EMBO/sd-character-level-ner huggingface dataset:
ACE2-protease co-expression and SARS-CoV-2 S-protein cleavage sites suggest a possible role for additional proteases in infection.Figure 6.(a) Multiple proteases are co-expressed with ACE2 in human lung scRNA-seq. Scatter plot of significance (y axis, -log10(adjusted P value)) and effect size (x axis) of co-expression of each protease gene (dot) with ACE within each indicated epithelial cell type (color). Dashed line: significance threshold. TMPRSS2 and PCSKs that significantly co-expressed with ACE2 are marked. (b) ACE2-protease co-expression with PCSKs, TMPRSS2 and CTSL across lung cell types. Significance (dot size, -log10(adjusted P value)) and effect size (color) for co-expression of ACE2 with selected proteases (columns) across cell types (rows). (c,d) Multiple proteases are expressed across lung cell types. (c) Distribution of expression (y axis) for ACE2, PCSKs and TMPRSS2 across lung cell types (x axis). White dot: median expression. (d) Proportion of cells (y axis) expressing ACE2, PCSK family or TMPRSS2 across lung cell types (x axis), ordered by compartment. (e) ACE2+PCSK+ dual positive cells across lung cell types. Fraction (y axis) of different ACE2+PCSK+ or ACE2+TMPRSS2+ dual positive cells across lung cell types (x axis). Dots: different individuals, line: median. (f) ACE2-protease co-expression analysis for the 20 most significant human proteases in AT2 cells. Significance (dot size, -log10(adjusted P value)) and effect size (color) for co-expression of ACE2 with different proteases (columns) across cell types (rows). (g) Additional protease expression in ACE2+TMPRSS2+ dual positive cells. Significance (y axis) and fold change (x axis) of differential expression for each human protease between ACE2+TMPRSS2+ dual positive vs dual negative cells within each indicated epithelial cell types (color). The top 20 most significantly differentially expressed proteases within AT2 cells and PCSKs across all epithelial cell types are highlighted.
Fig.Figure 2(A) Representative image of quadriceps from WTFlx and Ndufs3 smKO animals of 8 months of age. Muscle weight from Ndufs3 smKO males (black bar) and wild-type mice (white bar) from 6, and 8 months of age (n=5 each group). Bars represent means ± standard error (SEM). (B) Representative H&E, COX, and SDH staining of quadriceps from WTFlx and Ndufs3-Mlc1f smKO at 8 months old. (C) Cross-sectional area (CSA) of quadriceps muscle fibers. A minimum of 100 fibers/sample were analyzed (n =3/genotype). The percentage of central nuclei in skeletal muscle fibers of quadriceps muscle of WTFlx and Ndufs3 smKO at 8 months (n =3 mice for WTFlx and n=4 mice for Ndufs3 smKO). P values were calculated by Student's t test. (D) Serum lactate levels of WTFlx and Ndufs3-smKO animals at different ages. Ndufs3 smKO male mice (filled black squares) showed increased levels compared to matched WTFlx males (empty black squares). Error bars represent SEM. (E) BN-PAGE In-Gel Activities of Complex I and IV measured in homogenates from quadriceps of wild-type and Ndufs3-Mlc1f smKO animals at 2 and 4 months. (F-G) Western blots of muscle homogenates (quadriceps) of WTFlx and Ndufs3-Mlc1f smKO animals at different ages (2 and 4 months, respectively) using antibodies against PGC-1α, COX1 (complex IV subunit), NDUFS3, VDAC1, SDHA (complex II subunit), and β-actin. (H) Quantification of the western blots in panels F and G. Bars represent means ±SEM of n=4 for each group. P values were determined by Student's t test.
Figure 8Translation efficiency and UPF1 isoform expression conditionally alter target susceptibility by the NMD pathway.
