. **P < 0.01; ***P < 0.001 by two-tailed Student"s t test. n.s.: non-signif
B, C, Relative tumor volume (B) and weights (C) of PDX (BE564T) tumors after the treatment. *P<0.05 and ***P<0.001 by unpaired two-tailed t-test. (C) Data are the mean of tumor weights of each group (5 mice/group); error bar: SD
(a) IHC analysis for the microglia marker Iba1 in Emx1-Cre/Trim28-KO animals and controls. Scale bars: Low magnification 75 μm, high magnification 10 μm.
e expression of GFP-fused Cnot6l 3"-UTR in GV and MII oocytes with or without U01 F: Relative intensity of GFP signa after normalization by mCherry signal in the same oocyte The numbers of analyzed oocytes were indicated (n)
Western blot results showing the levels of CPEB1 in WT and Cnot6l-/- oocytes at the indicated time points after meiotic resumption. Total proteins fro 100 (B) oocytes are loaded in each lane α-tubulin (B) is blotted as a loading control. Experiments were performed three times with reproducible results; a representative result is shown
I Degradation of MAGE-A3/6 upon nutrient deprivation is dependent on Cul4A/B. HeLa cells were transfected with control siRNAs or siRNAs targeting both Cul4A and Cul4B. 72 hrs after treatment, cells were incubated for the indicated times with EBSS before harvesting and immunoblotting. Note, time 0 samples between two siRNA groups were normalized to more readily discern differences in MAGE-A3/6 degradation upon nutrient deprivation.
(C) Similar analysis of the same strains but grown in minimal M9 medium (with 10 µM MgSO4) supplemented with increasing concentrations of MnCl­­2. Black arrows denote full-length substrate (MgtE), red arrows denote the cleavage products generated by YqgP. (D) Western blots of four independent experiments shown in panel (C) were quantified by near-infrared fluorescence detection, quantified by densitometry and the results are displayed as fold activation of MgtE cleavage at 100 µM MnCl­­2 relative to 1 µM MnCl­­2 activity. Average values and all fours datapoints are plotted for each indicated YqgP variant.
(e) A histological section through a hair follicle (left, phase-contrast microscopy) stained for the stem-cell marker keratin 15 (K15) to identify the bulge region (dotted box), the stem-cell niche. DNA stain (DAPI) and the phase-contrast microscopy image show full follicle architecture. (f) Upper panels show MBd-accumulating cells in the bulge region (boxed) co-labelled with K15 and MKLP1. Enlargements (lower panels) of the boxed region highlight a cell with four MBds (asterisks). N, nucleus. Scale bar, 5 μm.
A. Protein sequence alignment of the HEAT8 hairpin and TAF1-TAND1, and the HEAT19 loop and TAF1-TAND2 (numbers represent amino acid positions). α-helices were assigned based on crystal structures and are depicted as blue cylinders. The Phe57 anchor residue of TAND2 is indicated 24[]. Black color highlights amino acid identity and gray shading indicates amino acids with similar properties.
Immunoblotting of the streptavidin precipitates of the mixture of biotin (100 μM) or biotin-Palbociclib (100 μM) THP1 cells (E). The data shown are representative of n=3 biological replicates.
Transwell assays showed the effect of ASS1WT and ASS1K234R on Caco-2-Vector or Caco-2-LOC113323 cell migration. Scale bar represents 100 μM..
Barplots reporting the average number of gain and sick phenotypes that are specific to each strain across all pairwise comparisons.
(D) qPCR quantification of shGAG and flGAG-POL normalized to ACT2 and to GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C SUBUNIT (GAPC) levels. qPCR was performed on n=3 biological replicates; bars: standard error. (**) = p-value < 0.01 (two-sided t-test between indicated values).
Analysis of the effect of TdT expression on the frequency of CSR as well as characteristics of Sμ-Sα recombination junctions resulting from the joining of DSBs with blunt ends. (j) Top: Schematic representation of the experimental design to analyze the effect of TdT expression on CSR in WT and Samhd1 KO cells. Bottom: Western blot analysis of the expression of TdT in WT and Samhd1 KO cells. Tubulin was used as a loading control.
