EMBO/sd-character-level-ner huggingface dataset:
(A,B) Effect of UK5099 treatment on norepinephrine-stimulated energy expenditure. Fully differentiated primary brown adipocytes were pre-treated with vehicle (DMSO) or 100 nM UK5099 for 2 h. OCR were measured in respirometry media supplemented with 5 mM glucose and 3 mM glutamine in the presence of vehicle or UK5099. Norepinephrine (NE; 1 µM), oligomycin A (Oligo; 4 µM), etomoxir (Eto; 40 µM) and antimycin A (AA; 4 µM) were injected where indicated. (A) Representative OCR traces averaging 4 technical replicates. (B) Quantification of non-stimulated OCR, NE-stimulated OCR, ATP-linked OCR, mitochondrial proton leak and Eto-sensitive OCR as shown in (A) from n=9 individual experiments. The effects of UK5099 treatment were normalized to vehicle for each experiment.
(C) In vivo epifluorescence microscopy following de novo expressed UapA-GFP in a germling maturing to young hypha at 180, 240, 300, 360 and 400 min after derepression of transcription via its native uapA promoter. During this developmental transition, UapA apical localization is gradually diminished. As the cell tip acquires a faster growth rate, UapA is completely retracted from the hyphal apex (see zoon-in panels on the right and white arrows).
(C) LncRNA CRNDE expression level was measured by qRT-PCR in adjacent normal tissue-derived macrophages (NTMs) and tumor-associated macrophages (TAMs) obtained from 7 cases of GC patients. Data information: Data are expressed as mean ± SD. Student's t-test **P<0.01.
(G - I) Boxplots showing FC (log2) in gene expression between indicated samples for 3 groups of genes classified according to H3K27me3 enrichments (as shown in E). Lower hinge, central line and upper hinge represent 25th, 50th (median) and 75th percentiles respectively. Upper/lower whiskers extend to the largest/smallest values no further than 1.5 * IQR from the upper/lower hinge, where IQR is inter-quartile range or distance between 25th and 75th percentiles. Outliers are not displayed. The notches extend $1.5*IQR/\sqrt{n}$ where n is a number of genes in each H3K27me3 class. Number of genes (n) in "Low", "Medium" and "High" H3K27me3 class used for boxplots are 9824, 2311, 2647 respectively. Expression changes were estimated using 2 or 3 biological replicates for each condition. Statistical significance was estimated using two-sided t-tests.
(A,B) Expression of mei2+ (B) using quantitative RT-PCR of RNA extracted from cells grown either in rich medium (dark gray) or starved for 4 hours (light grey). Cells of the following genotypes were analyzed: wild-type isogenic controls (WT), ppa2Η, par1Η, pab1Η, tsc1Η, and pab1Η tsc1Η. act1+ served as a control for normalization across samples. Values from a WT strain grown in rich medium were set at 1 to allow comparisons across culture conditions and mutant strains. Each column represents the mean value of 4 independent experiments, overlaid with individual data points and SE. Statistical significance was determined by 2-way ANOVA followed by Bonferroni's multiple comparison tests (n = 4).
Genetic interactions between condensin and (D) Gcn5 and Mst2. Fivefold serial dilutions of fission yeast strains were spotted onto complete medium.
(C) Digitonin-solubilized (1 or 4 g/g digitonin/protein ratio, as indicated) mitochondrial membranes from the indicated yeast strains (wild type, pex19Δ, pex19Δmsp1Δ) expressing Pex13-V5 (under its endogenous promotor) were separated by BN-PAGE with a 3-18% gradient and immunoblotted for PEX13-V5 (α-V5). Green box for wild type, orange box for pex19Δ, purple box for pex19Δmsp1Δ, indicates gel area of 300-130kDa correlated to complexome profiling heatmap. (D) Heatmap representing the protein abundance of Pex11, 13, 14, 17, 25 in digitonin-solubilized (3 g/g digitonin/protein ratio) mitochondrial membranes from the indicated yeast strains (wild type, pex19Δ, pex19Δmsp1Δ) expressing Pex13-V5 (under its endogenous promotor). Green box for wild type, orange box for pex19Δ, purple box for pex19Δmsp1Δ, indicates gel area of 300-130kDa correlated to complexome profiling heatmap. (E) Heatmap representing the protein abundance of Mdh3 and Pot1 in digitonin-solubilized (3 g/g digitonin/protein ratio) mitochondrial membranes from the indicated yeast strains (wild type, pex19Δ, pex19Δmsp1Δ) expressing Pex13-V5 (under its endogenous promotor).
