EMBO/sd-character-level-ner huggingface dataset:
GEMC1 is required for the generation of multiciliated tissues.Figure 4A. H&amp;amp;E staining of the nasal mucosa of E17.5 embryos of the indicated genotype. Normal respiratory pseudostratified columnar ciliated epithelium is shown in Gemc1+/+ embryos compared to the attenuated, flat columnar to squamous epithelium of Gemc1-/- embryos. Scale bars = 20 µm. B. PAS staining (purple) of the nasal mucosa of E18.5 embryos of the indicated genotype. Normal PAS positive goblet cells (inset, red arrows) are interspersed between MCCs (inset, black arrows) with their characteristic goblet or cup-like shape in Gemc1+/+ embryos. The Gemc1-/- mucosa has abundant PAS positive materials that accumulate in the apical borders of almost every columnar epithelial cell (inset, red arrows) and lacks typical goblet cells. Scale bars = 20 µm. C. Transmission electron micrographs of cross-sections of adult trachea from Gemc1+/+ animals revealed the presence of secretory cells (SC) and multiciliated cells (MCC). The apical membrane of MCCs accumulated basal bodies (BB) nucleating multiple cilia (C) and microvilli (MV). In the Gemc1-/- airway epithelium, no MCCs are identifiable and only secretory-like cells with MV at the apical surface are detectable. Scale bars = 5µm. Higher magnifications of the boxed regions are shown below, scale bars = 0.5µm. D. Lack of Ac-tubulin (top panel) and RFX3 (second panel from top) staining in the trachea of 1 month old mice. E. Cilia (Ac-tubulin staining) are not detectable in the ependymal cells of 2 month old Gemc1-/- mice (right panel). Choroid plexus (CP) and lateral ventricles (LV) are indicated. Scale bars = 20 µm
Figure 3Lyzs-Cre and p38γ/δLyzs-KO mice were fed a ND or a MCD diet for 3 weeks. (A) Representative H&amp;amp;E and oil red stained liver sections. Scale Bar: 50μm. (n=5-10). Lyzs-Cre and p38γ/δLyzs-KO mice were fed a ND or a MCD diet for 3 weeks. (B) Liver triglycerides (C) and plasma ALT at the end of the diet period. Lyzs-Cre and p38γ/δLyzs-KO mice were fed a ND or a MCD diet for 3 weeks. (D) Measurement of plasmaTNF-α and IL-6. Lyzs-Cre and p38γ/δLyzs-KO mice were fed a ND or a MCD diet for 3 weeks. (E) qRT-PCR analysis of myeloid cell markers and cytokine mRNA expression from liver tissue; mRNA expression was normalized to the amount of Gapdh mRNA. Lyzs-Cre and p38γ/δLyzs-KO mice were fed a ND or a MCD diet for 3 weeks. (F) qRT-PCR analysis of M1 and M2 polarization cell markers from liver infiltrated macrophages. mRNA expression was normalized to the amount of Gapdh mRNA. Data are means ± SEM (n=5-10). *P<0.05; **P<0.01; ***P<0.001 (2-way ANOVA coupled to Bonferroni's post tests).
Figure 1A. Map showing the EBV epitranscriptome in CNE2EBV with induced EBV reactivation, or HK1 cells with acute EBV infection. CNE2EBV cells were treated with NaB (2 mM) for 24 h to reactivate EBV. For acute EBV infection, RNA of HK1 cells was harvested at 24 hpi. The m6A peaks, identified based on all MeRIP-seq data using MACS2, are indicated as pink bars. The input and MeRIP coverage are indicated with gray and orange bars, respectively. B, C. Distribution of the m6A peaks across host mRNAs (B) and EBV mRNAs (C) was analyzed based on the MeRIP-seq data. D, E. Distribution of the m6A peaks across the host transcripts (D) and EBV transcripts (E) was analyzed based on three independent PA-m6A-seq experiments. PA-m6A-seq assays were performed in CNE2EBV cells following EBV reactivation, which was induced using TPA and NaB.
