EMBO/sd-character-level-ner huggingface dataset:
(J) HeLa cells were transfected with either WT GCS or GCS Δ3C for 16 hours and processed for cryo-immunolabeling. Distribution of indicated enzymes across the Golgi stack was quantified and represented as fraction of Gold particles in each cisterna. (n indicated in the graph; data are Mean ± SEM).
(b, c) Mouse fibroblasts stably expressing KFERQ-PS-CFP2 were photoconverted and maintained for 16 h in media supplemented (+) or not (−) with serum in the presence of 3-methyladenine (3-MA) to inhibit macroautophagy. (b) Representative images of the 3-MA-treated cells. (c) Quantification of the number of green fluorescence puncta per cell in 3-MA treated or not cells maintained in the presence (white bars) or absence (black bars) of serum. Values are mean+s.e. of 3 different experiments with >50 cells counted per experiment. No significant differences were detectable between samples supplemented or not with 3MA. Scale bars, 5 μm.
I. Representative images of CD31 and VE-Cadherin staining in intestinal wholemounts at an early disease stage (n= 5 WT, 5 ECko) in Casp8WT and Casp8ECko mice (red arrowheads point to VE-Cadherin 'empty' vessel patches). Scale bars: 25µm.
(j) In situ structure of the pig sperm DC microtubule doublet with the tubulin backbone in grey and microtubule inner protein densities colored individually. The gold and turquoise densities on the luminal side of the doublet are consistent with the positions of parts of the inner scaffold. This structure represents the DC doublets closest to the axoneme
B. Upper panel. Root growth model cartoon. Numbers (i=1,2,3...) label the order at which each cell (rectangle) entered the EZ (yellow) and the DZ (blue). ti is the time at which the i-th cell entered the EZ. Because of the irregularity in mitotic events at the meristem. ti - ti-1 is set to be stochastic. The simulations start with a single cell in the EZ. The EZ grows until it reaches the stationary regime, when it will be composed of nearly the same number of cells over time. All results in figures correspond to the stationary regime. Lower panel. Simulation of cell length exponential growth for three different cells (colors) of three simulated root files. Results herein correspond to the Sizer model.
Skin tumor outcomes in K14-IL33tg,ST2KO mice treated with DMBA/TPA carcinogenesis protocol in combination with SB431542 (test, n=6) or acetone (control, n=5). (F) Tumor latency (log-rank test)
TNFR1 expression in splenic neutrophils of wild-type, TNFR1 KO and SPRET mice determined by FACS. Neutrophils were defined by flow cytometry (FACS) as SSChighCD11b+Ly6GhighLy6Cmid and TNFR1+ cells from different strains were plotted in a histogram. In the insert, the median of TNFR1-PE signals were plotted and this shows that SPRET mice have an intermediate TNFR1 expression compared to WT mice.
(C) Per2 mRNA levels in WT (left) and CKO (right) cells were determined by qPCR over one circadian cycle (bottom), while PER2::LUC bioluminescence (top, min-max normalised) was recorded from parallel cultures. Per2 mRNA reported relative to Rns18s (bottom), n=3, ±SEM; PER2::LUC (top) presented as mean (solid) ±SEM (dashed), n=3. The WT mRNA trace was preferentially fit by a circadian damped sine wave compared with straight line (p=0.0412, extra sum-of-square F-test) whereas CKO data was not (ns).
(C) Grip strength of mice measured at day 12 post C26 injection, normalized to average strength of the control group (n=5-9). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by one-way Anova with Bonferroni's correction Data are mean ± SEM. ∗p < 0.05 and ∗∗∗p < 0.001 compared to control and #p < 0.05, ##p < 0.01, ###p < 0.001 compared to C26 untreated group.
The number of MLH1 foci in pachytene spermatocytes from 3-month-old males positively correlates with increasing Tex11 gene dosage.
Immunoblot analysis of anti-H3.1-HA pulldown of UBR7-LAP after deletion of H3.1 N-terminal tail (schematic, upper). 293T cells were co-transfected with UBR7-LAP and HA-tagged constructs. Numbers below blot indicate HA-normalized anti-GFP immunoblot signal relative to full-length H3.1-HA.
