EMBO/sd-character-level-ner huggingface dataset:
Monoculture experiments were performed to determine species' growth rates and lag times for each two-resource environment. For each pair of species, coculture competition experiments were performed in each two-resource environment, and qualitative competitive outcomes were determined There were 44 competitions in which both species could be assigned growth rates and lag times Each point represents one competition. Pie charts summarize the competitive outcomes for cases in which the slow-grower was the fast-switcher (above the Δtlag = 0 line) and in which the slow-grower was not the slow-switcher (on and below Δtlag = 0).
Experimental set-up: co-application of recAPPsα or CTα16 and BTX before LTP induction. Peptides and BTX inhibitor used for pre-incubation circulated throughout the whole LTP recording.
[A] DA induces genes involved in SA biosynthesis and signaling in Arabidopsis grown with Pi deficiency. Data information: qPCR results show values of means ± SE (n=3), two biological replicates were analyzed with similar results. Different letters denote significantly different means at p < 0.05, Tukey's multiple comparison test.
(D) GFP-LC3B immunoprecipitates endogenous FYCO1 from HeLa cell lysate. HeLa cells expressing GFP or GFP-LC3B were lysed and processed as in B. IP, immunoprecipitation; MM, molecular mass; WB, Western blot.
(G-I) FACS analysis of dormant (claret+) RM1 BD Irf- and RM1 BD Irf7 OE cells from bone at (G) day 11 post-IC injection (n = 4 per group) and (h) day 17 (n = 4-6 mice group/time point) with (I) D17 active (claret-) colony quantitation (mean +1) determined by multiphoton imaging and IMARIS interrogation (n = 9 bones from 3 mice per condition). Median shown. Upper and low box hinges denote first and third quartiles. Whiskers mark value limits.
E Time-lapse imaging of liquid droplets fusion after mixing 40 μM cGAS-mCherry with 10 μM G3BP1-mEGFP. Data information: Representative images are shown Scale bars 3 μm (E)
(A) VAMP7, Vti1b and syntaxin 7 distributions in endo‐lysosomal membranes from MSD, MPSIIIA and WT MEFs was evaluated by immonoblotting analysis of gradient fractions. To simplify the analysis the DRM, the intermediate‐I, the intermediate‐II and soluble fractions of the gradient were pooled separately and then subjected to immunoblotting. SNARE distribution was also analysed after loading WT cells with cholesterol and after MβCD treatment. In MSD and MPS‐IIIA MEFs, all analysed SNAREs abnormally accumulate in DRMs of lysosomal membranes. Cholesterol modulation results in a change of SNARE distribution.
(G) Immunofluorescence images of PDAC tissues from KPC mice treated with vehicle control and 5mg of tamoxifen, scale bar 100 μm
(A) The simplified biochemical network comprises amino acid biosynthetic and respiratory pathways in central carbon metabolism and a specialized metabolic pathway, aliphatic glucosinolate biosynthesis, studied in this paper.
Aci2 and Pa were both grown in monoculture in the two-resource environment. The same data is shown in both plots. The left plot shows the average of eight technical replicates on a log scale, while the right plot shows each of the replicates on a linear scale. Overlain on the left plot are growth rate fits of gAci2 = 0.88hr-1 and gPa = 0.67hr-1. Data Information: Data in A were collected at 400nm.
E) HeLa cells were co-transfected with 3'UTR TFG siRNA together with HA-TFGwtLIR or an empty vector (EV) or TFGmutLIR3 plasmids, expressed at near endogenous levels. Cells were cultured with complete (FED) or starvation (STV) media and grown in presence or absence of CLQ for 1h. ACTIN and LC3B-II protein levels are shown. Densitometry analysis of LC3B-II over actin for indicated conditions is shown in the graph (right). Data are mean value ± SEM. Statistical analysis was performed one-way ANOVA followed by Dunnett's multiple comparison test. *, P<0.05. (n=3 independent experiments).
(H) Immunoblot of lysates of peritoneal macrophages isolated from wild-type and Galectin-9 KO mice stimulated with AG (1 μg/ml) for indicated times. Data are representative of n=3 independent experiments.
