EMBO/sd-character-level-ner huggingface dataset:
Figure 1Schematic of Rod RNAi depletion and synchronization protocol. Representative still images of control, Rod depleted cells and Rod depleted cells supplemented with RNAi resistant Venus-Rod treated with nocodazole and time in minutes indicated. Scale bar, 5 μm. Time from NEBD to mitotic exit for the indicated conditions with each circle representing a single cell analyzed and mean time indicated by red line and standard error of mean shown. The number of cells counted and mean time indicated above. Immunofluorescence analysis of ZW10 and Mad1 upon depletion of Rod. Scale bar, 5 μm. Quantification of kinetochore intensities of the indicated proteins in control or Rod depleted cells with the signal normalized to CREST levels and Bub1 pSpT normalized to Bub1. Bar indicates mean and standard error of mean is shown by line. At least 200 kinetochores from 10 cells were analyzed and representative result from at least 2 independent experiments is shown. Time from NEBD to mitotic exit in control depleted, Rod depleted, Bub1 depleted and Rod and Bub1 co-depleted HeLa, U2OS and RPE1 cells. Cells were treated with nocodazole. Mad1 kinetochore levels in the indicated conditions normalized to level of CREST in HeLa cells. Cells were fixed at 45 min after releasing from RO3306 arrest into nocodazole. Bar indicates mean and standard error of mean is shown by line. At least 200 kinetochores from 10 cells were analyzed and representative result from at least 2 independent experiments is shown.
Figure 4A. Heatmaps for Spearman correlation. B. Principle component analysis reveals distinct clustering of AT2, Club and BASC populations. C. MA and Volcano plots, and Top50 DEGs (FDR<0.05, Log2FC>±0.585, Means>5) for visualization of pairwise differential gene expression analysis of BASCs and Club cells. D. MA and Volcano plots, and Top50 DEGs (FDR<0.05, Log2FC>±0.585, Means>5) for visualization of pairwise differential gene expression analysis of BASCs and AT2 cells. E. Heatmap of RNA-seq z-scores computed for the Top50 DEGs in BASC, AT2, and Club cells (FDR<0.05, Log2FC>±0.585, Means>5).
Figure 2(A) Experimental design used to assess the chronic effect of a transient 4D induction with BrdU and EdU given during Dox administration or 1h before sacrifice, respectively. From top to bottom: fluorescence pictures of the SVZ and absolute number of cells in 4D- (white bars) or 4D+ (black or red bars for all or RFP+ cells, respectively) mice scored positive for various markers as indicated. From top to bottom: fluorescence pictures of the SVZ and absolute number of cells in 4D- (white bars) or 4D+ (black or red bars for all or RFP+ cells, respectively) mice scored positive for various markers as indicated. Insets in (C) are magnified (right) with arrowheads pointing label-retaining NSC (white) or astrocytes (empty). From top to bottom: fluorescence pictures of the SVZ or proportions (C-E) of cells in 4D- (white bars) or 4D+ (black or red bars for all or RFP+ cells, respectively) mice scored positive for various markers as indicated. Arrowheads in (D) point cell doublets (among RFP+ protein-reteining cells in 4D+). From top to bottom: fluorescence pictures of OB (E) and absolute number or proportions of cells in 4D- (white bars) or 4D+ (black or red bars for all or RFP+ cells, respectively) mice scored positive for various markers as indicated. (E) GL=glomerular, EPL=external plexiform, MCL=mitral cell and GCL=granule cell layers.
Figure 2Normalized Hi-C contact maps for ΔrsaAvan::promoterless-rsaA and derivatives of ΔrsaAvan::PrsaA-rsaA with transcription terminators inserted 60, 560, 1060, or 2060 bp from the transcription start site. Only the region of the genome containing the van locus (dashed line) is shown. Above each Hi-C contact map is a schematic of the corresponding rsaA construct with the transcription terminator shown as a black hairpin and transcript as a wavy red line. Below each map is the corresponding directional preference plot. Normalized Hi-C contact maps for ΔrsaAvan::promoterless-rsaA and derivatives of ΔrsaAvan::PrsaA-rsaA with transcription terminators inserted 60, 560, 1060, or 2060 bp from the transcription start site. Only the region of the genome containing the van locus (dashed line) is shown. Above each Hi-C contact map is a schematic of the corresponding rsaA construct with the transcription terminator shown as a black hairpin and transcript as a wavy red line. Below each map is the corresponding directional preference plot.
