EMBO/sd-character-level-ner huggingface dataset:
Figure 4Volcano plot showing the differential metabolites between DMSO-treated and R406-treated samples. Red dots represent significantly upregulated metabolites and blue dots represent significantly downregulated metabolites in R406-treated cells. Dash lines represent 2-fold change, p-value < 0.05. Statistical significance was assessed by the method described previously (Love et al., 2014). KEGG analysis of these differential metabolites. Statistical significance was assessed by Benjamini-Hochberg method. Heatmap showing the normalized abundance (z score) of upregulated metabolites in R406-treated cells. Red indicates up-regulated metabolites, whereas blue indicates down-regulated metabolites. Stable isotope tracing mass spectrometry using 13C-labelled serine in cells treated with DMSO and R406. n = 3. Schematic diagram showing glycine, serine and threonine metabolism and downstream metabolic pathways. Metabolite abundance of SAM, SAH in samples treated with DMSO and R406. n = 6. Metabolite abundance of GSH and the SAH/SAM ratio (H) in samples treated with DMSO and R406. n = 6. The GSH and GSSG levels (J, K) and the ratio of GSH/GSSG (L) in samples treated with DMSO and R406. n = 3.
GBS exploit human CEACAM for enhanced adhesion to epithelial cells.Figure 4Adherence of GBS A909 to human CEACAM1 (CC1)-, CEACAM3 (CC3)-, CEACAM5 (CC5)-, CEACAM6 (CC6)- or CEACAM8 (CC8)-expressing, or an empty vector control, HeLa transfectants at MOI of 10 for 30 mins. Mean and SD for n = 4 independent replicates are shown. Confocal imaging of FITC-labelled GBS A909 strain adhesion to human CC1-expressing or empty vector control HeLa transfectants. Cell membranes were stained with AF-647 conjugated wheat germ agglutinin (WGA) (red) and nuclei with DAPI (blue). Scale bar: 26 μM. Adherence of A909 to human CC1-, CC3-, CC5-, CC6- or CC8-expressing, or an empty vector control, CHO transfectants at MOI of 10 for 30 mins. Mean and SD from n = 5 independent replicates is displayed. Adhesion of WT, ∆bac and ∆bac + pLZ.bac complemented A909 strains to human CC1- or CC5-expressing CHO transfectants, or empty vector control cells. Mean and SD from n = 5 independent replicates is displayed. Adhesion of FITC-labelled A909 to human CC1- -expressing, or control, CHO transfectants at an MOI of 10. Cell lines were detached and then incubated with FITC-labelled A909 for 30 mins at 4oC. The percentage of fluorescent cells was calculated for each population. Representative flow cytometry plots are shown (E), and the integrated results displaying the mean and SD from 3 independent replicates are reported in (F). Adhesion of FITC-labelled A909 strains to human CC1- expressing or control CHO transfectants at MOI of 10. Cell lines were detached and then incubated with FITC-labelled A909 strains for 30 mins at 4oC. Mean and SD for each population for n = 6 independent replicates is displayed
The cytotoxic synergy between mycolactone and BZ is maintained in BZ-resistant cells.Figure 4A Parental MM.1S (BzS) and MM.1S BzR cells were incubated with increasing concentrations of BZ for 24 h. The proportion of live (Annexin V- PI-) cells was then measured by flow cytometry as in Appendix Figure S1. Data are Mean % of live cells from technical duplicates, relative to vehicle controls. Data information: shown data are representative of 2 independent experiments with similar results. B Effect of mycolactone on MM.1S BzR cell viability after 48 and 72 h of treatment, as measured by exposure of Annexin V and incorporation of PI. Data are Mean % of live, apoptotic and dead cells from technical duplicates, relative to total cells. Data information: , shown data are representative of 2 independent experiments with similar results. C MM.1S BzR cells were treated for 24 h with mycolactone and/or BZ at the indicated concentrations, or vehicle as control. Data are Mean % ± SD of live, apoptotic and dead cells relative to total cells. N = 6 (cumulative data of 3 independent experiments with technical duplicates). D Synergy between mycolactone and BZ in the MM.1S BzR lines, when treated as in (C). Data are Mean Loewe scores ± SD, shown as heatmaps. Differences between treated cells and controls by Student's t-test: *p<0.05; N = 6 (cumulative data of 3 independent experiments with technical duplicates). E ATF4, CHOP, sXBP1 and BiP mRNA levels were quantified by qPCR in MM.1s BzR cells treated as in (C). sXBP1 mRNA levels were normalized to total (spliced + unspliced) XBP1 mRNA level. Data are Mean RNA fold changes (2-∆∆CT) ± SD, relative to untreated controls. N = 5 (cumulative data of 2 independent experiments with technical duplicates and triplicates), pairwise compared by nested one-Way ANOVA with Tukey's multiple comparison test, exact p-values indicated. Thapsigargin (Tg, 2 µM, 6h) was used as a positive control.
