EMBO/sd-character-level-ner huggingface dataset:
C oncogene induces invasion and metastatic dissemination via EV transfer in vivo A.Figure 5A. Cartoon of in vivo experimental approach. MDA-MB-231CFP;Cre and reported T47DDsRed cells were co‑injected in one mammary gland of 10 mice per experiment. B. Left: representative confocal images of mammary tumor formed by the co-injection of T47DDsRed reporter cells with either MDA-MB-231CFP;Cre;Control or MDA-MB-231CFP;Cre;HA-RASSF1C. Scale 200 μm. Right: averaged values for all mice for the percent of the eGFP+ or CFP+ cells as part of the whole tumor. Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001. C. Representative 3 hour migration paths of either MDA-MB-231CFP;Cre;Control (Control, left) or MDA‑MB‑231CFP;Cre;HA-RASSF1C (RASSF1C, right) within a single intravital imaging field of tumors co‑injected with T47DDsRed reporter cells. D. In vivo migration speed of MDA‑MB‑231CFP;Cre;Control or MDA‑MB‑231CFP;Cre;HA-RASSF1C in a mixed tumor with T47DDsRed cells. Values are an average of the totals from 5 mice each, measured from intravital time-lapse images. Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001. E. The normalized in vivo motility of T47DeGFP and T47DDsRed reporter cells in mixed tumors. A Non‑parametric Mann-Whitney U test was used to derive statistical significance. Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001. F. Cartoon representing the Cre-LoxP model exploited to follow up amoeboid motility in recombined reporter (T47DeGFP) cells. G. Quantification of distinct morphology of T47DeGFP in tumors from observed from a total of 30 positions in n=5 mice/group (Control or RASSF1C). Mesenchymal, Amoeboid or Hybrid motility were scored manually Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001. H. Quantification of the number of T47DeGFP metastatic events found in the lungs of mice with mammary gland tumors. Whole lung tile images were used for quantification, 6 of 10 μm sections each, 100 μm apart. Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001.
A model of Pom1 intermolecular auto-phosphorylation predicts Pom1 gradient’s system propertiesA.Figure 2Possible hypotheses for a buffering mechanism. In the cluster-based model, high local concentration leads to the formation of slow diffusing clusters, thus reducing the decay length at cell poles with high amplitude (Saunders et al, 2012). A cis-phosphorylation model provides no buffering. By contrast, in a trans-phosphorylation model, phosphorylation (and thus detachment) increases with local Pom1 concentration, providing a buffering mechanism reducing decay length at cell poles with high amplitude. Inverse correlation between Pom1/Tea4 and Tea4 observed experimentally following from the sub-linear relationship between Pom1 and Tea4 (see Fig. 1F, same data). Line shows linear regression (p-value<10-7). Relationship between Pom1/Tea4 and Tea4 predicted by the simple cluster-based and trans-phosphorylation models. The simple cluster-based model simply reflects the hypothesis that diffusion decreases with Pom1 concentration P. It illustrates that this hypothesis cannot alone explain the decreasing relationship between Pom1/Tea4 and Tea4 (red line). By contrast this relationship is well accounted for qualitatively and quantitatively by the trans-phosphorylation model (blue line; see also 1F). Combining both Pom1 clustering and trans-phosphorylation can also account for the decreasing relationship between Pom1/Tea4 and Tea4 (purple line).
Figure 3A. HEK293 or U2OS/MycBioID-FAM111A cell lines were induced with doxycycline for 24 h. Total protein from 105 cells was resolved by SDS-PAGE, and probed in western blots for both endogenous FAM111A (71 kDa) and MycBioID-FAM111A (110 kDa) as well as full length and cleaved PARP (116 and 89 kDa, respectively). The Tubulin western blot is a sample loading control. B. HEK293/MycBioID-FAM111A cell lines with no treatment (- Dox), or treated with doxycycline, along with DMSO or 100 μM Z-VAD-FMK for 24 h (total inhibition of PARP cleavage was also observed when 50 μM Z-VAD-FMK was used). Total protein from ~ 105 cells was resolved by SDS-PAGE, and probed in western blots with Myc, PARP, or Tubulin antibodies. C. HEK293 cell lines were treated with doxycycline and Z-VAD-FMK for 24 h. The colonies were fixed then stained with crystal violet. Cell growth was quantitated as total area on ImageJ. Values are mean ± s.e.m. of independent experiments (n = 3).