Figure 4A Pie charts of COVID-19 hospitalisation that were exclusively treated in general wards (Gen) or that required intensive care (ICU). Proportions of patients admitted to ICU that were non-diabetic (ND) or with type-2 diabetes (T2D). B Proportions of lymphocytes and monocytes in peripheral venous blood from T2D patients with COVID-19 either treated in Gen or requiring ICU admission. C Phenotypic analysis of lymphocyte and monocyte subpopulations in peripheral venous blood from T2D COVID-19 patients treated in Gen or requiring ICU treatment. D tSNE mapping of all cytometric acquired data with projections of population density, CD8 or IRF5 IRF5 expression. Maps are of representative profiles from each group.
Proposed model of RAD54 activity at ALT telomeres RAD54 functions downstream of presynaptic events to regulate the processing of D-loop structures (partial-X or PX junction), promoting telomere synthesis via BIR at ALT telomeres.Figure 5RAD54 functions downstream of presynaptic events to regulate the processing of D-loop structures (partial-X or PX junction), promoting telomere synthesis via BIR at ALT telomeres. RAD54 branch migration activity may function coordinately with BLM to promote BTR-dependent dissolution of recombination intermediates. Specifically, RAD54 may promote branch migration and ultimately, dissolution through regions of heterology either in the D-loop or that arise during error-prone DNA extension events. Alternatively, RAD54 may function to dissolve heterologous recombination intermediates to promote formation of more homologous intermediates that will lead to higher fidelity telomere extension events. In the absence of RAD54, like in the absence of BLM, ALT cells rely on nucleolytic cleavage of recombination intermediates by the SMX resolvase complex.
The systemic Stat3 inhibitor SH-4-54 confers protection from cognitive decline in APP/PS1 mice (A) APP/PS1 mice were systemically treated with SH-4-54 for 6 weeks and compared to age-matched APP/PS1 mice treated with vehicle.Figure 8APP/PS1 mice were systemically treated with SH-4-54 for 6 weeks and compared to age-matched APP/PS1 mice treated with vehicle. In the Morris Water Maze test, treatment with SH-4-54 led to significantly faster latencies to reach the hidden platform on the last training day (Two-way repeated-measures ANOVA followed by Bonferroni post-hoc test). The area under the curve (AUC) for the latency to reach the hidden platform was also smaller in APP/PS1 mice treated with the Stat3 inhibitor (Mann-Whitney test). The swimming velocity was not affected by the treatment (Mann-Whitney test). In the probe trial test, APP/PS1 mice treated with the Stat3 inhibitor spent significantly more time in the target quadrant (TQ) compared to the mean of all other quadrants (AO), whereas APP/PS1 mice treated with vehicle spent equal times in the target and all other quadrants (Wilcoxon matched-pairs signed rank test for all comparisons; APP/PS1-Stat3WT, n = 12 (5 female and 7 male) mice; APP/PS1-Stat3KO, n = 12 (4 female and 8 male) mice; age, 8 months). (E) To verify target engagement in the brain, the same mice assessed in the Morris Water Maze were anesthetized and imaged using in vivo two-photon microscopy of calcium activity. Systemic treatment with the Stat3 inhibitor reduced the hyperactive phenotype of cortical neurons (Mann-Whitney test).
1,25D3 induces autophagy in human macrophages co-infected with HIV and M.Figure 31,25D3 induces autophagy in human macrophages co-infected with HIV and M. tuberculosis.HIV (A), M. tuberculosis (TB) (B), and HIV/TB dual infected MDM (C) were treated for 7 days with 100 pmol/L 1,25D3, harvested and stained for HIVp17, mycobacteria, and saponin-resistant LC3B-II. Representative density plots from three donors are shown. (D) HIV/M. tuberculosis infected MDM (C) were treated for 7 days with 100 pmol/L 1,25D3, harvested and stained for HIVp17, mycobacteria, and saponin-resistant LC3B-II. Left, representative density plots from three donors from HIV/M. tuberculosis infected MDM are shown for HIV/M. tuberculosis co-infection. Right, histograms of saponin-resistant LC3B-II in macrophages that were HIV+M. tuberculosis− or HIV+day 7+ at day 7 post-infection.