Figure 8(A) Observation of inflorescences of 7-week-old wild-type (WT) Arabidopsis and the CDF4 transgenic plants. The asterisk represents the flower organ attached along the inflorescence. Scale bar indicates 1.5 cm. Selected abscission-related gene expression levels in (B) WT and proIDA::CDF4 lines by using qPCR analysis. The expression of these selected genes in the wild-type plant is given as 1. The relative expression level represents only the level of expression of the gene relative to the wild type. ACTIN2 was used as the internal control. Three independent experiments were conducted. Values are given as mean ± SD, n=3. *p<0.05 by Student's t test. Selected abscission-related gene expression levels in (C) WT and proIDA::CDF4RNAi lines by using qPCR analysis. The expression of these selected genes in the wild-type plant is given as 1. The relative expression level represents only the level of expression of the gene relative to the wild type. ACTIN2 was used as the internal control. Three independent experiments were conducted. Values are given as mean ± SD, n=3. *p<0.05 by Student's t test. D Schematic diagram indicating the locations of the putative CDF4 binding motif clusters (D1 to D5) in the approximately 1.8-kb promoter of PGAZAT. E Observation of GUS staining activity in the proPGAZAT::GUS and proPGAZAT::GUS & proIDA::CDF4. Scale bar indicates 0.5 cm. F ChIP-qPCR analysis of the relative binding of CDF4 to the promoter regions of PGAZAT. An anti-HA monoclonal antibody was used for DNA immunoprecipitation from 6-week-old pER8::CDF4-HA transgenic plants after estradiol induction. Black columns indicate the enrichment fold changes normalized to ACT2. Three independent experiments were conducted. Values are given as mean ± SD, n=3. *p<0.05 by Student's t test.
Fig.Figure 3(A) GAL-DGA1GAL-ARE2lro1Δ are1Δ (FYS118 strain) was grown on SC (synthetic minimal medium without dextrose) + raffinoseovernight, diluted to OD 0.4, and grown to mid-log phase in either SC + glucose or SC + galactose medium. Cells were shifted to SD-N for 2 h, stained with BODIPY, and visualized by fluorescencemicroscopy. Scale bar, 5 μm. (B) WT (BY4741) and GAL-DGA1 GAL-ARE2 lro1∆ are1∆ (FYS118) cells expressing GFP−Atg8 were grown as in A. Cells were lysed at the indicated times and subjected to SDS‒PAGE, followed by western blot analysis using anti-GFP antibodies. ( (C, D) WT (BY4741) and GAL-DGA1 GAL-ARE2 lro1∆ are1∆ (FYS118) cells expressing GFP−Atg8 (C) or GFP−Atg1 (D) were grown as in A and visualized by fluorescence microscopy after 2 h in SD-N. Scale bar, 5 μm. DIC, Differential interference contrast; SD-N, nitrogen-starvation medium; WT, wild-type.