F Quantification of CAL+ cells in the PL and IL cortex. Mock, n=4 mice; ZIKV, n=4 mice in B, D, and F. P = 0.0490 (PL in B), 0.0253 (IL in B), 0.0113 (PL in F). G CAL+ interneuron numbers plotted against social preference. Black solid lines represent regression line; grey lines indicate 95% confidence intervals in C, E, and G. Mock (black circles), n=4 mice; ZIKV (red circles), n=4 mice. P = 0.0054 (PL in C), 0.0226 (IL in C), 0.1765 (PL in E), 0.5840 (IL in E), 0.2983 (PL in G), 0.2109 (IL in G); linear regression. Data information: All data are presented as mean ± SEM. *P<0.05, **P<0.01. Two-tailed unpaired t-test unless described otherwise.
D, OTUB1 interacts with wt NRAS and active NRAS mutant. Flag-tagged NRAS proteins were immunoprecipitated using anti-Flag (M2) agarose from HEK293T cells overexpressing HA-tagged OTUB1 or empty vector (V).
EMSA analysis of the interaction of HAND2-AS1, INO80 and RUVBL2 with the BMPR1A promoter region.
C Probability density plots of single-cell mRNA distributions from smFISH as described in (B) before and after treatment with 20 ng/mL TNF for the indicated time points.
(B) Representative confocal imaging of NimB4-sGFP macrophages of embryo at stage 16; lateral (left) and ventral (right) views; Tissues were stained with anti-GFP (green, corresponding to NimB4-sGFP) and anti-SIMU antibodies (red, corresponding to macrophages). The arrows show the presence of NimB4-sGFP inside the embryonic macrophages. Scale bars = 20 μm
(F) The regrowth of MTs (i.e total tubulin intensity) was assessed in cells incubated at 37°C for 0, 60 and 150 seconds after ice-induced depolymerization (for 30 minutes). The graph represents the average of three independent experiments (calculating 10 cells per time point for each condition) (±S.E). Significant differences are noted as *p<0.05, Student's t-test
B, Effect of the deletion of hoxA or hoxB on red-light induction of the ccgA gene. A. alternata strains were grown for 36 h at 28°C. Samples were illuminated for 1 h in red light while controls were kept in the dark. The amount of ccgA transcript was quantified by qRT-PCR analyses with the histone 2B gene as housekeeping gene. Error bars represent the standard deviation (n = 3).
(E) Schematic illustration of CRISPR/Cas9-mediated genome editing of the non-essential RPS4Y gene on the Y chromosome with the insertion of a neomycin resistance cassette. (F) Experimental set-up for G, H.
(g) Nitrocellulose filters spotted with the indicated lipids (defined in e) were incubated with wild-type IRGMd, IRGMdS47N, and the IRGM isoform IRGMb at the indicated concentrations. GST control is shown in Supplementary Information, Figure S1d. Membranes in e-g were probed with anti-GST antibody.
(E) The molecular surface of hCAP-G in complex with hCAP-H. The structural model of hCAP-G is shown in white. hCAP-H is shown as a green ribbon model. Identical and homologous residues between hCAP-G and YCG1 are shown in blue and cyan, respectively.
(F) Mitochondria from the indicated yeast strains (pex19Δ, pex19Δmsp1Δ, and pex13Δmsp1Δpex19Δ) expressing Pex22-V5 (under its endogenous promotor) (HistodenzTM-purified) were separated by SDS-PAGE and immunoblotted for Pex22-V5 (α-Pex22-V5) and porin (α-porin). (G) Mitochondria from the indicated yeast strains (pex19Δ, pex19Δmsp1Δ, and pex13Δmsp1Δpex19Δ ) expressing Pot1-V5 (under its endogenous promotor) were separated by SDS-PAGE and immunoblotted for Pot1-V5 (α-Pot1-V5) and porin (α-porin). (H) Mitochondria from the indicated yeast strains (pex19Δ, pex19Δmsp1 Δ, and pex13Δmsp1Δpex19Δ) expressing Mdh3-V5 (under its endogenous promotor) (HistodenzTM-purified) were separated by SDS-PAGE and immunoblotted for Mdh3-V5 (α-Mdh3-V5) and porin (α-porin).
