EMBO/sd-character-level-ner huggingface dataset:
D) Top panel: representative images of Western Blot analysis of proteins extracted from ACM and HC C-MSC cultured in GM, hybridized with anti-CD36 and anti-PPARγ antibodies. Immunostaining of the housekeeping GAPDH is shown for normalization. Bottom panel: d.a. of PPARγ (n=18 biological replicates) and CD36 (n=17 vs. n=16 biological replicates) levels, normalized on GAPDH (Mann-Whitney test). Data information: mean ± SEM. * p<0.05, ** p<0.01.
(A) summ3-1 mutation in At2g11520. Exons are indicated with black boxes, UTRs with empty boxes, and introns with lines.
Regions that show reduced KDM6A binding in Hnf1a-/- chromatin are strongly bound by HNF1A and are highly enriched in HNF1 motifs. P-values in (D) were calculated with two-tailed Mann-Whitney U test
After five days of culture, significantly more nonviable structures are formed upon influence of Ndrg4-/- ENS-derived medium.
(M) Glial cell viability following treatment with senolytic compounds (azithromycin, fisetin). Data are represented as mean ± SEM. n=3; Student's t-test. Significantly different at p=0.0073*,0.0018**, 0.0286#, 0.0269##, 0.0045### in graph M.
(a) Hippocampal tissues obtained from Nrf2 (−/−) (6 months old, one male and two female) or wild-type (WT) (11 months old, two male and one female) mice were immunoblotted with a Nrf2 antibody, 12E8, PHF1, a monoclonal to total tau (Tau5) or a polyclonal to total tau (Tau) antibody. The asterisk to the left of the Nrf2 blot designates the position at which a nonspecific band migrated. The relative molecular masses (kDa) are indicated to the left of each blot. (b) Bar graphs represent the relative optical density of phosphorylated or total tau in the hippocampal tissues. n=6 (These data are based on the mouse hippocampi immunoblotted in Supplementary Fig. 1). Data shown are mean±s.e. and were analysed using Student's t-test. (**P0.01; ***P0.001)
F, Western blot of BT308NS showing phosphorylation of Aurora Kinase A at the indicated time points after IR in the absence (5 Gy) or in the presence (5 Gy + JNJ) of JNJ38877605. Total Aurora kinase A is also shown. H3 was used as loading control. Veh: non-irradiated vehicle-treated cells.
C: Treatment of COCS with POM1 reduces the levels of PIKfyve starting 48h post treatment. Each dot represents an individual experiment. Statistics: Unpaired t-test. **: p<0.01.
Histogram representation of the BAFF‐R surface staining on mature B cells from Tam‐treated mb1‐CreERT2;Sykfl/fl (solid line) or control mb1‐CreERT2mice (dashed line). Splenic transitional B cells derived from the BAFF‐R−/−mouse strain served as a negative control (dotted line).
B In vitro kinase assay with EDC3 (0.2μg) and AKT (0.1μg). Samples were analyzed by Western blotting with the indicated Abs.
Western blot detection of ARS proteins in HEK cells stably expressing mascRNA (mascRNA), the mutants (Anti-Mut1 and Mut1) or the scrambled RNA (Scramble). β-Tubulin was used as a loading control.
(K) The cartoon summarizes the effects of individual GALNT isoform KOs on signaling networks and subcellular location of protein substrates based on differential phosphoproteomic and O-glycoproteomic analyses.
Double immunolabeling of SYCP3 (red) and the cohesin cofactors WAPL (green, in Pds5AB cKO spread spermatocytes at the indicated stages. Sex bivalents (XY) are indicated. Scale bar, 10 μm.
A. Rab25 expression decreases nutrient withdrawal (24 h) induced cell death in ovarian A2780 and IOSE29 cells measured using the Cell death ELISA plus assay (left); cells were cultured in complete media (containing 5% FBS), serum free media (SF), complete media plus 2DG, serum and glucose free media (SF-glu), or in amino acid, glucose and SF Earls buffer salt solution (EBSS). (a) p < 0.01 versus control and (b) p < 0.05 versus pcDNA. (Right) Percentage of apoptotic cells (sub-G0 population) by flow cytometry in A2780 cells following glucose and serum withdrawal (Glu/SF). (a) p < 0.001 versus A2780pcDNA control and (b) p < 0.05 A2780Rab25 versus A2780pcDNA control.