H and I. ChIP analysis of mutant p53, YAP and H4 acetylated histone-bound chromatin from MDA-MB-468 cells on transduction with siRNAs oligos targeting endogenous YAP (siYAP) (H), NF-Y (siNF-YB) (I), or siGFP as a negative control (H and I). The experiment was performed in biological triplicates. The CCNA, CCNB2 and Cdk1 promoter occupancy was analyzed by RT-qPCR. Normalization was performed to the amount of input chromatin. The ChIP results were further normalised on the RT-qPCR of a region resulted negative for the recruitment of mutant p53 (Appendix Table S5). P-values were calculated with two tailed Student's t-test. Statistically significant results were referred with p-value<0.05.
D-G Relative mRNA gene expression as determined by RT-PCR, normalized to 36b4; n = 8/group. Anp: no significant differences; Bnp: *P = 0.01 versus WT sham, **P = 0.03 versus LXRα−/− sham; Myh6/Myh7: *P = 0.0002 versus WT sham, **P = 0.0003 versus LXRα−/− sham; Acta1: *P = 0.001 versus respective sham.
D U2OS:GFP‐parkin cells were treated as in (A) for the indicated time period, then fixed and immunostained for TOM20 (red). Cell boundaries are delineated in single‐channel images. Scale bars, 20 μm.
(A) Immunoblot of whole cell lysates of MEFs stably expressing ΔCys variants of BAK.
Levels of CoQ10 in fibroblasts of controls (C) and patients (P1-4) with primary CoQ10 deficiency (A).
A-L Only buffer (A), ferric iron (B), ferrous iron (C), ferrous iron-loaded DJA6 (D), DJA6J deletion (H), DJA6C224S (I), DJA6C241S (J), DJA6C267S (K), or DJA6C280S (L) was added to the reaction mixture (SUFBC2D complex, NFS2, SUFE1, MgCl2, NADPH and ATP). DMSO was added to the reaction mixture as a control to the iron chelator deferiprone (DFP) treatment (E). The reaction mixture containing ferrous iron-loaded DJA6 was treated with the iron chelator DFP (F). The reaction mixture containing ferrous iron was treated with the iron chelator DFP (G). UV-visible absorption spectra of the re-purified SUFBC2D complex from the reaction mixture were taken every 10 min for 50 min under anaerobic condition after addition of L-cysteine to initiate the reaction. A peak at 420 nm represents the iron-sulfur cluster in SUFBC2D complex. All data were based on three biological replicates, and similar results were observed.
F. Quantification and representative pictures for visualization of the PML protein (IF, green) and telomeres (FISH, red) in non-treated (NT) clone 35 cells and clone 35 treated with 4-OHT for 4 and 7 days. Arrows indicate co-localizations. Scale bar equals 10 µm. Bars represent data from three independent experiments ± SD. At least 150 cells were examined per condition per replicate. Significance was determined using one-way ANOVA. p-values are indicated on the graph. In all experiments, POT1 deletion was induced with 0.5 μM 4-OHT. Data information: 4-OHT - 4-hydroxytamoxifen, NT - non-treated cells, GRN163L - telomerase inhibitor Imitelstat, siNT -non-tagreting siRNA, negative control.
C) Results from WGCNA analyses, where lipids were separated in 12 modules and, labeled distinct colors, based on their internal correlations. Primary lipid classes, which comprise each module are listed as primary module members, with the number of species in each module/total number of species detected. The correlations between each of these lipid modules and relevant phenotypic traits are shown as a heatmap, where bicor (top) and p-value (bottom) are listed. Pvalues were calculated based on significance of regression (students test) and adjusted for multiple comparisons (FDR = 0.05)
D) HFs treated with paclitaxel alone showed a significant (adjusted p value = 0.0316 [*]) increase in the number of pH3+ cells in the matrix after washout. A significant (adjusted p value = 0.0278 [*]) increase in the number pH3+ cells was seen in HFs dual treated with both paclitaxel and palbociclib following drug washout. Palbociclib treatment alone showed no significant change in the number of pH3+ hair matrix keratinocytes after drug washout. Ordinary one-way ANOVA with multiple comparisons performed using N of 8-12 HFs from 3 patients. Values plotted represent the mean total number of cells counted per HF analysed. Error bars are standard error.