(K) The expression level of EPG-7::GFP is dramatically elevated and many EPG-7::GFP aggregates are formed in lgg-1 mutant embryos.
Immunoblot detection of ATG5 and BNIP3 from lysates of CntlKD (n=5), BNIP3KD (n=5) and ATG5KD (n=7) B16-F10 tumors. Densitometric quantifications relative to ACTIN levels are shown below each corresponding band.
western blot analysis of FoxO1 and ATGL in C2C12 cells transfected with Ago-183/96 and FoxO1 as indicated (n=5 per group for RT-PCR analysis).
(D) Proposed model of collagen recognition by autophagy. After synthesis, PC chains are subjected to quality control operated by the CANX/CRT chaperone system. Properly folded PC associates with HSP47 and is then secreted, whereas the misfolded fraction is sequestered by the CANX-FAM143B complex and delivered to lysosomes through ER-phagy.
C. In mouse embryonic fibroblasts, active (phosphorylated) cortactin is increased as compared to wild type, possibly compensating the lack of KV10.1.
Immuno-EM localization of NS5A and NS3 in HCV-infected cells.Huh7.5 cells were infected with 100 TCID50/cell of Jc1 and fixed 16 h post-infection. (A) Cells shown in panels b, c and e to g were post-fixed with 0.1% OsO4 providing best membrane preservation, especially in case of DMVs (f and g) and LDs (e). Both NS5A and NS3 localize predominantly to the ER (b and d) and 50-70 nm diameter single-membrane vesicles (SMVs; subpanel a, c and d). NS5A also localizes to lipid droplets (e).
A RPE cells expressing shRNAs specific to luciferase (shLuc) or lamin A/C (shLamin A/C) were serum-starved for 48 h and then stained for acetylated tubulin (Ac-tubulin, green) and CEP164 (red). The representative images show that the fluorescence intensity of CEP164 at the mother centriole of cilia-negative (left column) and cilia-positive (right column) basal bodies are similar. The graphs shown are the quantification of CEP164 at cilia-negative basal bodies and cilia-positive basal bodies.
schematic showing the immobilization of McjD to the surface: labeled McjD reconstituted in biotinylated DOPE lipid was immobilized to a PEG-biotin-coated surface in a flow cell via a neutravidin-tag on the proteoliposome. A typical surface scan is shown in false-color representation on the right (orange, double-labeled McjD; green, McjD with donor fluorophore only; red, McjD with acceptor fluorophore only)
N. FACS analysis of gp350 expression in CNE2EBV cells transfected with YTHDF1-specific siRNA (siY1-1 and siY1-2) or the siNC control following EBV reactivation. To measure gp350 expression in the reactivated CNE2EBV cells, cells were stained with anti-gp350 mAb (72A1) followed by an Alexa Fluor 594-conjugated secondary anti-mouse antibody and analyzed by FACS. The quantification of the ratio of GFP-positive and gp350-positive (GFP+/gp350+) cells from three independent experiments was shown.
Box plots with dot density plots showing that the apical area/basal area ratio was significantly smaller in REV cells than in LUZP1 KO cells [0.65 ± 0.16 (REV) vs. 1.30 ± 0.17 (LUZP1 KO)]. n = 10. **p < 0.01 (unpaired t-test). The value < 1.0 indicates apical constriction. The solid lines represent the medians and the boxes represent the inter-quartile ranges. The error bars extending from the box represents the data within 1.5 times of the interquartile range.
Residues on dynactin's pointed end (cartoon) that interact with cargo adaptors are shown as spheres, colored according to which adaptor they bind (yellow denotes binding to BICDR1, purple to Hook3 and green to BICD2). Binding sites 2-4 are shown in boxes.
C Excess amounts of parental C99 WT substrate compete crosslinking of C99-Bpa substrates to γ-secretase. Single and double asterisks indicate antibody crossreactivities to C99 monomer and dimer, respectively.
(F) TEM image of the same cell reveals large aggregates marked with 'A'. (G, H) Successive enlargement of the region marked in panel F shows an example of an aggregate-associated autophagosome.