(B) Antibody blocking assay. NSC-34 and SH-SY5Y cells were pre-treated with anti-PRPH or anti-IgG isotype antibodies, followed by EV-A71 S41 infection at MOI 10 and 0.01, respectively. Culture supernatants were harvested at 24h.p.i. and titrated by plaque assay.
5-week-old Sel1Lf/f and Sel1LAlb mice were injected i.v. once with AAV8-shCrebh or control AAV8-shLuc. Western blot analysis (H) of Ucp1 levels in inguinal white adipose tissue (iWAT) 5 weeks post injection (n=3 per group, 2 independent repeats). Hsp90, loading control for Western blot analysis.
A) Binding of TDP-43 to GU-rich RNA promotes liquid properties of TDP-43 condensates, as shown by the fusion of small condensates into larger droplets. This fluidity is impaired by the loss of RNA binding affinity or disease-linked mutations that alter phase separation, such as M337V and A321G, which could explain increased TDP-43 aggregation.
B, SidP does not impair the kinase activity of MavQ in vitro. MavQ was preincubated with increasing amounts of SidP, and the kinase activity of MavQ was measured by the ADP-Glo assay (B)
(C-D) iMEFgt/gt stably expressing cherry-tagged WT STING or K288R STING and either ev or V5-tagged m152 were stimulated with ISD (10 µg/ml) or mock stimulated. At 4 hpi total RNA was extracted to determine IFNb1 (C) and IL6 (D) transcripts by qRT-PCR. Data shown is combined from three (C) or two (D) out of three independent experiments.
Misfolded proteins are deposited at cytosolic CytoQ and nuclear INQ compartments, while amyloidogenic proteins are sequestered at IPOD next to the vacuole. CytoQ formation depends on Hsp42. Misfolded, cytosolic proteins are imported through nuclear pore complexes by Sis1 and other, so far unknown sorting factors. Protein aggregation inside the nucleus is triggered by Btn2, which transiently accumulates upon stress. INQ is located adjacent to the nucleolus and harbors cytosolic and nuclear misfolded proteins. DNA replication stress causes formation of Btn2‐dependent non‐canonical DNA stress foci at the INQ and might signal to checkpoint controls.
A. Volcano plots were used to demonstrate differentially expressed genes as determined by RNA-seq in either MM047CDK7i-R vs MM047 (top), MM074CDK7i-R vs MM074 (middle) or MM074BRAFi-R vs MM074 (bottom). Red dots show significantly over-(top) or under-(bottom) represented mRNA in drug-resistant cells compared to parental cells. All data were evaluated with the DESeq2 R package. The value for a given gene is the normalized gene expression value relative to the mean of all samples belonging to the same condition.
Wildtype SIRT7, but not its RF mutant, restore cellular respiration in Sirt7-deficient MEF cells Respiration flux was determined as indicated (D). (mean ± SD, n=3 experimental replicates, *p<0.05; **p<0.01; n.s.=not significant unpaired two-tailed t test)
Quiescent G0-phase wild-type, PEX1−/−, and PEX14−/− hTERT-RPE1 cells transfected with AcGFP1-tagged D4 as a cholesterol probe were immunostained with anti-pericentrin (white) and anti-acetylated tubulin (blue) antibodies. Cholesterol was stained with Filipin III (red). Arrows and arrowheads indicate primary cilia and cytosolic accumulations of AcGFP1-tagged D4, respectively. Scale bar, 5 μm. Quantification of the Filipin III intensity at primary cilia from (E). PEX1−/− and PEX14−/− hTERT-RPE1 cells had significant reductions in the ciliary signal of Filipin III (***p<0.001: one-way ANOVA with Tukey's HSD, n=3: 40-50 cells per experiment). In the boxplot, medians, 25th/75th percentile and min/max were represented by the central lines, the box limits, and the whiskers/error bars, representatively. Quantification of the AcGFP1-tagged D4 intensity at primary cilia from (E). The ciliary signal of AcGFP1-tagged D4 in PEX1−/− and PEX14−/− hTERT-RPE1 cells was significantly diminished (***p<0.001: one-way ANOVA with Tukey's HSD, n=3: 25-30 cells per experiment). In the boxplot, medians, 25th/75th percentile and min/max were represented by the central lines, the box limits, and the whiskers/error bars, representatively.