(C) Left: Shown is a line graph depicting normalized mRNA expression levels of the 9 TRs at the indicated time points during the reprogramming of MEFs. The data were plotted after normalization with the endogenous Gapdh using the "ΔCt method". The grey vertical dashed line depicts day 6 in which the expression levels of nearly all TRs peaks. Notice that the y-axis is broken to accommodate the large spread of expression levels. Right: Shown are western blots using antibodies specific for Irf6, Tead4, Taf1c, Rcan1 and Tfap4. Whole cell extracts were prepared from MEFs at day 6 of reprogramming and run side-by-side with extracts from control samples (day 0). Gapdh, mTOR and b-Tubulin were used as loading controls.
Figure 2. Dynamic reorganization of chromosomes during replication.. (F) Normalized contact frequencies between chr3 centromere (cen3; yellow arrowhead) and the rest of the genome for G1, G2 and ssc1 G2.
B Immunoblotting for the indicated proteins. Lysates of mock, wild-type YAP and YAP-5SA expressing cells were analyzed. Cells were treated either with PLX4032 (2 &amp;amp;#x3BC;M) or DMSO for 24 hr.
(D) Quantification of caspase-positive particles in the central brain area of larval brain. Values from at least five independent experiments are represented as mean ± SD total volume of caspase-positive particles (** P<0.01, by Mann-Whitney test).
B Deuteration of BAK in a membrane compared to inactive BAK is mapped onto the structure of inactive monomeric BAK
G Volcano plot showing DEGs in the offspring's hippocampus upon 5000 ppb ATO exposure (n = 2 mice for both control and ATO groups). Dash lines indicate fold change ≥ 2 or ≤ 0.5 and adjusted p value < 0.05. Genes to be further validated for expression levels are labelled.
Representative images of AβO immunoreactivity (detected using anti-oligomer monoclonal antibody NU4) in the hypothalamus of control, sham-operated adult cynomolgus macaques (Sh; n = 3) or macaques that received i.c.v. injections of AβOs (n = 3; see Materials and Methods). Nuclear staining (DAPI) is shown in blue. Insets show optical zoom images of the areas indicated by white dashed rectangles in the main panels. Scale bars = 100 and 20 μm for main panels and insets, respectively.
C Ratio of 35S-Cysteine and 35S-Methionine incorporation by in-vitro translation using wild-type mitohybrid ribosomes, mutant A1555G mitohybrid ribosomes, and MT-CO1 mRNA. Following immunoprecipitation, the MT-CO1 band was quantified by autoradiography, wild-type mitohybrid ribosomes were set as 1 (n=3), error bars indicate SEM; ****p<0.001 (Student's t-test).
(E) Hepatic growth hormone signaling target genes mRNA levels in the WT and L-HRD1 KO mice. (n=5 for each group). Data information: The data are representative of three independent experiments (mean ± s.d.).
3×105 MFC cells were subcutaneously injected into nude mice. Ten days after injection, BMDMs-exo, M2-exo, M2-si-control-exo, or M2-si-CRNDE-exo (10 µg) was injected into the center of the homograft tumors of mice (n=7 each group), followed by intraperitoneal injection of CDDP (10 mg/kg). Six days after CDDP treatment, all mice were sacrificed and the homograft tumors were collected. (D) LncRNA CRNDE expression in homograft tumors of mice. **P<0.01. Data information: Data are expressed as mean ± SD. : one-way ANOVA.
(M) Total PD-L1 and CD47 blotting analysis from DR5 resistant MDA-MB-436 cell lines after indicated DR5 agonist treatment (50nM, 6hr).
(C) Three-gate mechanism of topo II to pass one segment of DNA (T-segment) through another (G-segment). Upon ATP binding, the T-segment is captured by the entrance gate (N-gate) and passed through the transiently cleaved G-segment (DNA-gate). Upon re-ligation of the G-segment, the T-segment is released through the exit gate (C-gate).