Comparative profiling of AGO4‐ and AGO6‐dependent methylomesHeatmap depiction of the 3,731 DNA hypomethylation loci in ago4‐6.Figure 1A Heatmap depiction of the 3,731 DNA hypomethylation loci in ago4‐6. Each hypomethylated region corresponds to a colored horizontal bar, and the bars are clustered numerically into a column (y‐axis). Cytosines were examined as CG, CHG, and CHH. The color‐scaled methylation levels indicate the ratios of each type of methylated cytosines over total cytosines of the same type within the examined hypomethylated regions. B Heatmap depiction of the 3,678 DNA hypomethylation loci in ago6‐2. C Overlapping patterns of hypomethylated loci in ago4‐6 and ago6‐2. Upper panel, Venn diagram showing the numbers of the following three types of hypomethylation loci: (1) loci where ago4‐6 shows lower methylation levels than ago6‐2 (green alone); (2) loci where ago4‐6 and ago6‐2 show equal methylation levels (green and red overlap); and (3) loci where ago6‐2 shows lower methylation levels than ago4‐6 (red alone). Lower panel, box plots showing methylation levels at the three groups of loci.
scRNAseq identifies migration-dependent maturation of cortical interneurons A.Figure 2A. Schematic overview of experimental setup for single cell RNA-sequencing of human cortical interneurons from organoids. GFP+ cells from the dorsal and ventral regions of 70- or 90-day old organoid fusions were obtained by flow cytometry and sequenced individually. B. Visualization of single cell RNA-sequencing data from GFP+ cells from the different groups mentioned in 2A using UMAP after removal of stressed cells (EV3A-D). Clusters are color-coded according to the cell type. C. UMAPs depicting the expression of GABAergic markers DLX2 and DLX5, progenitor marker TOP2A, MGE marker SOX6, CGE marker NR2F2, and striatal marker ZFHX3. D. Proportions (Y-axis) and numbers (within bars) of cells arising from the different regions of a fusion are listed for each cluster. Numbers are down-sampled to 941 cells in the smallest region group for proper representation. UMAP depicting the fusion region from which the cells were isolated. E. Proportions (Y-axis) and numbers (within bars) of cells arising from the different fusion ages are listed for each cluster. Numbers are down-sampled to 1221 cells in the smallest age group for proper representation. UMAP depicting the fusion age at which the cells were isolated.
Figure 2A. Sequence similarity in combination to peptide length for 1000 random proteins derived from human proteome. Graph: bottom and top of the boxes are first and third quartiles, central band represents median, whiskers encompass minimum and maximum. B-C. Distribution of amino acids in homologues to Aβ KLVFFA (B) and LVFFAE (C) proteins. D. Binding of Biot-Aβ1-42 to homologue peptides derived from ~520 randomly selected proteins. E. Summary of Biot-Aβ1-42 binding throughout 8 membranes, color indicates the mean between membranes and the size of the outline the standard deviation. F. Heatmap of amino acid substitutions in membrane hits. G-H. Membrane top binders spell AD and PLAK, white space consists of random sequences. (sequences in AppendixTableS2)
a) STUB1 knockdown-induced repression of Δ133p53α is abrogated by bafilomycin A1 treatment.f4(a) STUB1 knockdown-induced repression of Δ133p53α is abrogated by bafilomycin A1 treatment. The siRNA transfection in MRC-5 fibroblasts was performed as in Fig. 3e. At 7 days after the initial transfection, the cells were untreated, treated with bafilomycin A1 (100 nM for 4 h) or treated with MG-132 (15 μM for 4 h), and examined in immunoblots as indicated. The results of Δ133p53α, full-length p53 and p62/SQSTM1 in untreated cells replicate those shown in Fig. 3c. The inhibition of autophagy by bafilomycin A1 was confirmed by increased levels of p62/SQSTM1 and LC3B. The inhibition of proteasomal degradation by MG-132 was confirmed by increased full-length p53. (b) STUB1 knockdown-induced repression of Δ133p53α is abrogated by knockdown of pro-autophagic proteins. MRC-5 fibroblasts (PDLs 30) were transfected for 4 days with control siRNA (−) or STUB1 siRNA (no. 1, +), in combination with control siRNA (c), p62/SQSTM1 siRNA (62), ATG5 siRNA (A5, no. 1 in Fig. 2a), ATG7 siRNA (A7, no. 1 in Fig. 2b) or Beclin-1 siRNA (B1, no. 2 in Fig. 2c), and examined in immunoblots for indicated proteins. (c) Δ133p53α is recruited to autophagosomes upon STUB1 downregulation. MRC-5 fibroblasts at early passage (PDLs 30; Y), those at or close to replicative senescence (PDLs 58; S (Rep)) and those induced to senesce by STUB1 knockdown (S (KD)) were used in immunoprecipitation (IP) with anti-STUB1, anti-Hsp70 and anti-LC3B antibodies, followed by immunoblots (IB) as indicated. Whole-protein lysates without IP (input) were also examined for Δ133p53α and β-actin levels. (d) Bafilomycin A1 stabilizes LC3B-interacting Δ133p53α in senescent cells. The same set of cells as in c were treated with bafilomycin A1 (+, 100 nM for 4 h) or untreated (−). These cells were used in IP with anti-LC3B antibody, followed by IB with anti-Δ133p53 antibody. Whole-protein lysates without IP were also examined in IB with anti-LC3B antibody. While untreated samples replicate the result shown in c, the differences between early passage and senescent cells become more evident with bafilomycin A1 treatment.
