EMBO/sd-character-level-ner huggingface dataset:
Characterization of the PfMev CLD-EcDPCK-mCherry-apt Δdpck line under permissive and non-permissive conditions A.Figure 5A.) Construct used to generate the PfMev CLD-EcDPCK-mCherry-apt parasite line. B.) Genotyping PCR confirming the deletion of the endogenous DPCK (Δdpck) using primer pairs C.) Live epifluorescence microscopy of the PfMev CLD-EcDPCK-mCherry-apt Δdpck line. This parasite line expresses api-SFG (green) and CLD-EcDPCK-mCherry (red) with DAPI marking the nuclei (blue). This parasite line was grown in the presence of 0.5μM aTc. D.) The PfMev CLD-EcDPCK-mCherry-apt Δdpck parasite line grown in the absence of aTc for 48 hours. The brightness of the red fluorescence image was increased to demonstrate the lack of mCherry signal associated with the parasite. E.) The PfMev CLD-EcDPCK-mCherry-apt Δdpck parasite line grown in the presence of 0.5μM aTc, and in the presence of 0.5μM Shield1 (Shld) for 48 hours. F.) The PfMev CLD-EcDPCK-mCherry-apt Δdpck parasite line grown in the absence of aTc, and in the presence of 0.5μM Shield1 (Shld) for 48 hours. The brightness of the red fluorescence image was increased to demonstrate the lack of mCherry signal associated with the parasite. Data information: All microscopy images represent fields that are 10µm long by 10µm wide. G.) Growth curve of the PfMev CLD-EcDPCK-mCherry-apt Δdpck parasite line grown either in the presence of 0.5μM aTc and the absence 0.5μM Shield1 (permissive condition, blue), or the absence of 0.5μM aTc and the presence of 0.5μM Shield1 (non-permissive condition, red). Pantothenate was supplied at 50nM in both conditions and the cultures were diluted 1:5 on day 4. Treatment under non-permissive conditions resulted in reduced parasite growth beginning at day 1 (two-way ANOVA, followed by Bonferroni's correction; *, P < 0.05). Error bars represent the standard error of the mean from two independent experiments, each conducted in quadruplicate.
Small-molecule driven cell type enrichment as a model for intestinal differentiation.Figure 1 (A) Illustration of the small intestinal crypt-villus structure and the organoid culture conditions that we use to enrich for specific cell types  (B) Fluorescence microscopy images of typical mouse small intestinal organoids under different culture conditions. Lgr5+ intestinal stem cells are labeled with GFP, which are ubiquitously present, restricted to the bottom of the crypts and absent in CV, ENR and EN, respectively. * is auto-fluorescence   (C) Pearson correlations between villus proteome and the different organoid samples when focusing on proteins that are significantly changing between CV, ENR and EN organoids, where the EN proteome correlates best with the villus proteome  (D) Schematic overview of the multi-omics approach we took to get a system-wide profile of cell type enriched organoid cultures
Mutant cfDNA has shorter fragments than non-mutant cfDNA in the CSF, plasma and urine samples of glioma patients.Figure 4A-C: Fragment size distributions for mutant (blue) and non-mutant (red) cfDNA reads, determined from the capture sequencing data for CSF samples (A), plasma samples (B) and urine samples (C).
Figure 5C2C12 cells were treated with 0, 0.5 and 2 mM SUC for 48 h. Representative images of MyHC-I and IIb immunofluorescent staining (green) in C2C12 cells (n=16). C2C12 cells were treated with 0, 0.5 and 2 mM SUC for 48 h. quantification of MyHC-I and IIb immunofluorescent staining (green) in C2C12 cells (n=16). C2C12 cells were treated with 0, 0.5 and 2 mM SUC for 48 h. The enzymes activity of (C) SDH, (D) LDH C2C12 cells were treated with 0, 0.5 and 2 mM SUC for 48 h. lactate production in C2C12 cells. C2C12 cells were treated with 0, 0.5 and 2 mM SUC for 48 h. Quantification of mitochondrial DNA contents in C2C12 cells. C2C12 cells were treated with 0, 0.5 and 2 mM SUC for 48 h. Mitochondrial electron microscopy showed the (H) mitochondrial density, (I) mitochondrial coverage, and (J) average mitochondrial area in C2C12 cell. Scale bar in (A) represents 50 μm, scale bar in (G) represents 0.5 μm.
