EMBO/sd-character-level-ner huggingface dataset:
a) Non-fasting blood glucose level was monitored weekly in Atg7+/+, Atg7+/−, Atg7+/+-ob/ob and Atg7+/−-ob/ob mice.f2(a) Non-fasting blood glucose level was monitored weekly in Atg7+/+, Atg7+/−, Atg7+/+-ob/ob and Atg7+/−-ob/ob mice. ***P0.001; two-way ANOVA. (b) IPGTT was done by glucose injection at 16 weeks of age as described in the Methods (left), and AUC calculated (right). *P0.05, **P0.01, ***P0.001; Student's t-test (left) and one-way ANOVA (right). (c) HOMA-IR index was calculated as described in Methods. *P0.05; one-way ANOVA. (d) ITT was performed by insulin injection at 16 weeks of age as described in the Methods. *P0.05, **P0.01, ***P0.001; Student's t-test. (e) Tissue lysates from Atg7+/+-ob/w, Atg7+/−-ob/w, Atg7+/+-ob/ob and Atg7+/−-ob/ob mice were prepared before and 7 min after injection of 5 U kg−1 regular insulin (Ins) into the tail vein, and subjected to immunoblot analysis using antibodies specific for phospho-Akt S473 and total Akt. Numbers below immunoblot bands indicate the fold changes normalized to control bands.
LIF/Stat3 activates mitochondrial respiration.Figure 3(A) Oxygen consumption rate (OCR) measured by SeaHorse Extracellular Flux assay of Stat3+/+ and Stat3-/- cells maintained in 2i condition in the presence of LIF. 200nM FCCP treatment, a mitochondria uncoupler, resulted in higher OCR increase in Stat3+/+ compared to Stat3-/- cells, showing a higher level of maximal mitochondrial electron transport chain (ETC) activity in Stat3+/+ cells. Injection of 200nM Antimycin shows similar non-mitochondrial respiration rates for both Stat3+/+ and Stat3-/- cells. Mean and s.e.m. of 5 technical replicates is shown. (B) Oxygen consumption rate (OCR) of Stat3+/+ cells cultured in 2i conditions without LIF or with LIF for several passages. 200nM FCCP and 200nM Antimycin were injected and resulted in a higher mitochondrial respiration activity in cells cultured in the presence of LIF. Mean and s.e.m. of 4 replicates is shown. See also Appendix Figure S3D. (C) Relative changes in oxygen consumption after 200nM FCCP treatment of Stat3+/+ cells cultured in 2i media in presence (dark blue bars) and absence of LIF (light blue bars). Mean and s.e.m. of >4 technical replicates of three independent experiments are shown. Unpaired t-test: * P<0.05. (D) Western blot of Stat3+/+ cells cultured in presence or absence of LIF. Note that protein levels of two mitochondrial markers (TOM20 and TIMM23) do not change in absence of LIF. GAPDH was used as a loading control. Relative mean intensity is shown below each band. (E) Mitochondrial DNA expression analysis of Stat3+/+ cells maintained in 2i in presence (dark blue bars) and absence (light blue bars) of LIF. The abundance of 3 mitochondrial genomic loci was measured and normalized to a nuclear genomic locus on chromosome 3. Mean and s.e.m of three independent biological replicates is shown. (F) BNGE analysis followed by Western Blot for a Complex-I protein (NDUFB8). ATPase serves as a loading control. RCS= Respiratory Chain Supercomplexes. See also Appendix Figure S3E and S3F.(G) Quantification of the chemiluminescent RCS/ATPase signal ratio (left) and ComplexI/ATPase signal ratio (right). Unpaired t-test: * P<0.05 ** P<0.01 *** P<0.001.
Figure 6: Average binding profile of ESRRB, KLF4, NANOG, OCT4 and SOX2 to Class I (green), Class II (orange) or all Nanog and Oct4 bound (grey dashed line) elements in ESCs. Read counts per base pair were normalised by library size and by subtracting the background (IgG) signal. B: Average FAIRE profile or ChIP-Seq profiles for H3K27ac, OCT4, Ep300 or OTX2 in ESCs or EpiLC for Class I and Class II elements. C: Results of a differential motif analysis in Class I and Class II peaks.