TEM reveals different numbers of microtubules at the apical end of sporozoites for the different lines. Each dot represents the numbers of microtubules counted per section. Red lines indicate median from 23 to 40 analysed sections per line.
D. STRING-based and Cytoscape-visualized network of phosphorylated kinases color-coded based on clusters shown in Figure 6C. The border of known regulatory sites is coloured in burgundy. The shape depends on the known function of the regulatory site.
Left, spider plots showing genes commonly expressed by monocytes and/or cMΦ in comparison to bMG (reference population, center). Bold genes are plotted as bar graphs (right). Data are derived from four independent experiments with 5-10 pooled mice per sample and shown as mean ± s.e.m.
B) Bar plot indicates average basal OCR and spare respiratory capacity in seahorse measurements. Data are presented as mean ± SD of one representative experiment (n = 4 wells). Samples were compared using Kruskal Wallis test followed by Dunnett's test for multiple pairwise comparisons. Corrected p values are indicated as follows *p < 0.05 and *** p < 0.001. Shapiro Wilk test was used to check data normality and Bartlett test was used to examine homogeneity of variances.
L. Quantitation of the percentage of normal, abnormal and missing rhabdomeres observed in the TEM images for the genotypes mentioned above, presented as a stacked graph plot; n=180 ommatidia from 3 different fly retinas for each. Data were quantified for significance using Student's t test. ***p<0.001, **p<0.01.
An mRNA-miRNA reaction network with two miRNA binding sites on the target mRNA (mmi-2 Model).
D Quantified fluorescence of UbG76V-GFP normalized to mRFP, as in (C). ****P<0.001, ANOVA with Dunnett's posthoc comparison to the wild-type control equivalent time point. N=20 animals per genotype and time point. Error bars indicate SEM.
AGS and ALPK1-KO cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TRAF6 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies.
A-G Five-day treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered). Effects on (D) locomotor activity. Compounds were administered by daily subcutaneous injections. Data represent means ± SEM;n = 8; *P < 0.05, **P < 0.01, ***P < 0.001.
A: upper panel: import of Aβ1-42 into mitochondria; lower panel: relative quantification from two independent experiments. Values of Aβ1-42 signal were normalized to HSP60 signal and the resulting value at 5 min without trypsin was arbitrarily chosen as 1. Error bars indicate ±SD. Statistical analysis was by unpaired, two-tail Student's t test. *p<0.05.
D) Scorpius-based ranking of all cells on a pseudotime from homeostatic to activated microglia. Whereas all cells within the WT groups are clustered within the homeostatic part of the pseudotime trajectory, APPtg-4M and APPtg-11M mice demonstrate a shift towards more activated microglia.
(left) representative photomicrographs of H&E stained tibialis anterior muscle sections from control and iNOS KO mice injected with or without LPS. Scale bars = 100 μm. (right) frequency histogram showing the distribution of muscle fiber minimum feret diameter in the tibialis anterior muscles from saline or LPS treated (top) WT control and (bottom) iNOS KO mice (n = 4). A total of 300 fibers per muscle were used for the analysis. Statistical comparisons, mean, and standard deviation of the mean are shown in the histogram legend.
Western blotting of N2a cell line that was transfected with AAV-PRKG2 for 48 hr. The blots were probed with anti-Ser259 (pMYRF) antibody. Note that overexpression of PRKG2 increased phosphorylation of N-terminal MYRF (nMYRF) in a dose-dependent manner.
E. ROCK1 and ROCK2 mRNA expression in human PDAC (n=146) from the TCGA research network. Significance (p value) of slope deviation from 0 determined by Deming regression.
The extreme C-terminal sequence of indicated secretory and mitochondrial proteins. The diGly, R__G and R_G_ motifs are labeled red.
5-week-old Sel1Lf/f and Sel1LAlb mice were injected i.v. once with AAV8-shCrebh or control AAV8-shLuc. qPCR analysis of hepatic growth-associated genes 5 weeks after injection (n=6 per group). Ribosomal L32, loading control for qPCR analysis.