Figure 6(A) Western blot analysis of total and pS776 wild-type and mutant Atxn1 in the brainstem of 8 weeks old SCA1 mice with heterozygous knockout of either one or both kinases. Mean ± SD, *P<0.05, **P<0.01, ****P<0.0001, one-way ANOVA, n = 7, 6, 4, 7 following the order of genotypes in the western blot, respectively. (B) Plethysmography data measuring breathing ability (total ventilated gas volume per minute) of 34 weeks old mice with different genotypes. Mean ± SD, *P<0.05, two-tailed t-test, n = 12, 13, 15, 13, 15, 9, 15, 13 following the order of genotypes in the graph, respectively. (C) Representative immunohistochemistry images of Iba1+ reactive microglia in the coronally sectioned hypoglossal nucleus of 36 weeks old mice with different genotypes. Yellow arrows indicates Iba1+ microglia, and larger pyramidal shaped cells are motoneurons. scale bar = 50 μm. (D) Quantification of the number of Iba1+ cells shown in (C). Mean ± SD, *P<0.05, ***P<0.001, one-way ANOVA, n = 3 mice per genotype, each dot is an averaged measurement from six sections per mouse. (E) Representative Hematoxylin and Eosin stained motoneurons in the coronally sectioned hypoglossal nucleus (white dashed line) of 36 weeks old mice with different genotypes. The motoneurons are dark purple with pyramidal shape within the nucleus. C: central canal. Scale bar = 100 μm. (F) Quantification of the number of motoneurons shown in (E). Mean ± SD, *P<0.05, one-way ANOVA, n = 3 mice per genotype, each dot is an averaged measurement from six sections per mouse. (G) Kaplan-Meier survival graphs of SCA1 mice with heterozygous knockout of either one or both kinases. The data of Msk1+/-, Rsk3+/-, and Msk1+/-; Rsk3+/- mice overlap those of wild-type mice. *P<0.05, Gehan-Breslow-Wilcoxon test, n = 15, 15, 12, 13, 22, 11, 20, 19 following the order of genotypes in the legend on top of the figure, respectively.
Figure 2 Figure 2. Removal of tumor-draining lymph node reduces distant organ metastasis of breast cancer cells (A and B) Schematic diagram of tumor resection with or without tumor-draining lymph node removal in 4T1 tumor-bearing mice.  Figure 2. Removal of tumor-draining lymph node reduces distant organ metastasis of breast cancer cells (A and B) Schematic diagram of tumor resection with or without tumor-draining lymph node removal in 4T1 tumor-bearing mice.  (C and D) Distant organ metastasis was examined by bioluminscent images of 4T1 tumor-bearing mice after tumor resection with (n=13 mice) or without (n=10 mice) tumor-draining lymph node dissection on week 5. The bioluminescent signal (pseudocolor) was recorded as photons per second per centimeter squared per steradian (p/s/cm2/sr) and the luminescent image was overlaid on the photographic image. For the additional details, see the methods section. (E and I) Summary table of distant organ metastasis derived from each surgery group. (F) Schematic diagram of tumor resection in inguinal lymph node pre-removed or sham control 4T1 tumor-bearing mice. (E and I) Summary table of distant organ metastasis derived from each surgery group.(G and H) Distant organ metastasis was examined by bioluminscent images of inguinal lymph node pre-removed tumor-bearing mice (n=9 mice) or sham surgery tumor-bearing mice (n=5 mice) after tumor resection on week 5. The bioluminescent signal (pseudocolor) was recorded as photons per second per centimeter squared per steradian (p/s/cm2/sr) and the luminescent image was overlaid on the photographic image. For the additional details, see the methods section.
