EMBO/sd-character-level-ner huggingface dataset:
Figure 1(a) Illustration of experimental protocol outlining DSS induced colitis in Lgr5GFP-CreERT2;ROSA26tdTomato mice. (b) RNAscope analysis of Lgr5 mRNA in DSS colitis demonstrating loss of Lgr5 transcript (N=3 per condition). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines indicate basement membrane. Scale bars =50µm (c) Hematoxylin and Eosin staining of the colonic epithelium following DSS induced damaged. Crypts are dramatically injured by d5. At d8 through d12, regenerating crypts are observed. Data information: Nuclei are counterstained with Dapi (blue); white dashed lines indicate basement membrane. Scale bars =50µm (d-e) Compared to untreated controls, DSS treatment ablates Lgr5-GFP+ stem cells and results in functional loss of tdTomato+ lineage tracing as early as d5. Lgr5-GFP+ stem cells reappear by d12 (N=3-4 per condition). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines indicate basement membrane. Scale bars =50µm Data are represented as mean ± SD (e) analyzed using Student's t-test. *P≤0.05, ** P≤0.01. (f) Effects of DSS colitis injury on RNA expression levels of stem (Lgr5 and Krt19) and progenitor (Atoh1 and Notch1) cell markers. Lgr5 mRNA expression is significantly decreased after exposure to DSS (N=6-7 per condition). Data are represented as mean ± SEM analyzed using Student's t-test. *P≤0.05, ** P≤0.01. (g) DSS and DT treatment of Lgr5DTR-GFP mice. Data are represented as mean ± SEM analyzed using Student's t-test. *P≤0.05, ** P≤0.01. Mice body weight (h) are comparable between three treatments: DSS+DT (N=12), only DSS (N=8) or only DT (N=3). Data are represented as mean ± SEM analyzed using Student's t-test. *P≤0.05, ** P≤0.01. Mice survival (i) are comparable between three treatments: DSS+DT (N=12), only DSS (N=8) or only DT (N=3). Data are represented as mean ± SEM analyzed using Student's t-test. *P≤0.05, ** P≤0.01. (j) Hematoxylin and Eosin staining of the colonic epithelium shows no morphological difference between DSS alone and DSS+DT treated mice. Data information: Nuclei are counterstained with Dapi (blue); white dashed lines indicate basement membrane. scale bar (j) =500µm. (k) The extent of epithelial damage is similar in mice treated with DSS alone versus DSS+DT (to ablate Lgr5+ stem cells) (N=3 DSS; N=6 DSS+DT). Data are represented as mean ± SEM analyzed using Student's t-test. *P≤0.05, ** P≤0.01. (l) RNAscope for Lgr5 in Lgr5DTR-GFP mice showing loss of Lgr5 transcripts after DT treatment (N=3-4 per condition). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines indicate basement membrane. Scale bars =50µm
Figure 6The representative graphs for quantification of the expected Nm32/A% and Nm34/A% ratios of G37-tRNAPhe(GAA), tRNALeu(UAA), tRNATrp(CCA), tRNAArg(ACG), tRNAArg(UCG), and A37-tRNAMet(CAU), which were isolated from WT, ftsj1 KO, and wdr6 KO cells by UPLC-MS/MS analysis. Error bars represent the standard deviation of three independent experiments. p values were determined using two-tailed Student's t-test for paired samples. ***p < 0.001. n.s., no significance. n.d., not detected.
Figure 7A Exon 1 of AS-RBM15 anti-sense RNA is used to enhance RBM15protein translation via incorporation into the RBM15mRNA-containing polysome via putative RNA interaction. Given that RBM15 protein translation in the presence of AS-RBM15 is rapamycin-resistant, the 5'CAP of RBM15 mRNA is needed for scanning of the protein translation initiation complex consisting of eIFs (eukaryotic initiation factors). The repeat elements such as AluSx may play no roles in protein translation. B During megakaryocyte terminal differentiation, AS-RBM15, activated by RUNX1 at transcriptional level, elevates RBM15protein via translation. Thus, AS-RBM15 increases the dosage range of RBM15 during MK terminal differentiation.