Figure 2A CD4+CD127-CD25hiFoxP3+CTLA4+ Treg induction from PBMCs incubated with CVF, CLys and CSN (10µg/ml) after 4h, 24h, 48h, 72h (plots and graphs shown), 120h and 168h. B Trafficking receptors (CXCR3, CCR4, CCR6 and CCR7) evaluation on induced Treg (CD25hiCD127-) and non-Treg cells (CD127+CD25-). C Induced Treg proliferation with Ki67 staining and Treg expression of IL-10 and IFNγ.
Role of TNF in fracture healing in vivo.Figure 1Addition of rhTNF at the fracture site on days 0 and 1 led to augmented healing, indicated by increased % callus mineralization, at day 28 after operation in a dose-dependent manner. Data are presented as mean ± SEM. Treatment with 1 ng TNF versus PBS control, ****P < 0.0001 by one-way ANOVA with Dunnett's multiple comparisons test. Addition of rhTNF at the fracture site must be given within the first 24 h to augment healing, indicated by % callus mineralization. Data are presented as mean ± SEM. 1 ng TNF versus PBS control treatment on days 0 and 1, ***P = 0.0009 by one-way ANOVA with Dunnett's multiple comparisons test. Treatment with systemic anti-TNF or local rmIL-10 led to impaired fracture repair at day 28, indicated by % callus mineralization. Data are presented as mean ± SEM. Treatment with PBS control versus anti-TNF, *P = 0.037, PBS control versus rmIL-10, *P = 0.037, by unpaired two-sided t-tests. Representative micro-CT images at the fracture site showing (from left to right): lateral view of tibia, cross-section, and cross and longitudinal sections with color overlay and 3D reconstruction. In the color overlays, the shade of blue corresponds to percentage mineralization: light blue denotes soft immature callus, whereas dark blue denotes hard mineralized callus. Scale bar, 2 mm. Representative ISH image (light field) showing TNF expression at the murine fracture site at 24 h after fracture. Scale bar, 250 μm. Red box indicates region of interest. High-power micrographs of region of interest from (E): at 24 h after fracture, mTNF expression (white signal on dark field, above) co-localized with polymorphonuclear cells found on the adjacent H&amp;amp;E section (below). Scale bar, 25 μm. Neutrophils were identified by their polymorphonuclear morphology as well as positive dark brown staining with anti-neutrophil elastase. High-power micrographs: at 7 days, TNF expression (white signal on dark field, above) co-localized with F4/80-positive cells (stained dark brown) extravasating from a blood vessel on the adjacent H&amp;amp;E section (below). Scale bar, 25 μm.
Figure 1A. NS1 dimer with one subunit in grey and the other colored by domain (green, β-roll; orange, wing with magenta connector subdomain; blue, central β-ladder). N-linked glycosylation sites are shown in sticks, and the glycans are shown in spheres.B. Topology diagram for the NS1 monomer, colored as the pattern in (A). Glycosylation sites are indicated with red hexagons and disulfide bonds with yellow circles.C. Side views of the NS1 dimer from the wing (left) and the end of the β-ladder (right). The β-roll (green), connector subdomain (orange) and the intertwined loop (yellow) of the wing domain form a discontinuous protrusion on one face of the β-ladder with the spaghetti loop (cyan) on the other face. The wing domain is omitted from the left image for clarity.