(A) overexpression of FUS does not affect expression of VAPB, PTPIP51 or mitofusin-2. Immunoblots of spinal cord proteins from three 10 week old FUS transgenic mice and three age-matched littermates are shown; FUS was detected via its HA-tag. Tubulin was used as a loading control.
Quantification of immunoprecipitation results of Figure 5G from three independent experiments. Data from 3 independent experiments were plotted with Mean % ± SD. *< 0.05 p-value and calculated by two-tailed paired t-test.
(B) Phosphorylation states of STAT1 in response to Mtb stimulation in Socs6-/- BMDMs were examined by western blotting. Fludarabine treatment concentration was 10 μM and the treatment time was 24 hours. Representative blots from n = 3 biological replicates are shown.
Liposome co-sedimentation assay using recombinant ATG16L1 protein and sonicated liposomes. Supernatant (S) and pellet (P) were analysed by immunoblotting against T7 tag to detect ATG16L1. Quantification of percentage protein in the pellet fraction was calculated from 3 independent experiments (right panel).
Cell-cycle flow cytometric analysis using Ki67/Hoechst-33342 staining of the percentage of LT-HSC in the G0 phase after nucleofection of cKit+ cells using the AmaxaTM P3 Primary Cell 4D-Nucleoeftcor kit, (J) Cells were nucleofected with miR-Scramble (CTRL) or miR-1246 mimic (n=3) for 72 hours,
Representative Southern blots showing DSB repair products in WT, rad59∆, rad52-R70A and rad59∆ rad52-R70A cells. DNA was digested with Bsp1286I and probed with a MAT-distal sequence (yellow box in panel B).
(F) Opti-prep purified supernatants from (E) were incubated with SupT1 target cells for 4 hours and virus-cell fusion was scored by flow cytometry. Mean + SD of 5-10 experiments (each performed with virus produced from an independent transfection) is shown. (G) Virus used in (E) were used to infect SupT1 cells and productive infection was scored at 48-60 hours by immunostaining with the KC57 antibody and flow cytometry. Expression of pCMV-MxA served as a negative control. The mean + SD of 5-10 experiments is shown.
a, Quantification of NHS-biotin-labelled RBCs or transferred CMFDA-labelled RBCs (n = 3).
(B) Left Panel: EC50 values (concentration of ACE2 needed for 50% binding) for Alpha and associated mutations. Colour code corresponds to location on S protein functional domains and lower EC50 values signifies higher affinity to ACE2 binding. Right Panel: EC50 values for Beta and associated mutations. Data set for N501Y and D614G reference mutations are duplicated between left and right panels as mutations are common to both variants.
A. Surface representation of F-actin ADP model, five monomers marked as n series from pointed to barbed end. A phalloidin molecule (yellow stick representation) bound between three actin monomers is highlighted.
(A, B) Selected proteins involved in DNA (A) and RNA (B) maintenance of control (143B, solid lines, grey bars) and ρ0 cells (dashed lines, colored bars). A, for POLG, UNG and TWNK, only abundances >1 MDa were quantified. Plots and gene names are in corresponding colors. Data are presented as mean ± SD (n=4). *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001 (Student's t-test for individual proteins and two-way ANOVA for changes of multiple proteins in a complex).
B The effects of apyrase (40, 80 and 160 U/ml) infusion into cerebral ventricle on social interaction time (n = 8, 10, 10, 10 mice. Interaction F3, 34 = 3.917, P = 0.0167; Target F1, 34 = 0.0004, P = 0.9834; Drug F3, 34 = 2.295, P = 0.0954; For target, Apyrase 80 U/ml vs control, P = 0.0008, Two-way ANOVA with Tukey's post-test).