GO term enrichment analysis of astrocyte clustersA - G Graphs showing top 10 enriched GO terms for each astrocyte cluster annotated in B.Figure 4A - G Graphs showing top 10 enriched GO terms for each astrocyte cluster annotated in Figure 1B. For all significantly enriched GO terms (analyzed by Gorilla)
Figure 5Heat map of metabolite relative levels in brown fat cells treated with or without 1mM asparagine. Quantification of representative metabolic intermediates of glycolysis in brown fat cells as in (A). n=3 independent experiments. Data information: Data represent means±SEM. *P<0.05; unpaired two-tailed Student's t test. Schematic illustration of key enzymes in glycolysis and tricarboxylic acid (TCA) cycle. Immunoblot detection of the glucose transporters, glycolysis and TCA key enzymes in primary brown fat cell line Asparagine was supplemented to cells during differentiation. Immunoblot detection of the glucose transporters, glycolysis and TCA key enzymes in immortalized brown fat cell line (E), BAT from mice fed asparagine (F) and injected asparaginase (G). Asparagine was supplemented to cells during differentiation.
Fig.Figure 7(A) Tumour sphere culture analysis of the tumour sphere formation ability of SNU-4th cells transfected with the above different mimics. Real-time PCR (B) analysis of EMT-related markers, stemness markers and drug resistance genes expression in SNU-4th cells transfected with the above different mimics. WB (C) analysis of EMT-related markers, stemness markers and drug resistance genes expression in SNU-4th cells transfected with the above different mimics. (D-E) Colony formation assay (D) and transwell assay (E) analysis of the colony-forming ability and migratory and invasive capability of SNU-4th cells transfected with the above different mimics. (F-G) Flow cytometric analysis of the rate of apoptosis (F) and SP cells (G) in SNU-4th cells transfected with the above different mimics. (H) Pearson correlation analysis of the correlation between the expression of circLMP2A and miR-3908. n = 69, P = 0.039, Pearson's correlation coefficient analysis. (I) Kaplan-Meier survival curves analysis of the correlation between miR-3908 expression and OS. n = 69, P = 0.049, log-rank test.
Gata1 and/or Gata2 modulates Scl binding in the enhancers of key hematopoietic transcription factors A Intersection of Scl binding sites in WT and Gata12KO Flk1+ MES shows Gata1‐ and/or Gata2‐dependent redistribution of Scl binding sites in a subset of target genes (two independent experiments).Figure 7A Intersection of Scl binding sites in WT and Gata12KOFlk1+MES shows Gata1‐ and/or Gata2‐dependent redistribution of Scl binding sites in a subset of target genes (two independent experiments). Selected GO terms among top 10 most enriched for Gata‐independent (blue) and Gata‐dependent (purple) Scl binding sites together with example genes reveal Gata1‐ and/or Gata2‐dependent functions for Scl‐mediated hematopoietic regulation. B-D SclChIP‐seq tracks in WT and Gata1,2KO Flk1+MES show Gata1‐ and 2‐independent Scl binding to cardiac regulators (Myocardin, Gata4) (B). B-D SclChIP‐seq tracks in WT and Gata1,2KO Flk1+MES show Gata1‐ and 2‐independent Scl binding to Gata1‐ and 2‐independent Scl binding to key hemato‐vascular regulators (Lyl1, Fli1) (C) and Gata1‐ and/or 2‐dependent Scl binding to key HSPC transcription factors (Myb, Runx1) (D).
Figure 1A. When an Anopheles mosquito feeds from an infected mammal, it takes up parasites with the bloodmeal. The parasites transform into motile ookinetes in the midgut. Myosin is essential for traversal of the midgut epithelium. Ookinetes transform into oocysts and develop into hundreds of sporozoites. Sporozoites egress from oocysts to float in the hemolymph. Active motility allows sporozoites to invade the salivary glands from where they are transmitted into the skin with the next bite. They traverse the skin and enter into a blood vessel. With the bloodstream they are transported until they reach the liver and actively invade a hepatocyte to develop into thousands of merozoites. These merozoites are released back into the bloodstream where they depend on myosin to actively invade red blood cells (RBCs) and multiply. Red and blue arrows indicate active and passive movements of the parasite, respectively. B. The motor protein MyoA localizes to the periphery of motile Plasmodium stages. Images show parasites expressing GFP-tagged MyoA. Nuclei were stained with Hoechst. Scale bar, 5 µm.
