EMBO/sd-character-level-ner huggingface dataset:
Phosphoregulation in proteins of the canonical MAPK pathways Representation of partial mating, high osmolarity and invasive growth MAPK KEGG pathway from the plasma membrane to the nucleus.Figure 6Representation of partial mating, high osmolarity and invasive growth MAPK KEGG pathway from the plasma membrane to the nucleus. Each heatmap displays log2 fold intensity changes over untreated of one or multiple co-occurring localized phosphorylation site(s) belonging to the indicated proteins. Heatmap rows correspond to treatments and columns to time points. Kinases substrate relationships (+p) and activating or inhibiting effect as stated by KEGG are indicated.
SARS-CoV-2 N phase separation enhanced by non-specific RNA binding.Figure 6A) Turbidity of N is increased in the presence of torula yeast RNA and homopolymeric RNAs. Error bars represent standard deviation of three replicates. B) DIC micrographs of MBP-N in the absence or presence of TEV (to cleave MBP from N to initiate with indicated RNA. In the absence of TEV, MBP-N in the presence of torula yeast RNA, polyC, or polyU RNA does not undergo LLPS. However, after cleavage of MBP, N phase separates. polyA RNA increases LLPS of N. Both in the absence and presence of TEV, polyG RNA induces aggregation of MBP-N. Sample conditions:50 µM MBP-N, 0.5 mg/mL RNA/polyX, 70 mM NaCl, 25˚C, 50 mM Tris pH 7.4. Scale bar represents 100 µm.
Figure 6A. Representative immunofluorescence images of F-actin (phalloidin) and DAPI show that treatment with ROCK inhibitor Y27632 but not depletion of EZH2 can prevent TGFβ1-induced actomyosin remodelling in AECs (scale bars 200 µm). B. Simple western analysis (Peggy Sue) of EZH2 immunoprecipitates shows abolition of TGFβ1-induced profibrotic transcriptional complex of EZH2/POL2/actin upon the convergent treatment of TGFβ1 and Y27632. Unspecific IgG binding was used as a negative control. Representative from 3 biological replicates is shown. Simple western analysis (Peggy Sue) of nuclear fractionation shows an increase in nuclear actin, ph-EZH2 and PO2-S2p levels in injured AECs. RNAi-mediated depletion of IPO9 (siIPO9) prevents injury-induced nuclear actin and POL2-S2p. D. Quantification shows mean + s.d. (n = 3 biological replicates, *p < 0.05, **p < 0.01, ***p < 0.001, ANOVA/Tukey's). E. qPCR analysis of profibrotic genes in MCs co-culture with AECs shows that depletion of IPO9 in TGFβ1-injured AECs blocks the fibrotic crosstalk with MCs. Data show mRNA levels of profibrotic genes normalised to S26 (mean + s.d., n = 3 biological replicates with 5 MCs donors, *p < 0.05, ***p < 0.001, ANOVA/Tukey's).