Figure 6Ratios of IgG to IgM derived from ELISA values plotted on a two-dimensional graph against blood glucose levels (left panel) and urine glucose levels (right panel) for n=5/group. Central bands: median, boxes: interquartile range, whiskers: max./min., statistical significance was calculated by using Mann-Whitney-U test, **P < 0.01. Serum anti-Insulin-IgM titers of mice immunized with InsA-peptide with a γ/µ ratio < 0.1 (black, n=5) and CI (grey, n=3) mice measured by ELISA at indicated days (coating: Insulin). Dots represent individual mice. Mean ± SD, statistical significance was calculated by using repeated measure ANOVA test, *P < 0.05. Blood glucose levels of InsA-peptide immunized mice (γ/µ < 0.1, black, n=5) and CI (grey, n=6) mice were assessed at indicated days post immunization with a commercial blood glucose monitor device. Dots represent individual mice. Mean ± SD, statistical significance was calculated by using Kruskal-Wallis test, all comparisons were not significant. Insulin-specific IgM affinity-maturation of InsA-peptide immunized mice at indicated days was measured by ELISA. Ratios of IgM binding to InsA(1) and InsA(4) (referring to molar antigen density) were calculated and plotted as relative units (n=5 for d7, d28; n=3 for d78). Dots represent individual mice. Mean ± SD, statistical significance was calculated by using repeated measure ANOVA test, **P < 0.01. Serum dilutions: 1:25. Coomassie stained SDS-page showing purified serum IgM of complex InsA peptide (cInsA) immunized and CI mice under reducing (+ β-ME), and non-reducing conditions. Representative of two independent experiments. Anti-Insulin affinity of PR-IgM (blue), primary IgM (red) and isotype control (black) measured by bio-layer interferometry. IgM binding to insulin was acquired in pm and used to calculate the dissociation constant shown in the graph (Kd = 1/Ka). Graph is showing antigen-antibody association phase. Data are representative for three independent experiments. Blood glucose levels of intravenously injected mice with purified IgM from control immunization (CI, n=5), complex InsA peptide (cInsA) immunization day 7 (total IgM d7, n=4) and day 85 (total IgM d85, n=5). Mean ± SD, statistical significance was calculated by using repeated measure ANOVA test showing comparison of red to black line, **P < 0.01, ***P < 0.001, ****P < 0.0001.
Figure 8A) Venn diagram showing the overlap between genes down-regulated or up-regulated in response to the indicated perturbations. B) Volcano plot showing the genes differentially expressed in ELF3-deleted CFPAC-1 cells. Differentially expressed genes were identified by comparing three ELF3-deleted clones with two wt clones. The Y-axis shows the -log10 of the q-values determined by Cuffdiff. C) Gene-ontology analysis on the set of differentially expressed genes in ELF3-KO cells. D) Scatter plots showing H3K27Ac (left) and H3K4me1 (right) levels at putative enhancers (TSS-distal genomic regions) in control vs. ELF3-KO cells. E) Volcano plot showing genes differentially expressed upon over-expression of ZEB1 in the low-grade PDAC cell line CFPAC-1. The Y-axis shows the -log10 of the q-values determined by Cuffdiff. F) A representative snapshot showing the differential effects of ZEB1 over-expression and KLF5 loss on the CLDN7 gene. G) Gene-ontology analysis on the set of differentially expressed genes in ZEB1-over-expressing CFPAC1 cells.
Proposed models of AV accumulation leading to elevated Aβ levels.Figure 8.Proposed models of AV accumulation leading to elevated Aβ levels. The schematic of macroautophagy depicts (A) the usual progression from autophagosomes (AP) to autophagolysosomes (APL) to lysosomes (L). Conditions that result in AV buildup (B and C) are expected to promote Aβ generation and accumulation, including impaired or delayed maturation of autophagosomes to lysosomes (B) or acute maximum induction of macroautophagy (C). Within neurons, AVs normally progress to lysosomes efficiently and are rarely seen in neurons (D). In AD, the disrupted retrograde transport of AVs in dendrites represents one of several possible mechanisms that impede the maturation of AVs to lysosomes, leading to Aβ generation in AVs and its delayed degradation in lysosomes (E).