E, First-order cell death kinetics for wild-type ColE9 or ColE9 K469C labelled with different AF dyes (AF488, AF568, AF647) against E. coli JW2203 with OmpF in the outer membrane. Cultures were incubated with 80 nM toxin at pH 7.5 and 37 oC and at various time points the reaction stopped using trypsin at 37 °C for 30 min, cells plated out and CFUs recorded. All time courses were conducted in the presence of chloramphenicol (20 µg/ml) to reversibly block cell division, which would otherwise compete with cell-killing. Control data shown are for cells with no ColE9 added but where growth was inhibited by the presence of chloramphenicol. Cell-killing half-lives, obtained from the fitted first-order plots shown (error bars represent the standard deviation across two biological replicates), were as follows: wild-type ColE9, 2.5 min; ColE9 K469CAF488, 4.1 min; ColE9 K469CAF647, 29.6 min; ColE9 K469CAF568, 78.8 min. The data show that the chemical nature of the fluorophore in the C-terminal DNase domain of ColE9 has a dramatic effect on the cell-killing kinetics of the colicin. The schematic shown alongside the kinetic data is a surface representation of AF568 (model Generated in coot), the fluorophore with the biggest impact on OmpF-mediated killing, manually grafted onto the structure of ColE9 OBS2 bound within subunit 2 of OmpF. The slow cell-death kinetics of ColE9 K469CAF568 likely reflects the time taken to pass this bulky molecule through the narrow eyelet of the porin.
B. EMSA analysis of yTBP binding to DNA. We incubated 5 nM FAM-labeled oligonucleotide (TGTATGTATATAAAAC) with indicated concentrations of purified yTBP (0.125 to 8 μM) and then analyzed binding by 6% non-denaturing PAGE. Band intensities of free DNA from the gels (Top panel) were quantified and plotted (Bottom panel).
D. Quantification. At least 200 cells were counted (n=3). Statistical analysis was performed using two-tailed unpaired student's t-tests. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001, n.s. not significant.
(D) Representative H&amp;amp;E staining of primary (arrow) and disseminated tumors (asterisk) arising from orthotopic xenograft of parental and SOX9-expressing medulloblastoma initiating cells (MIC and MIC-Sox9, respectively). Quantification of primary and metastatic tumors arising from both of MIC (n=16) and MIC-SOX9 (n=8) is shown in the histogram (p=0.0000136).
CSF extract was treated with Myc-XErp1 CaMKII- ZBR- (T195A C583A) IVT. An empty IVT reaction not expressing XErp1 was used as control. The extracts were treated with DMSO or CsA as indicated. Calcium was added, samples were taken at the indicated time points and immunoblotted for cyclin B2, pSer335 XErp1 and α-tubulin. The pSer335 XErp1 membrane was stripped and reprobed for the Myc-tag. Asterisks indicate unspecific bands.
(H) Box plot depicting the quantification of co-localization through Pearson's correlation coefficient between α-SNAP and AMPK in cortical neurons on the basal condition and on DHPG treatment for 5 minutes. The box extends from 25th to 75th percentile with the middlemost line representing the median of the dataset. Whiskers range from minimum to maximum data point. *p<0.01, n≥35 cells per group from 4 independent platings. Unpaired-sample t-test.
C. Synchronized PfCDPK7-KO or 3D7 ring/trophozoite stage parasites were labelled with BODIPY-ceramide and DAPI followed by live imaging as described for panel A. While tubular vesicular networks/structures (TVNs), vesicles were predominantly labeled in 3D7 parasites, most PfCDPK7-KO parasites did not exhibit TVN; instead, small punctate spots (white arrowheads) were seen in the iRBC cytoplasm (Scale bar-1 μm).
e) Representative micrograph showing hepatocyte from aged mouse containing a TAF located in close proximity to a neutrophil (labelled with Ly6G); f) schematic depicting experimental design; g) % of neutrophil migration towards conditioned media (CM) obtained from young (early passage) and replicatively senescent human fibroblasts. Media alone and fMLP were used as negative and positive controls respectively. Data are mean±S.E.M. of 3 independent experiments;
Reverse-phase HPLC analysis of whole-cell lysates from the siRNA-ALDH1A-treated HSCs in (E). Typical chromatograms of all-trans retinoic acid and 13-cis retinoic acid. The retention time is 14 min for 13-cis-RA and 23 min for all-trans RA.
B. Over-expression analysis of enriched KEGG pathways of significantly differentially expressed genes between low STAT3 versus high STAT3 groups in TCGA PRAD.
