EMBO/sd-character-level-ner huggingface dataset:
Figure 4(a) History-dependence due to slow relaxation to equilibrium can be augmented by negative inter-species interactions. Model analyses of six pairwise communities that experimentally displayed history-dependent behaviors and are coupled by mutual inhibitory interactions in the gLV model trained on T3. Network topology (left) and heat-map of history-dependent responses (right) across a range of inter-species interaction coefficient values. The line width and node size of the network diagram represents the magnitude of the inter-species interaction coefficients and steady-state monospecies abundance, respectively. The heat-map shows the absolute value of the difference in species absolute abundance at 72 hr for communities simulated using two initial conditions: x1 = 0.0158, x2 = 0.0008 or x1 = 0.0008, x2 = 0.0158 using the serial transfer experimental design. The black box denotes the boundaries of the set of α12 and α21 values yielding bistability in the model. The circle (red) indicates the inferred parameters based on training set T3. (b) Coupled positive and negative interactions can display robust species coexistence to variations in model parameters. Network diagram (inset) represents the magnitude, sign and direction of the inferred inter-species interactions between CH (x1) and ER (x2). Dashed (gray) and solid (orange) lines indicate a positive and negative interaction, respectively. The line width and node size denote the magnitude of the inter-species interaction coefficients and steady-state abundance of the monospecies, respectively. Heat-map of the ratio of x1 (CH) to x2 (ER) at 72 hr as a function of the inter-species interaction coefficients α12 and α21. Initial conditions for simulations were x1o = 0.0008, x2o = 0.0158. The circle (black) indicates the inferred parameter values for the CH, ER consortium for the gLV model trained on T3. (c) Heat-map (right) of the ratio of x1 to x2 at 72 hr across a broad range of growth rate parameter values (μ1 and μ2). Initial conditions for simulations were x1o = 0.0008, x2o = 0.0158. The line (white) outlines the parameter regimes for coexistence and single-species dominance at steady-state. The circle (black) represents the inferred parameter values for the CH, ER consortium. (d) Box plot of the fraction of parameter space that exhibits species coexistence across a range of growth rate parameters for all inferred positive/negative (+/-) or bidirectional negative (-/-) networks for the gLV model trained on T3. Growth rate parameters range from 0.05 to 1 hr-1 and 2500 combinations of growth rates within this range were evaluated. On each box, the red line represents the median, the edges of the box are the 25th and 75th percentiles, the whiskers extend to the most extreme data points that the algorithm considers not to be outliers, and the outliers are plotted as red crosses.
Figure 1(A) EM analysis of cortical synapses derived from WT and MPS-IIIA mice at different ages. The size of synaptic vesicles was quantified from 400-500 vesicles (taken from 5 mice for each genotype at each time point) and expressed as the average of vesicle diameter (nm). The number of synaptic vesicles per synapse was quantified from 20 different images (taken from 5 mice for each genotype at each time point), normalized by the length of synaptic cleft and expressed as % of WT. The synaptic density was measured from 20 different images (taken from 5 mice for each genotype at each time point) as the number of synapses/area(#/500μm2) and expressed as % of WT.Arrows indicate the synaptic cleft, while asterisks indicate abnormal vacuoles (B, C) The size of the lysosomal compartment was evaluated by WB (B) analysis in the brain of MPS-IIIA mice at indicated ages. Quantitation of WB by densitometry analysis (ImageJ) was shown (B). (B, C) The size of the lysosomal compartment was evaluated by IF (C) analysis in the brain of MPS-IIIA mice at indicated ages. (D) Extracellular recordings (fEPSPs) in hippocampal brain slices from 6 months-old WT and MPS-IIIA mice. The left panel shows representative fEPSP traces. Summary graphs show the fEPSPs slope as a function of either the applied stimulus intensity or the prevolley amplitude. Data are the average of the values from 9 slices (from 9 mice) in the WT group and 6 slices (from 5 mice) in the MPS-IIIA. *p<0.05, repeated measure ANOVA.