B. Quantification of the MCAK/Uba2 signal ratio normalised to each non-targeting control of 4 independent experiments. Error bars indicate standard deviation, asterisks the p-value of a two-tailed unpaired Student's t-test comparing each Fbxw5-directed siRNA sample with the according non-targeting control (*P < 0.05, **P < 0.01, ***P < 0.001).
D and E. HeLa cells were co-transfected with the indicated FUNDC1-MYC and FLAG-DRP1 constructs for 24 h. Cell lysates were analyzed by immunoprecipitation using anti-FLAG and immunoblotted with anti-MYC and anti-FLAG antibodies.
Violin plots displaying the average log2(fold-change) in gene expression between DOX and noDOX conditions on the chrX in Xist FL, Xist ΔA and Xist ΔB+C at day 2 of differentiation; violin plots represent the distribution of the values, the horizontal band is the median, the lower and upper hinges correspond to the 25th and 75th percentiles; p-values were calculated using paired Wilcoxon test; n = indicates the number of genes analyzed.
I. Similar to F, coverage profiles for ChIP factor occupancy for a putative regulatory element on Chr 5 near Zfp932, targeted by Chr 12 trans caQTL, showed greater occupancy of POU5F1 and increased open chromatin compared to D2. Distal ca-QTL target region used for quantification is indicated by a black box with LOD score below.
(P) qRT PCR analysis with total RNA isolated from control and IRGM knockdown HT-29 cells transfected with siRNA combinations as indicated that were infected with CHIKV (MOI 1, 24 h).
Walking speed of 10-day old adult male flies of the indicated genotypes was calculated. Mean ± SD. Unpaired two-tailed t-test, biological replicates: Control, n = 185, OGT, n = 148, TDP-43, n = 177, TDP-43/OGT, n = 187.
N2a cells treated with siBin1, siCD2AP or siControl.(G) Endocytosed BACE1 detected upon 5 min pulse with M1 and BACE1-GFP (insets), analysed by epifluorescence microscopy. Scale bars, 10 µm.(H) The amount of endocytosed BACE1 per cell was quantified as percentage of siControl normalized to BACE1-GFP (n=3, NsiControl=86, NsiBin1=72, NsiCD2AP=113; mean ± SEM).(I) Recycled BACE1 detected at the plasma membrane of non-permeabilized cells with M1, upon a 10 min pulse, acid stripping and 20 min chase, and BACE1-GFP (insets), analysed by epifluorescence microscopy. Scale bars, 10 µm.(J) The amount of recycled BACE1 was quantified as in (h) (n=3, NsiControl=94, NsiBin1=58, NsiCD2AP=109; ****P<0.0001 siBin1 vs. siControl, t-test, mean ± SEM).(K) Non-recycled BACE1 detected in acid-stripped permeabilized cells pulse-chased as in (i) with M1 and BACE1-GFP (insets), analysed by epifluorescence microscopy. Scale bars, 10 µm.(L) The amount of non-recycled BACE1 was quantified as in (h) (n=3, NsiControl=61, NsiBin1=51; ****P<0.0001 siBin1 vs. siControl, t-test; n=2, NsiCD2AP=37; mean ± SEM).
E Western blot of overexpressed FLAG‐tagged Matrin3 and PTB, in control siRNA and PTB/nPTB siRNA‐transfected cells, probed with anti‐FLAG to detect overexpressed proteins, anti‐PTB to detect the knockdown levels and anti‐actin to confirm protein loading. A titration of control sample (lane 1-12.5%, lane 2-25%, lane 3-50% and lane 4-100%) is also included to assess the levels of knockdown. The band present above the PTB doublet in lane 6 is FLAG‐tagged PTB.
D) Representative Western Blot of cytosolic cyt c and SMAC in HeLa wt and HeLa BAX/BAK DKO cells upon staurosporine (STS) treatment and Shigella flexneri infection (Sf).
(C) Gene set enrichment analysis showing significant enrichment of a megakaryocyte progenitor (MKP, Lin-Sca1-Kit+Itga2b+Slamf1+) signature in STAT5 knockdown cells. CLP, common lymphoid progenitor (Lin-Sca1lowKitlowIL7r+Flk2+); preGM, pre-grenulocyte/macrophage progenitors (Lin-Sca1-Kit+Itga2b-FcgRlowSlamf1-Englow); NES, normalized enrichment score.
