EMBO/sd-character-level-ner huggingface dataset:
j, Percentages of Tn (top), Tvm (middle), Tmem (bottom) among 60-wk-old or young mice (young KO, n=4; young WT, n=3; 60-wk-old KO, n=4; 60-wk-old WT, n=5).
(I) Densitometric quantification of the protein expression data Repression by ERS in the PP2 condition (average of 4 biological replicates) is shown relative to repression by ERS in vehicle condition. The bar graph shows means ± SD (standard deviations). One-sample t-test with BH correction for multiple testing was used to determine if the mean relative repression is statistically different from 100%.
e, Early suppression of mTORC1 signalling after birth was determined by immunoblotting of protein extracts from liver and heart of RagA+/+ (+/+), RagAGTP/+ (G/+) and RagAGTP/GTP (G/G) neonates immediately after Caesarean section (0 h) or after 1 h of fasting (1 h fast).
b) IOS analysis. ODI ± SEM of deprived animals treated with scr (N=5, black lines) and amiR-29a LNA (N=6, blue lines). Dashed lines connect pre- and post-MD ODI values of each animal. Solid lines represent the group average. Two-way ANOVA RM, treatment X time, p= 0.0074; post hoc Sidak's test, pre-MD scr vs post-MD scr, ns; pre-MD vs post-MD amiR-29a, p=0.0005.
F Structural comparison of H2A.B α2-α3 helices with their H2A counterparts. Structures of H2A-H2B dimer in the canonical nucleosome (yellow, PDB: 3LZ0) and H2A.B-H2B dimer in the H2A.B-NCP (orange) were superimposed for comparison. The dashed lines indicate the ~15 degrees kink of C-terminal region of H2A.B α2 helix.
Left: SMO-GFP reporter RPE cell line or RPE-1 wild type cells were infected with shGPR56strong or shLuc control followed by administration of doxycycline or the SMO agonist SAG as indicated. GPR56 KD significantly reduces the baseline and doxycycline induced SMO-GFP signal. Right: representative FACS histogram plots showing GFP intensity in shLuc versus shGPR56strong RPE cells with and without doxycycline. Unpaired t-test, bars and error bars represent mean and standard deviation of three biological replicates, *** p<0.0005, ** p<0.005, * p<0.05.
Analysis of cilia length in hTERT-RPE1 cells depleted of GEF DENND1B) and GAP (TBC1D10A regulators of RAB35. Cells transfected with indicated siRNAs were serum-starved for 48 h and stained for acetylated tubulin (acetyl. tub.) and DNA. Representative images are shown in (E). Regions within white boxes shown at higher magnifications to the right. Scale bars; 10 µm.
(C) Size distribution of the EVsin vivo in the CSF before (black; n=5) and 6 h after (grey; n=3) LPS treatment determined by NanoSight analysis.
A. and B. MTEC cultures were infected with a lentivirus expressing either GFP-GemC1 (GemC1) or GFP as a control and two days later transitioned to ALI culture conditions. Cells harvested at different time points during differentiation were co-stained with antibodies against GFP (green) to mark infected cells and endogenous McIdas(A) or Foxj1(B) (red). Arrows indicate infected cells that are McIdas or Foxj1 positive. Scale bars, 10 µm.C. and D. The percentage of infected cells expressing McIdas(C) or Foxj1(D) at each time point was quantified. Data are presented as the mean values of at least 10 independent fields obtained from at least two independent experiments for each condition. Error bars indicate ± SEM. *p<0.05, ***p<0.001. P-values were calculated by the non-parametrical two-tailed Mann-Whitney test.
a, b, Representative images of GFP-LC3 puncta (autophagosomes) in skeletal (vastus lateralis) (a) and cardiac muscle (b) from GFP-LC3 transgenic mice at serial time points after exercise. Scale bar, 20 µm. c, Quantification of data (mean ± s.e.m. of 10 tissue sections) in a and b. **P  0.01, ***P  0.001 (one-way ANOVA).
(D) cGAMP stimulation triggered EGFR-binding to STING. Raw 264.7 cells were transfected with cGAMP for 1h; cell lysates were immunoprecipitated with anti-STING antibody and analyzed by Western blot.