(A) The TVKS/T-motif has been conserved throughout metazoan evolution. The phospho-acceptor sites are indicated in red, the DFG- and APE motif flanking the activation loop (AL) are indicated in blue. Residues differing from human B-Raf are shown in grey or in red/blue with reduced intensity.
C. Immunoblot analysis of phosphorylated (p-) TBK1, IKKi, IRF3, P38, JNK1/2, ERK1/2 in peritoneal macrophage transfected with RKIP-specific or scrambled siRNA, followed by infection with VSV (MOI, 0.1). β-actin was used as a loading control.
A. MDCK cells were cultured on cell culture inserts for 4 days. On the last day, the culture medium was replaced with serum-free medium. sEVs released from the apical and basolateral sides of MDCK cells were purified by ultracentrifugation. Apical and basolateral sEVs (P100) were analyzed by silver staining.
FACS histogram plot (left) and summary bar graph from three replicate wells (right) showing reduction of GPR56 surface expression on the GPR56 positive AML cell line HEL only in conditions that contain the more specific CDK7 inhibitor YKL-5-124, but not those that contain only the specific CDK12/13 inhibitor THZ531. Unpaired t-test, bars and error bars represent mean and standard deviation of three individual treatments, *** p<0.0005, ** p<0.005, * p<0.05.
qRT-PCR gene expression analysis showing the fold-change of select DNA-damage response-genes panel in Molm-14-xenograft-derived: Cells from W1 plating, n=4, Data indicated by bars of fold-change calculated relative to matching controls, normalized to the endogenous control Gapdh and presented as means ± SEM.
a, b, Oral glucose tolerance test (OGTT) before (a, week 0) and after (b, week 4) 4 weeks of HFD.
(A) Spinal cord sections of mice overexpressing SODWT and SODG85R (disease end‐stage) were immunostained for BAG3 and SOD1. Arrows indicate SOD1‐ and BAG3‐positive aggregates in the neuropil. Scale bar, 20 μm.
Immunofluorescence microscopy and quantitative analysis for colocalization of M.tb with markers LC3 in Mavs -/- BMMs. Quantitative data are the mean ± SD of three independent infections and all data shown are representative of at least three independent experiments. Scale bar, 5 μM. n.s., not significant; * p < 0.05 , ** p < 0.01 and *** p < 0.001 by two-tailed Student's t-test.
and activity measurements (C) of culture supernatants from GAS strains 188, 188NADase-, and 188NADase(G330D).
The table shows parameters of mass spectrometry identification of CtUba4C202K and CtUba4C202S with lists of detected peptides containing the K-ε-GGH remnant motif of Urm1. In CtUba4C202K, the conjugation site on K202 was confirmed. In the TBH treated samples of CtUba4C202S several potential conjugation sites were found. We present only high confidence peptides reaching a Mascot score higher than 40, which were detected in all analyzed samples. Asterisks indicate ambiguous site localization of K-ε-GGH. #PSMs: number of peptide-to-spectrum matches; m/z: mass to charge ratio of precursor ion.
% of γH2A.X foci -positive nuclei (E) in α-actinin positive CMs from C57BL/6 mice. Data are mean ± SEM of n=4-7 mice per age group. 100 α-actinin positive CMs were quantified per mouse.
A) A pedigree of a Hodgkin Lymphoma family with POT1 Y36H mutation (adapted from and previously published in McMaster et al., 2018). More details of the subjects are listed in Appendix Table S1.
E. PolyQ proteins were expressed for 24 h before survivors were counted. Mean values and standard deviations from three independent experiments are shown.
(A) Schematic of the PIDD1 domain structure and of the different PIDD1 species generated by autoproteolysis. LRR = Leucin Rich Repeat Domain; ZU5 (N and C) domains = Domain present in ZO-1, Unc5-like netrin receptors and in ankyrins; UPA domain = conserved in UNC5, PIDD, and Ankyrins; DD = death domain.
D, Immunoblot analysis of protein lysates from ARPE-19 cells expressing TFE3-GFP-WT or mutants run under non-reducing condition.
G. Quantification of signal intensity of lamin B1 immunoreactivity in different neural cell types. F (3,82) = 173.1, P = 1.2 e-34, n = 12-30 cells per cell type, one-way ANOVA followed by Tukey-Kramer test (**P < 0.01).