exit from early endosomes.Figure 6(A) BACE1 carriers in axons of siBin1- or siControl-treated neurons expressing BACE1-GFP, analysed by epifluorescence microscopy. Scale bar, 10 µm. White rectangles indicate a BACE1-positive carrier magnified on the right. Scale bar, 1 µm.(B) Quantification of the percentage of siBin1- or siControl-treated neurons displaying extended BACE1 carriers (as shown in (a)); (n=3, NsiControl=67 cells, NsiBin1=68 cells; *P=0.0199, t-test, mean ± SEM).(C) Quantification of circularity of individual BACE1 carriers in axons and in dendrites of siBin1- or siControl-treated neurons. The percentage of BACE1 tubules (defined by circularity < 0.5; n=2, NAx=116 and NDd=134 of siControl carriers, NAx=71 and NDd=134 of siBin1 carriers; *P=0.0105 siBin1-axons compared to siControl-axons, t-test, mean ± SEM).(D) Quantification of average size (μm2) of individual BACE1 carriers in axons and in dendrites of siBin1- or siControl-treated neurons (n=2, NAx=116 and NDd=134 siControl, NAx=71 and NDd=134 siBin1; **P=0.0019, Mann-Whitney test, mean ± SEM). (E and F) BACE1 (green) exit in tubular carriers from Rab5-positive early endosomes (magenta) in axons of siBin1- (f) and siControl- (e) treated neurons expressing BACE1-GFP and Rab5-mCherry using time-lapse spinning-disk confocal microscopy (4 fps) (see EV movie 3). BACE1 and Rab5 are shown in axons at 0 sec and 4.75 sec. Scale bars, 10 µm. White rectangles indicate the region used in kymographs shown on the right. Arrows and kymographs (covering 3 or 4.75 sec) of merged BACE1 and Rab5 or BACE1 alone indicate in (E) a BACE1 punctum that exits in a tubular carrier from a Rab5-positive early endosome (asterisk) and in (F) a BACE1 tubule that emanates from a Rab5-positive early endosome. Scale bars, 1 µm
Figure 6A Measurement of catalase activity in vector control and CDF4RNAi plants. Ten-day-old green seedlings ("Young") and the third and fourth rosette leaves from 36-day-old plants ("Old") were used, respectively. Three independent experiments were conducted. Data are represented as means ± SD, n=3. Student's t test, *p<0.05. B qPCR analysis of CAT genes expression in the third and fourth rosette leaves from 36-day-old plants. The expression of CAT genes in the wild-type plant is given as 1. Three independent experiments were conducted. Data are represented as means ± SD, n=3. Student's t test, *p<0.05. C Schematic diagram indicating the locations of the putative CDF4- binding motif clusters (D1 to D5) in the promoter of CAT2. D ChIP-qPCR analysis of the relative binding of CDF4 to the promoter of CAT2. An anti-HA monoclonal antibody was used for DNA immunoprecipitation from 32-d-old pER8::CDF4-HA transgenic plants. Black columns indicate the enrichment fold-changes normalized to that of ACT2. Three independent experiments were conducted. Data are represented as means ± SD, n=3. Student's t test, *p<0.05. E Transient dual-luciferase reporter assay. The pGreenII-0800 LUC construct containing the CAT2 promoter and the p62-SK construct with or without CDF4 were transiently co-transformed into Col-0 protoplasts. Firefly luciferase (LUC) and Renilla luciferase (REN) activity were measured after culturing the protoplasts under low light conditions for 16 h. six independent experiments were conducted. Values are given as mean ± SD, n=6. *p<0.05 by Student's t test.
Fig.Figure 7A, B (A) Schematic of the spatially-restricted activation of ROS production at the plasma membrane after CIF stimulation (B) Comparison of the components of the cytoplasmic/nuclear signaling cascades induced by the flg22 bacterial pattern peptide (left) and the CIF peptides (right). Note that all of the signaling components in the two pathways belong to the same gene families, with the exception of the transcription factors. Components for which there is currently no direct experimental evidence are marked in gray, as are arrows indicating activation events that have not yet been experimentally established.
Pattern analysis associates proteins with patient prognosis.Figure 2A) Eight patterns of protein level changes between the three clinical groups: Adjacent normal, pre-treatment tumor and post-treatment tumor. B) Pattern 3 Protein network based on global pattern analysis: Node size and color is based on betweenness centrality score of each node in the network. Top 10% of the most central nodes are indicated C) Profile plot shows z-scored protein pattern of selected significantly changing oncogenes in pattern 3. Each line represents a patient and colored based on the distance to the median profile. D) Radial bar plot with percentages of proteins following each pattern (patient-wise pattern) in 35 patients E) Scatter plots show Spearman Rank correlations between percent of proteins following each pattern and relapse free survival (RFS) , based on patient-wise pattern analysis. Significance was determined using t-test, and p values were corrected using Benjamini Hochberg FDR correction.
