EMBO/sd-character-level-ner huggingface dataset:
Development of a 3D tissue model and in vivo live imaging during dermal maturation.Figure 4(x,y) cross-section of the computational model simulation of the dermal maturation process at the indicated Monte Carlo Steps (MCS). Colour code indicates epidermis (green), proliferating fibroblasts (blue), quiescent fibroblasts (yellow), ECM (grey) and adipocytes (brown). Abundance of the cell populations during the course of the simulation. Quantification of fibroblast proliferation and ECM density in the simulation. Live imaging of adult PDGFRαH2BEGFP mouse back skin. Representative time-lapse images of adult PDGFRαH2BEGFP (green) dermis with collagen shown as second harmonic generation (SHG) in purple at indicated imaging time points. Scale bar, 100 µm. In silico lineage tracing of fibroblasts. (E) Labelling of fibroblasts close to the epidermis at indicated MCS. (F) Labelling of fibroblasts in the middle of the dermis at indicated MCS. (G) Labelling of fibroblasts close to the inside of the body at indicated MCS.
a) Representative confocal images of LIPL-1::GFP and LIPL-3::TagRFP localization relative to the lysosomal marker PGP-2 show that LIPL-1 and LIPL-3 are localized to the lysosomal-related organelle.figf2(a) Representative confocal images of LIPL-1::GFP and LIPL-3::TagRFP localization relative to the lysosomal marker PGP-2 show that LIPL-1 and LIPL-3 are localized to the lysosomal-related organelle. (b) Acid lipase activity, measured in 1-day adult whole lysates, shows that lipl-1lipl-3 double mutant animals have reduced acidic lipolytic capacity. Mean±s.d. are presented relative to wild type (WT); significant differences are indicated; n = 4 independent experiments. (c) Oil Red O (ORO) staining and fatty acid methyl ester (FAME) analyses of wild-type and lipl-1(tm1954) lipl-3(tm4498) double mutant L3 larvae show that lysosomal lipases regulate cytosolic fat stores (see Fig. 2d for adult measurements). Means±s.e.m. are presented relative to wild type; significant differences are indicated; n = 3 independent experiments. (d) ORO quantification of wild-type and lipl-1(tm1954) lipl-3(tm4498) double mutant young adults fasted for 4 h shows that LIPL-1 and LIPL-3 contribute to fat mobilization following fasting. (Mean percentage ± s.e.m. relative to fed wild type). Wild-type fasted worms show 20% less ORO signal than animals fed ad libitum (P≤0.001), whereas lipl-1(tm1954) lipl-3(tm4498) double mutant worms show 7% reduction in ORO signal (a difference that is not significant to well-fed fat levels at P≤0.01 but it is significant at P≤0.05). n = 3 independent experiments. (e) Representative transmission electron microscopy images of well-fed and 6 h-fasted wild-type and lipl-1lipl-3 mutant animals (11,500×) show that the lipl mutants have more lipid-droplet stores in ad libitum fed and fasted conditions. Quantification of vesicle number and size is depicted as mean+s.e.m., n = 4 independent experiments. (f) Representative images of well-fed transgenic animals expressing LIPL-3::TagRFP and ATGL::GFP shows that LIPL-3 does not localize to lipid droplets. (g) ORO staining and quantification of wild-type and lipl-1(tm1954) lipl-3(tm4498) double mutant young adults treated post-developmentally (from L4) with RNAi against the essential autophagy genes lgg-1 and lgg-2 or vector control show that lipl-1 lipl-3 and the autophagy genes lgg-1 lgg-2 are in the same fat regulatory pathway. (Mean percentage+s.e.m. relative to wild type on vector control is depicted.) n = 4 independent experiments.