D. Pro-caspase-3 (Pro-CASP3) and activated caspase-3 (CASP3) expression analysis in GICs by immunoblotting. 2 µM rottlerin (Rott) inhibits prazosin (PRZ)-induced caspase-3 activation. V: vehicle. kDa: kilodaltons.
F: RAM, The number of memory errors increased in all groups with the numbers of baits already collected. This increase is considerably stronger in NexCre cTKO animals. [geno F(1,16) = 35.56, p < 0.0001; bait F(2,32) = 85.05, p < 0.0001 ; bait × geno F(2,32) = 3.138, p = 0.0570].
Single cell tracking analysis upon stimulation with Gas6 over 12 hour of Empty "E" or OPCML "O" (A) SKOV3 cell
G-I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV-1 BaL and DNA isolated 18 h post‐infection for qPCR.2LTR circles. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05, paired t‐test).
Relative SIE-(I) activities in Stat3-/- MEFs transfected with EV or the indicated STAT constructs and treated with LIF for 8 hours.
(F) RNA expression changes of selected genes associated with differential SEs. Top: genes significantly (FDR < 0.05) up-regulated by SEs in CLL. Bottom: Genes significantly down-regulated by SEs in CLL.
A. De novo protein synthesis measured by puromycin incorporation in shSCR, hTrmt13 knockdown cells (sh-1 and sh-2), and sh-1 with stable expression of wild type hTrmt13 (sh-1+hTrmt13) or enzymatically-inactive hTrmt13 (sh-1+E463A). Puromycin-labeled proteins were detected by immunoblotting. Representative images (left) and statistical analysis (right) are shown. Knockdown and overexpression efficiency of hTrmt13 in MDA-MB-231 verified by Western blots. Data information: Statistical analysis was performed using t-tests, and error bars represent mean ± SD for three independent experiments.
(A) Immunoblotting against the GFP or the GAPDH of proteins extracted from HEK293 cells transfected for 24 hours with 80 G4C2 repeats embedded in the human sense C9ORF72 and fused in all three possible frames with the GFP deleted of its ATG.
A) The ERMIT-based validation of the complex formation between AGR2 and LYPD3 or CD59, but not OS9. The monomeric AGR2 E60A was used as bait, while LYPD3, CD59 and OS9 were used as prays (n=6).
(E) Representative Western blot of IRP2 in mouse gastrocnemius and densitometric quantification (n=5). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001.
E and F) K562Mpl‐mKO2 cells submitted to the Duolink reaction. White arrow heads are pointing at example of Duolink positive reactions at the plasma membrane, while green arrow heads are pointing at positive Duolink reactions within the cytoplasm. Nuclei are labeled with Hoechst and scale bars = 5 µm. R: Pearson's correlation coefficient.
(B) Cumulative tube length for HUVEC recipient cells following treatment with 104 EVs isolated by UC from glutamine-replete and -depleted HCT116 cells or with vehicle (PBS). Both EV preparations promote tubulation, but the network is more stable with EVs from glutamine-depleted HCT116 cells.
(b) Denatured extracts from HEK293T cells stably expressing either FLAG-tagged wild-type p85β or FLAG-tagged p85β(Y655A) were immunoprecipitated (IP) with either an anti-FLAG resin or a 4G10 platinum resin and immunoblotted (IB) as indicated. Immunoblots of whole-cell lysates (WCL) are also shown in the last two lanes.
(e) LC3 puncta in Cx43−/− MOBs transfected with constructs coding for different forms of Cx43 (full length, CT, ΔCT258 or ΔCT245) tagged as indicated in the scheme. Left: Representative images. Merged fields (left) and LC3 channel in reverse black and white (right) are shown (images of GFP-Cx43 are shown in Fig. 2f). Right: Quantification of the average number of LC3 puncta per cell (n = 3 wells, 3 independent experiments, >50 cells per experiment).