Figure 5A. Luciferasereporter assay of wild-type (wt) and mutant (mut) ITPKB 3'UTR in HEK293 cells co-transfected with a synthetic miR-132 (miR-132) or a negative control (Neg Ctr) oligonucleotide. B. ELISA of Aβ40 and Aβ42 levels in HEK293-APPswecells transfected with a miR-132 antisense oligonucleotide (miR-132 inh), an siRNA against ITPKB (ITPKB siRNA) or both. The assays in A and B were performed in three independent experiments, each in triplicates. C. Western blot analysis of ITPKB knock down in APPPS1hippocampus using an siRNA oligonucleotide against ITPKB. Sample size, n=6 per group. Values were normalized to control-injected group (Ctr) and presented as mean ± SEM. D. ELISA of insoluble (Formic acid-soluble) Aβ40 and Aβ42 levels in the hippocampus of ITPKB siRNA- and control-injected animals at three months of age. Sample size, n=6 per group. Values were normalized to control group and presented as mean ± SEM. E, F. Western blot analysis of ITPKB levels upon miR-132 down- (E) or up-regulation (F) at six and three months of age, respectively. Sample size, n=9 per group for miR-132 down regulation and n=6 per group for miR-132 overexpression. Values were normalized to control groups and presented as mean ± SEM.
Figure 1Male C57BL/6J mice were fed with chow diet supplemented with 0, 0.5%, 1% SUC for 8 weeks. Serum SUA level Male C57BL/6J mice were fed with chow diet supplemented with 0, 0.5%, 1% SUC for 8 weeks. body weight gain Male C57BL/6J mice were fed with chow diet supplemented with 0, 0.5%, 1% SUC for 8 weeks. fat Male C57BL/6J mice were fed with chow diet supplemented with 0, 0.5%, 1% SUC for 8 weeks. lean mass Male C57BL/6J mice were fed with chow diet supplemented with 0, 0.5%, 1% SUC for 8 weeks. gastrocnemius index. Male C57BL/6J mice were fed with chow diet supplemented with 0, 0.5%, 1% SUC for 8 weeks. Gastrointestinal muscle fiber immunofluorescent laminin staining Male C57BL/6J mice were fed with chow diet supplemented with 0, 0.5%, 1% SUC for 8 weeks. frequency histogram of fiber cross-sectional area.
Figure 2(A, C) UBE2D3~Ub discharge assays with different TRIM25 and TRIM32 constructs, respectively. Assays were carried out with TRIM constructs as indicated and the reaction was monitored over 30 min. The asterisk indicates the band for the TRIM construct. (B, D) Quantification of the discharge assays using UBE2D1~UbAtto and TRIM25 or TRIM32, respectively. The loss of UBE2D1~UbAtto is plotted as the average of experimental triplicates (± s.d.). (E, G) K63 poly-ubiquitination assays using UBE2N/UBE2V1 and TRIM25 and TRIM32, respectively. Reactions were incubated for 30 minutes and samples taken at indicated times. The asterisk indicates the band for the TRIM construct. (F, H) Assays were quantified (see Materials and Methods) by supplementing the reaction with 1 uM UbAtto and integrating the loss of free UbAtto for TRIM25 and TRIM32, respectively. Assays were carried out in triplicate.
Figure 9A Model of how activated (GTP-bound) Rab35 at the ciliary and/or periciliary (pocket) membrane limits Arl13b ciliary levels. In one scenario, Rab35 inhibits Arl13b entry into cilia, possibly through an IFT pathway. In a second scenario, Rab35 promotes Arl13b exit/retrieval from ciliary (and periciliary) membranes via: (i) interaction with retrograde IFT, (ii) modulation of the transition zone membrane diffusion barriers that prevent Arl13b from exiting the cilum, and/or (iii) endocytic processes at or near the ciliary pocket that target Arl13b for degradation or recycling to non-ciliary plasma membrane destinations. B Ciliary membrane and ciliary length phenotypes following Rab35 disruption. In wild type cells, Arl13b, INPP5E and Smoothened (SMO; under conditions of Shh signal activation) all localise to the ciliary membrane. Arl13b promotes the ciliary localisation of INPP5E whilst limiting (or altering) the ciliary distribution of SMO ]. PI(4,5) P2 (blue line) is enriched within the proximal portion of the ciliary membrane.In Rab35-depleted cells, ciliary Arl13b levels are elevated, causing a concomitant increase and decrease in the ciliary levels of INPP5E and SMO, respectively. Rab35 disruption also leads to a reduction in the length of the proximal ciliary PI(4,5) P2 signal and a reduction in the frequency of PI(4,5) P2-positive cilia (thin blue line). Misregulation of ciliary membrane protein composition in Rab35-disrupted cells leads to a decrease in cilium length.