Figure 2Hierarchical clustering analysis of RNAseq expression profile from MSCs stimulated with LPS for 6 and 24 h. The heat-map shows the gene expression profile of non-primed MSCs and MSCs which were LPS primed for 6 and 24h. Red color represents upregulation, while blue color depicts down regulation in gene expression, each data point represents FPKM in log2 value. Pathway analysis depicts that cytokine-cytokine receptor interactions, genes encoding secreted soluble factors, an ensemble of genes encoding extracellular matrix, chemokine receptors which bind distinct chemokines, GPCR ligand binding, cytokine and inflammatory response, chemokine signaling pathway and IL-5 signaling are the most dominant pathways as assessed by transcriptional changes when non-primed and LPS primed MSCs were compared at 6 and 24 h after LPS priming. Venn diagram analysis displays up-regulated and down-regulated gene numbers indicated in blue and pink color, respectively. Purple color indicates the number of shared genes of the up-regulated and down-regulated genes at 6h and 24h after LPS stimulation. This implies rapid changes of expression of the same genes. Validation of the selected genes uncovered from global RNAseq analyses by qRT-PCR analyses displays up-regulation of CXCL-6 after LPS treatment. Validation of the selected genes uncovered from global RNAseq analyses by qRT-PCR analyses displays up-regulation of , IL-8 and IL-1β after LPS treatment. ELISA results depict an up-regulated expression of CXCL-6 after 24h of LPS treatment ELISA results depict a significantly increased IL-8 expression after 6 and 24h of LPS treatment. Western blot analysis showed up-regulation of IL-1β expression upon LPS priming of LPS primed MSCs. Actin served as control. Densitometry graph shows significant increase after 6h LPS stimulation compared to non-primed MSCs. Statistical analysis was performed using one way ANOVA, values are represented as mean ± SEM, n=3 biological replicates.
Selective restoration of FUS nuclear import in motor neurons rescues motor neuron loss.Figure 9(A) Double-immunolabeling of spinal cordneurons with ChAT (red) and N-terminal FUS antibody (green). Nuclei were visualized with DRAQ5 (blue). Cellular localization of FUS was analyzed in the ventral spinal cord of Fus+/+/ChAT-CRE (A1-A4), FusΔNLS/ΔNLS/- (A5-A8), and FusΔNLS/ΔNLS/ChAT-CRE (A9-A12).FUS was completely nuclear in ChAT+ neurons of Fus+/+/ChAT-CRE, while cytoplasmic in FusΔNLS/ΔNLS/-, In the ventral horn of FusΔNLS/ΔNLS/ChAT-CREmice, ChAT+ neurons (motor neurons, e.g. within the dashed square) displayed nuclearFUS immunoreactivity, while ChAT negative cells retained cytoplasmicFUS immunoreactivity (arrows) (B) Representative light microscopy images of spinal cord sections of Fus+/+/ChAT-CRE (B1, B4), FusΔNLS/ΔNLS/- (B2, B5) and FusΔNLS/ΔNLS/ChAT-CRE (B3, B6) mice at birth stained with cresyl violet (Nissl, B1-B3) or anti-choline acetyl transferase (ChAT, B4-B6).(C-D) Quantification of Nissl+ (C) and ChAT+ (D) motor neurons per spinal cord ventral horn. N=9 Fus+/+/ChAT-CRE, N=8 FusΔNLS/ΔNLS/- and N=4 FusΔNLS/ΔNLS/ChAT-CRE; for Nissl+ and N=11 Fus+/+/ChAT-CRE, N=7 FusΔNLS/ΔNLS/- and N=8 FusΔNLS/ΔNLS/ChAT-CRE; for ChAT+ (**) p<0.01 vs Fus+/+, (##) p<0.01 vs Fus∆NLS/+ ; (ns) non-significant; One way ANOVA followed by Tukey post hoc test.(E) Total numbers of caspase 3 (Cas3)/ChAT/DAPI triple positive cells in Fus+/+/ChAT-CRE, FusΔNLS/ΔNLS/- and FusΔNLS/ΔNLS/ChAT-CREmice. N=9 Fus+/+/ChAT-CRE, N=7 FusΔNLS/ΔNLS/- and N=8 FusΔNLS/ΔNLS/ChAT-CRE; (**) p<0.01 vs Fus+/+, (#) p<0.05 vs Fus∆NLS/+ ; (ns) non-significant; One way ANOVA followed by Tukey post hoc test.