Panel (F) depicts how many of the plants were harvested on different days (DOH), belong to different SNP subgroups or were RNA-sequenced in different batches. This panel also displays the variability in two discrete phenotypes, namely the number of leaves at harvest and whether or not leaf 16 was kinked. Panel (G) shows violin plots for the distribution of the coefficient of variance (CV) across the sampled plants for the levels of individual transcripts and metabolites. For visualization purposes, the transcript CV was capped at 2.0. Data information: In all violin plots, the median is indicated by the white circle. The black box extends from the 25th to the 75th percentile, and black whiskers extend from each end of the box to the most extreme values within 1.5 times the interquartile range from the respective end. Data points beyond this range are shown as black dots. The red open circle indicates the mean of the distribution, with red whiskers extending to 1 standard deviation above and below the mean.
Histogram of axonal (blue) and dendritic (purple) DCV fusion events upon repetitive electrical stimulation (16x50AP at 50 Hz).
(A) Phylogenetic tree of GNAT candidates from Arabidopsis thaliana (black letters), Saccharomyces cerevisiae (orange letters), and Escherichia coli (green letters) containing the acetyltransferase Pfam domains (PF0058, PF13302, PF13508, PF13673) GNAT family sequences were aligned with ClustalW, and a phylogenetic tree was designed by applying the Neighbor-Joining method. Bootstrap analysis was performed using 2000 replicates, whereby the resulting bootstrap values (values ≥ 20) are indicated next to the corresponding branches. The tree specific topology was tested by Maximum-Parsimony analysis. GNAT candidates with a putative organellar localization (TargetP1.1) were highlighted with a green background and named as GNAT1 to GNAT10 in relation to their position in the phylogenetic tree. Squares, triangles and circles describe the specific acetylation activity, which was reported in literature. The metabolic activity of GNAT2 corresponds to serotonin acetyltransferase
F Colocalization by immunofluorescence of Hwa (green signals) with lysosome (LAMP1, red signals) in Hela cells. Cells were co-transfected with Hwa-Flag, and ZNRF3-HA or ZNRF3ΔRING-HA. Magnification, 100 ×; scale bars: 10 μm.
A-C. Wild type embryos injected with control MO or with shox MO. C. Expression of col2a1 at 55 hpf was examined by in situ hybridization in wild type embryos injected with control MO and with shox MO. Arrow and dotted line indicate the pectoral fin.
BMDMs were treated with palmitic acid (0, 100 μM, or 200 μM) for 12 h and transfected with HT-DNA (2 μg/mL) for 6 h before RT-qPCR analysis of Ifna4 (K), IFNb1 (L) expression. Data information: 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
E Effect of GSK-J4 (40 μM), a specific KDM6A inhibitor, on high glucose-mediated changes in levels of nephrin, WT-1 and H3K27me3. *P < 0.05 versus normal controls, #P < 0.05 versus untreated HG-incubated cells (Parametric ANOVA and a Bonferroni post hoc test; n = 3).
A Sec63-mNeon images of the cortical ER of WT and Δice2 cells harboring the inducible system (SSY1405, 1603). Cells were untreated or treated with 800 nM estradiol for 6 h.
YAP knockdown was sufficient to induce caspase-3 activation/PARP cleavage in hypoxia and was not further enhanced by GPRC5A depletion.
(E) 12 µM of MDH alone and a 1:1 ratio of either MDH:UgpB or MDH:MBP were incubated at 37°C for 60 min in the presence of CHO and then fractionated via centrifugation for use in a solubility assay as described above (C) . The pellet fraction was concentrated 5-fold. In some samples (+G3P), 120 µM of G3P was added prior to the addition of any other protein. Addition of G3P inactivates UgpB's ability to inhibit protein aggregation.
Coomassie blue stained SDS-PAGE gel (15%) of purified human CST complex (CTC1 wild- type and ∆700N).
Quantification of signalosome components and mitotic Wnt target expression level by immunoblotting in natural mitotic cells treated for 1 hour with DMSO or MDC, an inhibitor of clathrin-mediated-endocytosis.
(C) IL-1β levels in supernatants of primary human macrophages (MDM) subjected to knockdowns and sequentially treated with LPS and LLOMe.
C) enriched KEGG pathways enriched by ATAC-DEGs. Rich factor represents the ratio of the number of mapped genes to the number of all the annotated genes located in the pathway.