CFTR splicing assay was examined in cells expressing various TDP-43 constructs by PCR analysis. The numbers represented the relative ratios of exon 9 exclusion (-) vs. inclusion (+) (top panel). Both endogenous (endo.) and exogenous (exo.) TDP-43 protein levels in the indicated samples were examined by immunoblotting (bottom panel).
D, Double immunostaining for GFP and TH as a marker for dopaminergic neurons in the dorsal striatum of GFP-control, ALNe-218 and ALN-treated animals. Arrowheads indicate GFP+/TH- cells with neuronal morphology. No GFP+/TH+ cell could be detected in any of the experimental groups. Scale bars indicate 20 µm. Data information: Scale bars indicate 20 µm.
(G) Heat-map displaying the mean expression level of MMR genes (measured in TPM) in Gata6wt (n=10) and Gata6mut (n=3) SebC.
(B) Representative images and H3K9me2 nuclear signal intensity of HeLa cells transfected with the indicated siRNAs and either pEGFP-C1 (RNH1-) or pEGFP-M27 (RNH1+). At least three experiments were performed. The median of each population in a representative experiment with at least 100 cells per condition is shown. Boxes and whiskers indicate 25-75 and 10-90 percentiles, respectively. *p<0.05, **p<0.01, ***p<0.001 (one-tailed paired t-test). Black stars denote significant increases whereas red stars denote significant decreases.
c Dot plot showing dynamics of scaled intensities over time of selected phospho-sites associated with the keyword "Cell projection" (dots color-coded per cluster). The linear structure of the selected proteins with the corresponding regulated phospho-sites are depicted below.
(B) Quantification of radiolabeled polymers. Green columns are for the ERLAD-competent ATZNNN and ATZQNQ variants (see Fig. 3B, 3G, 3J, 3K), red columns are for the ERLAD-incompetent ATZQQN and ATZQQQ (see Fig. 3H, 3I, 3J, 3K) (mean, n=5 for ATZNNN, n=3 for ATZQNQ, n=4 ATZQQN and n=4 for ATZQQQ). Two-way ANOVA and Sidak's multiple comparison test, ns P>0.05, * P<0.005, ** P<0.01, *** P<0.001, **** P<0.0001.
Scatter plots of PD-1/LAG-3-expressing CD8 T cells after activation by A459-SC3 cells in a sample of G1 and G2 patients within CD28+ and CD28negative populations as indicated in the figure.
(D-F) RAW264.7 macrophages were treated with 1 mM LLOMe for 30 min. (D) Endogenous LRRK2 and (E) Rab8A recruitment to LAMP-1 positive compartments was visualised by immunofluorescence. Scale bar = 10 μm. (F) Quantification of D-E. Data represents the mean ± SEM of three independent biological experiments.
Protein blots of polyGln proteins expressed in transfected HEK293T cells with interrupted or pure polyGln repeats; EV: empty vector; n=3 transfections
(D) Relative mRNA level of sinhcaf in zebrafish PG, PV, EV, MV and FG follicles was measured using RT-qPCR. Data shown are mean ± SEM (n = 3, biological replicates). Data information: EV, early vitellogenic stage (early stage III); FG, full-grown stage (late stage III); MV, mid vitellogenic stage (mid stage III); PG, primary growth (stage I); PV, previtellogenic stage (stage II).
(F) Schematic representation of circSLC8A1-Ago2 complex binding and its effect on miR-128 targets.
E Immunoblotting of HEK293T cells co-transfected for 48 h with GFP-TLR7, plus HA-SHP2, HA-SHP2 mutant vectors, followed by immunoprecipitation with anti-GFP beads.
Engagement of the FcR by opsonized particles of multiple sizes and shapes (small or large beads, rod bacteria) commonly recruits the second messenger, NAADP, which activates TPC channels across the macrophage endo-lysosomal network. Local Ca2+ nanodomains around TPCs activate the Ca2+-dependent protein phosphatase, calcineurin (CaN), which dephosphorylates and thereby activates dynamin (Dyn-2). For clarity, only one dynamin-dependent event is shown (phagosome scission) but others are not excluded. TRPML1 Ca2+ nanodomains are only activated by large (6 µm) beads, a specialist secondary signal to additionally drive lysosomal exocytosis (via Synaptotagmin 7, Syn 7) and thereby provide supplementary lysosomal membrane (red-dashed lines) to the larger phagosome.