Three representative protomers within a VCP hexamer are shown in the model.figf6Three representative protomers within a VCP hexamer are shown in the model. The D2 in the central protomer (N) is highlighted. The conformational changes observed in the four nucleotide states apo, ATP, ATP‡ and ADP over a cycle of ATP hydrolysis are schematically represented. The largest conformational changes occur between the preactivated states i and ii (apo and ATP) and the activated states iii and iv (ATP‡ and ADP). (i) In the apo state, the D2 domain (dark yellow) and D1-D2 linker (orange) are in a disordered state. (ii) Upon ATP binding, only small conformational changes occur. (iii) ATP interactions with D2 elements induce major conformational changes that result in an overall more ordered D2 and D1-D2 linker (orange) in the activated ATP state (ATP‡; red), with formation of the allosteric inhibitor binding site (violet). (iv) ATP hydrolysis leading to the ADP state induces a repositioning of the arginine finger (indicated by the dotted arrow) that in turn assists γ-phosphate release in the N + 1 protomer. Binding of allosteric inhibitors, which most likely occurs through interactions with the ISS motif, hampers the movement of the arginine finger toward the γ-phosphate, thus preventing ATP hydrolysis propagation and freezing D2 in the ADP-bound state.
CTD shortening alters putative enhancers and delays transcription induction.Figure 6A- Histogram showing the distribution of a number of putative eRNAs paired to genes in RPB1-52R and RPB1-25R cells upon 15 and 30 min TPA treatment (200 nM) as well as in the DMSO controls. B- Box plots showing RNA synthesis levels (RPK) of putative eRNAs paired with genes upregulated (adjusted p value < 0.05, log2 fold change >=1) in RPB1-52R and RPB1-25R cells upon 15 min of TPA treatment (200 nM). p value = 0.000732 (Mann-Whitney U test) Box limits are the first and third quartiles, the band inside the box is the median. The ends of the whiskers extend the box by 1.5 times the interquartile range. Two independent biological replicates were analyzed. C- Box plots showing RNA synthesis levels (RPK) of putative enhancer eRNAs paired with genes upregulated (adjusted p value < 0.05, log2 fold change >=1) in RPB1-52R and RPB1-25R cells upon 30 min of TPA treatment (200 nM). p value = 2.77e-5 (Mann-Whitney U test) Box limits are the first and third quartiles, the band inside the box is the median. The ends of the whiskers extend the box by 1.5 times the interquartile range. Two independent biological replicates were analyzed. D- Exemplary genome browser view showing TT-seq read coverage over DUSP1 gene as well a region giving rise to a putative eRNA mapped to it in RPB1-52R and RPB1-25R cells upon 15 min of TPA treatment (200 nM). E - Venn diagrams showing overlaps between groups of genes upregulated upon 15 min TPA treatment in RPB1-52R and RPB1-25R cells (left panel), 30 min TPA treatment in RPB1-52R and RPB1-25R cells (middle panel) as well as triple overlap between genes upregulated upon 15 min TPA in RPB1-52R and RPB1-25R cells with those upregulated upon 30 min TPA in RPB1-25R cells (right panel). Genes showing adjusted p value < 0.05 and log2 fold change >= 1 were considered upregulated.
Figure 1(A) Side-view of the overall structure of the S. cerevisiae CIII2/CIV supercomplex and its position in the mitochondrial inner membrane (IM). IMS: intermembrane space Zoom-in of the CIII2/CIV interaction sites with residues and distances annotated. The inner-membrane protein-lipid-protein interactions (Rip1-CL-Cox5a), where Rip1 is marked in gold, CL in grey, and Cox5a in red (B) Zoom-in of the CIII2/CIV interaction sites with residues and distances annotated. the mitochondrial matrix, protein-protein interaction of Cor1 (blue), and Cox5a (red) (C) are shown. (D) Blue-native gel electrophoresis of S. cerevisiae strains with indicated mutations in Cor1.