AosR rewires transcriptome in response to oxidative stress.Figure 3Volcano plots were obtained from DEseq2 analysis across three biological replicates of Rv vs Rv∆aosR. DEGs are highlighted as red dots (log2 fold change<1; p adj<0.1). P values were calculated using DEseq2, which uses Wald test and were adjusted for multiple testing using Benjamini-Hotchberg method. Numbers in top quadrants reveal upregulated (in green) and downregulated (in red) in Rv compared with Rv∆aosR. b. Heat map indicates log2 fold changes of enriched (green) and depleted (red) genes in Rv compared with Rv∆aosR. Color intensity indicates relative higher upregulation and downregulation, respectively. Same as (a) under oxidative conditions. Venn diagram illustrating the common set of genes between RvandRv∆aosR under oxidative conditions compared with Rv∆aosR in normoxic and oxidative conditions. Same as (b) under oxidative conditions. DEGs are clustered according to their functional category. The analysis was performed as explained in Appendix Fig S1. Bar graphs depicting the percentage of enriched (green) and depleted (red) DEGs plotted in (e) belonging to a particular functional category. Relative gene expression of selected DEGs measured by qRT-PCR in Rv compared with Rv treated with CHP (g) and Rv as compared with Rv∆aosR under oxidative conditions (h). Data were normalized with respect to 16s rRNA and results are expressed as mean log2 fold change + SD of three independent replicates and is representative of one of two biological replicates.
DAPk family proteins do not induce cell death via the mitochondrial pathway.Figure 2.(A) Scoring loss of mitochondrial membrane potential (ΔΨm). 293 cells expressing luciferase (black), DRP-1 Δ73 (pink), DAPk ΔCaM (purple), and Bax (green) were assayed for loss of mitochondrial membrane potential 24 h after transfection using flow cytometric analysis of TMRM fluorescence. The fraction of TMRM-negative cells calculated from three experiments is shown in the graph below. The small increase in TMRM fluorescence in the kinase-transfected cells is not statistically significant. (B) Scoring the release of cytochrome C from mitochondria. 293 cells cotransfected with luciferase (1 and 2), Bax (3 and 6), DRP-1 Δ73 (7 and 8), or DAPk ΔCaM (9 and 10) and GFP constructs were incubated for 24 h and immunostained using anti-cytochrome C antibodies. Cells were visualized for cytochrome C (left) or GFP (right) fluorescence. Bax-transfected spread (3 and 4) or blebbed (5 and 6) cells are shown. In fields that also contain nontransfected cells, arrows point to GFP-positive cytochrome C-stained cells. (C) Assessing the effects of Bcl-2 and Bcl-XL. 293 cells were cotransfected with luciferase, DRP-1 Δ73, DAPk ΔCaM, or Bax, and either Bcl-2 or Bcl-XL together with GFP. GFP-positive cells were visualized by fluorescent microscopy and scored for the appearance of cell death morphology 24 h after transfection. Total cell death refers to the sum of all morphological changes observed.
Figure 6(A) Top: Rose plot visualizing the acrophases (based on rhythmic genes in the liver transcriptome from (Atger et al., 2015)) of genes exhibiting heat-induced (orange, n=797) and cold-induced (blue, n=828) upregulation of GE in mouse hepatocytes, respectively. Bottom: Acrophases of genes with cold-induced (blue, n=55) and heat-induced (orange, n=47) poison exon events, respectively. Numbers indicate respective ZT, with the left half representing night (at which mice are active and have an elevated body temperature) and the right half representing day (at which mice are asleep with lower body temperature). The black circles represent expected normal distribution if data would be randomly sampled. (B) Correlation of rhythmic Srsf10 expression (orange, left y-axis) and exon 3 inclusion (black, right y-axis) in mouse liver samples from the indicated ZTs (n=4, mean +/- SEM). Quantifications were obtained by RNA-seq analysis of datasets from (Atger et al., 2015). (C) Representative Western blot of SRSF10 protein levels from mouse liver nuclear extracts (NX) from different ZTs. The different SRSF10 variants are highlighted on the right. SRSF10-fl and SRSF10-2 are the result of differential last exon usage. hnRNP L was used as a loading control. The asterisks could represent hyperphosphorylated SRSF10-fl through higher CLK activity during the day.