Figure 4(A) Germinal center (GC) response induced by eOD-GT8 60mer immunization in WT mice adoptively transferred with CD45.2 B cells from CLK21, CLK09, CLK19 mice on Day 8. 8-week-old CD45.1 mice were transferred with 5×105 (1 in 104) of isolated CD45.2 B cells from CLK21, CLK09 and CLK19 KI one day before the immunization with eOD-GT8 60mer, on day8, the spleenocytes were isolated and detected by FACS. First column shows the frequency of total GC (CD38loCD95+) among B cells gated from SSL, the second column shows the frequency of CD45.2 B cells among total GC, third column shows the frequency of eOD-GT8 binding B cells among GC CD45.2 B cells; fourth column shows the frequency of eOD-GT8 binding B cells that do not bind the VRC01 epitope-knockout, eOD-GT8-KO; diagrams at right show eOD-GT8 KD affinities for CLK21 (green, affinity 440 nM), CLK09 (blue, affinity 350 nM) and CLK19 (orange, affinity 1.8 µM). (B) Quantification of GCs, CD45.2 cells and CD45.2 binder frequency in adoptively transferred mice. X-axis represents CLK21, CLK09 and CLK19 adoptively transferred mice group that immunized with eOD-GT8 60mer. Y-axis represents the frequency of total GC (left) among B cells, the frequency of CD45.2 cells within GCs and the frequency of eOD-GT8-CD45.2 binders. Each circle represents one mouse. n=5 mice/group for CLK21 and CLK09, n=3 mice/group for CLK19. Bars indicate geometric mean and geometric SD from mice in each group. (C) Immunohistochemistry of day 8 spleen sections for host mouse receiving 5x105 isolated CD45.2 B cells from CLK09 (left) and CLK19 (right) KI mouse. Green, B220; Blue, CD3; White, CD45.2; Red, GL7.White arrows indicate the CD45.2 B cells.
a) Fluorescence microscopy of immortalized GFP-LC3–transduced lymphoblasts from donors homozygous for the normal ATG16L1*300T allele (300T) or risk allele ATG16L1*300A (300A), left unstimulated or treated for 2 h with rapamycin (50 μg/ml) or for 4 h with MDP (20 μg/ml).figf5(a) Fluorescence microscopy of immortalized GFP-LC3-transduced lymphoblasts from donors homozygous for the normal ATG16L1*300T allele (300T) or risk allele ATG16L1*300A (300A), left unstimulated or treated for 2 h with rapamycin (50 μg/ml) or for 4 h with MDP (20 μg/ml). Green, GFP-LC3. Scale bar, 5 μm. (b) Induction of GFP-LC3 signals by rapamycin, MDP or Gram-positive peptidoglycan (PG+; 20 μg/ml) in cells treated as described in a, presented relative to GFP-LC3 signals in unstimulated control cells. *P 0.05 (t-test). Data represent three independent experiments (error bars (b), s.d.).
Systemic Trf1 depletion in healthy tissues does not compromise tissue function nor organism viability.Figure 6Trf1lox/loxhUBC-CreERT2 genetic mouse model. Trf1 expression levels in the indicated tissues of wild-type and Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet for 7 weeks. Representative images of TRF1 immunofluorescence and quantification of the percentage of TRF1-positive cells in skin and intestine sections of wild-type and Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet for 7 weeks. Survival curve of wild-type and Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet for 7 weeks. Quantification of the histological alterations observed in tamoxifen-treated Trf1lox/lox hUBC-CreERT2 mice and 4 months after tamoxifen retrieval compared to their wild-type counterparts. Quantification of blood cell populations in wild-type and Trf1lox/lox hUBC-CreERT2mice subjected to a tamoxifen-containing diet for 7 weeks and after 3 weeks and 4 months of tamoxifen retrieval. Trf1 expression levels in blood, intestine, skin, and bone marrow of Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet either for 7 weeks or for 6 months and after 3 weeks tamoxifen retrieval compared to wild-type mice.