Figure 2(A) Immunoblot analysis of ENKD1 and GAPDH in MEFs cultured in serum-free medium for 48 h. (B-D) Immunofluorescence images (B) and quantification of the percentage of ciliated cells (C, n = 3 independent experiments) and ciliary length (D, n = 70 cilia from three independent experiments) for MEFs cultured in serum-free medium and stained with antibodies against acetylated α-tubulin and γ-tubulin and DAPI. To quantify the percentage of ciliated cells (C), >100 cells were analyzed for each experiment. Scale bar, 5 µm. (E) Immunoblot analysis of ENKD1 and β-actin in RPE1 cells transfected with control or ENKD1 siRNAs and cultured in serum-free medium for 48 h. Immunofluorescence images (F) and quantification of the percentage of ciliated cells (G, n = 3 independent experiments) for RPE1 cells transfected with control or ENKD1 siRNAs, cultured in serum-free medium, and stained with antibodies against acetylated α-tubulin and γ-tubulin and DAPI. To quantify the percentage of ciliated cells (G), >150 cells were analyzed for each experiment. Scale bar, 5 µm. quantification of ciliary length (H, n = 100 cilia from three independent experiments) for RPE1 cells transfected with control or ENKD1 siRNAs, cultured in serum-free medium (I, J) Immunofluorescence images (I) and quantification of the percentage of ciliated cells (J, n = 3 independent experiments) for RPE1 cells transfected with control or ENKD1 siRNAs, cultured in serum-free medium, and stained with antibodies against Arl13b and Centrin and DAPI. To quantify the percentage of ciliated cells (J), >80 cells were analyzed for each experiment. Scale bar, 2 µm. (K, L) Immunofluorescence images (K) and quantification of the percentage of ciliated cells (L, n = 3 independent experiments) for RPE1 cells transfected with control or ENKD1 siRNAs and plasmids expressing GFP, GFP-ENKD1, GFP-ENKD1-N, GFP-ENKD1-M, or GFP-ENKD1-C, cultured in serum-free medium, and stained with the antibody against acetylated α-tubulin and DAPI. The siRNA-resistant forms of ENKD1 were used for these rescue experiments. To quantify the percentage of ciliated cells (L), >120 cells were analyzed for each experiment. Scale bar, 3 µm.
Figure 4IPs were carried out from RNase A-treated S-phase HeLa cell lysate using the Lsm11 antibody and IgG (A) followed by western blotting with indicated antibodies. 2 % of input was loaded. * indicates a nonspecific band. The white line delineates the boundary where irrelevant lanes have been removed from the same blot IPs were carried out from RNase A-treated S-phase HeLa cell lysate using the ALYREF antibody and IgG (B), followed by western blotting with indicated antibodies. 2 % of input was loaded. * indicates a nonspecific band. The white line delineates the boundary where irrelevant lanes have been removed from the same blot (C) Pull-down of purified His-Cntl (PGK1) or His-Lsm11 using equal amount of GST and GST-ALYREF proteins in the presence of RNase A. Proteins pulled down were separated by SDS-PAGE followed by coomassie staining. * indicates a nonspecific band. Cntl or ALYREF siRNA treated Flag-Lsm11 stable expression cells were used for IPs with IgG or the Flag antibody. The immunoprecipitates were subjected western analysis (D). * indicates the antibody heavy chain. Cntl or ALYREF siRNA treated Flag-Lsm11 stable expression cells were used for IPs with IgG or the Flag antibody. The immunoprecipitates were subjected to RT-qPCRs (E) * indicates the antibody heavy chain. The bars show the relative IP efficiencies of histone pre-mRNAs to U7 snRNA. Error bars represent standard deviations from biological repeats (n=3). Statistical analysis was performed using Student's t-test. *P < 0.05, **P < 0.01, ***P< 0.001. (F) Graphic displays that ALYREF interacts with Lsm11 and facilitates U7-snRNP recruitment.