D qRT-PCR analysis of tiTERRA in cells carrying no tiTEL (CAF13), one tiTEL (CAF545) or two tiTELs (CAF110) cultured in EMM medium in presence or absence of Thiamine (THI; repressed and induced condition, respectively) for 24 h. RNA was reverse transcribed with oC and cDNA was amplified with oF3 and oR3 oligonucleotides to detect only tiTERRA (graph on the left) or with oF1 and oR1 oligonucleotides to detect simultaneously tiTERRA and natural TERRA (on the right). Values are normalized to ACT1 mRNA and expressed as fold increase over CAF545 in uninduced conditions (THI+). Bars and error bars are averages and SD from 3 independent experiments. * P < 0.05, ** P < 0.01 (relative to CAF545 THI+; two-tailed Student's t test).
SILAC-based proteomics data identify known (red) & novel (green) hypoxia-induced proteins in SW620 cells. One sample T-test was performed.
C) Cells were treated as in (B). Protein lysates were prepared and analyzed by SDS-PAGE followed by immunoblotting using the indicated antibodies (n=3). The dotted line indicates the juxtaposition of two non-adjacent lanes.
Micrographs collected in the GFP channel for each truncation (columns) of each studied MRP (rows) grouped by the N-terminus targeting properties based on theoretical expectation summarized in (B) with the MRPs possessing MTS-like N-termini in panel (C)
MPHs from Raptor flox/flox mice were infected with Ad-GFP or Ad-shDOCK5 or Ad-shDOCK5 + Ad-Cre. The lysates were immunoblotted with indicated antibodies or β-actin. The levels of DOCK5 and Raptor protein, and total and phosphorylated mTOR and S6K1.
C) Left panel: representative images of Western Blot of CD36, PPARγ and GAPDH protein expression of ACM and HC C-MSC protein extracts in AM supplemented or not with 20μg/ml 13HODE, 5mmol/L NAC or both (n=8 biological replicates). Right panels: d.a. normalized on the house-keeping GAPDH (Two-Way Anova). Data information: mean ± SEM. * p<0.05, ** p<0.01, *** p<0.001.
STK38 kinase activity is required and sufficient for nutrient-starvation induced autophagy. (D) HeLa cells were transiently transfected with siRNA targeting the 3'UTR region of endogenous STK38 (or with non-targeting siRNA (siNT)) and then transiently transfected with the indicated STK38 mutants expressing plasmids 48h after. The next day, the cells were incubated with DMEM or EBSS for 4 hours and overall p62 level was quantified for autophagy estimation (n = 3 independent experiments, mean ± SEM; ***p<0.001, ns, not significant, Student's t test).
C) Q-PCR analysis reveals a progressive increase in the YAP-TEAD target gene Ctgf in Lats1/2 dKO intestines at 3-days and 7-days post i.p. injection with tamoxifen, as well as similarly increased TEAD1 and TEAD4 expression, confirming that TEAD1 and TEAD4 are YAP-responsive genes. Notably, Axin2 and TEAD2 exhibit a mild but progressive decline over 3 to 7 days after Lats1/2 deletion, consistent with Axin2 being a known Wnt-specific target gene, and with Wnt signalling remaining active in Lats1/2 dKO intestines.
C: Representative images of FISH analysis with an RNA probe of ELDR (red) and DAPI staining (blue) in formalin fixed paraffin embedded OSCC tissue. An unrelated probe was used as negative control. Magnification: 40X; inset magnification 100X and scale bar 10 µm.
A) Hierarchical clustering of the Pearson correlation coefficients of transposon insertion profiles for gene pairs. Insets show clustering of the IRA1/IRA2 and SWC3/SWC4 gene pairs (bottom inset, black arrows) and high correlation of the SYS1/GEF1/SPF1 cluster with DRS2 and MVP1 (top inset, blue arrows).