Binding of ATG16L1 to lipids is required for PAS recruitment.Figure 4ATG16L1-/- stably expressing the indicated Flag-S-ATG16L1 constructs were amino acid starved for 2 hr prior to immunofluorescence analyses using antibodies against Flag tag (green) and ATG5 (red). Scale bar: 9 μm. Right panels show quantifications of average number of Flag- and ATG5-positive dots per cell. ATG16L1-/- stably expressing the indicated Flag-S-ATG16L1 constructs were amino acid starved for 2 hr prior to immunofluorescence analyses using antibodies against S tag (to detect ATG16L1, red) and WIPI2 (green). Scale bar: 9 μm. Lower panel shows quantification of average number of WIPI2 positive dots per cell. Average intensities of individual Flag-ATG16L1 dots in (A). Underlying grey circles represent individual data points. Dots were quantified (n=1225 for ATG16L1WT; n=334 for ATG16L1LD). WIPI2-/- cells reconstituted with the indicated Flag-S-ATG16L1 constructs were amino acid starved for 2 hr prior to immunofluorescence analyses using antibodies against Flag tag (green) and FIP200 (red). Scale bar: 9 μm. Lower panel shows quantification of average number of Flag positive dots per puncta-positive cell.
Figure 4Rose plots indicating the number of all detected and differently expressed tissues-enhanced proteins in mild (left) and severe patients (right) compared with healthy controls. Tissues labeled in orange represented tissues with the largest proportions (100% of all detected tissue-enhanced proteins) of altered tissues-enhanced proteins. Heatmap indicating expression patterns of proteins related to organ function among control, mild and severe patient groups. Values for each protein in three groups (rows) are color-coded based on expression level, low (green) and high (red) z-scored FOT. Systematic summary of brain-enhanced expressed proteins and signaling cascades significantly altered in COVID-19 patients (neurotransmitters transport, synthesis). Values for each protein at all analyzed samples (columns) are color-coded based on the expression level, low (green) and high (red) z-scored FOT. Network summarizing lung-enhanced expressed proteins and signaling cascades significantly altered in COVID-19 patients (HIF-1α signaling pathway). Network summarizing liver-enhanced expressed proteins and signaling cascades significantly altered in COVID-19 patients (Lipid metabolism). Boxplots indicating the expression level of known brain dysfunctional biomarkers in control (n=12), mild (n=13) and severe (n=18) patients. Differences between groups were estimated using Kruskal-Wallis test. The horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.