D Co-immunoprecipitation of FER with HERK1-GFP in Arabidopsis seedlings expressing pFER::HERK1-GFP. Numbers indicate molecular weight marker sizes in kDa. Assays were performed twice with similar results. CBB refers to Coomassie Brilliant Blue staining of total proteins.
proteins in HFSC colonies from Sirt7+/+, Sirt7-/- and Sirt7-TG mice Nfatc1 protein levels were quantified using Image J Plus 6.0 (E, n = 3 mice for each group).
Above: t-SNE plots for Cd74 and H2-Aa expression. Below: Typical immunofluorescence pictures for CD74 (red) and H2-Aa (red) in CX3CR1+ cells in the ciliary body and the peripheral stroma and epithelium of the cornea (green). Two animals were examined. Scale bars represent 50 µm.
ROS, mitochondrial mass (MitoTracker green), mtDNA copy number measurements in mESCs treated with CAP in 2iL (mean values ± SD). n = 3 biological replicates.
Boxplots of poly(A) tail lengths for mRNAs whose abundance decreased ('DOWN', dark green) or increased ('UP', light green) in PABP-depleted cells as compared to cells expressing PABP. Solid horizonal middle lines in box plots denote the median; lower and upper box limits correspond to first and third quartiles; whiskers extend from box limits to the most extreme values. Wilcoxon-Mann-Whitney tests (two-sided) were used to determine differences between upregulated mRNAs and downregulated mRNAs relative to each other and to the background (mRNAs whose abundance did not change in the absence of PABP relative to PABP-expressing cells). (D and E) Comparison of log2-fold change in transcript abundances within PABP-depleted cells relative to cells expressing PABP versus their reported P-body log2-fold enrichment status (Hubstenberger et al., 2017). The Pearson's correlation coefficient (R=0.73) and the corresponding p-value (p<2.2e-16) are reported with a corresponding trendline (black) and 95% confidence interval (gray). (D) Points in dark green indicate mRNAs that are downregulated in PABP-depleted cells and depleted from P-bodies. Points in light green indicate mRNAs that are upregulated in PABP-depleted cells and enriched in P-bodies. Transcript numbers in each quadrant are listed. (E) Nuclear-encoded mRNAs encoding cytoplasmic ribosomes (orange), mitochondrial ribosomes (blue) and proteins with mitochondrial functions (green) that are downregulated in PABP-depleted cells relative to PABP-expressing cells and are predominantly depleted from P-bodies. Proteins with mitochondrial functions were defined based on an inventory of human mitochondrial proteins (Calvo et al, 2016).
(A) Colony formation of WT and TM induced Gata6 iKO keratinocytes stained with hematoxylin. Primary keratinocytes were isolated from induced iKO newborn mice, plated on feeder cells, and stained with hematoxylin at day 7 after plating (top). Phase contrast images of cells are shown below. Scale bars: 30 m. (B) Quantification of colony formation from (A), average SD from n=3 mice in each genotype.
Cardiac glycogen content in 17 weeks old male Vegfb+/+ (n=6), Vegfb+/- (n=6) and Vegfb-/- mice (n=5) presented as mean ± SEM. Statistical evaluation using one-way ANOVA and Dunnett´s multiple comparisons test, p-value: * <0.05 (compared to Vegfb+/+).
(D-F) (D) Total red blood cell (RBC) count, (E) hematocrit (HCT) and (F) hemoglobin (HGB) content were determined by ADVIA in the blood of sick mice of the indicated genotypes or at the termination of the experiment for healthy controls. Data are presented as mean ±SEM. Each data point represents one individual mouse. Statistical significance was assessed using Student's t-test comparing tamoxifen-treated RosaCreERT2+/Ki;GFP-Chimeras (n=6) with Bcl-xfl/fl;RosaCreERT2+/Ki;GFP-Chimeras (n=21), Bcl-xfl/fl;RosaCreERT2+/Ki;Bim+/-;GFP-Chimeras (n=20), Bcl-xfl/fl;RosaCreERT2+/Ki;Bim-/-;GFP-Chimeras (n=12), Bcl-xfl/fl;RosaCreERT2+/Ki;Puma+/-;GFP-Chimeras (n=15), Bcl-xfl/fl;RosaCreERT2+/Ki;Puma-/-;GFP-Chimeras (n=10) and Bcl-xfl/fl;RosaCreERT2+/Ki; Bim+/-;Puma+/-;GFP-Chimeras (n=17) ; ***p<0.001; ****p<0.0001. Data for the Bcl-xfl/fl;RosaCreERT2+/Ki;GFP-Chimeras and RosaCreERT2+/Ki;GFP-Chimeras
Fluorescence t 1/2 values of FRAP on Swi6‐EGFP heterochromatic loci. The box bounds the interquartile range (IQR) divided by the median, and whiskers extend to a maximum of 1.5 × IQR beyond the box.