L. AP half-width recorded in Centrinone-B treated (n = 43 cells in 3 independent experiments) and control human iPSC-derived neurons (n = 59 cells in 4 independent experiments). Data information: Data represents mean ± SEM. Chi-square-test including post-hoc analysis with Mann Whitney test after-hyperpolarization *** p<0.001, ** p<0.01, * p < 0.05, ns p>0.05
C) The left panel contains the structure of the RG loopCENP-A binding site in the CA-CCpep-CNNT complex. R81CENP-A of the RG loop is recognized by CENP-N. The right panel displays a superposition of the structure of CENPC-CT in the CA-CCCT complex on the CA-CCpep-CNNT complex shown in the left panel. The model of CM peptide in the CA-CCpep-CNNT complex has been removed for clarity. The CENPC motif region in CENPC-CT is shown in pink. Structural collision between the CM downstream region of CENPC-CT and CENPN-NT is shown at the RG loop of the CENP-A nucleosome.
(C) Representative EM micrographs showing the morphology of mitochondria in siCtrl, siORP5 and siORP8-treated cells. Scale bar, 1 μm. (D) Quantifications of the number of mitochondria with altered morphology in the indicated siRNA conditions. % altered mitochondria ±SEM, n=25 cells and 632-710 mitochondria. *P<0,001 compared to siCtrl.
a-d, Representative 3D deconvolved MIP images from live imaging of Nrl.Gfp+/+ (green) P8 photoreceptors at DIV1-3, labelled with SiR-actin (red) (N = 7 independent cultures). Photoreceptors exhibit a variety of processes, including (a) neurites (blue arrow), (b) nascent inner segment-like protrusions (yellow arrow), and (c) short and (d) long (magenta arrows) actin+ve nanotube-like (herein termed PhNTs) connections; Scale bar = 5 µm;
Rhythmic Srsf10 productive mRNA levels (relative to Gapdh) were analyzed by RT-qPCR. For each clone, expression is normalized to time point 52h For Srsf10 two independently generated clones were investigated (∆E3 A and B). Statistical significance was determined by unpaired t-test and is indicated by asterisks: p values: **p<0.01, ****p<0.0001.
F. Schematic drawing of an NMD reporter whose transcription can be repressed by doxycycline addition to the culture
PLS regression analysis of codon usage of HTE (n=100) versus LTE (n=100) proteins at ( (TP 4 ( Visualized by scores. Eclipse in represents Hoteling T2 limit at p-value of 0.01 (F-test)
B. UTP6 in U-2 OS cells exemplify proteins localized to whole nucleoli (HPA025936).
A) Wild-type FUS localizes to the nucleus and binds, presumably in conjunction with other hnRNPs, its direct pre-mRNA targets to regulate splicing of minor introns. B) Mutations inactivating the NLS of FUS (= first hit) reduce the nuclear abundance of FUS, resulting in deregulated splicing of the direct targets (i.e. FUS-dependent minor introns), whereas other minor intron-containing mRNAs are not yet affected. C) Over time, due to repeated stress (= second hit), mutant FUS leads to the formation of cytoplasmic aggregates, which further reduces the amount of FUS in the nucleus due to trapping of wild-type FUS in these aggregates along with U11 and U12 snRNAs. This affects now not only the splicing of FUS-dependent minor introns, but leads to a general inhibition of minor intron-containing mRNAs due to the reduction of nuclear U11 and U12 snRNAs.
D Percentage of live animals raised on the indicated feeding RNAi (or empty vector control) bacteria assayed after 6-hour exposure to heat shock. 100% of control animals of the same genotype but not given heat shock survived. ***P<0.001, **P<0.01, *P<0.05, ANOVA, Tukey's multiple comparison test compared to wild type. N=3 trials. Error bars indicate SEM.
(F) Molecular model of the interaction between the ACP and the ER domains of ctFAS in cartoon representation. The model was derived from a rigid fit from (B) and subsequently flexibly refined for clash removal and interface energetics optimization.
The mRNA expression profiling on specific markers of stem cells (B) and transit amplifying cells captured on P7 incisors CLE followed by analysis using real-time RT-PCR (C). qRT- PCR results are in arbitrary values after normalization for GapDH. Statistics was performed on triplicates using one-way ANOVA followed by Bonferroni's test.