Striatal infusion of the high dose of cholesterol increases endogenous cholesterol catabolism and synthesis in the striatum of HD mice.Figure 4(A) Schematic pathway of cholesterol synthesis and cholesterol precursors and catabolites in the brain. Green arrows indicate enzymes with downregulated mRNA in HD, and red arrows indicate cholesterol precursors or metabolites that were decreased per ID-MS; SREBP2-dependent genes are in bold. Here, lanosterol, 7-lathosterol, desmosterol, and 24S-OHC (highlighted in the boxes) were measured by ID-MS. (B) 24S-OHC level measured by mass spectrometry in the infused and contralateral striatum of wt, R6/2‐ACSF, and R6/2 chol-high mice at 12 weeks of age after a 4-week striatal infusion of cholesterol (N=4/group). All values are expressed as % above the mean of wt, and these data are shown as scatterplots with means±standard error. Each dot corresponds to the value obtained from each animal. (C-E) Lanosterol (C), lathosterol (D), and desmosterol (E) level measured by mass spectrometry in the infused and contralateral striatum of wt, R6/2 ACSF, and R6/2 chol-high mice at 12 weeks of age after 4-week striatal infusion of cholesterol (N=4/group). All values are expressed as % above the mean of wt, and these data are shown as scatterplots with means±standard error. Each dot corresponds to the value obtained from each animal. (F-I) Nuclear (white arrows) and perinuclear (yellow arrows) localization of endogenous SREBP2 in the striatum of wt, R6/2 and R6/2-chol mice. Representative confocal image (F and H) and relative quantification (G and I) of SREBP2 (red) in wt and R6/2 mice and in the infused and contralateral striatum of R6/2 chol-high mice (N=4). Hoechst (Ho, blue) was used to counterstain nuclei. Scale bar in F and H: 10 µm. Graphs in (G and I) represents the intensity of SREBP2 normalized on nuclei (%). Data are shown as scatterplots with means±standard error. Each dot corresponds to the value obtained from each image. Statistics: Student's t-test (**p<0.01; ****p<0.0001). J, K Representative high-magnification confocal images of immunostaining against SREBP2 (red) and NeuN (J) or GFAP (K) (green) on coronal sections of brains from R6/2 chol-high mice. A cell in the infused striatum, positive for NeuN and GFAP respectively, is shown. Hoechst (Ho, blue) was used to counterstain nuclei. Scale bars: 1 µm.
Figure 3a and b, Schematic representation of the potential acetylation domain organization of ISX and its lysine mutants (AC1‒AC3). Data information: Each experiment was repeated at least three times. c, Recombinant PCAF acetylates His6-ISX at lysine residue 69 by in vitro acetylation assay. Acetylated ISX was detected by anti-acetyl Lysine antibody. Data information: Each experiment was repeated at least three times. d and e, The protein levels of GFP-tagged WT or mutant ISX, PCAF and BRD4 were determined in cytosol, nuclei, and anti-GFP immunoprecipites of A549 cells by Western blotting. Acetylated ISX was detected by anti-acetyl Lysine antibody. Data information: Each experiment was repeated at least three times. f, The protein levels of total and acetylated histone H3 were determined in anti-histone H3 immunoprecipites of A549 cells by Western blotting. Data information: Each experiment was repeated at least three times. The cell migration (wound healing, g) activity were determined in A549 cells with GFP-tagged wild or ISX mutants. Data are presented as mean ± SD in graph (***, p < 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Scale bar, 100μm. Data information: Each experiment was repeated at least three times. h, The cell invasion (transwell, h) activity were determined in A549 cells with GFP-tagged wild or ISX mutants. Data are presented as mean ± SD in graph (***, p < 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Scale bar, 100μm. Data information: Each experiment was repeated at least three times. i, Schematic representation of tumor xenograft metastasis activity of constitutively expressing RFP A549 cells transfected with wild type or ISX AC3 mutant cDNA. Modified A549 cells were directly injected into lung to form xenograft tumor mass. Data information: Each experiment was repeated at least three times. j. Tumor xenografts metastasis activity of constitutively expressing RFP A549 cells transfected with wild type or ISX AC3 mutant cDNA were imaged by IVIS imaging system at fifth weeks Data information: Each experiment was repeated at least three times. k, Kaplan-Meier survival curve analysis of nude mice xenograft injected with A549 cells carrying GFP, ISX-GFP and ISX Ac-GFP (AC3) (n = 10). p = 0.0003. p‐values were calculated by log‐rank (Mantel-Cox) test comparing the two Kaplan-Meier curves. Data information: Each experiment was repeated at least three times.
Figure 1(A) Generation of RNA samples from mouse primary hepatocytes for analysis of temperature-dependent AS-decay. (B) Automatic cluster-mapping of the temperature-dependent splicing changes in CHX, based on changes in PSI (percent spliced in). Categories (right) were manually assigned. (C) Examples for cold-induced (blue) or heat-induced (red) AS-decay via exon inclusion or exon skipping. In each example, on top a simplified exon-intron structure is given, PTCs and the length of frameshift inducing exons are highlighted. Predicted splicing changes were validated by radioactive RT-PCR with primers binding to the surrounding constitutive exons. Box plots show median PSI of validation PCRs of four different samples from at least two different mice, whiskers show min to max. Individual data points are shown as circles. (D) Classification of temperature-dependence in genes with CHX-dependent splicing events. Number of genes and percentages are indicated. (E) GO-term analysis of temperature-controlled AS-decay genes. All expressed genes (mean tpm > 0) served as background.