(g) Maximum dP/dt was examined using cardiac catheterization with graded dobutamine infusion in WT and Parkin Tg aged littermates (n=8 per group).
C) Representative images of colony formation in soft agar upon PYCR1 KO. Scale bar: 100 μm.
I, Cell viability of BT308NS, measured 72 h after IR (5 Gy) in the absence (vehicle) or in the presence of MET (JNJ38877605), Aurora Kinase A (MLN8237), or AKT (Ly294002) inhibitors (fold vs. non-irradiated vehicle-treated cells, mock). *: t-test (5 Gy + inhibitor) vs. (5 Gy + vehicle), p<0.01.
B-C. Analysis of the collagen network in cell-derived matrices (CDMs) produced by wt and Sharpincpdm MSFs using COL1A1 immunolabelling. B. Maximum intensity projections of confocal images are shown. Scale bars represent 50 μm. C. Quantification of distinct collagen fibre bundles in wt and Sharpincpdm CDM samples (n = 5). Mean ± SEM.
Schematic representation of TAp73α and K3R. K3R is a mutant TAp73α in which three lysine (K) residues in the C-terminal region are replaced with arginine (R).
I Lung weight of experimental mice from (H). Mann-Whitney test. **P-value of the comparison = 0.0055. Median ± IQR.
F. Surface illustration of the yCP. The β5 and β6 subunits are depicted in dark gray, with the residue ranges that correspond to mammalian β5 and β6 subunits in the chimeric proteasomes highlighted in gold and blue, respectively. The β5' and β6' subunits of the second β-ring are hidden on the back of 20S proteasome.
D. GSEA revealed that Hnf1aaKO pancreas showed increased transcripts involved in oncogenic pathways such as EMT, MAPK, KRAS, PI3K-AKT.
D Immunoblot analysis of retinal lysates from 6-7 week old WT and NYKO mice. GFAP was used as a marker for reactive astrogliosis and SDHA as a loading control. Data were analyzed using unpaired t-test, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001, ns = not significant. Data are means ± SEM.
(F) Gastric cancer cells after lncPSCA-knockout or stably overexpressing lncPSCA and control cells were treated with cycloheximide (CHX) or vehicle for the indicated periods of time. DDX5 levels were analyzed by Western blot.
E Following treatment with 10 μM metformin for 7 days, protein levels in WM115 and S462 cells were measured by immunoblotting.
Representative BLI traces showing increased binding of Nxph1 to Nrxn1 LNS2SS2A+ and Nrxn1 LNS2SS2AB+ compared to that of Nrxn1 LNS2SS2-. Replicate numbers are shown in E.
C (Left) Detection of XBP1 mRNA splicing in shFAM20C HepG2 cells expressing RNAi-resistant codon-altered Fam20C wild-type (WT) or its inactive D478A mutant (DA) treated with or without 5 μM Tg for 1 h. Fam20C expression levels were shown by protein immunoblotting. (Right) Quantification of XBP1 mRNA splicing levels. Data information: data were shown as mean ± SEM of three independent experiments. *p < 0.05, **p < 0.01 (two-tailed Student's t-test).
(G) ﻿YFP-B56α pull down from cells stably expressing the indicated LxxIxE binding pocket variants of B56α and subsequent immunoblotting of indicated proteins. Representative of 4 independent experiments.
A. A diagram for generation of Pbk K64K65 → AA KI mice using CRISPR/Cas9 system.
Relative proliferation of mESCs as in (J) (mean values ± SD). n = 3 biological replicates.