(B) Starvation‐induced protein degradation of Δatg8 harbouring the different mutants was tested as described above. API, aminopeptidase I; GFP, green fluorescent protein; mAPI, mature aminopeptidase I; pAPI, premature aminopeptidase I; WT, wild type.
(F) Left: Barbed end growth velocities (dots) in 1uM profilin-actin as a function of measured mCherry-WAVE1 surface density. NPF surface density was varied using varying amounts of dark mCherry competitor (see Methods). The red line is a linear fit to the data. Error bars are SD. Right: Surface mCherry-WAVE1 fluorescence and corresponding kymographs of barbed end growth for indicated examples.
D. Correlation of SARS-CoV-2 expression with ACE2 expression across all infected cell types from ileum organoids at 24 hpi. (n=146) Gray area represents the standard error to the fitted line.
[A] (This study) In phosphate (Pi)-sufficient plants, diacetyl (DA) partially suppresses the immune system including the production of reactive oxygen species (ROS), primes salicylic acid (SA) accumulation, and increases the competitiveness of GB03 against pathogens, resulting in enhanced symbiont colonization without compromised resistance to the pathogen Pst DC3000. As a result of the mutualistic association, plant growth is promoted. In P-deficient plants, DA simultaneously elevates the levels of salicylic acid (SA) and jasmonic acid (JA), resulting in strong activation of phytohormone-mediated immunity and consequently plant hypersensitivity to P deficiency. As a result, plants display stress symptoms.
(d) Lys 11 represents a tunable node through which curvature dependence of the lipidation reaction can be controlled. Lipidation assays were run as in b. Total GL1 lipidation was assessed from reactions with wild-type Atg3 or mutant forms of Atg3 in which position Lys 11 was changed as indicated. Lipidation efficiency on low PE/low curvature liposomes (30% PE, 400 nm) increases with increasing hydrophobicity of the new amino acid, while liposomes with high PE (55%) or high curvature (sonicated) are good substrates for all active forms of Atg3. Left: Coomassie gels of individual lipidation reactions. Right: densitometry of Coomassie-stained gels revealed the ratio of GL1-PE to the sum of all three GL1 species as in Fig. 2. Light grey bars are sonicated liposomes; dark grey bars are 400 nm extruded liposomes. For b,c, P values were calculated between sonicated and 400 nm samples of the same mutant. For d, P values represent comparison with WT protein on the same liposome size and composition. For all panels, n = 3 independent experiments, error bars represent standard deviation and **P 0.05; *P 0.01. Uncropped gels in Supplementary Fig. 7.
(A) Control HeLa cells or cells transfected with the indicated siRNAs were treated for 3 hr with cycloheximide, lysed, and incubated with agarose-bound wheat germ agglutinin to capture glycosylated membrane proteins. Total cell lysates (left) and lectin pull-down samples (right) were assayed by western blotting. The experiment was repeated three times, and representative data are shown.
C) Significance values from GSEA using combined CTNNB1 gene sets. Each treatment group was compared to tumor-free control transcriptomes. *FDR < 1e-5 determined, set to 1e-5 for plot.
(C) 786-0 cells were treated with or without aa starvation for 6 hours and then treated with CHX (1 μM) for the indicated times. The protein level of GDH1 was determined by western blotting (left), and the relative GDH1 protein levels were calculated (right). CHX: cycloheximide. Unpaired t-test was used. Data information: The data are represented as mean ± SEM of three independent experiments. The unpaired t-test were used (N.S.: not significant; ***p < 0.001).
qPCR analysis of glut1 and glut2 expression in WT, hs:dnYap and hs:Yap transgenic embryos heat shocked at 24 hpf and isolated at 30 hpf. n>3, *p<0.05, **p<0.01, ****p<0.0001, two-sided Student's t-test; values represent the mean ± s.e.m
(e) HE (left) and immunohistochemical DAPK1 (right) staining of adjacent brain sections. Compared with those in saline (top) and TAT-GluN2B-treated (middle) controls, TAT-GluN2BCTM treatment (bottom) selectively reduced infarct area (left) and DAPK1 levels (right) ipsilaterally. Black outlining delineates infarct areas as visualized with HE staining.