A schematic example representing c-Jun-mediated adaptive resistance to vemurafenib-induced apoptosis In the sensitive cell line (e.Figure 7In the sensitive cell line (e.g., MMACSF), vemurafenib shifts the majority of the cell population toward quiescence (represented as pRbLowcells) and fully inhibits pERK, p-cJun, and pS6 in these cells, leading to high levels of apoptosis. In the relatively resistant cell line with p-cJun up-regulation (e.g., WM1552C), vemurafenib significantly inhibits pERK and induces quiescence in the majority of cell population, but high levels of p-cJun lead to incomplete suppression of pS6 and protect cells from apoptosis. Combination of a selective JNK inhibitor, JNK-IN-8, with vemurafenib inhibits p-cJun and pS6 in quiescent cells and increases the fraction of apoptotic cells.
Full transcriptome profiles of SARS-CoV-2 Patients with NGS, qRT-PCR, and LAMP.Figure 2.LAMP.(a) Clinical samples tested by qRT-PCR (Positive, dark red or Negative, light grey) were sequenced and run through the LAMP assay. These results were compared to the buffer blanks (Negative Control), dark grey, Synthetic RNAs or Vero 6 cell extracts with SARS-CoV-2 infection (Positive Controls, light red), and Subway Samples (Environmental, blue). Read proportions are shown on the y-axis. (b) SARS-CoV-2 abundance, as measured with NGS and percentage of reads (y-axis) is compared to the Ct Threshold for qRT-PCR (x-axis), with lower Ct values representing higher viral abundance, and the LAMP reaction output (Fluorimeter values, black to yellow scale). (c,d) Read mapping to archaea (red), bacteria (green), fungi (yellow), human (blue), and SARS-CoV-2 (orange), and other viruses (grey), across the clinical controls (CN, CP), environmental samples, qRT-PCR negative, and qRT-PCR positive samples.
Figure 2A. Detection of polyubiquitylated species of endogenous Sufu co-immunopurified from DAOY cells transfected with Myc-tagged ubiquitin (Ub) either in the presence of non-targeting siRNA (Control) or two siRNAs against Fbxl17 (1) and (2). MG132 (10µM) was added in all samples. B. Detection of polyubiquitylated species of Sufu upon co-transfection of HEK293T cells with HA-tagged Sufu and Myc-tagged ubiquitin (Ub) either in the presence of non-targeting siRNA (Control) or two siRNAs against Fbxl17 (1) and (2). MG132 (10µM) was added in all samples. C. Fbxl17 mRNA relative levels in DAOY and HEK293T cells upon Fbxl17 depletion with either a non-targeting siRNA (Control) or two siRNAs to Fbxl17 (1) and (2). D. Detection of ubiquitylated Sufuco-immunoprecipitated from HEK293T cells co-transfected with HA-tagged Sufu, Myc-ubiquitin (Ub) along with either Flag-tagged Fbxl17 wild type (WT) or a mutant lacking the F-box domain (Fbxl17ΔF). MG132 (10µM) was added in all samples. E. Detection of ubiquitylated Sufuco-immunoprecipitated from HEK293T cells co-transfected with Myc-tagged ubiquitin (Ub), Flag-tagged Fbxl17 and HA-tagged Sufu WT or Sufu mutant K257R. MG132 (10µM) was added in all samples.