Figure 9(A) Heatmap of CPT1A protein expression as measured in proteome analysis of Tnfaip2-/- and WT ESCs and during differentiation induction of EB cultures (n=5 biological replicates). The colour scale represents average log2ratios. (B) Expression of Cpt1a mRNA as determined by qRT-PCR in WT and Tnfaip2-/- EBs at the indicated days of differentiation induction [n=3 biological replicates; log-transformed data were normally distributed (P>0.05 as per Shapiro-Wilk test) and analyzed by multiple t-tests with Holm-Sidak correction for multiple comparisons]. Differentiation-induced WT EBs and Tnfaip2-/- EBs were treated with palmitic acid (PA) and palmitoyl-L-carnitine (PC) (8μM each) or a vehicle control (C,D) The diameters of the rosette structure of differentiated WT EBs and Tnfaip2-/- EBs were measured on day-3 after differentiation induction. (n=3 repeat experiments with 7-62 EBs per experiment per group): (C) Representative photographs (scale bar: 0.02 mm) and (D) quantification of the diameter of the rosette structure of the indicated groups [data were not normally distributed (P<0.05 as per Shapiro-Wilk test) and thus analyzed by Mann-Whitney U test with Holm Sidak correction for multiple comparisons]. RNA-seq was conducted on day-3 of differentiation induction of Tnfaip2-/- EBs that were either treated with PA/PC or with a vehicle control (n=3 independent pools of 7-62 EBs per group). The heat maps depict the intersection of DEGs with the following gene sets (E) "stem cell maintenance: positive and negative regulators", RNA-seq was conducted on day-3 of differentiation induction of Tnfaip2-/- EBs that were either treated with PA/PC or with a vehicle control (n=3 independent pools of 7-62 EBs per group). The heat maps depict the intersection of DEGs with the following gene sets ;, (F) "mesoderm development" RNA-seq was conducted on day-3 of differentiation induction of Tnfaip2-/- EBs that were either treated with PA/PC or with a vehicle control (n=3 independent pools of 7-62 EBs per group). The heat maps depict the intersection of DEGs with the following gene sets (G) "ectoderm development". Five other stem cell-related genes (Tfcp2l1, Dppa3, Fbxo15, Zfp42 and Klf2) were additionally incorporated based on literature searches. The asterisks indicate the reverted changes in gene expression that were seen in Tnfaip2-/- EBs versus WT EBs The color scale represents the gene-wise z-score calculated from normalized gene expression levels. (H) Representative image of immunofluorescence staining against ectodermal marker (SOX1) and the mesodermal marker (T alias Brachyury) on day-3 of differentiation induction of Tnfaip2-/- EBs +/- co-treatment with PA/PC. Three repeat experiments were conducted with a total number of 9 EBs per group
Cardiac GATA4 becomes downregulated within the first postnatal week and is necessary for myocardial regeneration.Figure 1(A) Cardiac GATA4 protein abundance analyzed by immunoblotting. GAPDH was the loading control. + denotes positive control for GATA4 from cardiomyocytes infected with a GATA4 overexpressing adenovirus.(B) Densitometric quantification of the immunoblot shown under (A); ***p=0.0003 for P1 vs. P7 and P1 vs. P21; p<0.0001 for P1 vs. P60. The number within bars indicates the number of mice analyzed in that particular group. (C) Immunoblot of cardiac GATA4 abundance in control (Con) and cardiomyocyte specific Gata4 knock-out mice (CM-G4-KO) at postnatal day (P) 1.(D) Quantification of the immunoblot shown in (C); *p=0.018. (E) Cardiac immunofluorescence staining and its quantification from Con and CM-G4-KO mice at P1. Scale bar: 25 µm; ****p<0.0001. (F) Transversal sections of mouse hearts 7 days after cryoinjury as indicated, stained with Sirius-Red . Scale bar: 500 µm. The quantification of the left ventricular (LV) scar area (red, arrows) 7 days after injury is shown on the right; **p=0.0027.(G) The quantification of the LV scar area of the indicated mice 21 days after cryoinjury; *p=0.0261.(H) The quantification of the LV scar area of the indicated mice 60 days after cryoinjury; ****p<0.0001. (I) Echocardiography analysis of left ventricular systolic function (measured as fractional area change) in the indicated mice 7 days after cryoinjury; *p=0.033 between Con mice after sham or cryoinjury and p=0.04 between Con and CM-G4-KO mice after cryoinjury.