Figure 3A-C Metal concentrations in the WT, dja6 dja5 and RNAi mutants. Fe concentrations in total leaves (A and B) and total chloroplast (C) from 4-week-old WT, dja6 dja5 and RNAi mutants were quantified by inductively coupled plasma mass spectrometry, and are shown as means ± SEM (n = 3 biological replicates) of μg g-1 dry weight (DW). WT and RNAi mutants used in (A and C) were grown on soil, while WT and dja6 dja5 seedlings used in (B) were grown on MS medium with 2% sucrose. Similar results were obtained in two additional independent biological experiments. Asterisks indicate significant differences from the value of WT (two-sample Student's t-test; *, P < 0.05; **, P < 0.01; ***, P < 0.001). D Volcano plot of the result from quantitative transcriptome profiling in WT and dja6 dja5 mutant. Statistical analysis was performed using Student's t-test. Data on the X-axis represent the Log2-ratio of FC (fold change) between the absolute abundances of transcripts identified from dja6 dja5 against WT. The Y-axis represents the Log10 of FDR (false discovery rate). All DEGs (differentially expressed genes) with FDR < 0.01 and FC > 2 are marked in grey, while all iron-related DEGs with FDR < 0.01 and FC > 2 are marked in red. The iron-related DEGs labeled with red dots within the black boxes are referred to in the text. All data are based on three biological replicates.
Figure 8Resting CD4+ T cells purified from patient samples (n= 18, Appendix Table S3) were treated with 30 µM of each PH compound for 24 hours, and HIV-1 RNA was measured in culture supernatants. Results are presented as HIV virions/mL.
Figure 5Length distribution of total small RNAs from BmN4 cells overexpressed with AcGFP, mCherry-Siwi or mCherry-Siwi-D670A. Two peaks (20-nt and 27-nt) correspond to siRNA/miRNA and piRNA respectively. MA plot of differential piRNA expression analysis between Siwi-D670A and Siwi overexpressed libraries. Each dot represents the mapped piRNA (> 25-nt) on a predicted silkworm gene. Predicted CDSs with mean RPM > 2 between two independent naive libraries were categorized into non-TE genes (red), potential-TE genes (orange) and TEs (blue) (see also Figure EV4A and Materials and Methods). Siwi-D670A overexpression up-regulates non-TE gene-derived piRNAs while TE-derived piRNAs are not affected. See also Figures EV4 and EV5. Split violin plots of piRNA expression fold change between AcGFP (control) and piRNA factor(s) overexpressed libraries. Overexpression of Siwi-D670A, BmVasa-E339Q and both mutants increase non-TE-derived piRNA (red, 626 genes) while TE-derived piRNA (blue, 818 genes) does not change. Bonferroni-corrected P-values and the effect sizes (r) were calculated by Asymptotic Wilcoxon rank sum test. Normalized coverage per million (CPM) of mapped piRNA reads (> 25-nt) on the CDS region of 4 representative genes. Colored areas represent reads from Siwi-D670A-overexpressed library and the grey areas represent reads from wild-type Siwi-overexpressed library. (Top) piRNA reads mapped to both sense and antisense directions on a TE gene (putative reverse transcriptase) and a potential TE gene (uncharacterized protein) with similar RPM between the two libraries. (Bottom) piRNA reads mapped to the sense direction on non-TE genes (ribosomal protein S9 and eIF4E-1) with elevated RPM in the Siwi-D670A library. Elevated peaks appear to spread around the pre-existing peaks on these genes in the wild-type library. Fold changes of piRNA expression levels in UTRs and CDS between Siwi-D670A and Siwi overexpressed libraries. Non-TE-derived piRNAs are similarly up-regulated across 5′ UTR (non-TE: 105 genes, TE: 274 genes), CDS (non-TE: 628 genes, TE: 811 genes), and 3′ UTR (non-TE: 126 genes, TE: 257 genes). Bonferroni-corrected P-values were calculated by Asymptotic Wilcoxon rank sum test. Fold changes of piRNA expression levels in introns (15,065 annotated regions), intergenic regions (11,124 annotated regions), and exons (10,177 annotated regions) between Siwi-D670A and Siwi overexpressed libraries. Only exon-derived piRNAs are up-regulated by Siwi-D670A overexpression, suggesting that the process is strictly cytoplasmic. Bonferroni-corrected P-values and the effect sizes (r) were calculated by Asymptotic Wilcoxon rank sum test.