(E) Control or dBI‐1 knockdown adult flies were exposed to nutrient starvation and then animal viability was monitored over time for several days. In all, 100 individuals were monitored in each condition. Data represent mean and standard error (N=3). Two‐way ANOVA was used to analyse statistical significance between groups.
E tRNA-bound species of FLAG-tagged Sec61β from experiment shown in panel (D) were quantified and expressed relative to the value obtained for the control-depleted RRL. Shown is the mean with standard error of mean for n=4 biological replicates. Statistical significance was calculated using unpaired t test with Welch's correction. ns - not significant.
C Heat map of changes in relative mRNA abundance for genes encoding NMD factors, as determined from RNA-seq following transfection of HEK-293 cells with a siRNA that targets both UPF1 isoforms (UPF1total) or a siRNA that specifically targets the UPF1LL isoform.
Profile reporting the position of regions annotated "LTR" in RepeatMasker relative to PEs from the indicated tissues. Red and blue horizontal lines materialize the level of LTR density expected in a random sequence from pancreatic islets and human embryonic stem cell line HUES6, respectively.
3B) Transduced nt and PINK1 knockdown (kd) SH-SY5Y cells were cultivated either in RPMI+5% FCS or starved for 24 h and 40 h in HBSS. The LAMP-2 and actin content were determined by western blotting. A representative blot after 40 h starvation in HBSS is shown on the right. The relative LAMP-2 content of untreated cells was set as 1. Cells with stable PINK1 knockdown exhibited after 40 h a reduced LAMP-2/actin ratio compared to the nt cells; n = 4, p<0.05.
USP36 SUMOylates Nhp2 and Nop58 in vitro. In vitro SUMOylation assays were performed by incubating recombinant Nhp2 (F, G) or Nop58 (H) (0.1 μM) with SUMO E1 (30 nM), Ubc9 (50 nM), SUMO2 (4 μM) in the absence or presence of USP361-800 (50 nM, 1x; 100 nM, 2x) and/or ATP (2.5 mM) at 37ºC for two hours or the indicated times. The reactions were assayed by IB using anti-Nhp2 and anti-Nop58 antibodies, respectively.
(E) Position relative to the nuclear envelope (Zone 1 of the lacO-tagged GAL1-GAL10 locus in the indicated strains grown either 12h on glucose, or 90 min galactose or galactose + 0.2M HU. The third panel shows the relative retention at the nuclear periphery (Zone 1) on galactose + HU. The number of cells is >300 for each condition.
(F) GmLMM1 interacts with NbBAK1, GmBAK1a, and GmBAK1b. The indicated constructs were transiently expressed in N. benthamiana and the interactions were examined by Co-IP assays. Data information: The experiments were performed two times (F), as biological replicates, with similar results.
G, Enrichment of biological processes in altFUS interacting proteins compared to the Human mitochondrial proteome (Fisher's Exact test with FDR < 0.1 %). The number of proteins identified in each GO term is indicated next to the corresponding bar.
Microarray analysis was performed following doxycycline-regulated specific AR-V7 depletion (using a tet-plKO backbone) in 22Rv1 PC cells compared to doxycycline-treated shGFP controls. The genes that were significantly regulated by shAR-V7 (in either direction, p value < 0.05) were distributed among the gene modules defined by WGCNA in panel A. Upregulated genes (red) are those in which expression decreased following AR-V7 depletion and conversely downregulated genes (blue) are those that increased following AR-V7 depletion.
(C) Venn diagrams showing the total, positively and negatively regulated genesets identified by GSEA upon the loss of function of Prmt1 and β-catenin in Hoxa9-/- LSK-MLL-ENL cells.
(e) Production of IFN-γ and TNF in cells obtained 8 d after infection and stimulated ex vivo with various peptides (above plots), gated on total CD8+ T cells. Numbers in quadrants indicate percent cells in each.
(F). Kaplan-Meier survival curve of secondary recipient mice transplanted with Ctnnb1-/- LSK-MLL-ENL leukemic cells with vector control or shPrmt1. See also Appendix figure S6.