D, E Zoomed-in binding interfaces of NKG2D with MICA (D) or ULBP3 (E), corresponding with the configuration (shown as gray dashed box in (A) and (B), respectively).
e, The bands from a-d were quantified from 3 independent experiments. The mean with SEM is shown.
(C) Sirt5 deficiency inhibits NADPH production in MEFs. 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<0.001 (two-tailed unpaired t-test).
FACS analysis of Lysotracker (B) dye fluorescence in RCS treated with the indicated FGF ligands (50 ng/mL) for 16h. Fluorescence intensities were expressed as % relative to vehicle (5% ABS). Mean +/- standard error of the mean (sem) of N=3 biological replicates/treatment. Analysis of variance one way (ANOVA) p<0.002 (B) Tukey's post hoc test ***p<0.0005.
(J Analysis of the extent of signal spreading in the z-dimension (apico-basla) of basal myosin-II. Myosin-II signal intensity was plotted along the apicobasal axis and a Gaussian curve fitted to the basal peak. The width of the Gaussian fit was used as a parameter to estimate myosin-II signal spreading in the z-dimension, which was limited to 4 µm (N=3). In each box plot, the central mark, the bottom, and the top edge of each box indicates the median, the 25th and 75th percentile, respectively. Whiskers extent to the most extreme data point
(c) Labelling intensity of PtdIns(3) P in wild-type yeast cultured in S(-NC) for 4 h (average±s.e.m.). PtdIns(3) P was found in both leaflets of the autophagosome and autophagic body membrane, and the labelling was much stronger in the EF than in the PF. In the vacuolar membrane, significant labelling was found in the EF, albeit at much lower levels than in the PF. The experiment was repeated three times, and the number of colloidal gold particles per μm2 was measured in more than ten randomly selected images.
Schematic representation of the notion that an increase in the expression of MCOLN1 results in a proportional increase in ML-SA1-induced Ca2+ release in HN31 cells.
(G) Quantification of CTxB retrograde transport in BMMs following siRNA-mediated depletion of Stx6 (siStx6) after AlexaFluor™488-CTxB binding on ice followed by 30 min incubation at 37˚C. Data are means ± SD from n=3 independent experiments, in which 100 cells were analyzed per experiment. The asterisk indicates a statistically significant difference (P=0.0114, unpaired Student's t test) compared to the siNT control.
(A) Immunoblot of protein lysates from wild-type, PERK-KO and GCN2-KO MEF cells incubated in the presence of DMSO (Control), Tunicamycin (0.1 µg/ml), or starved in EBSS for 16 h. Data are representative of three independent experiments.
C. Representative time-lapse spinning disk confocal images of n = 3 of live COS7 cells stably expressing GFP-TMD (green) marked ER and SiR-lysosome-stained LE/Lys (orange) . Zoom insets highlight regions of interest containing a mobile endosome as denoted by the white arrow. First row represents ER (GFP-TMD) (green), the second row shows MDA generated ER movement (magenta), third row shows a merge of the two preceding channels and the fourth row shows a merge of ER (green) and LE/Lys (orange). Samples were treated with either DMSO or 2µm paclitaxel. Scale bar: 30µm and zoom insets 3µm. All images acquired for 90 frames at 1Hz.Images related to movie EV7 and 8 D. Kymograph of panel (C). E. MDA quantification of panel (C) normalized to control cells, showing the average ER movement surrounding LE/Lys under control or treated conditions and the overall average ER mobility under control or treatment conditions. Graph represents mean ±s.d. of analyses at multiple locations within the same cell (n = 20 cells per condition from 3 independent experiments). Significance two-tailed student t-test **** P<0.0001; ns = not significant.
(A) UMAP representation of the whole scRNAseq dataset (0 dpa and 3 dpa) showing the cell density distribution of the 3 dpa sample. (B - E) Expression of snap25 (neuronal marker), leptin, sox2 (progenitor marker) and foxm1 on the same UMAP representation as in (A). (F) UMAP representation of the 16 clusters identified in the scRNAseq dataset
C. Schematic illustration for the lactate uptake assay with 2 well chamber. Cells were seeded on a glass bottom dish. BMECs and adenoviral laconic-infected HBVPs were separated by 2 well chamber. After attachment, the 2 well chamber was removed for cell migration.