Cholesterol dysregulation contributes to stress pathway induction and cell death A Immunofluorescence (IF) images of HCT116 cells treated as indicated for 12h (Imipramine and Domperidone, each 30 µM) and stained for cholesterol content using filipin III.Figure 6A Immunofluorescence (IF) images of HCT116 cells treated as indicated for 12h (Imipramine and Domperidone, each 30 µM) and stained for cholesterol content using filipin III. B Immunofluorescence (IF) images of HCT116 cells treated with Domperidone and co-stained for cholesterol and Lamp1. C Ratio of toxicity and viability of HCT116 spheroids (3D) treated as indicated (NEN 1.2 µM, Domperidone (Domp) 30 µM). Cyclodextrin content in the medium is indicated in percentage (%CD). Data information: data are presented as mean (SD) (N=3) and were analyzed by a one-way ANOVA with Tukey post-hoc test or a two-way ANOVA with Tukey post-hoc test * p< 0.05; ** p< 0.01;*** p< 0.001; **** p < 0.0001. D Ratio of toxicity and viability of U87 spheroids (3D) treated as indicated (NEN 1.2 µM, Domperidone (Domp), Imipramine (Imi), Amitriptyline (Ami), Desipramine (Desi), each 30 µM, Clomipramine (Clomi 20 µM, Cyclodextrin (CD) 0.75%). Data information: , data are presented as mean (SD) (N=3) and were analyzed by a one-way ANOVA with Tukey post-hoc test or a two-way ANOVA with Tukey post-hoc test * p< 0.05; ** p< 0.01;*** p< 0.001; **** p < 0.0001. E Relative mRNA expression levels of the specified genes in HCT116 cells, treated as indicated for 16h (NEN (N) 1.2 µM, Domperidone (D) 30 µM, Cyclodextrin (CyD) 0.75%). F Immunoblot analysis of HCT116 whole cell lysates using antibodies against gammaH2AX and treated as indicated for 16h (NEN 1.2 µM, Domperidone (Domp) 30 µM, Cyclodextrin (CD) 0.75%). Data information: data are presented as mean (SD) (N=3) and were analyzed by a one-way ANOVA with Tukey post-hoc test * p< 0.05; ** p< 0.01;*** p< 0.001; **** p < 0.0001.
TRAIL induces TAK1‐dependent AMPK activation and autophagy in retinal pigment epithelial cells.Figure 6(A) The lysates of hTERT-RPE1 cells transfected with indicated siRNAs for 48 h and left untreated or treated with 500 ng/ml TRAIL for 2 h were analysed by immunoblotting. (B) hTERT-RPE1-eGFP-LC3 cells transfected with indicated siRNAs for 48 h were left untreated or treated with 500 ng/ml TRAIL for 24 h and analysed for LC3 translocation (left) and sub‐G1 DNA content (middle) and AMPKα expression (right). (C) hTERT-RPE1-eGFP-LC3 cells were transfected with indicated siRNAs for 48 h and analysed for the indicated mRNAs (top). After 48 h, cells were left untreated or treated with 500 ng/ml TRAIL for 2 h, and analysed for P‐ACC and GAPDH (loading control) expression by immunoblotting. Similar results were obtained in two independent experiments. (D) Cells transfected as described in (C) and left untreated or treated with 500 ng/ml TRAIL, 10 μM ionomycin or starved for amino acids and glucose for 24 h were analysed for LC3 translocation. (E) Lysates of wild‐type (WT) MEFs and MEFs with an inactive TAK1 knock‐in (TAK1Δ) treated with 500 ng/ml TRAIL were analysed by immunoblotting. Similar results were obtained in two independent experiments. (F) WT and TAK1Δ MEFs left untreated and treated with 250 or 500 ng/ml TRAIL were analysed for cell death by the LDH release assay. Similar results were obtained in two independent experiments (A, C and E). The values represent mean±s.d. for two (D) or a minimum of three independent experiments (B, F). *P‐value 0.05, **P‐value 0.01 and ***P‐value 0.001 as compared with cells treated in the same way, but transfected without siRNA (B, D) or the wild‐type cells (F).
Immune response and physiology of monkeys immunized with recombinant adenovirus vaccine.Figure 1.Immune response and physiology of monkeys immunized with recombinant adenovirus vaccine. Time course of antibody response. Serum samples were diluted 40-fold prior to ELISA analysis. Animals in the high-dose and low-dose group were immunized with 1×109 and 1×108 pfu virus each time, respectively. Arrows indicate the time point for immunization. Immune response and physiology of monkeys immunized with recombinant adenovirus vaccine. Determination of virus neutralization antibody titer using 96-well microneutralization assay. An arbitrate titer of 2 was assigned to animals in the placebo and control group since there was no detectable neutralization activity in these samples. Statistical significance between different data sets was calculated using t-test. Immune response and physiology of monkeys immunized with recombinant adenovirus vaccine. ELISPOT analysis of IFN-γ response in PBMC samples. Pool A and B contain peptides corresponding to S1-orf8 fusion and N, respectively. Data represent two animals from each group. Immune response and physiology of monkeys immunized with recombinant adenovirus vaccine. Average food consumption after live virus challenge.