(B) Gene set enrichment analysis (GSEA) of expression changes induced by Vitamin C treatment, for genes upregulated in Treg cells vs conventional T cells (GSE7460, left panel), genes upregulated in WT Treg cells vs CD4+ naïve T cells (our data, middle panel) and genes upregulated in WT Treg cells vs Tet2/3 DKO Treg cells (our data, right panel), presented as enrichment score (Y-axis) and overlap of genes from each set (X-axis, shown on the bottom) with genes expressed higher in TGFβ + VitC and TGFβ + RA + VitC compared to TGFβ alone and TGFβ + RA, respectively. Data are from two biological replicates.
G. Wnt inhibition reduces the expression and protein levels of HR and FA pathway genes in a Wnt-addicted colorectal cancer patient-derived xenograft. Mice with CRC PDX driven by a RSPO3 translocation were treated with vehicle or ETC-159 for 56 hours before harvesting. (G) Tumor lysates were analyzed by SDS-PAGE and immunoblotted with the indicated antibodies. Each lane represents an individual tumor.
(A) Flow chart illustrates A151 administration and experimental design. Mice received daily intraperitoneal (IP) injections of A151 (300μg) or an equal volume of phosphate-buffered saline (PBS) vehicle for 3 consecutive days starting immediately after reperfusion.
Representative fluorescence pictures and quantification (below the fluorescence pictures) of dissected adult gonads relative to the number of mitotic cells from wild-type animals fed bacteria transformed with either vector expressing dsRNA against gfp (con) or frh-1 and stained with DAPI (blue) and either anti-PARP-1 (red) (A Scale bar: 20µ (A Data information: Data are presented as mean ± SD. For each panel N=2, 8-10 worms per replicate and condition
C, Transcriptomic signature indicative of PI3Kα activation in the same cohorte. Genes whose expression is increased only in metastatic patients are underlined. The unsupervised hierarchy of each sample is shown in the top part of the figure; the unsupervised hierarchy of genes is shown on the left; the list of genes is detailed on the right. Blue=low expression, Red=high expression.
C: Cal27, JHU029 and JHU022 cells were transfected with control or ELDR siRNA (50nM), and cell proliferation was analyzed at the indicated time points. n = 3 biological replicates. Data are represented as the mean ± SD,
As in B and C but with transfection order reversed (green =Cry1 expression in ProkR2+ cells only, n=6) (p=0.006; baseline vs. ProkR2.Cre *p=0.03, baseline vs. ProkR2.Cre and Prok2.Cre **p=0.009, ProkR2.Cre vs. ProkR2.Cre and Prok2.Cre ns. p=0.1).
C. (left) Jurkat cells were treated for 24 h with H2O2 (50 μM) or PMA/ionomycin (200 + 300 ng/ml). Basal and phospho-active form of ATM, and GSNOR were assessed by Western blot. Vinculin was used as loading control. (right) Phospho:basal level ratios of ATM along with densitometry of GSNOR immunoreactive bands are expressed as arbitrary units. Values shown represent the means ± SD of n = 3 independent experiments. *, p<0.05.
(F-I) Functional gene annotation of altered cellular pathways in (F) TAM-MG, (G) TAM-MDM, (H) TIL-CD4 and (I) TIL-CD8 compared to control cell types from tumor-free animals. Cutoffs: basemean >20 and adjusted p-value (padj) <0.05. Adjusted p-values were obtained by Wald test and corrected for multiple testing using the Benjamini and Hochberg method. All DEGs based on padj were subjected to analysis.
Relative expression of Oct4 and Sox2 after hnRNPLL overexpression. The data represent the means ± SD (n=3, from biological repeats). ***P＜0.001. T-test was used to determine the significance.
A, B Schematic diagram of Drosophila (D. melanogaster) CYLD (dCYLD) and human (H. sapiens) CYLD (A), and a multiple amino acid sequence alignment of a catalytic region of the ubiquitin carboxyl-terminal hydrolase (UCH) domain in different species (B). dCYLD is 639 amino acids in length, and contains one cytoskeletal-associated protein-glycine-conserved (CAP-Gly) domain (Red) and the UCH domain (Green) (A). Human CYLD is 965 amino acids in length and contains three CAP-Gly domains, an unstructured phosphorylation region (Phos-site (Pink); specific for CYLD chordata species), and a UCH domain (Green). A conserved active Cys (C284 in Drosophila) is indicated by * (B).