(C) Diffusion map, displaying diffusion component (DC) 1, 2 and 4, generated from the mRNA expression profiles reconstructing the developmental trajectories of the αβ and γδ developmental lineages across human thymocyte subsets. The line connecting the different subsets is reflecting the developmental stages of human T cell development.
(L-O) Lateral images of the FLS (L, N; dotted line) or dorsolateral CCV region from where the FLS normally sprouts (M, O; dotted line) fixed at 36 hpf in lyve1b:EGFP embryos that have been fluorescently immunostained with anti-PROX1 (green) and anti-GFP (red). These show no change in the number of Prox1-positive lymphatic progenitors in the ccbe1 morpholino-injected (M) and sFLT4 mRNA-injected (O) embryos compared with control morpholino-injected (L) and uninjected (N) embryos. (P) Quantitation of the percentage of dorsolateral CCV ECs that are lymphatic progenitors relative to the total number of dorsolateral CCV ECs in control morpholino-injected (n = 26), ccbe1 morpholino-injected (n = 27), uninjected (n = 28) and sFLT4 mRNA-injected embryos (n = 32). (Q) Quantitation of the total number of dorsolateral region CCV ECs in 36 hpf embryos that were uninjected or injected with control morpholino (n = 26), ccbe1 morpholino (n = 27), or sFLT4 mRNA (n = 32).
(e)HeLa were transfected with the indicated siRNAs and vector encoding GFP-IRGMd, and labelled with MTR. The percentage of cells with mitochondrial morphologies ranging from normal, punctiform (dots) and elongated were quantified.
(b) Glutamine synthetase reporter plasmids carrying mutations in putative FOXO-binding sites were transfected in HEK293 cells together with Renilla and FOXO3(A3) as indicated. Luciferase activity was measured 40 h after transfection. Data are depicted as relative luciferase units (RLU) compared with the control. Shown are mean ± s.e.m. values (n=3)
(A, B) Representative images and quantification of 14 DIV neurons transduced with mCh, mCh-TSG101, or mCh-Rab35, treated for 5 h with either DMSO (CON) or Bafilomycin (Baf) to block lysosomal degradation, and immunostained for Tau and LAMP1. Overexpression of Rab35 or TSG101 increases Tau accumulation in lysosomes of Baf-treated neurons, indicating that Rab35/ESCRT pathway activation stimulates sorting of Tau into lysosomes (scale bar: 5 μm)(n=25-27 cells/condition; for TSG101, 2-way ANOVA, Baf x TSG101 interaction F1, 99=4,075 p=0.04, overall Baf effect F1, 99=10,30 p=0.0018, Sidak posthoc analysis ***p=0.0007; for Rab35, 2-way ANOVA, Baf x Ra35 interaction F1, 101=5,36 p=0.02, overall Baf effect F1, 101=12,01 p=0.0008, Sidak posthoc analysis ***p=0.0001). All numeric data represent mean ± SEM
(F) Co-immunoprecipitation of PARP1 with endogenous KLF4 is independent on DNA. The DNA binding inhibitor EtBr was added to the MDA-MB-231 cell lyses followed by immunoprecipitation of KLF4 complex.
A, B. Cycloheximide (CHX) assay. (A) N2a cells transfected with Atoh1-GST, Ccnd1 and Cdk4 plasmids 2 days prior were harvested after 0, 4 and 8 hr treatments of 50ug/mL CHX and lysates were subjected to immunoblotting with anti-Atoh1 or β-actin as a housekeeping control. (B) Quantification of relative levels of ATOH1 to the β-ACTIN. N2a transfected with only Atoh1-GST is referred as WT and N2a transfected with Atoh1-GST, Ccnd1 and Cdk4 plasmids is referred as 4D. Same experiments were performed three times. Error bars are representing as Mean ± SEM.
(A) Co-purification of Rtf1-PK in cells expressing Mog1-TAP (+,+). A non-tagged strain (-,-) and cells expressing only Rtf1-PK (+,-) were included as negative controls for co-purification. Inputs and IPs are depicted for each strain.
(C) β-catenin ChIP-seq enrichment over ENCODE TCF7L2 (also known as TCF4) ChIP peaks in HEK293T cells. The data represent the mean ± 95% C.I. obtained from three independent experiments (N = 3)
E Heme quantification by absorbance at 400 nm of the soluble NPC cell lysates. All data are presented as means + SEM of at least three independent experiments (One-way ANOVA).