Figure 2(A-I) Ovol2 protein expression revealed by indirect immunofluorescence. Enlarged images of the boxed areas in (E) are shown as (F-I) to indicate Ovol2 protein distribution in the intermediate regions (F-H) between the proliferative zone (D) and the migrating front (I). White dashed line indicates the wound margin. DAPI stains the nuclei. (J) RT-qPCR analysis of unwounded skin, and microdissected wound regions (n=3 mice)
Figure 1(A) Schematic to scale of human MYH3 gene on chromosome 17. Noncoding regions are displayed in pink. Coiled coil domain (840-1933 bp) displayed in purple. Motor domain (86-779 bp) displayed in yellow. Actin binding site (656-678 / 758-772 bp) shown in cyan. Location of R672H mutation is enlarged and labelled. (B) Schematic to scale of zebrafish smyhc1 gene on chromosome 24. Noncoding regions are displayed in pink. Coiled coil domain (842-1929 bp) displayed in purple. Motor domain (85-778 bp) displayed in yellow. Actin binding site (655-677 bp) displayed in cyan. Location of R672H mutation is enlarged and labeled. (C) Aligned DNA and amino acid sequences of MYH3 and smyhc1 alleles surrounding the smyhc1R673H and MYH3 R672H substitutions. The smyhc1- allele has a 7 base pair deletion that results in a frameshift in which one errant amino acid precedes a premature stop codon. The smyhc1R673H allele results from a G>A transition single point mutation. (D) Western blot of whole zebrafish larvae, Smyhc1 stained with the F59 antibody. smyhc1+/+ larvae express Smyhc1 at 24hpf, but not at 48hpf. smyhc1-/- larvae do not express Smyhc1. (E) Smyhc1 immunohistochemistry stain of 24 hpf (hour post fertilization) zebrafish larvae. Filamentous actin is stained with phalloidin (red). Nuclei are stained with DAPI (blue). Smyhc1 is stained with the F59 antibody (green) (Elworthy et al, 2008). smyhc1+/+, smyhc1R673H/+, and smyhc1R673H/R673H larvae display Smyhc1 in the muscle fibers at 24hpf. smyhc1-/- larvae at 24 do not stain positively for Smyhc1. Scale bar represents 50 µm.
Figure 5(A) Representative images of COS7 cells transiently transfected with GFP-COP1 WT or GFP-COP1 NESmut (V238A/L242A) (green) and empty vector or 3xFLAG-CRM1 (grayscale). Cells were stained with anti-FLAG (Cell Signaling) and anti-rabbit Alexa Fluor 680. Nuclei were counterstained with DAPI (blue). Scale bar, 10 µm. (B) Representative images of COS7 cells transfected with GFP-COP1 WT (green), the indicated TRIB1-HA constructs (red), and empty vector or 3xFLAG-CRM1 (grayscale). Cells were stained with anti-FLAG (Cell Signaling), anti-HA (Sigma), anti-rabbit Alexa Fluor 680, and anti-mouse Alexa Fluor 568. Nuclei were counterstained with DAPI (blue). Scale bar, 10 µm. (C) Quantification of the average ratio of nuclear/cytoplasmic fluorescence of GFP-COP1 constructs in (A) and (B). Mean values ± S.E.M. are shown for three independent experiments where 50 individual cells per experiment were analyzed. Significance was calculated using the Student t test (ns, not significant; *p < 0.01; ****p < 0.00001). (D) A hypothesized model for inhibition of COP1 nuclear export by TRIB1 through NES masking. In this model, binding of the PSL to the WD40 domain stabilizes a conformation in which the NES, located in the distal putative coiled coil domain, is exposed. This could be achieved by an effective reduction of the distance between the WD40 domain and the putative coiled coil domain, resulting from PSL binding. Loss of this proximity upon TRIB1 binding could then induce a conformational change in the coiled coil domain that results in NES masking. (E) Representative images of COS7 cells transiently transfected with the indicated GFP-COP1 constructs (green) and 3xFLAG-CRM1 (grayscale). Cells were stained with anti-FLAG (Sigma) and anti-mouse Alexa Fluor 568. Nuclei were counterstained with DAPI (blue). Scale bar, 10 µm. (F) Quantification of the average ratio of nuclear/cytoplasmic fluorescence of GFP-COP1 constructs in (E) and Figure EV6C. Mean values ± S.E.M. are shown for three independent experiments where 50 individual cells per experiment were analyzed. Significance was calculated using the Student t test (ns, not significant; ****p < 0.00001). (G) Quantification of percentage of cells observed in (E) and Figure EV6C with the indicated GFP-COP1 construct exhibiting nuclear (Nuc), nuclear and cytoplasmic (Nuc/Cyt), or cytoplasmic (Cyt) localization. Mean values ± S.E.M. are shown for three independent experiments where 50 individual cells per experiment were analyzed.