Figure 4Structure of SR34 RNA isoforms. Large black boxes indicate exons, narrow black boxes indicate UTRs, black lines indicate introns. Colored boxes indicate protein domains affected by an AS event. RS domain: Arg/Ser-rich domain. Red arrows indicate probes used for gel electrophoresis. Protein domains were retrieved from Uniprot database (https://www.uniprot.org). Analyses of RT-PCR products of SR34 transcripts on 8% acrylamide gel. Quantification of the ratio of SR34 isoforms detected in the gel in (B) RNAs were extracted from WT and RNAi-ASCO1 14-day-old plants. The asterisk (*) indicates a significant difference as determined by Student's T test (p < 0.05, n = 3 biological replicates). Error bars show mean +/- standard deviation. Structure of NUDT7 RNA isoforms. Large black boxes indicate exons, narrow black boxes indicate UTRs, black lines indicate introns. Colored boxes indicate protein domains affected by an AS event. RS domain: Arg/Ser-rich domain. Red arrows indicate probes used for gel electrophoresis. Protein domains were retrieved from Uniprot database (https://www.uniprot.org). Analyses of RT-PCR products of NUDT7 transcripts on 8% acrylamide gel. Quantification of the ratio of NUDT7 isoforms detected in the gel in (E) respectively. RNAs were extracted from WT and RNAi-ASCO1 14-day-old plants. The asterisk (*) indicates a significant difference as determined by Student's T test (p < 0.05, n = 3 biological replicates). Error bars show mean +/- standard deviation.
Figure 5A Genetic interactions of ICE2 with selected lipid synthesis genes. CDP, cytidine diphosphate; DAG, diacylglycerol; PA, phosphatidic acid; PI/PS/PE/PC, phosphatidyl-inositol/serine/ethanolamine/choline; TAG, triacylglycerol. B Growth assays of untreated WT, Δice2, Δnem1, Δnem1 Δice2, Δspo7, Δspo7 Δice2, Δpah1 and Δpah1 Δice2 cells (SSY1404, 2356, 2482, 2484, 2481, 2483, 2807, 2808). Numbers represent areas under the curves and serve as growth indices. Mean + s.e.m., n = 3 biological replicates. Data for WT and ∆ice2 cells are the same in the left and middle panels. C, D Lipidomic analysis of WT, Δice2, Δnem1, Δice2 Δnem1, Δspo7 and Δice2 Δspo7 cells (SSY1404, 2356, 2482, 2484, 2481, 2483). Mean + s.e.m., n = 4 biological replicates. Asterisks indicate statistical significance compared with WT cells, as judged by a two-tailed Student's t-test assuming equal variance. *, P < 0.05; **, P < 0.01. Data for WT and Δice2 cells are the same as in both panels. E Sec63-mNeon images of untreated WT, Δnem1, Δnem1Δice2, Δspo7 and Δspo7 Δice2 cells (SSY1404, 2482, 2484, 2481, 2483).
Model of RAB21-mediated WASH/retromer cargo sorting.Figure 8RAB21 is required for endosomal sorting of direct clathrin-independent cargos. RAB21 associates with WASH/retromer subcomplexes at endosomes. RAB21 could either i) recruit WASH/retromer or ii) be recruited by WASH/retromer or iii) be part of a positive feedback loop that would allow WASH/retromer and RAB21 recruitment at endosomes. Endosomal RAB21 would be required for WASH-mediated F-actin polymerization. Although the data does not directly demonstrate a direct link between F-actin generation and cargo sorting, we propose that RAB21-dependent F-actin generation would be required for sorting of a CIE cargo subclass (MCT1, SLC3A2, Basigin and CD44), while it would not be required for other cargos (CI-MPR or Glut1). In RAB21 knockout cells, decreased WASH/retromer endosomal localization is observed, which results in reduced endosomal F-actin and direct CIE cargos misrouting. This ultimately leads to the lysosomal degradation of these misrouted cargos (demonstrated for SLC3A2). Dotted line between VARP and RAB21 indicates that their co-regulation with the retromer is speculative.