Human IFITMs inhibit SARS-CoV-2 Spike-pseudotyped lentivirus infections.Figure 1(A, B) HEK293T cells transduced with the indicated FLAG-tagged IFITM expression constructs or vector control plus transient transfection of ACE2 were infected with HIV-1expressing a luciferase reporter gene pseudotyped with (A) SARS-CoV-2 Spike (HIV-SARS-2) or (B) SARS-CoV Spike (HIV-SARS-1). Measurement of luciferase activity 72 h post infection served as a readout for infection. Luciferase readings were normalized to vector control, which was set to a value of 100. Bars in (A and B) represent averages with individual data points from 3-5 independent experiments shown as circles. Error bars represent SD. #p<0.05 compared to vector control by ANOVA followed by Tukey's multiple comparisons test. Not indicated in (A), IFITM1 was also significantly different from IFITM2 and IFITM3. C) Representative example flow cytometry plots from cells transfected as in A/B demonstrate high transfection efficiency and expression of each of the FLAG-tagged IFITMs. D) Caco-2 cells were transfected as in (A/B) and infected with HIV-SARS-2. Luciferase readings at 72 h post infection were normalized to vector control, which was set to a value of 100. Bars represent averages with individual data points from 4 independent experiments shown as circles. Error bars represent SD. #p<0.05 compared to vector control by ANOVA followed by Tukey's multiple comparisons test. E) Caco-2 cells were transfected with the indicated siRNAs for 48 h followed by treatment with IFNβ for 24 h. Western blotting of cell lysates is shown. F) Cells were infected with HIV-SARS-2. Luciferase readings at 48 h post infection were normalized to vector control, which was set to a value of 100. Bars represent averages with individual data points from 3-7 independent experiments shown as circles. Error bars represent SD. #p<0.05 by ANOVA followed by Tukey's multiple comparisons test for the comparisons indicated by lines.
Overview of the transcriptional events following osmotic stress.Figure 9 A We speculate that under normal conditions, ERF8 represses the other network genes. Upon mild osmotic stress (indicated with a red arrow), some genes of the network can be phosphorylated (PTM), a hypothesis based on literature and the abundance under normal conditions. Subsequently, the expression of the network genes increases during four groups of transcriptional induction. The direct transcriptional regulations of the core network members (ERF6, ERF8, ERF9, ERF59 and ERF98) are depicted with green and red arrows, representing activation and repression respectively. The regulatory connections of the core network members that were identified when evaluating the effect of two TFs together on a shared target gene, are depicted with dashed green and red arrows, representing activation and repression respectively. The latter regulatory interactions occur in the presence of a necessary transcriptional partner. The color of the nodes represents the strength of the induction. FC = Fold change. B Schematic representation of the feed forward loop the network is composed of. Upon input, such as mild osmotic stress, activators of the core network are induced (A) and activates downstream TFs (C). These TFs or another unknown component could induce the expression of the repressors of the core network (B), which in turn leads to the repression of the downstream TFs (C), restoring the original state of the network.
Figure 3Figure 3a. CDK12 inhibition results in differential expression of a subset of genes. Comparison of log2 fold-changes versus log2 mean expression in 3'end RNA-seq data shows differentially regulated genes after inhibition of CDK12. Down- (log2 fold-change < -1) and up-regulated (log2 fold-change >1) genes are shown in blue and red, respectively. Figure 3b. CDK12 inhibition down-regulates DNA damage- and cell cycle-related genes. GO analysis using the Gorilla webserver of enriched cellular functions in 1491 genes down-regulated (log2 fold-change <-1.0; p<0.01) in 3'end RNA-seq data upon CDK12 inhibition. Functions related to DNA replication and cell cycle are marked by the red rectangle. Figure 3c. Outline of formation and activation of DNA replication complexes in G1/S phase. Origin recognition, pre-replication and pre-initiation complexes are depicted; Genes dependent on CDK12 kinase activity (log2 fold-change<-0.85; p<0.01) are shown in red. Figure 3d. Validation of RNA-seq for select DNA replication genes by RT-qPCR. Graph shows relative levels of mRNAs of described genes in serum arrested and released (0 h G0/G1) AS CDK12 HCT116 cells either treated (3-MB-PP1) or not (CTRL) with the inhibitor for indicated times after the release. mRNA levels were normalized to B2M mRNA expression and mRNA levels for each gene at the time of release (0 h) was set as 1. n=3 replicates, error bars indicate SEM. Figure 3e. Protein levels of core DNA replication factors are dependent on the CDK12 kinase activity. Western blot analyses of protein expression by the depicted antibodies in serum synchronized and released (0 h) cells either treated or not with 3-MB-PP1 for the indicated times after the release. FUS is a loading control. A representative Western blot of 3 replicates is shown. Figure 3f. CDK12 inhibition affects loading of CDC6 and CDT1 DNA replication factors to chromatin. Western blotting analyses of chromatin association of the indicated DNA replication factors in serum synchronized and released AS CDK12 HCT116 cells treated or not with 3-MB-PP1 for the indicated times. Histone H2A serves as a loading control of chromatin fractions. A=asynchronous cells, 0 h=time of release. A representative Western blot of 3 replicates is shown.