Fig.Figure 1(a) Phylogenetic tree of the apelin, angiotensin, and bradykinin receptor, Scale (0.1). The Ciona intestinalis AGTR like gene served as an outgroup. The ω parameters of two fish branches are shown. Scale: The unit of evolutionary distance is the number of amino acid substitutions at each position. (b) Conservation of the apelin/angiotensin/bradykinin peptide receptor subfamily among all vertebrates except for the GPR15-C10ORF99 pair. * Indicated that these three fish species did not undergo a third round of whole-genome duplication during fish evolution. (c) Result of rapidly evolving genes (REGs). This calculates the χ2 critical value and P value for conducting the likelihood ratio test. The genes with P <0.05 were considered. (d) GPR15 underwent positive selection in fishes. The parameters for each branch are shown; the dN/dS ratio was calculated with the whole protein-coding region. **P-value < 0.01, * P-value < 0.05, NA: not available.
LC3 and p62 accumulate in IBMPFD muscle tissue.Figure 1.(A and B) Immunoblot of 9-mo-old quadricepsmuscle lysates from control (cont) or VCP-WT, -RH9, or -RH12 mutant transgenic lines with p62 (A) or LC3 (B) antibodies. Note the increase in p62 and LC3II isoforms in mutant animals. Densitometric quantification is from more than six 9-mo-old animals/group. LC3 and p62 levels are normalized to loading control. Error bars represent the standard error from six independent experiments. **, P < 0.001. AU, arbitrary unit. (C) p62 immunostaining of tibialis anterior (TA) or quadriceps (Quad) muscle from 9-mo-old control, VCP-WT, or one of two VCP-RH transgenic lines (RH9 or RH12). Note accumulations of p62 in the middle of myofibers or along subsarcolemmal regions. (D) Histochemistry and immunohistochemistry of quadriceps muscle from VCP-RH-expressing transgenic mice. Hematoxylin and eosin (H&amp;amp;E) staining of a 15-mo-old animal with an RV, p62 immunostaining of an RV from a 12-mo-old animal, LC3 immunostaining of an RV, and subsarcolemmal accumulations of LC3 from a 12-mo-old animal. The bracket highlights one LC3-positive myofiber. A single muscle fiber is outlined in white. (C and D) Arrows denote vacuoles or accumulations of p62 or LC3. Bars, 30 µm.
Figure 3A, B. Aggregate number of detected and undetected cysteines (A) and lysines (B) in 3,840 CpDAA-containing proteins. C. Heatmap of missense score correlations for all possible non-synonymous SNVs at CpD Cysteine (29,541 missense) for eight pathogenicity scores. Overall, Spearman's rank r were between 0.36 and 0.91. Data information: color intensity represents two-tailed Spearman's rank-order correlation coefficients between 0 and 1. D. CpD Lysine (41,850 missense) heatmap for missense score correlations for all possible non-synonymous SNVs. Spearman's rank r between 0.16 and 0.81. Data information: color intensity represents two-tailed Spearman's rank-order correlation coefficients between 0 and 1. E. Odds of predicted deleterious Cys>Trp (red) missense at detected (n=6,057) versus undetected (n=34,049) residues in 3840 detected proteins. Deleterious missense defined by CADD38, FATHMM, and DANN score thresholds (y axis). CADD38 OR = 0.76, p = 3.40e-22; FATHMM OR = 0.92 , p = 0.02; DANN OR = 0.690 , p = 6.69e-26. Odds of predicted deleterious Lys>Ile (blue) missense at detected (n=3,581) versus undetected (n=63,385) residues in 3840 detected proteins. CADD38 OR = 1.80, p = 1.03e-53; FATHMM OR = 1.55, p = 3.47e-33; DANN OR = 1.75, p = 9.21e-14. *p < 0.0042 Bonferroni adjusted (two-tailed Fisher's Exact test) Data information: 95% confidence intervals (line segments) and odds ratios (squares). F. Odds of ClinVar pathogenic variant overlapping detected (6,057 Cys; 8,868 Lys) versus undetected (34,050 Cys; 140,652 Lys) residues in 3,840 detected proteins. Cys detected in ClinVar pathogenic site (red, OR = 1.17, p = 0.457) and Lys detected at ClinVar Pathogenic site (light blue, OR = 2.76, p = 1.03e-04). Combined Cys and Lys (dark blue, OR = 2.26, p = 9.99e-07) *p < 0.0167 Bonferroni adjusted (two-tailed Fisher's Exact test). Data information: 95% confidence intervals (line segments) and odds ratios (squares).