Figure 1(A-H) Six to eight weeks old female outbred CD-1 mice were infected via tail vein injection with 5x107 CFU of WT S. aureus Newman or isogenic mutant strains grown in TSB medium to an OD600 of 0.5. Organs were harvested after (A-D) four days or (E-H) eight days post-infection, and bacterial burdens in the (A and E) liver, (B and F) heart, (C and G) spleen and (D and H) kidney were determined. Data represent mean ± SEM (n=7 biological replicates).. * Denotes p < 0.05, ** denotes p < 0.005 and *** denotes p < 0.0007, using the Mann-Whitney test.
Figure 3A Time-lapse imaging of cGAS-G3BP1 condensates. Data information: Representative images are shown Scale bars, 10 μm 45 μM cGAS-mCherry, 10 μM G3BP1-mEGFP were used in the assays. B Fluorescence intensity distribution on cGAS-G3BP1 droplets. A quantitative analysis of a representative cGAS-G3BP1 droplet is shown. Along the white line on the merged image, the fluorescence intensity of both G3BP1 and cGAS channels were recorded. Data information: Representative images are shown Scale bars, 10 μm 45 μM cGAS-mCherry, 10 μM G3BP1-mEGFP were used in the assays. C Time-lapse imaging of cGAS-DNA droplets in the presence of G3BP1-mEGFP. Data information: Representative images are shown Scale bars, 10 μm 45 μM cGAS-mCherry, 10 μM G3BP1-mEGFP, 2 μM dsDNA were used in the assays. D cGAS, G3BP1 and Cy5-dsDNA were incubated. A quantitative analysis of a representative cGAS-DNA droplet is shown. Along the white line on the merged image, the fluorescence intensity of G3BP1, cGAS and dsDNA channels were recorded. Data information: Representative images are shown Scale bars, 10 μm 45 μM cGAS-mCherry, 10 μM G3BP1-mEGFP, 2 μM dsDNA were used in the assays. E Time-lapse imaging of condensates formed by cGAS, G3BP1 and dsRNA. Data information: Representative images are shown Scale bars, 10 μm 45 μM cGAS-mCherry, 10 μM G3BP1-mEGFP 2 μM dsRNA were used in the assays. F cGAS, G3BP1 and Cy5-dsRNA were incubated. Similar quantification analysis as in D was performed. Data information: Representative images are shown Scale bars, 5 μm 45 μM cGAS-mCherry, 10 μM G3BP1-mEGFP, 2 μM dsRNA were used in the assays.
Inflammation-mediated loss of Complex II and IV integrity are reversed with GW274150.Figure 7Western blot analysis for ETC protein complex subunits. (left) Quantification of SDHB (Complex II; CII) normalized to VDAC (Outer Mitochondrial Membrane; OMM) and relative to untreated control. (right) Quantification of MTCO1 (Complex IV; CIV) normalized to VDAC and relative to untreated control.
REV3L facilitates replication in pericentromeric heterochromatin, preventing DNA double-strand breaks.Figure 6A. Representative fibers of newly synthesized DNA labeled with IdU (red) for 30 minutes and CldU (green) for 30 minutes in HeLa cells transfected with non-targeting siRNA (siNT) or siRNA against Rev3l. SatIII probe is visualized in blue. Scale bar: 10 μm = 20kb. Relative Rev3l mRNA level normalized to GAPDH mRNA level is shown (top panel). Distribution of fork speeds (kb/min) and fork ratios (IdU/CldU track length) are shown in dot plots for SatIII and global DNA (bottom panel). The number of fibers analyzed is indicated in (n). Bars represent the median ± interquartile range (Mann-Whitney test. ns: not significant, * p<0.05; ** p<0.01, *** p< 0.001 and ****: p<0.0001). The presented data are representative of 3 biological repeats. B. Asynchronous Rev3l+/+ and Rev3l-/- MEFs were fixed with PFA then subjected to in situ proximity ligation assay (PLA) using 53BP1 and HP1α antibodies then PLA foci were counted in both cell lines (more than 150 nuclei for each condition were counted). p-values were calculated by Mann-Whitney test ( ****: p<0.0001). Red lines indicate the mean values. Error bars: SEM. Controls with a single antibody are also shown. Experiments were repeated three times. Representative images