Figure 4Heatmaps summarizing proteomic analyses (iTRAQ) performed in SK-Mel-28 and SK-Mel-147 after treatment with BO-110 (1µg/ml, 10 h). Shown are Hallmark gene sets with NES>1. See also Datasets EV1,2 for additional information. REACTOME gene set analysis of protein changes in SK-Mel-28 and SK-Mel-147 cell lines treated with BO-110 (1µg/ml, 10 h). Type I IFN mRNA induction (IFNA2 and IFNB1) in SK-Mel-147 melanoma cells treated for 16 h with the indicated amounts of BO-110 (in mg/ml). Data correspond to the mean ± SD of three experiments with three technical replicates normalized to vehicle control. Statistical significance was determined by ANOVA. Heatmap showing differentially deregulated signaling cascades in SK-Mel-147 and HLEC treated with 1µg/ml B0-110 for 10 h (versus vehicle-treated controls). Data correspond to mRNA expression profiles analyzed by GSEA using the Hallmark genesets. The scale indicates the normalized enrichment score (NES). Heatmap depicting expression changes in interferon-related genes (GO:0034340) in SK-Mel-147 melanoma cells (left panel) and HLEC (right panel) treated with vehicle or 0.5 g/ml of BO-110 for 10 hours. CD274, LAG3 and PDCD1 genes were also included as a reference.
Ubiquitination and recruitment of Atg proteins.Figure 2.(A and B) NIH3T3 cells stably expressing mStr-Ub and GFP-tagged LC3, Atg5, WIPI-1, Atg14L1, or ULK1 were transfected with Effectene-coated latex beads for 30 min. Then, live cells were observed at 1-min intervals by fluorescence microscopy. Bar, 3 µm. The time after Ub localization was measured for at least 30 cases for each combination. Each value represents the mean ± SD. Statistical analysis was performed by Student's unpaired t test. *, P < 0.05; NS, not significant. (C) NIH3T3 cells stably expressing GFP-tagged Ub, LC3, Atg5, WIPI-1, Atg14L1, Atg9L1, or ULK1 were transfected with Effectene-coated beads for 3 h in the presence or absence (mock) of 30 µM UBEI-41 (a ubiquitin E1-specific inhibitor) and subjected to immunocytochemistry for galectin3. The percentages of GFP-positive per galectin3-positive beads were enumerated. At least 30 beads were counted (n = 3). The values are the mean ± SD. Statistical analysis was performed by Student's unpaired t test. *, P < 0.05. (D and E) Parent NIH3T3 cells, Atg4B mutant overexpressing NIH3T3 cells stably expressing GFP-tagged LC3, Atg5, WIPI-1, Atg14L1, Atg9L1, or ULK1 were transfected with Effectene-coated latex beads for 3 h and subjected to immunocytochemistry for galectin3. The percentages of Atg-positive per galectin3-positive beads were enumerated. At least 30 beads were counted (n = 3). The values are the mean ± SD. (E) wild-type MEFs, and Atg5-KO MEFs stably expressing GFP-tagged LC3, Atg5, WIPI-1, Atg14L1, Atg9L1, or ULK1 were transfected with Effectene-coated latex beads for 3 h and subjected to immunocytochemistry for galectin3. The percentages of Atg-positive per galectin3-positive beads were enumerated. At least 30 beads were counted (n = 3). The values are the mean ± SD.