Figure 2(A) Left, example of a large PMD on chromosome 2 derived from a consensus of CLL samples (n=11). Right, genome-wide quantification of PMDs across CLL samples (n=11) and NBCs (n=6). Red, methylated DNA; blue, unmethylated DNA. (B) Expression of genes located inside (blue) and outside (grey) the PMD regions. (C) Fraction of differentially expressed genes inside or outside PMD regions. Up- and downregulated genes are shown in red and green, respectively. (D) Upper panel: Average signal of histone modification marks normalized to H3 and standard deviation in 5-kb windows around the ±50 kb flanking regions of PMD boundaries. Normalized fold changes were calculated by dividing to the average signal flanking outside the PMD boundaries. Blue box, within PMDs; thin line, outside PMDs, nor. - normalized. Lower panel: Distribution of bound CTCF sites in CLL cells as determined by ChIP-seq (blue line) around the ±50 kb flanking regions of PMD boundaries in 5 kb windows. The height of the curves gives the sum of the next nearest CTCF peak at the given distance to the PMD boundary. (E) Percentage of somatic mutations located inside (blue) or outside (grey) the PMD regions. Red line represents the expected ratio based on the genomic length of PMD and non-PMD regions. Mutation data were from (Puente et al, 2015).
Figure 6(A, B) Representative images of heart sections of animals kept on a ketogenic diet or control diet for two weeks stained against ERG and Ki67 or EdU, double positive cells are indicated by arrowheads, and quantification of double positive cells in heart sections per high power field (HPF). Scale bar: 50 μm. Data are presented as mean ± SD. n≥3; *, p<0.05; **, p<0.01; ***, p<0.001 unpaired Student's t-test. (C, D) Quantification of Ki67+/ERG+ cells in heart sections of mice kept on a ketogenic diet or control diet for four weeks or six weeks. Data are presented as mean ± SD. n≥3; *, p<0.05; **, p<0.01; ***, p<0.001 unpaired Student's t-test. (E) Quantification of CD31+ area in heart sections of mice kept on a ketogenic diet or control diet for four months. Data are presented as mean ± SD. n≥3; *, p<0.05; **, p<0.01; ***, p<0.001 unpaired Student's t-test. (F) Quantification of Ki67+ endothelial cells in several organs of mice kept on a ketogenic diet or control diet for four weeks (gastrocnemius and soleus muscle) or two weeks (brain, lungs, subcutaneous adipose tissue, liver). Data are presented as mean ± SD. n≥3; *, p<0.05; **, p<0.01; ***, p<0.001 unpaired Student's t-test.
Figure 7One thousand ESCs of the indicated genotypes were placed into hanging-drop cultures to form embryoid bodies (EBs). After 3 days (referred to as day-0), differentiation was induced by exposure to differentiation medium (days-1 to days-3 after medium change). (A) Representative photographs of EBs of the indicated genotypes at day-0 and day-3 after differentiation induction (experiments were conducted in 3 biological replicates; n=5-42 EBs per biological replicate, scale bar: 0.02 mm). RNA-seq analysis was conducted on Tnfaip2-/- EBs vs. WT EBs on day-3 of differentiation induction of EBs (n=3 biological replicates). The heat maps depict the intersection of DEGs with the following gene sets (B) "stem cell maintenance: positive and negative regulators", RNA-seq analysis was conducted on Tnfaip2-/- EBs vs. WT EBs on day-3 of differentiation induction of EBs (n=3 biological replicates). The heat maps depict the intersection of DEGs with the following gene sets ;, (C) "mesoderm development" RNA-seq analysis was conducted on Tnfaip2-/- EBs vs. WT EBs on day-3 of differentiation induction of EBs (n=3 biological replicates). The heat maps depict the intersection of DEGs with the following gene (D) "ectoderm development" Tnfaip2 and 5 other stem cell-related genes (Tfcp2l1, Dppa3, Fbxo15, Zfp42 and Klf2) were additionally incorporated based on literature searches. The color scale represents the gene-wise z-score calculated from normalized gene expression levels. The asterisk refers to the gene identified in this study. (E) Representative image of immunofluorescence staining against the ectodermal marker (SOX1) and the mesodermal marker (T alias Brachyury) in WT and Tnfaip2-/- EBs on day-3 of differentiation induction. (3 repeat experiments were conducted on a total number of 9-10 EBs per genotype, scale bar: 20µm). (F) mRNA expression of Tnfaip2 measured by RT-qPCR in ESCs on the indicated days of differentiation induction of WT EBs [n=3 biological replicates; log-transformed data were normally distributed (P>0.05 as per Shapiro-Wilk test), the P value for the upregulation of Tnfaip2 on consecutive time points (day-0, -2 and -3) was calculated starting with the probability of maximum rank-based difference, i.e. having two groups of three data points perfectly separating, p1,b = 0.1 (bidirectional) and P1,u = 0.05 (unidirectional); the probability of finding a triple series of max. difference starting at some timepoint is Ptriple,tp = p1,b · p1,u · p1,u, and finding such a triple somewhere across the 4-step time series is Ptriple = Ptriple,tp + (1- p1,u) · Ptriple,tp = 0.0005.