The abundance of individual lipid classes (mean ± SEM) within the set of six membrane GL and GPL extracted from 4DO fat body samples. w- n = 7, dTorKO n = 7, dLap1-/- n = 4. One-Way ANOVA with Bonferroni's post hoc test. * p < 0.05 and ** p < 0.01.
(K) iWAT weight of C57BL/6J and ADX mice 6h after normoxia or hypoxia. N = 5-6 per group. Data information: All bars represent mean ± SEM. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. ****P<0.0001, ***P<0.001, **P<0.01, *P≤0.05.
Western blot analysis of MsrB2, pp53(S15) and LC3 I/II in Meg-01 cell after 25 mM HG treatment for 24 hrs. GAPDH was used as the loading control. Quantification analysis on individual groups. GAPDH served as the loading control. (MsrB2: shCon/HG vs. shCon; **p=0.0017, shMsrB2/HG vs. shCon/HG; *p=0.0189, pp53: shMsrB2/HG vs. shCon/HG; *p=0.0317, LC3II: shCon/HG vs. shCon; *p=0.0215, shMsrB2/HG vs. shCon/HG; *p=0.0158, n=3) The nonparametric t test was performed for comparisons of 2 groups. Analysis was performed with Prism software (GraphPad Software, Inc, La Jolla, CA). A difference of P<0.05 was considered significant.
(C) T47DML cells treated or not with hormone were subjected to micrococcal nuclease (MNase) digestion of chromatin followed by high-throughput paired-end DNA sequencing (MNase-seq). Snapshot of the genome browser for the BCAS1 gene is depicted. The expected MNase protection pattern around the TSS and gene body is observed and coincides with regions enriched in H2A.Z, H3K27ac and H3K4me3.
B. Average speed of salivary gland sporozoites. Data points represent individual sporozoites of 3 independent biological replicates. Shown is the mean ± SEM. P-values are calculated using the Kruskal Wallis test followed by the Dunns multiple comparison test.
G. Chromatin immunoprecipitation (ChIP) of wild-type plants and PROSOG1:SOG1-Myc lines and anti-MYC antibody. The promoter region of CYCB1;1 is enriched in SOG1-MYC after cisplatin treatment.H. Structure of genes tested by ChIP with an antibody anti-MYC in PROSOG1:SOG1-Myc and wild-type plants. Red arrowheads indicate the primer binding sites for PCR. A total of four regions were tested as indicated by arrowheads. Asterisks indicates significant differences within a 5% confidence interval (Student's t-test).
E) Overexpression of GFP-TDP-43 variants with different mutations that either block (CC and AA mutation, red labels) or mimic phosphorylation (DD and EE, green label) at S403/404 or S409/410 in motor neuron-like NSC-34 cells. Western blot showed a specific signal for total TDP-43 (top panel), TDP-43pS403/404 (middle panel) and TDP-43p409/410 (lower panel) and load control SOD1 (bottom panel).
Experimental strategy of the laboratory selection experiments: an sRNA library was generated using the rybB scaffold with nine randomized nucleotides at the 5' end, cloned into a broad-range plasmid backbone, and transferred into V. cholerae ΔrpoE cells. These colonies were pooled, grown to OD600 of 0.2 and treated with ethanol (3.5% final conc.) for 6 hours. Surviving cells were recovered on agar plates, pooled and subjected to another round of selection (3 selections total). After each selection, the plasmids of surviving cells were analyzed using high-throughput sequencing.
B. Quantification of phosphorylation events in response to TNF-α stimulation. The bar chart shows the fraction of phosphorylation sites that were differentially regulated upon TNF-α stimulation.
(e) The proportions of EGFP-positive cells with EGFP-HDQ74 aggregates in wild-type (Atg5+/+) and knockout (Atg5−/−) Atg5 MEFs, transfected with EGFP-HDQ74 for 4 h and then treated for 48 h with drugs (all 1 μM) or DMSO (control). Error bars show 95% confidence interval. ***P 0.001; **P 0.01; *P 0.05; NS, nonsignificant.