Figure 6(A) Knockdown of UHMK1 blocked NCOA3 binding to ATF4. SGC7901 cells were treated as indicated. Co-IP was carried out with mouse immunoglobulin G (IgG) or anti-NCOA3 antibody. Then Western blotting was performed. (B) BGC823 cells were transfected with Flag-NCOA3 or NCOA3-S1062A/T1067A with or without His-tagged UHMK1. Co-IP was performed using an anti-Flag antibody. (C) Proximity ligation assay of the interaction between different NCOA3 proteins and ATF4 in BGC823 cells. Confocal images were acquired with a Nikon A1 microscope and the Nikon Elements software suite. Maximum projection images are shown (original magnification ×120). Scale bars=20μm. (D) Computational molecular docking analysis to investigate the molecular mechanism by which NCOA3-S1062/T1067 phosphorylation is involved in the interaction of NCOA3 binding to ATF4. Based on the predictions of ZDOCK software, S1062 and T1067 of NCOA3 are located in the interface between ATF4 and NCOA3, and S1062/T1067 phosphorylation greatly enhances the binding affinity of NCOA3 for ATF4 by increasing NCOA3 hydrophilicity. (E) (Ei) ChIP data from BGC823 cells are presented as indicated. (Eii) NCOA3-S1062/T1067 phosphorylation by UHMK1 enhanced the expression of critical genes as indicated (three biological replicates). (F) (Fi and Fii) The effects of WT-NCOA3 and the NCOA3-S1062A/T1067A, and NCOA3-S1062E/T1067E mutants on BGC823 cell proliferation, invasion, and migration (three biological replicates). Data information: Unpaired, two-tailed statistical significance was assessed by Student's t‐test.Data represent mean ± SD. *P< 0.05, **P< 0.01, ***P< 0.001. (G, H) The effects of WT-NCOA3, and the NCOA3-S1062A/T1067A, and NCOA3-S1062E/T1067E mutants on GC growth and metastasis in the mouse model (n = 10 mice/group). Scale bars=1cm. Data information: Unpaired, two-tailed statistical significance was assessed by Student's t‐test.Data represent mean ± SD. *P< 0.05, **P< 0.01, ***P< 0.001.
Fig.Figure 5A Number of unique and shared OCRs (TSS and distal) in T-ALLs and in healthy T-cell precursors. B Unsupervised learning by PCA of all TSS and distal peaks collected in the combined analysis of healthy and leukemic T-cells. C log2 fold changes of 292 genes which are differentially expressed (x-axis, RNA-Seq: non-sorted bulk thymi vs. T-ALLs) and differentially accessible (y-axis, ATAC-Seq: sorted T-cell populations vs. T-ALLs) in T-ALLs in comparison to healthy T-cell precursors. Dot size and color indicate the frequency (number of patients having dysregulation of the gene). Genes with ≥5/19 frequency are shown on the plot. Protein coding genes with ≥12/19 frequency are labelled. For plotting the average LFC values of ATAC and RNA are used per gene per quartile. Q1 - 4 stands for the quadrant 1 - 4. D Heatmap of VST normalized read counts (each row is also normalized by the row mean) of differentially expressed genes (pval<0.1; DESeq2) in three patients in comparison to remaining 16. Orange triangles indicate three patients with no DAB1 but high SPI1 expression and motif counts.
Figure 6A. Gross morphology of testes from MFN1f/f-Cre compared to their wild-type littermates. B. Histological studies of testis sections from wild-type mice or MFN1f/f-Cre littermates at different time points postnatal. Red stars: tubules with spermatocytes. C. IHF of PLZF (day 14 postnatal), MILI, MVH, and GASZ/CytC (day 7) of testes sections. Scale bars for PLZF are 50 m and 10 m for others. D. EM of testical sections from wild-type neonatal mice or MFN1f/f-Cre littermates. N: nucleus. E. Histochemistry of respiratory enzymes, COX, NADH, and SDH on testical sections from mice 10 days postnatal. Scale bar: 100 m.
Role of CatSper in chemosensory signaling pathways of sea urchin and mammalian spermSignaling pathways in sperm of A.Figure 8A Signaling pathways in sperm of A. punctulata (upper panel) and humans (lower panel). Questionmarks above dashed lines in the lower panel indicate that the mechanism of how ΔpHi is produced and the hyperpolarization by Slo3 has not been firmly established. Solid lines indicate that the action of ΔpHi on CatSper and of ΔpHi and Ca2+ on Slo3 activity has been firmly established. B Model of the pHi‐induced change in the voltage dependence and Vthr of CatSper; the resact‐induced hyperpolarization (black arrow) evokes a rapid alkalization that shifts the voltage dependence of CatSper activation to more negative values (blue arrow) and, thereby, primes CatSper to open during the subsequent depolarization (red arrow). C Changes in pHi evoked by repetitive release (arrows) of cGMP from caged cGMP. The first UV flash was delivered at t = 0.