EPG-7 directly interacts with multiple Atg proteins.Figure 5.(A) EPG-7 coimmunoprecipitates with ATG-9::HA. (B) EPG-7 directly interacts with ATG-9 in a GST pull-down assay. (C and D) Coimmunoprecipitation reveals that EPG-7 associates with LGG-3 (C) (C and D) Coimmunoprecipitation reveals that EPG-7 associates with LGG-1 (D). (E) EPG-7 directly interacts with LGG-3. (F) EPG-7 fragments containing amino acids 852-1003 or 1004-1142, but not 762-851, interact with LGG-1. (G) Fragments of EPG-7 containing amino acids 762-851 or 852-1003 directly interact with ATG-18. (H) Fragments of EPG-7 containing amino acids 1-704 or 1143-1330 directly interact with UNC-51. (I) SQST-1 associates with LGG-1 in vivo. Embryonic extracts from epg-7 mutants show that interaction of SQST-1 with LGG-1 is EPG-7 independent. (J) Fragments of SQST-1 containing amino acids 351-499 and 604-693, but not 500-603, interact with LGG-1. (K) Fragments of SQST-1-containing amino acids 418-499 and 604-630 bind to LGG-1. Mutating the putative LIR in the 604-630 fragment (605YPDL608 to APDA) does not affect the binding. (L and M) SQST-1(del LGG-1-1+2)::GFP, in which the two LGG-1-binding fragments (amino acids 418-499 and 604-630) are deleted, is weakly expressed and diffusely localized in the cytoplasm in sqst-1(ok2892) mutants. (N and O) Loss of function of lgg-1 dramatically elevates the expression level of SQST-1(del LGG-1-1+2)::GFP, which forms a large number of aggregates. (L and N) DIC images of the embryos shown in M and O, respectively (P) SQST-1(del LGG-1-1+2)::GFP aggregates colocalize with EPG-7 in lgg-1;sqst-1 mutants. Insets show a magnified view.
Figure 4HEK293 Tet-off experiments showing the degradation of REL-OPT and REL-WT transcripts under vehicle (DMSO)- and cycloheximide (CHX)-treatment, post-doxycycline addition. data is representative of 3 independent experiments each with 3 replicates. The data represents the mean ± SD for 3 replicates. A two-way ANOVA with Holm-Sidak multiple comparisons was performed. P-values are denoted as follows: p < 0.05 (*), p<0.01 (**) and p<0.001 (***). HEK293 Tet-off experiments showing the degradation of IL6-OPT, IL6-WT and IL6-DE transcripts (B), under vehicle (DMSO)- and cycloheximide (CHX)-treatment, post-doxycycline addition. data is representative of 3 independent experiments each with 3 replicates. The data represents the mean ± SD for 3 replicates. A two-way ANOVA with Holm-Sidak multiple comparisons was performed. P-values are denoted as follows: p < 0.05 (*), p<0.01 (**) and p<0.001 (***). HEK293 Tet-off experiments showing the degradation of REL-OPT and REL-WT transcripts (C) under vehicle (PBS)- and anisomycin (ANI)-treatment, post-doxycycline addition. data is representative of 3 independent experiments each with 3 replicates. The data represents the mean ± SD for 3 replicates. A two-way ANOVA with Holm-Sidak multiple comparisons was performed. P-values are denoted as follows: p < 0.05 (*), p<0.01 (**) and p<0.001 (***). HEK293 Tet-off experiments showing the degradation of IL6-OPT, IL6-WT and IL6-DE transcripts (D), under vehicle (PBS)- and anisomycin (ANI)-treatment, post-doxycycline addition. data is representative of 3 independent experiments each with 3 replicates. The data represents the mean ± SD for 3 replicates. A two-way ANOVA with Holm-Sidak multiple comparisons was performed. P-values are denoted as follows: p < 0.05 (*), p<0.01 (**) and p<0.001 (***). HEK293 Tet-off experiments showing the degradation of REL-OPT, REL-OPT (+1 Frameshift) and REL-WT transcripts (E) post-doxycycline addition. data is representative of 3 independent experiments each with 3 replicates. The data represents the mean ± SD for 3 replicates. A two-way ANOVA with Holm-Sidak multiple comparisons was performed. P-values are denoted as follows: p < 0.05 (*), p<0.01 (**) and p<0.001 (***). HEK293 Tet-off experiments showing the degradation of IL6-OPT, IL6-WT, IL6-DE and IL6-OPT (+1 Frameshift) transcripts (F) post-doxycycline addition. data is representative of 3 independent experiments each with 3 replicates. The data represents the mean ± SD for 3 replicates. A two-way ANOVA with Holm-Sidak multiple comparisons was performed. P-values are denoted as follows: p < 0.05 (*), p<0.01 (**) and p<0.001 (***).