(d) Hel308 DNA helicase DNA (pdb 2PR6; backbone in orange, bases in gray bonds) after aligning the RecA domains of Hel308 with those of FRH (cyan, RNA in yellow); see also Appendix Fig S4. The superposition indicates that the KOW module is positioned to interact with double stranded RNA that is being unwound by the RecA and DHSCT domains.
E Echocardiography analysis of left ventricular dimensions and cardiac function at 1 week post-I/R in mice. ** p < 0.0001, n = 15 mice in the sham-operated group and n = 10 mice in the I/R group.
D283 cells were treated with DMSO (vehicle, black), with LY364947 (red) or with SB431542 (orange). Growth curve experiments showing cell proliferation upon TGFβ/Activin signaling inhibition. The p-values were determined by unpaired t-test and two-way ANOVA *p < 0.05, **p < 0.01, ***p < 0.001.
(F) Cell growth assay in BT549 cells with GFP or MIG-6 knockdown in the absence and presence of gefitinib for 72 hours.
E. Effect of CCL2 on KCl-induced MCH release. The perifusion of hypothalamic tissues with 60mM KCl for 30 min induces an up to 3.1-fold increase in MCH release. CCL2 (100 nM) dramatically blunts KCl-induced MCH release, an effect partially by the addition of INCB3344 (10µM) (3 to 5 independent experiments, 3 chambers per condition in each experiment). * or $ p<0.05, ** p<0.01, *** p<0.001. * KCl vs KCl+CCL2 conditions. $ KCl+CCL2 vs KCl+CCL2+INCB3344 conditions. Data are expressed as mean fold-increase in MCH release per chamber vs basal secretion, ± SEM.
D) HRP-Lamp1 vesicles show less colocalization with glycogen in UAS-HRP-Lamp1;Dmef2-Gal4 larvae starved and treated with CQ.
Representative immunohistochemistry of GFP+ stem cells per crypt, n=60~70 crypts from n=3 mice per group. Scale 50 µm.
Whole exome sequencing was initially performed on DNA extracted from peripheral blood leukocytes of 111 individuals from the 18 most extensive families from our cohort (76 with DP and 35 controls). The exome sequences were aligned to the UCSC hg19 reference genome. Picard tools and the genome analysis toolkit were used to mark PCR duplicates, realign around indels, recalibrate quality scores and call variants. Variants were analyzed further and filtered for potential causal variants using filters for quality control, predicted functional annotation, minor allele frequency (MAF), segregation with trait, variants in multiple families and biological relevance (See methods and Table EV1 for further information on filtering criteria). Targeted exome sequencing using a Fluidigm array of 28 candidate genes identified post-filtering was then performed in a further 42 families from the same cohort (288 individuals, 178 with DP and 110 controls). Variants post targeted re-sequencing were filtered using the same criteria as the whole exome sequencing data. Rare variant burden testing was performed for all genes selected for targeted re-sequencing, in order to rank candidate genes post targeted re-sequencing. A multiple comparison adjustment was applied to the set of 28 p values post hoc (Benjamini et al., 2001). Screening of 100 further cohort controls was via conventional Sanger sequencing. Functional annotation of the variants as described elsewhere in methods. DP - delayed puberty. *data unpublished.
E. STAT2 levels in MEFs were decreased by transfection with siRNAs for 48 hrs after which the cells were infected with ZIKV (MOI=5) for another 48 hrs. The silencing efficiency was determined by immunoblotting. Representative panels are shown. The experiment was repeated three times.
(B) Immunoblots of protein lysates from ARPE-19 cells infected as indicated in (A). Data are representative of three independent experiments.
The graph shows the variations of the total amount of tubulin per cell with respect to the content of actin at the centrosome. The two lines correspond to linear regressions of the two sets of data relative to cells transfected with centrin1-VCA-GFP or centrin1-GFP.
I TFEB homodimer formation detected by glutaraldehyde (GA) crosslinking. Purified recombinant GST-tagged TFEB or TFEB mutants was incubated with or without glutaraldehyde, then the products were analyzed by immunoblotting using anti-TFEB.
Live imaging of adult PDGFRαH2BEGFP mouse back skin. Representative time-lapse images of adult PDGFRαH2BEGFP (green) dermis with collagen shown as second harmonic generation (SHG) in purple at indicated imaging time points. Scale bar, 100 µm.