Methylation of H3K9 spreads across natural boundaries and heterochromatin becomes derepressed in swi6∆ cells.Figure 4H3K9me2 ChIP‐seq enrichment profiles for swi6+ and swi6∆ cells on centromere 1. Centromeric repeat elements (dg/dh) are indicated. Inverted repeats (IRC1) constitute heterochromatin boundaries in wild‐type cells (Cam et al, 2005). The y‐axes represent log2 ChIP‐seq enrichments in 200‐bp genomically tiled windows calculated over clr4Δ cells. Two independent biological replicates for each genotype were performed (replicates 1 and 2). Positions of genomic elements on the plus and minus strands are indicated. Blue, protein‐coding genes; white, repeats; green, long terminal repeat (LTR). H3K9me2 ChIP‐seq enrichment profiles for swi6+ and swi6∆ cells on the telomere of the right arm of chromosome 1. Two independent biological replicates for each genotype were performed (replicates 1 and 2). Differential expression of transcripts coming from centromere 1 assessed by tiling microarray gene expression analysis. Expression data for swi6+ and swi6∆ cells were taken from a previous publication (Woolcock et al, 2012).
ssRNA40 and CL097 induce autophagy in macrophages through TLR8.Figure 2Macrophages transduced with non-specific scrambled shRNA (shNS) or TLR8 shRNA (shTLR8) were treated for 24 h with CL097, ssRNA40, ssRNA41 or rapamycin (Rapa). (A) Cells were lysed and immunoblot performed with antibodies to TLR8 and β-actin. (B) Immunoblots of LC3B isoforms using antibody to LC3B or β-actin. (C) Cells were fixed and permeabilized then stained with antibody to LC3B (green) and Hoechst 33342 (blue). Scale bars indicate 10 µm. Left, representative fluorescence microscopy images from three donors are shown. When puncta are not present, LC3B staining gives rise to a diffuse cytoplasmic pattern. Right, percentage of cells with LC3B puncta. Bar charts are presented as the means ± s.e.m., n = 4. * p<0.05.
Knockdown of beclin 1 suppresses abnormal autolysosomal puncta formation and embryonic senescence caused by Spns1 deficiency in zebrafish.Figure 3(A) Effect of beclin 1 knockdown on EGFP-LC3 puncta formation in spns1-depleted zebrafish embryos. Injection of control (water) injection, spns1 MO (4 ng/embryo) or coinjection of spns1 MO (4 ng/embryo) and beclin 1 MO (12 ng/embryo) into Tg(CMV:EGFP-LC3) fish was performed to assess whether the beclin 1 knockdown reduces or eliminates aggregated LC3 puncta induced by Spns1 depletion at 84 hpf. Scale bar, 10 µm. Quantification of data presented in panel A (n = 12) is shown in the right graph; the number (n) of animals is for each morphant or water-injected control. Three independent areas (periderm or basal epidermal cells above the eye) were selected from individual animals. (B) Effect of beclin 1 knockdown on EGFP-GABARAP as well as mCherry-LC3 puncta formation in spns1-depleted zebrafish embryos. Injection of control (water), spns1 MO or coinjection of spns1 MO and beclin 1 MO into Tg(CMV:EGFP-GABARAP;mCherry-LC3) fish was performed to evaluate whether the beclin 1 knockdown reduces or eliminates the aggregation of GFP-GABARAP puncta in comparison with those of LC3 caused by the Spns1 depletion at 84 hpf. Scale bar, 10 µm. Quantification of data presented in the top row (green; EGFP) (n = 9), middle row (red; mCherry) (n = 12), and bottom row (yellow; merge of EGFP and mCherry) (n = 9) in panel B is shown in the right graphs; the number (n) of animals is for each morphant or water-injected control. Three independent areas (periderm or basal epidermal cells above the eye) were selected from individual animals. (C) Effect of beclin 1 knockdown on embryonic senescence in spns1 morphant. By using the same injection samples [injection of control (water), spns1 MO or coinjection of spns1 MO and beclin 1 MO into Tg(CMV:EGFP-GABARAP;mCherry-LC3) fish], SA-β-gal staining was performed to assess whether the beclin 1 knockdown has any impact on the embryonic senescence caused by Spns1 depletion at 84 hpf. Representative images of individual fish by bright field (BF, live samples) and SA-β-gal (SABG) staining are shown in the upper and middle panels, respectively. Scale bar, 250 µm. Lower panels are larger magnification images of corresponding SA-β-gal samples shown in the middle panels and the fluorescence images of nuclei counterstained with DAPI. Scale bar, 10 µm. Quantification of data presented in the middle row (SABG) in panel C (n = 12) is shown in the right graph; the number (n) of animals is for each morphant or water-injected control. Error bars represent the mean ± S.D., *p<0.005.