LC8 Promotes the Bim-Beclin 1 Interaction.Figure 6(A) Bim-147 does not bind to Beclin 1. Beclin 1-Flag/vector (IP negative control), Beclin 1-Flag/Myc-BimEL-1-147aa (Myc-147), or Beclin 1-Flag/Myc-BimEL-ΔBH3 (Myc-ΔBH3) were transfected into HeLa cells. Anti-Myc (Rabbit) was used for immunoprecipitation. (B) Bim-147 is competent for LC8 binding. LC8/vector (IP negative control), LC8/Myc-BimEL-1-147aa (Myc-147), or LC8/Myc-BimEL-ΔBH3 (Myc-ΔBH3) were transfected into HeLa cells. Anti-Myc (Rabbit) was used for immunoprecipitation. (C) Mutating LC8 binding consensus sites within Bim disrupts the Bim-LC8 interaction. Bim(EL) EE/vector (IP negative control), Bim(EL) EE/Myc-LC8, Bim(EL) EE-S109A, S113A, T114A (AAA)/ Myc-LC8, or Bim(EL) EE-T116E/ Myc-LC8 were transfected into HeLa cells. Anti-Myc (Rabbit) was used for immunoprecipitation. Data are shown as mean ± SD. ∗∗∗p < 0.001. (D) Mutating LC8 binding consensus sites within Bim disrupts the Bim-Beclin 1 interaction. Bim(EL) EE/vector (IP negative control), Bim(EL) EE/Beclin 1-Flag, Bim(EL) EE-S109A, S113A, T114A (AAA)/Beclin 1-Flag, or Bim(EL) EE-T116E/Beclin 1-Flag were transfected into HeLa cells. Anti-Flag (M2) was used for immunoprecipitation. Data are shown as mean ± SD. ∗∗∗p < 0.001. (E) Bim-S does not bind to LC8. BimEL-EE (EL)/vector (IP negative control), BimEL-EE (EL)/Myc-LC8, BimL-EE (L)/Myc-LC8, or BimS-EE (S)/Myc-LC8 were transfected into HeLa cells. Anti-Myc (Rabbit) was used for immunoprecipitation. (F) Model of LC8 promoting Beclin 1-Bim interaction. In nutrients, LC8 binds the Bim consensus sequence (DKSTQTP). This enables a transition of the Bim C terminus from a disordered state to α helices and a β sheet (Barbar, 2008), which favors the Bim-Beclin 1 interaction. In starvation conditions, Bim is phosphorylated at T116 within the consensus sequence (DKSTQpTP) leading to its dissociation from LC8 (Lei and Davis, 2003). Bim returns to the disordered state, which binds to Beclin 1 less effectively. Grey boxes, higher degree of disorder; white box, lower degree of disorder (Barbar, 2008). (G) LC8 enhances Bim-Beclin 1 interaction in vitro. His-Bim, His-LC8 and GST-Beclin 1 were expressed in BL21(DE3) E. coli and purified. Two micrograms of His-Bim was combined with 2 μg GST without or with 1 μg His-LC8 (as controls); 2 μg His-Bim was combined with 2 μg GST-Beclin 1 without or with 1 μg His-LC8. The mixtures were incubated in buffer A for 3 hr. Glutathione beads were then used to pull down GST or GST-Beclin 1. The pulldown products were detected with anti-Bim and anti-Beclin 1. (H) LC8 siRNA knockdown reduces the Bim-Beclin 1 interaction. Control siRNA or LC8 siRNA were transfected into HeLa cells. After 48 hr, HA-Bim(EL) EE/vector (IP negative control) or HA-Bim(EL) EE/Beclin 1-Flag was transfected into control siRNA transfected HeLa cells; HA-Bim(EL) EE/Beclin 1-Flag was transfected into LC8 siRNA-transfected HeLa cells. Anti-Flag (M2) was used for immunoprecipitation. Note that in the presence of BimEE, endogenous LC8 was pulled down by Beclin 1 when cells were treated with control siRNA. Data are shown as mean ± SD. ∗∗∗p < 0.001.