Mispositioning of the substrate cleavage domain by PS1 FAD mutations.Figure 5A PS1 FAD mutations display little or no effect on substrate interactions at the exosites. Asterisks indicate antibody crossreactivities to C99 monomer. B PS1 FAD mutations alter substrate binding to the PS1 NTF in the γ-secretase cleavage domain. The weak PS1 A246E FAD mutation alters substrate interactions predominantly at V49 and L52, whereas the highly pathogenic PS1 L166P FAD mutation causes more broad changes over the whole cleavage domain. Arrows denote changes in binding of individual residues. Corresponding quantitation of substrate binding is shown below the immunoblots. Bars denote the mean ± S.E. (n = 3). Yellow line indicates level of substrate binding to PS1 WT, which was set to 1. Blue and red bars indicate increases or decreases in binding, respectively. C Both mutants decrease crosslinking to the PS1 CTF. D Model depicting substrate mispositioning of the PS1 FAD mutants in the active site region. Red lightning mark indicates corresponding substrate miscleavage.
| 1,6-hexanediol treatments (1,6HD) differentiate early and late viral replication factories (a) Replication factories in MA104-NSP5-EGFP cells infected with RV at 4 HPI dissolve after >30 s post application of 4% (v/v) 1,6HD added to the cell culture medium (middle panel).Figure 3(a) Replication factories in MA104-NSP5-EGFP cells infected with RV at 4 HPI dissolve after >30 s post application of 4% (v/v) 1,6HD added to the cell culture medium (middle panel). Removal of 1,6HD results reassembly of multiple EGFP-NSP5-containing droplets dispersed in the cytosol (right panel). Bottom, replication factories at 12 HPI: before application of 1,6HD (left), 2 min after application (middle), and 15 min after removal of 1,6HD from cell culture medium (left). Note larger viral factories that remain refractory to 1,6HD treatment. Scale bar, 50 µm. (b) Sensitivity of RV replication factories to aliphatic alcohols at 4 HPI. Left to right -1,6-hexanediol (1,6HD); 1,3-propylene diol (1,3PD); 1,2-propylene diol, or propylene glycol (PG); glycerol (Gly); polyethylene glycol 200 (PEG200). Top panels - before application and bottom panels - 1 min after application of these compounds (4.5% v/v). Scale bar, 30 µm.