Figure 6(A-D) Female C57/BL6 animals were treated with 3,4-DC for 24 h. Following, liver and heart tissue was excised and cells were subjected to subcellular fractionation. Thereafter proteins were separated by SDS PAGE and immunoblots were performed to detect the nuclear translocation of TFEB and TFE3 (A, C). GAPDH and H3 were used as controls for cytosolic and nuclear fractions, respectively. Band intensities of nuclear TFEB, TFE3 and H3 were measured and ratios of nuclear TFs versus H3 (TFsnuc/H3) were calculated in (B, D). Data are means ± SEM of at least three mice (*** = p < 0.001 versus Ctr) GFP-LC3 expressing mice were i.p. injected with 3,4-DC for 24 h. Leupeptin (Leu) was used to test autophagic flux in vivo and GFP-LC3 dots were measured in liver tissue. Data are means ± SEM of at least three mice (*= p < 0.05 versus ctr without Leu; #= p < 0.05 versus ctr with Leu). C57/BL6 mice were i.p. injected with 3,4-DC or were starved for 24 hours. Following liver tissue was excised and subjected to SDS PAGE and immunoblot GAPDH was measured as a loading control. Band intensities of GAPDH and LC3-II were measured and ratios LC3-II versus GAPDH (LC3-II/GAPDH) were calculated Data are means ± SEM of at least three mice (* = p < 0.05, ** = p < 0.01). GFP-LC3 expressing mice were i.p. injected with 3,4-DC for 24 h. Leupeptin (Leu) was used to test autophagic flux in vivo and GFP-LC3 dots were measured in heart (I, J) tissue. Data are means ± SEM of at least three mice (*= p < 0.05 versus ctr without Leu; #= p < 0.05 versus ctr with Leu). C57/BL6 mice were i.p. injected with 3,4-DC or were starved for 24 hours. Following heart tissue was excised and subjected to SDS PAGE and immunoblot GAPDH was measured as a loading control. Band intensities of GAPDH and LC3-II were measured and ratios LC3-II versus GAPDH (LC3-II/GAPDH) were calculated Data are means ± SEM of at least three mice (* = p < 0.05, ** = p < 0.01).
Figure 4(A, B) Longitudinal intraindividual stability of NfL (A) and pNfH (B) serum levels over 6 weeks, assessed in both ataxic (red) and preataxic (green) SCA3 and control (blue) subjects (n=21). Data of the same individuals are linked by lines. ICC, intraclass correlation coefficient (estimate and 95% CI). (C) Sample size estimations were performed for future intervention trials using the reduction of Nf levels towards control levels as outcome measure. The estimated number of subjects per study arm is plotted over the assumed therapeutic effect for lowering the Nf level in SCA3 subjects to levels observed in healthy controls (NfL: dashed line, pNfH: dotted line).
Figure 4(A) Top Panel: Schematic representation of the S protein colour coded for the functional regions: N-terminal domain (NTD), receptor binding domain (RBD), fusion peptide (FP), heptad repeat 1,2 (HR1, HR2), transmembrane anchor (TA), C-terminal domain (CTD). Bottom left Panel: Vero GFP-split cells were transfected with S plasmids containing each of the individual mutations associated with Alpha variant in the D614G background. The amount of fusion was quantified at 20h and normalized to D614G reference plasmid. Bottom right Panel: Quantified fusion for each of the individual S protein mutations associated with the Beta variant. Colour code of each mutation corresponds to S protein functional regions represented in the schematic on the Top Panel. Data set for N501Y and D614G reference mutations are duplicated between bottom left and bottom right panels for presentation as these mutations are common to both variants. (B) Left Panel: Quantified fusion of the Alpha + E484K variant S protein normalized to D614G S. Right Panel: Representative images of fusion at 20h. Scale bar: 200 µm. Top and bottom are the same images with and without Hoechst channel.