Figure 5A. Representative immunofluorescence images of SV40 LT localization 72 h after transfection into U2OS cells infected with control or FAM111A shRNA. Images were taken with a Zeiss Axio Imager. LT is shown in green, and DAPI blue. Scale bar: 100 μm. B. Quantification of LT positive cells described in A and fixed at indicated times post transfection. Five hundred or more cells were counted for each condition. C. Quantification of RFP marker distribution upon co-transfection with SV40 LT variants into U2OS cells infected with control or FAM111A shRNA. Cells were fixed at the indicated times. Five hundred or more cells were counted for each condition. In B & C, values are mean ± s.d. of independent experiments (n = 3). *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001 (two-tailed unpaired t-test). D. Western blot analysis of control or FAM111A-depleted U2OS cells transfected with SV40 LT variants. Cells were collected and lysed at indicated timepoints after SV40 transfection, immunoblotted with FAM111A, LT, or PARP antibodies. Cdc2-PSTAIR was used as a loading control.
a, Macrophages were stimulated with LPS (100 ng ml-1) for the indicated time period.figf3a, Macrophages were stimulated with LPS (100 ng ml-1) for the indicated time period. The number of endogenous LC3 dots within each cell was counted. The results shown are mean + s.d. (n > 100). b, Expression levels of p62 and LC3 in macrophages. c, IL-1b and IL-6 production by wild-type or Atg7-deficient macrophages stimulated with LPS. Statistical significance was determined by the Student's t-test. *P,0.01. d, Macrophages were pre-treated with or without 10 mM 3MA and then stimulated with the indicated ligands.
Schematics for nutrient pulse systems.Figure 1Three separate systems were used to pulse glucose to starved E. coli. The spin flask system (i) and plate reader system (ii) provided glucose pulses at defined frequencies. In the real-time metabolomics configuration (Link et al, 2015), another pump circulated culture and injected 2 µL of culture directly into a time of flight (QTOF) mass spectrometer every 10-15 s from the spin flask system. A microfluidic platform (iii) reproduced the pulse feeding and tracked division events. A pulsing period is defined as the time between the start of successive glucose medium exposures. During each pulse, glucose medium was flowed for 10 seconds, and the no glucose buffer was flowed in the intervening period
Figure 4A: The E14tg2a ESCs were transduced with lentiviral shRNAs targeting genes Esrra, S100a8, or Hcfc2 and induced to form EBs. The day 6 EB cells were analyzed by flow cytometry to measure the Mesoderm-Endothelium cells (Flk1+/Cxcr4-) and Endoderm cells (Cxcr4+/Flk1-). The percentages of Mesoderm-Endothelium cells (Flk1+/Cxcr4-) were decreased on day 6 with shRNA knockdown of Group XII genes Esrra, S100a8, and Hcfc2 compared to control as quantified by flow cytometric analysis.B: Knockdown of Esrra, S100a8, and Hcfc2 showed that the ratios of percentage of Mesoderm-Endothelium population vs Endoderm population were decreased as measured by Flk1+/Cxcr4- vs. Flk1-/Cxcr4+ on day 6. The data were generated based on the quantification of flow cytometry analyses. Error bars represent standard deviation (SD), n=2. Student's t-test, *p<0.05. C: The E14tg2a ESCs were transduced with lentiviral shRNAs targeting genes Atp5g3, Bub1b, Eci1, or Dis3l and induced to form EBs. The day 6 EB cells were analyzed by flow cytometry to measure the Mesoderm-Endothelium cells (Flk1+/Cxcr4-) and Endoderm cells (Cxcr4+/Flk1-). Flow cytometric analysis showed that Endoderm cells (Cxcr4+/Flk1-) were deceased while Mesoderm-Endothelium cells (Flk1+/Cxcr4-) were slightly increased in