Figure 4(A) BMDM from wt or Trem2 ko mice were cultured on APP/PS1micebrain cryosections incubated with or without mAb11 (1 µg/ml) or an isotype control (IC; 1 µg/ml) for 24 h. Sections were then probed with methoxy-X04. Scale bar, 500 µm.(B) The amyloid plaque load was quantified from the entire sagittal section. Sections incubated with medium (no cell) were set as baseline. (n = 6, +/- SEM; 2 way ANOVA, interaction P<0.0001, genotype P<0.0001, treatment P<0.0001; Tukey's multiple comparisons tests; wt vs. ko for the following conditions: no antibody P=0.0304, IC P=0.0049, mAb11 P=0.0212; wt : IC vs. wt : mAb11 P=0.0008; ko : IC vs. ko : mAb11 P=0.0001). (C, D) Equal numbers of wt and Trem2 ko BMDM were added and cell numbers were analyzed after termination of experiments by quantifying the CD68 positive cells on top of the sections. (n = 4, +/-SEM; t-test; n.s., nonsignificant, P=0.5004). Scale bar, 200 µm. (E) Aβ was extracted by urea buffer from replicate slices of the experiment shown in (A) and total Aβ was identified by western blotting.
Figure 1(A) % Fat mass/body weight of recipient mice (n=34 per group, Student t-test *p<0.05, ***p<0.001) MF: mesenteric fat, EF: epididymal fat. CC-R: Control chow-feces recipients, HF-R: High fat diet-feces recipients. (B) Oil red-O staining of livers after 2 weeks of diet challenge (Diet) or fecal transplantation (FT). Fat vesicles were photographed at 100x magnification. CC: Control chow, HF: High fat diet. Scale bar 0.1mm.(C) Fold change in lipid droplet area (n=3-5 each group, diet: Mann-Whitney Rank sum test *p<0.05; fecal transplantation: unpaired, two-tailed Student t-test p=0.1). (D) Cladogram generated from LEfSe analysis showing the differentially abundant microbiota from CC-R and HF-R.
Mesenchymal heterogeneity in the liver malignant sites (A) Key marker genes for the four mesenchymal clusters (RBP1, COL1A1, RGS5, and MYH11).Figure 3Key marker genes for the four mesenchymal clusters (RBP1, COL1A1, RGS5, and MYH11). Light gray dots denote cells originating from non-tumor samples. Dark gray dots denote cells originating from the tumor samples. Left - Representative smFISH image of patient p1 stained for RGS5 and COL1A1 showing distinct spatial localization of CAFs and Pericytes. Scale bar 10µm. Dashed lines mark the shortest distance of cells (2a) and (2b) from the cell (1). Middle - zoom-in of (1) from left panel, showing a blood vessel like structure formed by endothelial cells marked by PDGFB (magenta) wrapped by pericytes marked by RGS5 (green). Dashed lines are two consecutive cell layers of endothelial cells and pericytes. Scale bar 2.5µm. Right - zoom-in of (2a and b) from the left panel, showing two distant CAFs expressing high COL1A1 signal but not RGS5. DAPI used for nuclei staining. Scale bar 2.5µm. Violin plot of the distance from blood vessels of low/high RGS5 expressing cells (n=358 and n= 360 respectively) and low/high COL1A1 expressing cells (n=359 and n= 359 respectively). 'p' is the p-value determined by Wilcoxon rank-sum test. Empty circles are the medians over all repeats. Schematic representation of the top-ranked interaction (bona-fide) detected by NicheNet (Methods). Results are sorted by the prior interaction potential between pericytes and tumor LVECt cells. Pathway enrichment analysis for all bona-fide genes (Datasets EV4) using Enrichr tool. Images in this figure are representative images out of eight independent experiments over four patients.