CLEC12A Knockdown and the ATG16L1 T300A SNP Act Additively to Impair LC3-Bacteria Colocalization.Figure 2(A) Representative epifluorescent images showing impaired antibacterial autophagy in ATG16L1 KO HeLa cells complemented with the indicated ATG16L1 protein in the presence of control siRNA or CLEC12A siRNA. The scale bars represent 10 μm. (B) Percentage of LC3-Salmonella colocalization in WT HeLa cells, ATG16L1 KO HeLa cells, and ATG16L1 KO HeLa cells stably expressing ATG16L1∗300T or ∗300A alleles in the presence of control siRNA or CLEC12A siRNA. Data are shown as means ± SD; n = 75. Data shown are representative of three independent experiments.
Long-term BACE1 inhibition after AAV-VHH-B9 delivery reduces cognitive deficits in AppNL-G-F mice.Figure 2(A) Experimental timeline illustrating key points in the development of amyloidosis in the AppNL-G-F mouse line along with key experimental manipulations. This longitudinal design allowed pathology to be performed on animals used in behavioral experiments (Figures 3, 4 and 5). (B) Sociability and social recognition memory in AppNL-G-F (KI) mice and C57Bl/6J wild type (WT) controls were tested using a standard protocol (top). During sociability, control (grey plots) and AppNL-G-F (colored plots) mice showed more interest in a strange mouse in an adjacent testing chamber [S1] than in an empty chamber [E]. This behavior was similar irrespective of VHH-B9 or GFP treatment. Social recognition memory (preference for a novel mouse in S2 over S1) was observed in controls (grey plots) expressing VHH-B9 or GFP. In AppNL-G-F mice (magenta plots), VHH-B9 prevented deficits in social recognition memory. Data are presented as violin plots. Median and quartiles (thick and thin white lines respectively) indicate spread of data. Sociability *p=0.01, ***p=0.0005, ****p=0.0001; Preference for social novelty *p=0.04, **p=0.006, (2-way ANOVA with post-hoc multiple comparisons using Šídák correction). Behavioral experiments with AppNL-G-F: AAV-VHH-B9, n=17; AAV-GFP, n=16. Experiments with C57Bl/6J mice: AAV-VHH-B9, n=18; AAV-GFP, n=18, non-injected, n=18. (C) Representative sagittal section from an AppNL-G-F mouse injected at 6 weeks of age with AAV-VHH-B9. The brain was harvested 12 months post-injection and sagittal sections were immunostained for the cMyc tag fused to VHH-B9. Note the widespread expression throughout the brain. Scale bar: 1 mm. Boxed sections are displayed at higher magnification in the images below. PF cortex, Prefrontal cortex: DG, Dentate gyrus. Scale bars: 50 µm.