the cells with shRNA knockdown of Group XI genes Atp5g3, Bub1b, Eci1, and Dis3l compared to control.D: Knockdown of Atp5g3, Bub1b, Eci1, or Dis3l led to increase of Mesoderm-Endothelium/Endoderm population ratio as quantified based on the flow cytometry data. Error bars represent standard deviation (SD), n=3. Student's t-test, *p<0.05. E: The E14tg2a ESCs were transduced with lentiviral shRNAs targeting genes Wbp5, Rbm26, Gdpd4, and Nrxn1 and differentiated towards HSPCs. The differentiated cells on day 20 were analyzed by flow cytometry. Silencing of group IV genes including Wbp5, Rbm26, Gdpd4, and Nrxn1 decreased overall LK, LS, and LSK population on day 20.F: Quantification of LK+LSK+LS cell fractions with Wbp5, Rbm26, Gdpd4, and Nrxn1 silencing based on flow cytometric analyses. Error bars represent standard deviation (SD), n=2. Student's t-test, *p<0.05. G: The E14tg2a ESCs were transduced with lentiviral shRNAs targeting genes Ap2a1, Mettl22, Lrsam1, or Hal and differentiated towards HSPCs. The differentiated cells on day 20 were analyzed by flow cytometry. Flow cytometric analysis showed notable reduction of LSK population on day 20 with Group X genes Ap2a1, Mettl22, Lrsam1, or Hal knockdown.H: Quantification of flow cytometric analyses showed knockdown of Ap2a1, Mettl22, Lrsam1, and Hal significantly impaired generation of LSK population on day 20 in vitro compared to control. Error bars represent standard deviation (SD), n=3. Student's t-test, *p<0.05.
Figure 10A and B Neutralization of SARS-CoV-2 B.1.351/Beta by the indicated VHH antibody constructs. The neutralization experiment was performed as described in Fig 3A, with the difference being that a mutant-optimized anti-RBD/S1 VHH cocktail was used for immunofluorescence staining Two titrations for the Re9F06 trimer are shown, corresponding to the standard (upper row) or a five-fold higher virus inoculum (lower row) that was used for even more stringent neutralization conditions.
Tracking individual mitochondria over time reveals that fusion and fission are paired.Figure 2(A) An INS1 cell expressing mtPA‐GFP and co‐labeled with TMRE. The two mitochondria fused 20 s after photoactivation (arrow in '20 s'). Then, a voltage difference was established between the two poles (120 s) and they were later physically separated (120 s). The pattern is qualitatively similar to that shown in Figure 3Bi. Scale bar, 2 μm. (B) Fusion and fission time chart for individual mitochondria. Individual mitochondria tagged with mtPA‐GFP were monitored for a period of 1 h and the occurrence of fusion and fission was recorded. Mitochondria in INS1 and COS7 cells spend 77s (±71 s) and 87 s (±78 s), respectively, in the post‐fusion, connected state, and an average of 1434s and 1172 s, respectively, in the solitary, post‐fission state. (C) Fusion triggers fission. Cumulative probability of the occurrence of fission events at different intervals after fusion events occur (fraction of all fission events occurring after the given time interval). The data are fit to a hyperbolic function representing linkage between the two events (INS1, R2=0.98; COS7, R2=0.96). The straight line shows the predicted linear growth rate in fission event probability over time that would be expected if the fission had occurred independently from the fusion events (dashed lines INS1, R2=0.77; COS7, R2=0.84; see Supplementary data). (D) Fission does not trigger fusion. Cumulative probability of the occurrence of fusion events at different intervals after the fission event occurred. The data points were fitted to a linear relationship (R2=0.92), as predicted if fusion occurred independently of fission (0.05 versus 0.06%/second, respectively; see Supplementary data).