are shown. Scale bar= 5 μm. C. Asynchronous Rev3l+/+ and Rev3l-/- MEFs were subjected to PLA as by using γH2AX and HP1β antibodies and processed as in (B). p-values were calculated by Mann-Whitney test ( *: p<0.05). Red lines indicate the mean values. Error bars: SEM. Controls with a single antibody are also shown. Three independent experiments were performed. D. RPE cells were transfected with non-targeting siRNA (siNT) or siRNA against Rev3l then 72h later cells were subjected to PLA by using 53BP1 and HP1α antibodies and processed as in (B). p-values were calculated by Mann-Whitney test ( ****: p<0.0001). Red lines indicate the mean values. Error bars: SEM. Three independent experiments were performed. E. HeLa cells were transfected with non-targeting siRNA (siNT) or siRNA against Rev3l then 72 h later cells were subjected to PLA by using 53BP1 and HP1α antibodies and processed as in (B). p-values were calculated by Mann-Whitney test ( ***: p<0.001). Red lines indicate the mean values. Error bars: SEM. Three independent experiments were performed. Rev3l+/+ and Rev3l-/- MEFs were incubated with or without 0.23 μM aphidicolin for 24h before metaphase spreading. FISH was performed using major satellite probe to quantify breaks in pericentromeric regions (F). Representative images of chromosomes showing abnormalities (see arrows) in pericentromeric regions from Rev3l-/- MEFs. Chromosomes were labelled with DAPI Error bars indicate standard error of the mean for three independent experiments. Mann-Whitney test (ns: not significant, * p<0.05; *** p< 0.001). G. breaks in non-pericentromic regions were quantified (G). Error bars indicate standard error of the mean for three independent experiments. Mann-Whitney test (ns: not significant, * p<0.05; *** p< 0.001).
Compartment‐specific aggregases control protein aggregation in S.Figure 9Misfolded proteins are deposited at cytosolic CytoQ and nuclear INQ compartments, while amyloidogenic proteins are sequestered at IPOD next to the vacuole. CytoQ formation depends on Hsp42. Misfolded, cytosolic proteins are imported through nuclear pore complexes by Sis1 and other, so far unknown sorting factors. Protein aggregation inside the nucleus is triggered by Btn2, which transiently accumulates upon stress. INQ is located adjacent to the nucleolus and harbors cytosolic and nuclear misfolded proteins. DNA replication stress causes formation of Btn2‐dependent non‐canonical DNA stress foci at the INQ and might signal to checkpoint controls.
Activation of PDGFR-β in mesenchymal cells in Foxd1Cre::Pdgfrb+/J mice results in progressive interstitial fibrosis, inflammation and tubular damage (A) Histological stainings and its histomorphometric quantification (B) of kidney cortex for α-SMA of wt (25 weeks) and Foxd1Cre::Pdgfrb+/J mice of an age of 6 and 35 weeks show expansion of myofibroblasts in the interstitium of the transgenic mice.Figure 4Histological stainings and its histomorphometric quantification (B) of kidney cortex for α-SMA of wt (25 weeks) and Foxd1Cre::Pdgfrb+/J mice of an age of 6 and 35 weeks show expansion of myofibroblasts in the interstitium of the transgenic mice. Collagen I staining and its histomorphometric quantification (D) show the progression of interstitial fibrosis in the time course. The tubular stress marker Lipocalin-2 (LCN2) is not expressed in early time points but increases in time course in late stages when fibrosis is more prominent, as seen on histological staining The tubular stress marker Lipocalin-2 (LCN2) is not expressed in early time points but increases in time course in late stages when fibrosis is more prominent and mRNA level A slight, but significant increase in interstitial ErHr3 positive stained macrophages was observed, particularly at later stages (G). For evaluation, ErHr3 positive cells were counted on 20 view fields on 40x magnification (H).