F. flp/FRT clones mutant for Rpp3018.2specifically in the germline (star) and/or the follicular cells (arrows) are detected by the absence of GFP. Magnifications show mutant oocytes with Orb mislocalization next to the karyosome (dotted circle) instead of being localized to the posterior, as seen in stage 3 (st.3) wild-type clones. Scale bar, 10µm.
A. CEM-GFP cells were pre-treated with 50 ng/μL of Vs for 15 min and infected with 0.1 moi of CXCR4-using HIV-1 (NL-4.3) and GFP fluorescence was measured at 488 nm as an indicator of HIV LTR activity. Vs treatment was repeated every 24 h for the experiment.
C Representative FACS plots of CD45+ CD4 T cells in the spinal cords of mice on day 12 of EAE. Cells were gated as single live CD45+.
D Immunohistochemistry for SOX9 and EpCAM (brown staining) on consecutive sections from severe (IS6) fibrosis and normal fetal liver at 18 weeks post-conception (wpc). Dual immunofluorescence confirms SOX9 and EpCAM in the same cell in severe fibrosis.
B. Morphometric analysis demonstrates a decrease in muscle fiber size of the wild−type control mice compared with sgk1tg transgenic littermates (p = 0.0015).
Immunoblot of BACE1 or GAPDH (loading control) from immortalized MEFs treated with a proteasome inhibitor (MG132) or a lysosome inhibitor (chloroquine; CQ).
(G) FRET ratio between STIM1 and SERCA2 in response to store depletion and its enhancement by ANO8. Data information: The first number in parenthesis indicates the number of similar experiments performed and the second number is the number of cells analyzed. All results are given as mean±s.e.m of the indicated number of experiments or cells analyzed, and difference were analyzed by unpaired t test.
RT-qPCR analysis of Syk expression in MEFs infected with shNC and shSyk viruses. n = 3.
A, B The oocytes were exposed to different concentrations of NO3- in N free MBS for 1.5 h at pH5.5. Net NO3- accumulation was fitted with both Michaelis-Menten and Linear Regression in A for high affinity range and Linear Regression in B for low affinity. Values are the mean ± SE (biological replicates: n=3) with 3-4 oocytes in each sample.
CHME3 treated with negative control, EB1 or CLIP170 siRNAs were either lysed and analyzed by WB Molecular weight markers (in kDa) are shown to the right of WBs in A.
Human peripheral blood mononuclear cells (PBMCs) were cultivated for 48h in RPMI containing 80mg/dl glucose (NC) and supplemented with 10mM beta-hydroxybutyrate (BHB). T cell stimulation was performed through CD3/CD28 Dynabeads at a bead:cell ratio of 1:8. C Confocal microscopy images of human CD4+/CD8+ T cells, stained with MitoTracker green, representative of two individual experiments.
Genome browser view of FUS gene, centered on altFUS. The 'Transcript' track contains the beginning of the canonical FUS transcript (ENST00000254108) in blue. The 'Protein' track contains the beginning of the FUS protein (green) and the whole altFUS protein (red). In G, the 'Peptide' track contains all the peptides identified by a peptide-centric approach. The peptides indicated matched better to at least one spectrum than any known protein, and are coloured in yellow if they matched better than any known protein with any PTM The peptides sequences are indicated and are unique to altFUS or its isoform.
G Immunohistochemistry staining of αSMA in primary skinfibroblasts isolated from healthy mice after treatment with TGFβ ± 4μ8C. Scale bars = 20 μm.
(B) Peak values of Ca2+ transients in MEFs transfected with PERK-ΔN or PERK shRNA. Error bars represent ±SD from six independent experiments.
A: Schematic domain composition of PBANKA_1317200, showing predicted ER signal peptide (red), apicoplast transit peptide (green), transmembrane helices (dark grey), NADP(H) binding (pink) and NAD(H) binding (blue) modules. Functional NTH domains I, II and III are indicated.