E. Average number of γ-H2AX foci per cell in cells that were not treated (NT) or exposed to 2 Gy ionizing radiation. N=2.
(A) Schematic showing presence of tumor cells capable of optimal and non-optimal apoptotic activation by DR5 agonists constitute heterogeneous tumors.
Detailed view of the wMelOTU (pink) active site region and its coordination of the Ub C-terminus (red). Residues that coordinate Ub or stabilize the active site are shown with ball and stick representation.
(B) The percent of the cell surface area covered by GFP-LC3 vesicles was quantified using the Image J software. n>70 cells in three experiment, *P0.01.
(A) HeLa cells were transfected with siRNAs for autophagy-related gene ATG5 (siATG5) or with a non-silencing siRNA (siC). Depletion of ATG5, which decreased the levels of the ATG5-ATG12 covalent complex, was confirmed by Western blot. Loading control: transferrin receptor (TfR).
Schematic illustration depicting the analysis criteria for random section electron micrographs (not drawn to scale). Synaptic vesicles (SVs) were categorized as ribbon-associated SVs (RA-SVs, green) or membrane-proximal SVs (MP-SVs, yellow).
(e) HEK293 cells expressing GFP-tagged LRRK2 and transduced with lentivirus control (Ctr) or carrying shRNA against LAMP-2A (L2A(−)), incubated or not with NL for 12 h and immunoblotted for the indicated proteins.
(F) Immunofluorescence analysis of the old APPPS1 slice in co-culture (14 DIV) treated with cytochalasin D (CytoD) and vehicle control (Ctr) and immunostained with M3.2 (green) and CD68 (red). Inhibition of phagocytosis by CytoD blocks amyloid plaque clearance. Scale bar: 50 µm.(G) Quantitative analysis of core-only plaques in the old APPPS1 slice in co-culture (14 DIV) treated with CytoD and Ctr reveals a decreased number of core-only plaques upon CytoD treatment. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques. The values represent mean ± SEM from 3 independent experiments, including total of 6 independent slice culture dishes (***P < 0.001).
(F) Representative immunoblot of Grk5 protein levels and quantification in cytoplasmic and nuclear fractions from left ventricle lysates of WT and Cand2 KO mice after TAC surgery. Lamin B - nuclear marker, Gapdh - cytoplasmic marker. Analyzed by One-way ANOVA, n=3 biological replicates. Data information: Error bars indicate means ± SEM. * - P ≤ 0.05, *** - P ≤ 0.001.
Figure 1. Comparison of genome structures recovered from five synchronized stages over the cell cycle. (B) 3D average representation of the Hi-C contact map of a yeast G1 population. The color code reflects chromosomal arm lengths and, centromeres, telomeres and rDNA are highlighted.
Localization of α 1S subunit. Whole skeletal muscle fibres enzymatically isolated from Ctrl (A-D) or ΔDHPR (E-H) FDB muscles 6 months post injection were processed for immuno‐fluorescent labelling for α1 S subunit (red) and laminin (green). Scale bars, 10 μm; Arrows indicate α1 S subunit expression on sarcolemma; antibody labelling was visualized by serial confocal microscopy and represented as movies of the optical sections (Supplementary Movies S5A and S5B). (D, H) Present projections of confocal Z‐series (step between each frame is 1 μm) along XZ and YZ planes as indicated.
(b) RagA/RagC and TSC1/TSC2 independently regulate S6K phosphorylation. HEK293 cells were transfected with 200 ng of each Rag and/or ′ constructs as indicated. Amino acid starvation for 1 h (-AA) is indicated. Phosphorylation and protein levels of the transfected proteins were determined by immunoblotting with appropriate antibodies, as indicated.
(e) Predicted metabolite interchange network representing metabolites that were secreted or utilized by distinct organisms based on a two-fold threshold. Arrows point from the source species to the consumer organism. Node size and line width are proportional to the total number of secreted metabolites and number of predicted metabolite interactions, respectively. Species at the top and bottom of the network are primarily producers or consumers, respectively.