OPCML/AXL ratio is predictive of patient outcome in silico.Figure 8 The relative ratio of OPCML to AXL was calculated and above median values were defined as High OPCML/AXL (red), and below median values were defined as Low OPCML/AXL (green). Kaplan-Meier curves showing overall patient survival of High OPCML/AXL and Low OPCML/AXL cancer patient groups from (A) Ovarian GSE9891, (B) Ovarian GSE26712, (C) Ovarian TCGA, (D) Ovarian GSE31245, (E) Ovarian GSE73614, (F) Low Grade Glioma TCGA, (G) Lung TCGA, (H) Gastric GSE15459, (I) Gastric GSE62254, (J) Colorectal GSE17536, (K) Colorectal GSE41258, (L) Renal TCGA. HR, Hazard Ratio
Figure 8In wild-type animals, RPB-9 promotes Integrator-dependent cleavage of nascent motif-dependent piRNA precursors. piRNA precursors are then processed into mature piRNAs, which trigger a potent 22G siRNAs amplification response. As a result, complementary target transcripts are silenced. In rpb-9 mutants, transcription termination is defective and leads to longer piRNA precursors. As a consequence, the amount of mature piRNAs is decreased and the amplification response impaired. Target transcripts fail to be silenced.
Figure 5(A) Representative image of an NK cell (red) interacting with four DCs (green). (B, C, D) Plot of the confinement ratio (CR, black squares), the normalized NK speed Vthr(ti) (red circles) and the digitalized NK-DC distance, DistD(ti) (green triangles) as a function of time for the NK cell reported in the image. The B, C and D panels correspond respectively to the interaction with the DC1, DC2 and DC4 displayed in (A). For reference also the normalized distance Dist(ti) is reported in the plots (blue down triangles). The time periods in which all the three conditions discussed in the text are fulfilled are marked with red striped rectangles in the plots. The green up-triangles indicate the parameter TonToff defined as TonToff = -1 if Dist(ti) < d = 25 µm and TonToff = -1 if Dist(ti) d and indicate the putative interactions according to a more simplified algorithm based on the DC-NK cell distance alone.
Figure 6A. Ovaries of different genotypes were dissected for RNA extraction. RT-qPCR was performed using transposable elements specific oligonucleotides. The boxplots show several pooled transposon fold changes obtained for different genotypes after normalization to control heterozygous Rpp3018.2/CyO. Homozygous and transheterozygous Rpp30 flies (yellow and orange, respectively) show transposon overexpression, whereas Rpp3018.2/Rpp30PE ovaries carrying the ubiRpp30GFP transgene are similar to control. aubHN/QC42 ovaries (grey) were used as positive control. Arrows point to some highly expressed transposons. B. Scatter plot showing the expression of canonical transposable elements from RNA sequencing data obtained from white virgins versus Rpp3018.2 ovaries. Arrows point to P-element (P-ele) and I-element (I-ele). Transposons are indicated as red or black dots (significant or not significant fold change, respectively). Genes are indicated as yellow or grey dots (significant or not significant fold change, respectively). C. Significant transposons fold changes (p<0.05) were pooled and shown in a boxplot (grey). Note that the median value (black bar) is above 0. Arrow indicates the P-element (P-ele). Fold changes of individual transposons are shown in a barplot. Red bars, upregulated transposons. Blue bars, downregulated transposons. D. Testes from control heterozygous, transheterozygous Rpp3018.2/Rpp30PE or aubHN/QC42 were fixed and stained for Stellate crystal formation. Z-projections are shown.
Figure 4Micro-CT analyses of trabecular bone from Grounded and Tail suspended model (n=5 independent biological replicates). Scale bar=1 mm. Data were compared using an unpaired t‐test (* indicates P < 0.05, ** indicates P < 0.01), error bars are standard deviations. Micro-CT analyses of cortical bone (n = 5 independent biological replicates). Scale bar=1 mm. Data were compared using an unpaired t‐test (* indicates P < 0.05, ** indicates P < 0.01), error bars are standard deviations..