Figure 7(A) Two control and BSCL2fibroblast cell lines were delipidated and treated with OA for 1 h, fixed and stained with LD540. Maximum intensity projections of deconvolved confocal z-stacks. (B) Control and BSCL2fibroblasts were incubated with OA for 75-90 min, LDs were stained with LD540 and cells imaged live with widefield microscopy. Insets show overlay of two subsequent frames (400 ms apart). (C) Analysis of (B). Bars = 1 - [Pearson's colocalization coefficient between subsequent frames/ROI], ± SEM, n=120-140 ROIs (60-70 cells), 2 experiments, **p<0.005 (Mann Whitney test). (D) Control and BSCL2fibroblasts were transfected with ER marker plasmid (sfGFP-ER-3) for 24 h and treated with OA for 10-60 min. LipidTox Deep Red or LD540 was used to label LDs and cells were imaged live by airyscan microscopy. Examples of LDs with high mobility are shown, blue arrowheads indicate a LD moving along the ER, orange arrowheads indicate LDs moving independent of the ER. (E) Analysis of ER associated movement of LDs from live airyscan microscopy as in (D). Bars: % of LDs/ROI displaying indicated mode of movement, mean ± SEM, n= 50-42 ROIs (218-374 LDs), 2 experiments, **p<0.005 (Mann Whitney test). (F) Control and BSCL2fibroblasts were treated with OA for 1 h, fixed and stained with anti-ACSL3 antibodies and LD540. Representative sections of peripheral ER areas, maximum intensity projections of deconvolved confocal z-stacks. (G) Analysis of (F), with insets illustrating assigned categories of ACSL3 LD association. Insets are the same as in Fig 4F. Bars: % of LDs/ROI showing the category indicated, mean ± SEM, n= 11-10 peripheral ROIs from 11-10 cells/group (1200-2019 LDs), 2 experiments, **p<0.005 (unpaired T-test). (H) Delipidated fibroblasts were pulsed for 20 min with 0.1 mM alkyne-OA either directly (1) or after pre-incubation with 0.1 mM OA for 1 h (2), and chased in the presence of 0.1 mM OA for 40 min. Bars: % of alkyne-OA in neutral lipids (triacylglycerol and cholesterol esters), normalized to control cells in (1), mean ± SEM, n=11-12 samples, 2 experiments, *p<0.05 (unpaired T-test). For C,E,G and H the results are pooled of 2 controls and 2 patients.
Choroid plexus macrophages properties are controlled by complex microbiota.Figure 3(A) UMAP plot illustrating the color-coded aggregated transcript counts of published core signature genes for CAMs and microglia. The scale bars represent color coded sequencing depth-corrected log transformed transcript counts. (B) UMAP representation of 487 individual choroid plexus cells from lateral and fourth ventricles of SPF (green dots) and GF (yellow dots) mice. (C) UMAP representation of the choroid plexus cells of SPF and GF mice color-coded for the Seurat cluster assignment. The color-clusters mappings are indicated on the right hand side of the plot. The cell type annotations are based on published gene expression profiles. (D) Stacked bar plot (Marimekko chart) presenting the color-coded relative contribution of choroid plexus cells derived from SPF (green) and GF (yellow) mice. Ranges of p-values are provided for significantly enriched regions per cluster, based on hypergeometric tests. Benjamini-Hochberg correction was applied to correct for multiple testing (*P < 0.05; **P < 0.01). (E) Volcano plots of the differential gene expression analysis of n=51 SPF and 136 GF stromal cpMΦs (left) and n= 85 SPF and 134 GF Kolmer epiplexus cell (CPepi) cells (right) based on Wilcoxon Rank Sum tests. The shown genes are filtered based on an avg. log2FC > 0.2 and adjusted p-value < 0.05. (F) Heatmap of the top 10 differentially expressed genes per cluster (adjusted p-value of <0.05 based on Wilcoxon Rank Sum tests). The scale bar represents color-coded Pearson residuals. (G) UMAP maps color-coded for transcript counts of genes enriched in subsets of choroid plexus cells. The scale bars represent color coded sequencing depth-corrected log transformed transcript counts. (H) Representative Iba1+ immunohistochemistry in the choroid plexus of SPF, GF, ABX-treated, ASF, recolonized ASF, sDMDMm2, TLR2,3,4,7,9-deficient, SCFA-treated GF mice or FFAR2-deficient mice. Scale bar = 50 µm. (I-O) Quantification of stromal CPMΦ. Each symbol represents one mouse. Three to four sections per mouse were examined. Means ± s.e.m. are indicated. Significant differences were evaluated by unpaired t-test or one-way ANOVA followed by Tukey's post-hoc comparison test and marked with asterisks (*P < 0.05, **P < 0.01, ***P < 0.001). Data are representative of at least two independent experiments.