Figure 7A. Transient overexpression of GEMC1 leads to increased levels of FOXJ1 and MCIDAS expression (RT-QPCR) in HEK293T cells. Results for MCIDAS are graphed on a smaller scale in the right panel: V = vector and G = GEMC1. The mean and standard deviation of 3 individual experiments in HEK293T cells are graphed. Similar induction of FOXJ1 was observed in U2OS and T98G (Fig EV3). B. Both the CC and the TIRT domain of GEMC1 are required to activate FOXJ1 (RT-QPCR). A corresponding Western blot showing relative expression levels of the mutant GFP tagged GEMC1 variants is shown from HEK293T cells. The mean and standard deviation of 3 individual experiments in HEK293T cells are graphed. Similar results were also observed in U2OS (Fig EV3). C. Activation of FOXJ1 by GEMC1 is inhibited by the co-expression of Geminin (compare 3rd and 4th lanes). Example Western blot is shown below. Results graphed are the mean and standard deviation of 3 individual experiments in HEK293T cells. D. Co-expression of GEMC1 and Multicilin results in similar levels of FOXJ1 expression (measured by RT-QPCR) as Multicilin alone in HEK293T cells. The mean and standard deviation of 4 individual experiments in HEK293T cells are graphed. E and F. The activation of FOXJ1 by GEMC1 is partially dependent on Multicilin. HEK293T cells were transfected with a control siRNA (siC) or 2 different siRNAs against MCIDAS (si1 and si2) prior to being transfected with GFP or GFP-GEMC1 expression vectors. Relative MCIDAS (E) and FOXJ1 (F) expression levels were assessed by RT-QPCR. The mean and standard deviation of a representative experiment performed in triplicate is graphed. An additional experiment is presented in Fig EV3. G. Model for the role of GEMC1 in the differentiation of MCCs. Inhibition of Notch signaling by Mir34/449 is required for MCC differentiation and the ability of GEMC1 and Multicilin to activate transcription(Kyrousi et al, 2015; Liu et al, 2007; Marcet et al, 2011; Stubbs et al, 2012; Tsao et al, 2009). GEMC1 acts early, in conjunction with E2F4/5-DP1 (EDG), to activate genes including Multicilin and FoxJ1, likely through direct interaction with E2F4 at the promoters of FoxJ1 and some other E2F target genes (dotted line) (Fig 5, 6 and 7). The activation of Multicilin leads to further amplification of the transcriptional program through E2Fs (EDM complex)(Ma et al, 2014) and GEMC1 and Multicilin may form heterocomplexes (Fig 6E) with E2F4/5-DP1 (EDM-EDG) (Caillat et al, 2013). This leads to the optimal activation of FOXJ1, MYB, RFX3, and other transcription factors required for the expression of CCDC78, DEUP1, CCNO and other downstream components of the MCC differentiation pathway(Funk et al, 2015; Klos Dehring et al, 2013; Ma et al, 2014; Tan et al, 2013; Wallmeier et al, 2014; Zhao et al, 2013). See discussion for further details.
Figure 3A t-SNE plots showing the original (left) and re-clustered (right) adipogenic lineage cells by integrated analysis of homeostatic and stress conditions. Top 15 PCs were chosen for the clustering. B Dot plots showing the gene expression patterns of selected genes in each cluster. C Stacked bar charts showing the cell cycle status in all clusters. D Flow cytometry analysis of BrdU incorporation in uncultured Lepr-Cre+Notch3+/- BMSCs (n=4 independent experiments). Eight-week-old Lepr-Cre; tdTomato mice were given a single intraperitoneal injection of BrdU (100 mg/kg body mass) and maintained on 0.5 mg/ml of BrdU in the drinking water for 14 days. E Immunofluorescent images of the distal femur in 8-week-old Lepr-Cre; tdTomato mice. Notch3 (green), tdTomato (red), CD31 (gray), DAPI (blue). Sinusoid (a), arteriole (b), artery (c) and avascular bone marrow (BM, d) regions were shown. Arrowheads indicated Notch3+ tdTomato+ adventitial cells closely associated with ECs. Arrows indicated Notch3- tdTomato+ reticular cells in the bone marrow that were not associated with ECs. Scale bars were 10 µm. F Localization quantification of Lepr-Cre+Notch3+ cells relative to bone marrow ECs (n=5 biological replicates from three independent experiments). Cells within 5 µm diameter of ECs were considered adjacent. G G Graphical illustration of the 3D co-culture system. H Volcano plot showing DEGs in the bulk RNA-seq analysis (n=3 biological replicates). Green dots represent down-regulated genes. Red dots represent up-regulated genes. I qPCR analysis of Notch3 and Cdk6 expression (n=3 independent experiments). J Flow cytometry analysis of BrdU incorporation in Lepr-Cre+Notch3+/- BMSCs after 3D co-cultured with bone marrow ECs (n=3 independent experiments). BrdU was administered at a final concentration of 10 µM from culture day 1 to day 5. K, L GO terms (K) and KEGG pathways (L) enriched in up-regulated genes. M Representative confocal images of BMSCs 3D co-cultured with bone marrow ECs. Z-stack projection was shown. Notch3 (green), tdTomato (red), CD31 (gray), DAPI (blue). Arrowheads indicated Notch3+tdTomato+ adventitial cells. Arrows indicated bone marrow ECs. Scale bar was 50 µm. N Localization quantification of Lepr-Cre+Notch3+ cells relative to bone marrow ECs after 3D co-culture (n=3 biological replicates from three independent experiments). Cells within 25 µm diameter of ECs were considered adjacent. O Heatmap showing the average expression levels (column-wide Z score) of secreted factors with clustering.