Figure 3A Workflow for single-cell profiling of dorsal skin from the sham, IMQ, IMQ+SHP099 three groups. The number of cells used in the integration was shown for each sample group (right). Each group consists of two samples, including two mice per sample in the sham group and three mice in the model and SHP099 administration groups. B UMAP visualization of all cells. Clusters are colored and labeled according to their inferred cell type identities. C UMAP plot of cells colored by cell subsets. D Heatmap displayed the top 20 differentially expressed genes for each cluster (left). Selected genes for each cluster are highlighted (middle). Feature plots of expression distribution for cluster-speciﬁc marker genes (right). Violin plot showed the relative expression of 47 inflammation-associated genes based on sample groups and cell clusters. Relative expression of selected cluster-specific genes in each cluster. High-density bar charts showed the distribution of the normalized expression levels of genes.
Figure 8LysoTracker-stained acidic compartments in zebrafish larvae brains at 3 and 5 dpf. Total signal was increased across the brains of vps16 crispants at 5 dpf, and abnormal, large puncta observed in the optic tectum from 3 dpf (arrows). LysoTracker signal colocalizes with the astroglial reporter slc1a2b:citrine and does not appear to overlap with the pan-neuronal reporter elavl3:GCaMP5G. The puncta indicated in A exist within cells expressing the mpeg1:EGFP transgene, revealing microglia with a grossly altered cellular morphology. Microglia at 3 dpf contain an increased number of acidic compartments as compared to controls. Global GFP-Lc3 signal is increased in unstimulated vps16 embryos (left panel), with clusters of puncta present particularly along the midline of the optic tectum (right panel, magnified view) and anterior hindbrain. Magnified view of the anterior hindbrain showing numerous GFP-Lc3 puncta in the vps16 embryo that do not colocalize with LysoTracker.
Figure 2A-D. Resistance to bacterial pathogens was tested by exposing worms to Pseudomonas aeruginosa strain PA14 in a slow kill assay. Both nuo-6 and isp-1 long-lived mitochondrial mutants show increased resistance compared to wild-type worms (A). Disruption of components of the p38-mediated innate immune signaling pathway (nsy-1, sek-1, pmk-1, atf-7) markedly decreases resistance to PA14 in wild-type (B), nuo-6 (C) and isp-1 (D) worms. All strains were tested in a single parallel experiment. Two biological replicates per strain were performed with a total of at least 175 animals per strain. Data information: ***p<0.001. Statistical significance for survival plots was determined with the log-rank test. Significance is indicated between the strain listed on top and all other strains. Data from panel A is repeated in panels B, C, and D for direct comparison.
Figure 6(A) Schematic representation of the UBQLN1, UBQLN4, and STI-II mutant proteins used in this study. (B) UBQLN4 dominantly co-precipitates IL-2Rα ΔSS over UBQLN1. Precipitates of Flag-tagged UBQLN1 or UBQLN4 from HeLa cell lysates were probed with IL-2Rα ΔSS. (C) The complete amino acid sequences of human UBQLN1 and UBQLN4 were analyzed using the disorder/order structure prediction program PONDR-FIT. The STI-II region of UBQLN4 is indicated by the red box, and that of UBQLN1 is boxed blue. Note that the disorder tendency of the UBL, STI-I, and UBA regions is nearly identical between UBQLN1 and UBQLN4 (indicated by black and green boxes), while that of the STI-II region is quite distinct, and the STI-II of UBQLN4 shows a high probability of an ordered structure. The numbers denote the corresponding amino acid positions in these proteins. (D) Amino acid sequence alignments of the STI-II regions of UBQLN1 and UBQLN4. UBQLN4-specific residues are shown as red characters. HS: Homo sapiens (Mammalia), MM: Mus musculus (Mammalia), GG: Gallus gallus (Aves), PS: Pelodiscus sinensis (Reptilia), and XL: Xenopus laevis (Amphibia). (E) Substitution of the STI-II sequence of UBQLN4 with that of UBQLN1 (designated as the 4-STI-II-1 mutant protein) abolished its high affinity to the IL-2Rα ΔSS client protein. (F) Substitution of the STI-II sequence of UBQLN1 with that of UBQLN4 (designated as the 1-STI-II-4) did not enable UBQLN1 to recognize IL-2Rα ΔSS.