Figure 1A-D Cells were infected at the indicated MOI. Viral replication (Left) and release (Right) were assessed by flow cytometry and RT-qPCR. A) Caco2/TC7 cells (MOI 0.01) B) Calu-3 cells (MOI 0.001) C) Vero cells (MOI 0,01) D) primary human airway epithelial cells (HAEC) virus release (Right) and infectious virus release (Left) (MOI 0.01). Data are mean ± SD of at least 3 independent experiments. Statistical analysis: Mixed-effect analysis or Two‐way ANOVA compared to D614G reference, ns: non‐significant, *P < 0. 05, ****P < 0.0001.
Figure 1(A, B) Flies form well-organized compound eyes when they carry GMR-GAL4 without a target gene (A) but develop rough eyes when GMR-GAL4 drives expression of UAS-Foxn1 (B). Panel B shows the typical severity of the rough-eye phenotype. Data information: Representative phenotypes are shown in all panels. Scale bars, 100 μm. (C, D) Bristles are pigmented and properly shaped when flies carry hs-GAL4 without a target gene (C) but are often white, bent, and shortened when hs-GAL4 drives expression of UAS-Foxn1 (D). Flies in panels C and D were raised at 25°C. Arrows denote examples of white bristles. Data information: Representative phenotypes are shown in all panels. Scale bars, 100 μm.
Figure 2Representative confocal images of WT and PS-DKO cells treated with the indicated SMase inhibitors (10 µM desipramine or 5 µM GW4869) or DMSO (VEH) for 12-16h. (A) Endogenous levels of lipid droplets (LDs) were visualized by incubation with LipidTox. Graph shows the Lipidtox fluorescence intensity/cell. Endogenous levels of free cholesterol revealed by filipin staining of (B) WT cells under the indicated treatments. Graphs show the filipin fluorescence intensity as a percentage over VEH. Endogenous levels of free cholesterol revealed by filipin staining of (C) PS-DKO cells under the indicated treatments. Graphs show the filipin fluorescence intensity as a percentage over VEH.
Figure 1A, Normalized weight of Ssrp1fl/fl; CreERT2+/+ mice of different ages (weeks) after the start of tamoxifen (TMX) treatment. A. Mean weight (%) ± SD. P < 0.05 for all tamoxifen treated groups versus vehicle (ANOVA). Log-rank test p = 0.032 for the oldest male age group versus all other male groups; p = 0.013 for all females versus all males; for all other comparisons p > 0.05. n = 6-10 mice. , B. survival of Ssrp1fl/fl; CreERT2+/+ mice of different ages (weeks) after the start of tamoxifen (TMX) treatment. B. Kaplan-Meier survival curves. Log-rank test p = 0.032 for the oldest male age group versus all other male groups; p = 0.013 for all females versus all males; for all other comparisons p > 0.05. n = 6-10 mice. C. Normalized blood cell counts in Ssrp1fl/fl; CreERT2+/+ mice treated with vehicle or tamoxifen on day 7 after start of treatment. Mean ± SD, * indicates p < 0.05 (unpaired t-test). n = 3 mice. D. Photographs of vehicle- or tamoxifen-treated Ssrp1fl/fl; CreERT2+/+ mice seven days after start of treatment. E. Gross pathology examination of Ssrp1fl/fl; CreERT2+/+ mouse euthanized due to 20% weight loss after treatment with tamoxifen. Vehicle-treated mouse is shown for comparison. Green and blue ovals indicate subcutaneous and inguinal fat deposits, respectively. F. MRI image of Ssrp1fl/fl; CreERT2+/+ mouse before and after tamoxifen treatment.
Protein correlation profiling (PCP) analysis using the median profile of the PA28αβ regulator as the reference profile.Figure 2Protein correlation profiling (PCP) analysis using the median profile of the PA28αβ regulator as the reference profileProfiles of the PA28α, PA28β, and the β2i proteins (blue, red and green lines, respectively). Plot of the χ2 values of the experimental replicate 2 as a function of the χ2 values of the experimental replicate 1.A zoom of the graph in (B) is represented and χ2 coordinates for PA28α, PA28β, and β2i proteins are highlighted as blue, red, and green dots, respectively. Light gray dots represent the χ2 coordinates of the proteins quantified in all the fractions of the gradient. The median profile of the PA28α and PA28β subunits was used as the reference profile for the calculation of the χ2 values.