is elevated in NPC tissue and plasma and is a potential diagnostic biomarker A, Western blotting showing cellular INSL5 in the immortalized NPEC and NPC cell lines after inhibition of protein secretion by BFA, and β-actin was used as a loading control.Figure 1A, Western blotting showing cellular INSL5 in the immortalized NPEC and NPC cell lines after inhibition of protein secretion by BFA, and β-actin was used as a loading control. B, ELISA assay showing secreted INSL5 in the supernatants of NPECs and NPC cell lines. For NPECs, n=3; for NPC, n=7. C, The concentration of plasma INSL5 in healthy controls (normal EBV (-)), non-tumor individuals with VCA-IgA positive (normal EBV (+)) and NPC patients, in training cohort. D, ROC of the diagnostic prediction model with plasma INSL5 level in the training cohort. E, The concentration of plasma INSL5 in healthy controls (normal EBV (-)), non-tumor individuals with VCA-IgA positive (normal EBV (+)) and NPC patients, in validation cohort 1(GZ). F, The concentration of plasma INSL5 in healthy controls (normal EBV (-)), non-tumor individuals with VCA-IgA positive (normal EBV (+)) and NPC patients, in validation cohort 2(ZS). G, Confusion table of binary results of the diagnostic prediction model in the training cohort, validation cohorts and the whole cohort. H, ROC of the diagnostic prediction model with plasma INSL5 level in the whole cohort. I, ROC of the diagnostic prediction model with plasma INSL5 level in individuals with VCA-IgA-negative plasma in all three cohorts. J, Confusion table of binary results of the diagnostic prediction model in VCA-IgA-negative individuals in the training cohort, validation cohorts and the whole cohort.
FOXD3 binds to MERVL and MSR elements.Figure 1(A) Transcription factor binding sites with Transfac IDs predicted by PROMO in repeat element consensus sequences. (B) Electrophoretic mobility shift assay (EMSA) with increasing concentration (0, 15nM, 30nM, 60nM, 1.25μM and 2.5μM) of GST-FOXD3 and fixed concentration (50nM) of 5'-Cy5 labelled dsDNA oligonucleotides (35 bp each) from Sox15 promoter (positive control), MSR, MERVL-LTR, MERVL-int, L1MdA and Hprt promoter (negative control). The experiment was repeated 3 times. (D) ChIP-qPCR enrichment of FOXD3 in mESCs using primers specific for MSR, MERVL-LTR, MERVL-int (including and excluding the FOXD3 cognate motif), L1MdA promoter sequences. Sox15 promoter and Actb promoter primers are used as positive and negative control respectively. Data is represented as percentage of input and the average of 3 biological replicates is plotted. Error bar indicates standard error of the mean (SEM). Asterisks indicate statistically significant differences compared to no antibody control levels (*: p< 0.05, paired t-test). (C): Metadata analysis plots of FOXD3 ChIP-Seq (blue) and input (green) over MSR, MERVL-int, MT2_Mm and L1MdA consensus sequences including 1 kb flanking the start (RS) and end (RE) of each repeat. Y axes indicate normalized reads per genome coverage (RPGC). Predicted FOXD3 binding sites are marked in yellow and enrichment of FOXD3 over input is indicated in red. FOXD3 enrichment is seen in MSR, MERVL-int, MERVL-LTR but not in L1MdA.