Figure 1A. Schematic for the experimental workflow and the computational pipeline employed for the discovery and annotation of endothelium-enriched long non-coding RNAs. B. Distribution of Translation Efficiency Score (TES) across novel lncRNAs identified in this study and RefSeq genes. Box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend till 5th and 95th percentiles. C. Differential expression analysis revealed 156 endothelial-enriched lncRNAs with a fold change of at least 10 (closed circles) and 685 lncRNAs at 2 fold (open circles). D. UCSC browser snapshot of the zebrafish vascular endothelial associated lncRNA 2 (veal2) transcript. 5' RACE and 3' RACE data confirmed ends of the veal2 transcript. E. Ribosomal pull down shows lack of occupancy of ribosomes on veal2. fli1a and actb were used as positive controls. F-I. e-GFP fusion assay confirms lack of peptide formation from veal2 sequence. (F-G) mitfa-eGFP fused transcript. (H-I) veal2-eGFP fused transcript. Arrowheads indicating e-GFP expression in mitfa-eGFP injected embryos. Scale bar-100μm. J. Relative abundance analysis from different subcellular fractions revealed veal2 is a cytoplasmic lncRNA. Bar graph represents the relative abundance of veal2 and actb transcripts across different fractions of the cell. Data from three different experiments plotted as mean percentage values ± standard deviation. K. Relative expression of veal2 across Fluorescence activated cell sorted (FACS) GFP(+) endothelial cells (EC) and GFP(-) non endothelial cells (NEC). fli1a and actb were taken as positive control and normalization control, respectively. Data from three different experiments represented as fold change relative to EC values ± standard deviation. L. Whole mount in situ expression analysis of the veal2 transcript across different stages of zebrafish embryos. (LI,II) 1K cell stage, (LIII,IV) 10 hpf stage, (LV,IV) 28 hpf stage. LI,III,V- antisense-veal2 probe. (LII,IV,VI) sense-veal2 probe. Magnification-2.5X, Scale bars-100μm. M-N. Expression of veal2 transcript (FPKM scores) across (M) 11 developmental stages and (N) all publically available RNAseq data of zebrafish's different tissues or cell types compiled by ZFLNC database (Hu et al, 2018).
Figure 2C57BL/6 mice were treated with mouse recombinant IL-33 or PBS daily for 5 consecutive days. (A, B) Representative FACS analysis showing the proportion of Tregs (CD4+Foxp3+) in the CD4+ T cell compartment from the spleens (A) and kidneys (B) at day 3 after treatment in C57BL/6 mice receiving PBS (n=4) or IL-33 (n=6). C57BL/6 mice were treated with mouse recombinant IL-33 or PBS daily for 5 consecutive days. (C, D) Representative FACS analysis showing the proportion of ILC2s (Lin-GATA-3+) in the CD45+ leukocyte compartment from the spleens (C) and kidneys (D) at day 3 after treatment in C57BL/6 mice receiving PBS (n=4) or IL-33 (n=6). (E, F) proportion of Tregs (E) and ILC2s (F) in the spleen and kidney in PBS-injected controls (n=4) and at weeks 1-12 after IL-33 treatment (n=4-6 per IL-33-treated group). Data information: Data shown are the mean ± SEM; Statistical analysis was performed with an unpaired t-test, **P<0.01, ***P<0.001.