A The percentages of WT or Arhgap45−/− CD45.2+ cells (Key: left side) among CD45.2 + WT CD45.1 cells found in the BM of control and Arhgap45−/− competitive BM chimeras are shown. B The percentages of WT or Arhgap45−/− CD45.2+ cells among CD45.2 + WT CD45.1 cells found in the blood of control and Arhgap45−/− competitive BM are shown. C The percentages of WT or Arhgap45∆T/∆T CD45.2+ cells among CD45.2 + WT CD45.1 cells found in the BM of control and Arhgap45∆T/∆T competitive BM are shown. D The percentages of WT or Arhgap45∆T/∆T CD45.2+ cells among CD45.2 + WT CD45.1 cells found in the blood of control and Arhgap45∆T/∆T competitive BM are shown. E The percentages of WT or Arhgap45−/− CD45.2+ cells among CD45.2 + WT CD45.1 cells found in the thymus of control and Arhgap45−/− competitive BM chimeras are shown. F The percentages of WT or Arhgap45−/− CD45.2+ cells among the CD45.2 + WT CD45.1 cells found in mesenteric LNs (mLN) and spleen of control and Arhgap45−/− competitive BM chimeras are shown. G The percentages of WT or Arhgap45∆T/∆T CD45.2+ cells among CD45.2 + WT CD45.1 cells found in thymus of control and Arhgap45∆T/∆T competitive BM are shown. H The percentages of WT or Arhgap45∆T/∆T CD45.2+ cells among CD45.2 + WT CD45.1 cells found in mesenteric LNs (mLN) and spleen of control and Arhgap45∆T/∆T competitive BM are shown. Data information: Each dot represents an individual mouse and results in (A) to (H) are representative of two experiments with a total of 5-10 mice per group. Consistent with previous reports (Jafri et al, 2017), competitively transplanted mice exhibit a bias in favor of CD45.2 reconstitution. *P ≤ 0.033, ** P ≤ 0.002, *** P ≤ 0.001, **** P ≤ 0.0001; unpaired Student's t test. Mean and SD are also shown.
Heatmap showing the expression profile of cell proliferation-related genes in LIF-treated or control IECs (Ctrl) (K).
(A) Morphological phenotypes of transgenic plants over-expressing MEKK2-FLAG protein in WT and summ3-17 background. Line 1 and 2 express MEKK2-FLAG in WT background. Line 3-5 express MEKK2-FLAG in the summ3-17 mutant background. The photograph shows four-week-old soil grown plants. Expression of MEKK2-FLAG was detected by western blot using an anti-FLAG antibody.
(I) qRT-PCR results of RSK3 mRNA levels after knockdown of ZBTB7B in Daoy cells (n = 2). Data information: Mean ± SD, *P<0.05, **P<0.01, ***P<0.001 ****P<0.0001, one-way ANOVA.
Combined IF and DNA FISH for RAD54 (IF) and telomeres (FISH) in U2OS-TRF1-FOK1-WT or U2OS-TRF1-FOK1-D450A (nuclease dead) cells. Cells were treated as in E immediately prior to staining. Scale bars = 10 µm Quantification of data from F. RAD54 foci were detected using particle analysis in Fiji. At least a total of 300 cells were counted from 3 repeated experiments. Values shown are mean±sem. Values were compared using Kruskal-Wallis test followed by Dunn's multiple comparison test. Quantification of data from F. RAD54 foci were detected using particle analysis in Fiji. Cells were counted as positive if they counted 8 or more RAD54 foci that colocalized with telomeres. Values shown are mean±sem of n=3 biological replicates. Values were compared using standard two-way ANOVA followed by Sidak's multiple comparison test.
(H-I) THP-1 cells were treated with DMSO or 2-BP (50 μM) (H) or palmitic acid (100 μM) (I) for 12 h. Six hours after transfection with HT-DNA (2 μg/mL), cGAMP was extracted and quantified by cGAMP ELISA. Data information: 2-BP: 2-bromopalmitate Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.005; ***, P˂0.001
B MARS- or MARS2-catalysed HTL production from Hcy (20 μM) was carried out in vitro in the presence of different AHT concentrations. The amount of HTL produced in each reaction was determined by thin layer chromatography.