Transient expression of phagocytic molecules and exposure of the “eat-me” signal phosphatidylserine (PS) in the outer nuclear layer during rod degeneration.Figure 2A-C Microglia infiltrating the ONL demonstrate upregulation of the phagocytic molecule, CD68. Top images in (A) show composites of CD68 (red), Iba1 (green), and DAPI (blue) staining; bottom images show the same field with CD68 staining only. At P18, non-infiltrating microglia expressed low or undetectable levels of CD68, a lysosome-associated membrane protein. At P21-23, microglia infiltrating the ONL strongly upregulated CD68 (arrowheads). At P30, CD68 immunopositivity in ONL microglia decreased and was mostly confined to amoeboid cells in the subretinal space. (B) Magnified view of inset in (A) demonstrates localization of CD68 to microglia phagosomes. (C) CD68 expression (area of immunopositivity as a fraction of the ONL) demonstrated a peaked at P22 and decreased by P30. Scale bar, 20 μm. D-F Upregulation of MFG-E8, a secreted glycoprotein that serves as a bridging molecule for phagocytosis receptors, in the ONL. (D) MFG-E8 was low or absent in the ONL at P18, but emerged at P21-23, localizing to photoreceptor cell bodies in a column-like pattern (arrow) and as a punctate signal within infiltrating microglia (arrowhead), before decreasing throughout the ONL at P30. (E) A magnified orthogonal view of the inset from (D) demonstrating punctate MFG-E8 immunopositivity within ONL microglia. (F) Quantification of MFG-E8 expression demonstrated a prominent emergence at P22 and a subsequent decrement by P30. Scale bar, 20 μm. G-K Increase in phosphatidylserine (PS) exposure in the ONL during photoreceptor degeneration. (G) At P18, PS immunopositivity is near absent in the ONL, but increased significantly in ONLsomata at P21-23, before decreasing at P30. (H) Quantitation of PS exposure by image analysis (by fractional area of PS immunopositivity within the ONL (top), and the mean intensity of PS staining in the ONL (bottom)) demonstrated a transient increase at P22. (I) Co-immunolabeling of rods with rhodopsin at P22 demonstrates that PS exposure was present in a majority of rods (inset shows at high magnification the co-labeling of PS and rhodopsin in multiple rodsomata). (J) Conversely, immunolabeling of cones with conearrestin demonstrates the sparse co-localization of PS in cones (inset shows close juxtaposition but no colocalization of PS and arrestin labeling). (K) Scoring of rhodopsin+rods and arrestin+cones for PS co-labeling demonstrates that a large majority of rods, but only a small minority of cones, showed PS exposure (two-sided unpaired t-test, n = 3 animals at P22). Scale bars = 20 μm.
14 hemocyte populations can be distinguished in WL by single cell RNA seq.Figure 2A) UMAP projection representing the 14 clusters of cells identified in the hemocyte pools from OregonR WL (NI dataset). B) Number of cells and proportion of each cluster in the NI dataset. C) GO terms enrichment analysis for each cluster. The x-axis is the GO term enrichment, the color gradient (black to light blue) indicates the p-value, the number of genes and the GO term category (CC: cellular compound, BP: biological process, MF: molecular function) are indicated between brackets. D) Top 5 markers of each cluster. The expression levels is represented by the gradient of purple levels) and the percentage of cells with the size of the dots.