Wildtype (WT) HSCs compensate for the lymphopoietic deficiencies of co-transplanted mutant HSCs in blood production.Figure 1 A We co-transplanted barcoded WT HSCs with competitor WT, B cell deficient (uMT-/-), or B and T cell deficient (NSG or Rag2-/-γc-/-) HSCs into irradiated recipient mice. Peripheral blood was harvested from recipient mice at 6 to 8 months after transplantation and sorted into granulocytes (Gr), B, CD4 T, and CD8 T cells for population and clonal level analyses  B-C Competitor donor derived Gr, B, CD4 T, and CD8 T cells in the peripheral blood. In the control group, competitor donor cells are WT HSCs. In the deficient group, competitor donor cells are uMT-/- or NSG HSCs Data information: Data are shown as percentages of the total number of white blood cells (WBCs). Data were collected at month 7 post transplantation for the uMT-/- group and month 8 post-transplantation for the NSG group, and presented as mean ± SEM. n=7 mice for the uMT-/- group and n=6 for the NSG group. *p<0.05, **p<0.01, ***p<0.001 (two-tailed and two-sample equal variance Student"s t-test)  D-E WT donor derived Gr, B, CD4 T, and CD8 T cells in the peripheral blood Data information: Data are shown as percentages of the total number of white blood cells (WBCs). Data were collected at month 7 post transplantation for the uMT-/- group and month 8 post-transplantation for the NSG group, and presented as mean ± SEM. n=7 mice for the uMT-/- group and n=6 for the NSG group. *p<0.05, **p<0.01, ***p<0.001 (two-tailed and two-sample equal variance Student"s t-test)  F-G Total production of Gr, B, CD4 T, and CD8 T cells in the peripheral blood (derived from WT HSCs, competitor HSCs, helper whole bone marrow cells, and residual host cells) shown as percentages of the total number of white blood cells (WBCs). Data information: Data are shown as percentages of the total number of white blood cells (WBCs). Data were collected at month 7 post transplantation for the uMT-/- group and month 8 post-transplantation for the NSG group, and presented as mean ± SEM. n=7 mice for the uMT-/- group and n=6 for the NSG group. *p<0.05, **p<0.01, ***p<0.001 (two-tailed and two-sample equal variance Student"s t-test)
| Disruption of iron influx systems partially restores tolerance of the ∆vxrAB mutant against PenG exposure.Figure 6(A) Time-dependent killing experiment in the presence of PenG. (B) and (C) Iron uptake mutants restore ∆vxrAB growth on 10% sucrose. The indicated strains were grown to exponential phase (OD600~0.5) in LB medium and spot-plated on 10% Sucrose plates with or without additional iron sulfate. An example is shown in (B), quantification of cfu is shown in (C). Data information: Data are average of 3 independent biological replicates, error bars represent standard deviation. ∗∗∗ P<0.0003; ∗∗∗∗ P<0.0001 (paired t-test).
An ULK1-independent ATG13-ATG101 complex regulates basal ATG9A function and p62/SQSTM1 turnover.Figure 8During adaptor-mediated basal autophagy, an ULK1-inpependent ATG13-ATG101 complex interacts with ATG9A at p62/SQSTM1 clusters and promotes the ATG9A-mediated turnover of these clusters. Upon loss of the ULK1-indpendent ATG13-ATG101 complex, or disruption of the ATG13-ATG101-ATG9A interaction, the p62/SQSTM1 clusters accumulate, resulting in an accumulation of ATG9A at p62/SQSTM1 clusters.
Figure 4A. Eight weeks old mice were injected with liposomes coupled to scrambled siRNA (siScr) or sequences targeting MST1 MST2 (siMST). Each dot is representing an independent animal. The % of Mst1 Mst2 mRNA remaining in the liver was tested by RT-PCR, 1, 3 and 6 days post injection and calculated compared to control non-transfected livers. Unpaired, two-tailed Student t-test was used to calculate the significance of mRNA remaining in comparison to non-transfected control livers at each time point. B. Western blot detection of MST1, p-LATS1 and β-actin 1, 3 and 6 days post siRNA injection. A representative animal from each time point is shown. C. Western blot detection of YAP1, p-YAP1, H3 and p-H3, 3 days post siRNA injection. Two representative animals from each group are shown. All samples were run on the same blot. The blot is split due to non-consecutive loading of the samples. D. Quantitative RT-PCR analysis of RNA isolated from mouse liver for FoxM1B, Birc5 and cyclin B1, 1, 3 and 6 days post injection. Log2 fold change was calculated using non-transfected mouse liver as control. Unpaired two tailed Student t-test was used to calculate the significance of fold change of in comparison to a panel non-transfected control livers. E. HNF4α and Ki67 were detected by IHC and cells positive for both were classified as proliferating hepatocytes. Ki67 positive hepatocytes are indicated with an asterisk and Ki67 negative bile ducts/biliary cells with an arrow in tissue 3 days post siRNA delivery. The percentages of positive hepatocytes at day 3 and day 6-post injection are graphed. Two-tailed Student t-test was used to calculate the significance of percentage of positive hepatocytes in comparison to non-transfected control livers.
Figure 7In normal condition, FTO demethylases m6A modification of Hif1a mRNA, which in turn prevents YTHDC2-mediated mRNA translation and thermogenic gene expression, thereby increasing white adipocytes differentiation and lipid accumulation, leading to HFD-induced obesity. FTO deficiency in adipose tissue increases mRNA m6A level of Hif1a transcript, leading to YTHDC2-mediated transltion and enhanced protein expression of HIF1A. Subsequently, HIF1A promotes transcription and expression of thermogenic genes, including Ppargc1a, Prdm16, Pparg, which results in white adipocytes browning and thermogenesis, thereby resisting obesity.