C. NCOA4 KO MEFs reconstituted with hNCOA4-myc were cultured with 10 μg/ml FAC for the indicated times and fixed for imaging. Cells were immunostained with ferritin and myc antibodies. Scale bar, 10μm.
(D) Validation of interaction between ectopically expressed KLF4 and PARP1. 293T cells were transfected with FLAG-KLF4 and Myc-PARP. Whole cell lysates or IP complex pulled down by anti-FLAG antibody were analyzed by Western blotting.
(B) ACE2 cell surface expression on Caco-2 and Calu-3 was determined by quantitative real-time PCR. Data information: Data show the mean values and error bars are the SEM. Statistical analysis was performed using ordinary one-way ANOVA with Tukey's multiple-comparison test. *P≤0.05, **P≤0.01 (n=5 Caco-2 donors measured in monoplo), *p=0.0460 (n=5 Calu-3 donors measured in monoplo)
Partial least squares discriminant analysis (PLS-DA) model and used the variable importance in projection (VIP) score was used to assess the contribution of each genus, shown as a scores plot in (E) VIP score cut off of 1(n=4-5 mice per group).
JQ1 treatment inhibits microglial expression of inflammatory cytokines in the rd10 retina. Intravitreal injection of JQ1 (or vehicle) was performed at PN14, as described in Fig. 1. Retinas were collected at PN24. a Homogenates were prepared from retinas (3 groups, total 12 mice) and used for qRT-PCR. Quantification: normalization to GAPDH mRNA; mean ± SEM; n = 3 independent homogenation/qRT-PCR experiments; *P < 0.05, **P < 0.01 compared to rd10 vehicle control. b Retinal homogenates were used for determination of MCP-1 protein levels by ELISA. Quantification: normalization to WT mice injected with vehicle; mean ± SEM; n = 3 experiments; *P < 0.05. c Retinal microglia were purified from dissociated rd10 retinas via flow sorting, as described in 'Methods'. Sorting was performed five times using retinas collected from five groups of rd10 mice (four mice each). Sorted microglial cells (CD11b + CD45low) were then subjected to qRT-PCR. Quantification: normalization to GAPDH mRNA; mean ± SEM; n = 5; *P < 0.05, **P < 0.01, compared to rd10 vehicle control. d Microglial cells were isolated and purified from B6 mouse brains. Cells were pre-incubated with vehicle (DMSO) or JQ1 (0.5 μM) for 12 h, and then induced for inflammatory cytokine expression with LPS (1 μg/ml) for another 2 h prior to qRT-PCR assay. Quantification: normalization to GAPDH mRNA; mean ± SEM; n = 3 independent experiments; *P < 0.05, **P < 0.01 compared to vehicle + LPS
E Immunoblotting of the transfected wild-type DNMT3A, C520A/C524A and C541A mutants in 293T cells upon 1 μg/mL ATO treatment for the indicated durations.
M-P Representative images of lectin stained choroidal flat mounts 7 and 14 days after laser coagulation in control mice (M, N) and IFN-b treated animals (O, P). Dashed lines indicate CNV areas and the asterisk marks the central optic nerve head. Scale bar: 200 µmQ Quantification of lectin-stained CNV areas with ImageJ software. Bars show mean ± SD. (n = 7-12 RPE/choroidal flat mounts; One-way ANOVA followed by Tukey's post-test: **p = 0.0038).
(F) Western blot analysis of endogenous Atg8a from third instar muscle lysate. 6 hrs starvation induces lipidated Atg8a-II in Dmef2-Gal4 control at both 18 hrs and 48 hrs PS, but not in DTS at 48 hrs PS.
, Selective secreted metabolites with significant change linked to urea cycle components from healthy (n=3; blue) and regressed (n=3; green) mammary glands. Values represent metabolite abundance levels as quantified by the area under the curve (AUC) of the marker fragment ions/transitions for each metabolite. Values are plotted on the log2 scale. Statistics were calculated using the limma package n R with the significance threshold corresponding to a Benjamini-Hochberg adjusted p-value ≤ 0.05 (residual compared to normal). ata information: umbers of replicates correspond to individual mice or humans. ox plots: midline, median; box, 25-75th percentile; whisker, minimum to maximum. umbers marking comparisons (gray lines) show p values (corresponding statistical tests are described in individual panel legends).