Inhibition of FGFR signaling in keratinocytes promotes IFN and ISG expression (A,B) qRT-PCR for different ISGs relative to Rps29 using epidermal RNA from 8 week-old (A) or 5 day- or 9 day-old (B) K5-R1/R2 and control (CTRL) mice.Figure 1(A qRT-PCR for different ISGs relative to Rps29 using epidermal RNA from 8 week-old (A) K5-R1/R2 and control (CTRL) mice. qRT-PCR for different ISGs relative to Rps29 using epidermal RNA from 5 day- or 9 day-old (B) K5-R1/R2 and control (CTRL) mice. (C) Confocal microscopy images of epidermal sheets from back skin of K5-R1/R2 and CTRL mice stained for IRF7 and K14, counterstained with DAPI. Arrows denote nuclear IRF7 (red) in basal and suprabasal keratinocytes of K5-R1/R2 mice. The strong red staining of the stratum corneum (sc) is unspecific background and is more pronounced in K5-R1/R2 mice due to the increased thickness of this layer. (D) qRT-PCR for different ISGs, Ifnb, and Ifnl3 relative to Rps29 using RNA from freshly isolated, non-cultured keratinocytes of K5-R1/R2 and control (CTRL) mice at P7. (E) qRT-PCR for ISGs relative to Rps29 using RNA from primary keratinocytes of neonatal CTRL and K5-R1/R2 mice. (F) qRT-PCR for ISGs and Cre relative to Rps29 using RNA from primary keratinocytes of neonatal K5-Cre and wild-type (WT) mice. (G) Western blot analysis of total (L) and nuclear (N) lysates from immortalized (imm.) keratinocytes of CTRL and K5-R1/R2 mice for IRF1, IRF7, IRF9, Lamin A/C (nuclear marker, loading control) and GAPDH (cytosolic marker, loading control). (H) qRT-PCR for RSAD2 and ISG15 relative to RPLP0 using RNA from HaCaT keratinocytes treated for 48 h with the FGFR inhibitor BGJ398 (3.5 μM) or vehicle in the presence of serum.
Figure 5(A) Fluorescent western blot analysis of Atxn1, Msk1, and Rsk3 in seven different brain regions of wild-type mice at 9 weeks old (n = 3). Each protein levels were represented relative to the protein levels in brainstem. Mean ± SD, **P<0.01, ***P<0.001 ****P<0.0001, one-way ANOVA. Data information: BS: brainstem, CBM: cerebellum, MB: midbrain, ST: striatum, HC: hippocampus, CTX: cortex, OB: olfactory bulbs. (B) Representative BaseScope assay images of Rsk3 in the whole brain sagittal sections of wild-type (top) and Rsk3-/- mice (bottom) at 5-6 weeks old. The areas within the black squares are magnified in the right panels in each genotype. Scale bar = 2 mm in whole brain images; 50 μm in the magnified images. Data information: BS: brainstem, CBM: cerebellum (C) Representative IF images of Msk1 in the whole brain sagittal sections of wild-type (top) and Msk1-/- mice (bottom) at 6 months old. The areas within the white squares are magnified in the right panels in each genotype. Scale bar = 2 mm in whole brain images; 50 μm in the magnified images. Data information: BS: brainstem, CBM: cerebellum (D) Western blot analysis of total and active form of Rsk3 and Msk1 in the cerebella and brainstem of 12 weeks old WT and SCA1 mice (n = 4). Relative Rsk3 and Msk1 levels were represented into log2 scale. The protein levels of the two kinases are significantly different between the two brain regions. Mean ± SD, *P<0.05, **P<0.01, ****P <0.0001, two-way ANOVA. Data information: BS: brainstem, CBM: cerebellum (E) Western blot analysis of ATXN1, RSK3, pRSK3, MSK1, and pMSK1 in the postmortem cerebella, pons, and medulla oblongata of human controls and SCA1 patients (n = 3 per genotype). Total protein was used for normalization, and protein levels are represented relative to cerebellar protein levels in control group. C: Cerebellum, P: Pons, M: medulla oblongata. Values from P and M are combined and presented in BS. Mean ± SEM, *P<0.05, **P<0.01, two-way ANOVA, n = 3 (CBM) and 6 (BS). Data information: BS: brainstem, CBM: cerebellum