Figure 9Primary hippocampal neurons (DIV6+4) were cotransfected with shTDP and GFP to visualize neuron morphology. Dendritic morphology from at least 23 neurons per condition per experiment was quantified by Sholl analysis and statistically evaluated using two-way ANOVA with Bonferroni's (B, D) or Tukey's (F, H) post-test. Scale bar represents 100 µm. (A, B) TDP-43 knockdown (DIV6+5) significantly reduces dendrite branching compared to control: at 25, 37.5 and 87.5 µm radius p < 0.05, at 50 µm p < 0.01 and from 62.5 to 75 µm p < 0.001. Primary hippocampal neurons (DIV6+4) were cotransfected with VPS4B or appropriate controls and GFP to visualize neuron morphology. Dendritic morphology from at least 23 neurons per condition per experiment was quantified by Sholl analysis and statistically evaluated using two-way ANOVA with Bonferroni's (B, D) or Tukey's (F, H) post-test. Scale bar represents 100 µm. (C, D) VPS4B transfection (DIV6+4) significantly reduces dendrite complexity: at 25 µm radius p < 0.05, from 37.5 to 75 µm p < 0.001 and from 87.5 to 100 µm p < 0.01. Primary hippocampal neurons (DIV6+4) were cotransfected with shTDP or appropriate controls and GFP to visualize neuron morphology. Dendritic morphology from at least 23 neurons per condition per experiment was quantified by Sholl analysis and statistically evaluated using two-way ANOVA with Bonferroni's (B, D) or Tukey's (F, H) post-test. Scale bar represents 100 µm. (E, F) Two days after shRNA transfection neurons were treated with 1 nM NRG1-beta 1 (NRG1) or vehicle and analyzed at DIV6+5. shCtrl vs. shTDP: at 25 and 87.5 µm radius p < 0.05, from 37.5 to 75 µm p < 0.001. shCtrl vs. shCtrl + NRG1: from 37.5 to 62.5 µm p < 0.05. shTDP vs. shTDP+NRG1: no significant difference. Primary hippocampal neurons (DIV6+4) were cotransfected with shTDP or appropriate controls and GFP to visualize neuron morphology. Dendritic morphology from at least 23 neurons per condition per experiment was quantified by Sholl analysis and statistically evaluated using two-way ANOVA with Bonferroni's (B, D) or Tukey's (F, H) post-test. Scale bar represents 100 µm. (G, H) Transfection of the indicated combinations of shCtrl, shTDP, ErbB4 or vector control (DIV6+5). shCtrl + Ctrl vs. shTDP + Ctrl: from 25 to 75 µm radius p < 0.001, at 87 and 112.5 µm p < 0.01 and at 100 µm p < 0.05. shTDP + Ctrl vs. shTDP + ErbB4: from 25 to 100 µm radius p < 0.001, at 112.5 µm p < 0.01. shCtrl + Ctrl vs. shTDP + ErbB4: no significant differences.
Figure 1A. Proline structure, Arginine structure, and the mutation site image, produced by the HoPE server, depicting the P522 in green with the R522 mutation in red B. Flexibility (RMSD) differences between the wild type and mutated protein, significant differences are highlighted in the figure. RMSD was measured per residue over the whole simulation time using the GROMACS tool g_rms and here averages were plotted with standard deviations represented in the error bars. Data were analysed using a Mann-Whitney U test in the R statistical package. C. Wild type and Mutated structures overlaid in MOE. In this image most of the structure is light grey with the SH2 domain highlighted in blue (P522) and orange (R522), the inset shows a closer view of the SH2 domain with both the P522 and R522 variants highlighted.
Unlike wild-type NAV3, mutant cancer alleles are devoid of persistency induction and metastasis suppression.Figure 6A MCF10A cells were plated on collagen, and 24 h later, they were treated with EGF (10 ng/ml). Shown are trajectories of cells transiently expressing the indicated forms of NAV3. Red tracks indicate relatively low persistence (< 0.6).B Quantification of migration parameters (from A) is shown as mean ± SEM (60 cells and three experiments). C HEK293 cells previously transfected with EGFP-NAV3 (WT), EGFP-NAV3-D1047N or EGFP-NAV3-A459P were treated with cycloheximide (CHX; 50 μg/ml) or with the solvent, DMSO, for the indicated time intervals, followed by cell lysis and immunoblotting using anti-EGFP and anti-α-tubulin antibodies. The signals obtained were quantified and normalized to time zero (untreated cells; right panel). D, E The indicated mCherry-expressing MDA-MB-231 derivatives were injected intravenously (1.5 × 105 per mouse) using 5-week-old female SCID mice. Four weeks later, lungs were photographed and the numbers of lung metastases were determined.