(A) Maternal behavior can be induced in female mice, which have never been exposed to pups (naive females) by repeated social exposure to pups (trial 1-5). Virgin female mice start to retrieve pups and engage in maternal care responses (pup grooming, crouching, nest building), thereby becoming attached to the nest location as indicated by the tracking path.
(D) WB analysis of the polyubiquitination of GP130 in HEK293T cells co-transfected with Flag-GP130, Myc-NEDD4L, HA-Ub or its mutants expressing only one lysine (K-only), respectively, which followed by denaturation-IP with ANTI-FLAG M2 beads and WB analysis with anti-HA antibodies.
(F) Vinculin was knocked down as described in (D) and the levels of vinculin and YAP target gene expression was analyzed using RT-qPCR (Mean ± SD; n=3; ***P≤0.001, ****P≤0.0001, T-test).
(D) Immunoblotting analysis of ubiquitin ligases and proteasomal subunits in XO8 GSCs and XO8 GSC-derived cells in the course of differentiation (P1-P7). (E) Similar to (E) except that XO6 GSCs were used.
Matrix showing significant overlap of stringent specific phenotype mutants (p-value < 0.05; significance was determined using Fisher's exact tests). Circle size corresponds to the log value of the overlap odds ratio. Orange circles denote same-compartment phenotype pairs. Dark blue fill colour indicates phenotype pairs with at least one enriched protein complex in the overlapping set. LE: late endosome.
Expression of CALIC in primary skin tumors (P) and their metastases (M). Expression of CALIC in primary skin tumors of patients without (w/o) or with (w) metastases.
(A) GFP-PAQR3 transfected HeLa cells were fixed for immunofluorescence staining with indicated antibodies before or after glucose starvation (GS) for 4 h. The nuclei were stained with Hoechst 33342. Scale bar: 10 μm.
GPS reporter cells expressing peptide libraries ending with a random (X) or Gly (G) residue were treated with dominant-negative (DN) cullins and analyzed. Data are presented as mean ± standard deviation from nine replicates. GPS reporter cells carrying indicated libraries were treated with shRNAs against various BC-box proteins and analyzed. VHL and FEM1C serve as unrelated BC-box protein controls. Data are presented as mean ± standard deviation from nine replicates.
(D) TMEM59 ID (amino acids 263-323) suffices for HA-LC3A lipidation. 293 cells were transfected with the indicated CD16:7 chimera (Control: empty chimera) and vectors encoding HA-LC3A and GST, subjected to aggregation with the shown amounts of anti‐CD16 antibody and lysed for western blotting. The right panel shows control WBs demonstrating equal loading (ACTIN), transfection (GST) and chimera expression (CD16) in unaggregated samples, as all experimental points per chimera derive from a single transfection.
A, B A bidirectional transcription module at the MpFGMYB/SUF locus acts as a toggle switch between male (A) and female (B) sexual differentiation in M. polymorpha. MpFGMYB expression is activated by one or more unknown cues associated with reproductive growth. In males, MpFGMYB expression is suppressed by constitutively expressed antisense SUF, allowing an unknown factor (M) to activate both autosomal and Y-chromosomal genes to promote male differentiation (A). A dominant "Feminizer" on the X chromosome directly or indirectly suppresses SUF expression, allowing expression of MpFGMYB and downstream autosomal and X-chromosomal genes to promote female differentiation (B). Genes on the X and Y chromosomes are dispensable for the sexual morphologies of the gametophytes, but required for the differentiation of functional gametes. C In A. thaliana, three FGMYB genes promote female differentiation in the embryo sac, a highly reduced female gametophyte of flowering plants. FGMYB expression is regulated at the transcriptional level after the formation of sporophytic female floral organs
X and Y chromosome mapping. Genes with high expression (up) are shown in orange and low expression (down) are shown in blue. The defined ratio of up or down genes is > 1.5 and < two-thirds, respectively. The comparison is (each female vs the average for males) or (each male vs the average for females). The location controls for the expressed genes (exp. genes) on the X-chromosome and Y-chromosome are plotted (red squares) for genes whose FPKM averages were above 1 for females or males.