Figure 5 (A) Luc-reporter assays in P19 cells. Luc-reporters containing SOX3 and SOX9 bound CRMs around the astrocyte specific genes Fgfbp3 and Ttyh1 were strongly activated by SOX9 in synergy with NFIA; an activation that could be efficiently blocked by SOX3. No activation of these reporters could be detected with SOX10 or SOX11. (B) Luc-reporters containing SOX9 and SOX10 bound DNA-regions around the astrocyte genes Aldh1l1 and Atp1a2, which are not expressed in SOX10+ oligodendrocytes, could not be activated by SOX9 or SOX10  (C) Luc-reporters containing SOX9 and SOX10 bound CRMs around the oligodendrocyte specific genes Plekhb1 and Mid2 were activated in an additive manner by SOX9 and SOX10. No activation could be detected with SOX11. (D) Luc-reporters containing SOX3 and SOX11 bound CRMs of the neuronal genes Tubb3 and Lhx2, which are sequentially bound by SOX3 and SOX11, could be activated by SOX11 and efficiently repressed by SOX3. No activation could be detected with SOX10 (E) Forced expression of SOX3 for 96 hrs in differentiating GPCs blocked the formation of astrocytes but not oligodendrocytes. Scale bar, 25µm. (F) Statistical view of Fig. 5E. Bars represents mean values (of 3 experiments) of cells expressing GFAP or SOX10 in GFP or Sox3-transduced cells. Error bars in figure 5 indicate standard deviation of 3-7 individual samples and three-star significance > 0.001 (t-test). (*) 0,05<P<0,01; (**) 0,01<P<0,001; (***) P<0,001
Therapeutic effect of R-III on CCl4-induced liver fibrosis.Figure 4Representative macroscopic pictures of livers from control and CCl4-, CCl4/albumin-, CCl4/RBP-, and CCl4/R-III-treated mice. Liver sections were stained with H&amp;amp;E and Sirius red, and also subjected to immunohistochemistry for type I collagen. Scale bar, 200 μm.
Figure 4A U2OS cells stably expressing HA‐Flag‐ATG9A transfected with siRNA targeting AP2A1 (40 nM), or siRNA AllStar control (40 nM) were treated with KU0063794 or DMSO (6 h) 4 days post‐transfection, fixed, and stained with anti‐HA antibody. B Co‐localization of HA‐Flag‐ATG9A with TGN46. C Lysates of U2OS cells transfected with siRNA targeting AP2A1, or siRNA control AllStars analyzed by SDS-PAGE. D U2OS cells stably expressing mCherry−ATG9 were transiently transfected with GFP−Dynamin 2 or GFP−Dynamin 2 (K44A), 20 h post−transfection cells were fixed and with anti−TBC1D5 antibody. ATG9A and Dynamin 2co−localization is indicated by arrows.
USP45 co‐immunoprecipitates with components of the SLX4 complexSchematic representation of the domain architecture of human USP45 protein.Figure 1A Schematic representation of the domain architecture of human USP45 protein. B Endogenous USP45 was immunoprecipitated (IP) from wild‐type (WT) and USP45 knockout (KO) KBM7 cells lines. The immunoprecipitates were resolved on a polyacrylamide gel and stained with Instant Blue. The gel was divided into the indicated sections, and proteins identified by mass spectrometry are detailed in Supplementary Table S1. The key proteins that we focus on in this study are indicated. C Endogenous USP45 was immunoprecipitated from the WT and KO KBM7 cell lines and subjected to immunoblotting with the indicated antibodies. D Endogenous USP45 was immunoprecipitated from WT and USP45 KO U2OS cells lines and analysed as in (B). Mascot scores of the interactors are detailed in Supplementary Table S2. E Endogenous USP45 was immunoprecipitated from the WT or KO U2OS cell lines and subjected to immunoblotting with the indicated antibodies. Similar results were obtained in at least two separate experiments. F Schematic representation of the SLX4 complex.