Figure 6A) Manhattan plot of genome-wide association for expression of Ifi203 in liver. Red line shows Bonferroni-corrected threshold and blue shows an FDR =0.01 pvalue of significance calculated based on FaST-LMM pvalues. B-D) Allelic variation plots showing the peak SNP for Ifi203 expression (rs31614030) at the CC or TT allele (x-axis) plotted against expression of Ifi203 (B), levels of hepatic PC(38:3) (C), and plasma insulin levels (D). Red line shows Bonferroni-corrected threshold and blue shows an FDR =0.01 pvalue of significance calculated based on FaST-LMM pvalues. E-G) Correlation between the parameters listed above showing significant relationships between hepatic Ifi203 and PC(38:3) (E), hepatic Ifi203 and plasma insulin levels (F) or PC (38:3) and plasma insulin (G). Pvalues were calculated based on significance of regression (students test) and adjusted for multiple comparisons (FDR = 0.05) H) Experimental design for validation of Ifi203 as a regulator of total hepatic PC levels on a HF/HS diet. Mice receiving the control virus (open bars) or shIfi203 (black bars) were analyzed for liver expression of Ifi203 (I), total PC levels in liver (J) P-values calculated using a students t-test between groups. Data represent means ± SEM (n =4-5 per group). Mice receiving the control virus (open bars) or shIfi203 (black bars) were analyzed for liver expression of Pemt (K), total liver TAG content (L), or plasma insulin levels (M). P-values calculated using a students t-test between groups. Data represent means ± SEM (n =4-5 per group).
The RecA and arch-elbow domains of FRH compared to Mtr4.Figure 4(A) The two RecA domains are rotated relative to one another in FRH (cyan, large cell) compared to Mtr4 (green, RNA backbone in orange). The change in positioning of RecA-2 with respect to RecA-1 results in an overall displacement from the Mtr4 domain juxtaposition that ranges from 1.1 - 4.0 Å throughout RecA-2 with the largest differences at the external helices. (B) Comparison of arch domains conformations from Mtr4 (green) and FRH (large cell in cyan, small cell in marine) after superposition of the most N-terminal helical region. The isolated KOW modules of FRH, Mtr4 (with FRH superimposed), and Ski2 have considerably different loop configurations.
Figure 1A CUEDC2protein levels in mouse tissues. Adult (12-week-old) mouse was sacrifices and total protein was extracted from the liver, kidney, lung, spleen, heart, stomach, intestine, prostate, testis, brain, and thymus. B (top) In vivo cardiac ischemia-reperfusion model protocol (30-minute ischemia followed by indicated times of reperfusion). (bottom) Mice were subjected to reversible ischemia in vivo for 30 minutes and reperfused for different time period. Protein was extracted from the area at risk of heart at the indicated time points and subjected to immunoblot analysis of CUEDC2 and CUEDC1. Representative results were shown from 2 mice at each time point, and experiments were repeated for three times. C Isolated primary ratneonatal cardiomyocytes were treated to hypoxia with serum free-medium for 6h and reoxygenated accompanying adding serum back for different time period in vitro and the protein level of CUEDC2 was tested at different time points during reoxygenation. Each experiment was repeated for three times. D CUEDC2 protein level was plotted using the immunohistochemical scores as described in methods. (left) Plot of CUEDC2 scores in each BZ and DZ (n = 9 patients). (right) Representative images from immunohistochemistry staining for CUEDC2 in tissues from patients who suffered acute myocardial infarctions. The boxed areas in the left images are magnified in the middle and right images. DZ, distant zone; BZ, border zone. Scale bars, 250 μm (left), 50 μm (middle and right). * p = 0.001.