Figure 2A) The JAK inhibitor baricitinib (Ba) blocked LIF-induced STAT3 phosphorylation. BCE cells were pre-incubated with DMSO, baricitinib (2 μM), cobimetinib (Co) (150 nM) or BEZ235 (BE) (5 nM) for 1 hour and were then treated with vehicle or LIF (10 ng/ml, Sigma) for 15 minutes. Ctrl, no pre-incubation with inhibitors. B) Baricitinib suppressed LIF-induced BCE cell growth. BCE cells were pre-incubated with DMSO, baricitinib, cobimetinib, or BEZ235 for 1 hour and then treated with vehicle, LIF (10 ng/ml) or VEGF (10 ng/ml). Cell proliferation was analyzed after 6 days, n=3. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. C) and D) STAT3 knockdown in BCE cells. BCE cells were transfected with siNegative and siRNAs targeting STAT3. qRT-PCR were performed to examine STAT3 mRNA levels. STAT3 level in siNegative was set as 1. Data from three independent experiments were averaged and are presented in C. In D, cells transfected with siRNAs were treated with LIF (10 ng/ml) or vehicle for 15 minutes. Whole-cell lysates were subjected to Western blotting with the indicated antibodies. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. E) LIF-induced BCE cell growth was abolished by STAT3 knockdown. BCE cells with STAT3 knockdown were cultured with LIF (10 ng/ml, Sigma) or vehicle. Cell proliferation was analyzed after 3 days. Fluorescence reading at 590 nm for each vehicle group was set as 1, n=3. siNegative, negative control siRNA not targeting any known genes. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test.
Figure 4A. Real-time PCR analysis of the genes coding for the pro-inflammatory cytokines IL-1β, IL-6, TNF-α in the hypothalamus of icv CCL2 injected mice at different times after injection (from 1h to 18h), normalized to values in icv saline injected mice (n = 6 per group). B-E. Study of gene and protein hypothalamic expression of the chemokine CCL2 (B, C) in icv CCL2 injected mice. Real-time PCR analysis for CCL2 (B) at different times after injection (from 1h to 24h), normalized to values in control icv saline injected mice (n = 6 per group). B-E. Study of gene and protein hypothalamic expression of the chemokine CCL2 (B, C) in icv CCL2 injected mice. Measurement of CCL2 (C) concentration by EIA after icv CCL2 injection (black bars) or icv saline injection (grey bars) in mice at 1h, 6h and 18h after injection. B-E. Study of gene and protein hypothalamic expression of MCH peptide (D, E) in icv CCL2 injected mice. Real-time PCR analysis for MCH (D) at different times after injection (from 1h to 24h), normalized to values in control icv saline injected mice (n = 6 per group). B-E. Study of gene and protein hypothalamic expression of MCH peptide (D, E) in icv CCL2 injected mice. Measurement of MCH (E) concentration by EIA after icv CCL2 injection (black bars) or icv saline injection (grey bars) in mice at 1h, 6h and 18h after injection. Cerebellum was used as negative control (3 independent experiments, n=6 per group in each experiment). F. The decrease in MCH mRNA levels observed 18h after icv CCL2 injection is abolished by the CCR2 antagonist INCB3344 (10μM) and in CCR2 KO mice, as shown by real-time PCR analysis for MCH in the hypothalamus. Results were normalized to values in icv saline injected WT mice (n=6 per group). Data are expressed as means ± SEM. ** or $$ p<0.01. * saline vs icv CCL2 injection in WT mice. $ icv CCL2 injection in WT mice vs CCL2+INCB3344 icv injection in WT mice or icv CCL2 injection in CCR2 KO mice.