EMBO/sd-character-level-ner huggingface dataset:
Astrogenesis in the postnatal dentate gyrus (DG).Figure 1A Scheme illustrates developmental fate-mapping experiment using NestinCreERT2; CAG CAT GFP (from now on referred to as NestinCreERT2; GFP) mice to monitor radial glia-like neural stem cells (rNSCs) and their generated progeny. B Experimental scheme of tamoxifen injection paradigm: perinatal mice were injected twice (12 h apart) to label early perinatal rNSCs and killed at postnatal day (P) 3, 7, 10, or 14 to analyse the rNSC-generated progeny within the DG layers hilus, granular zone (GZ), and molecular layer (ML). C Confocal images of rNSC-derived astrocytes expressing GFP (green) and astrocyte-specific markers (ACSBG1, GFAP, S100β; magenta) at different timepoints (P7, P10, P14); lower pictures depict single-channel images the astrocyte markers (grey) used above. Data information: ; scale bars (C = 10 µm, D Representative pictures of recombined astrocytes (GFP+/ACSBG1+; arrowheads) during DG development (P3, P7, P10, P14). E, Quantification of total numbers of recombined astrocytes (GFP+/ACSBG1+) per area at postnatal timepoints in the total DG (E) Data information: All data are represented as mean ± SEM; number of experimental animals throughout figure: n = 5 (P3) and n = 6 (P7, P10, P14), (E indicated by red dots dotted lines mark GZ borders; scale bars (D = 50 µm. , F Quantification of total numbers of recombined astrocytes (GFP+/ACSBG1+) per area at postnatal timepoints in the distinct DG compartments (F), i.e. hilus, GZ, and ML indicated by different colours. G Representative images of proliferating astrocytes (ACSBG1+, cyan; arrowheads) in combination with cell cycle markers KI67 or MCM2 (magenta; P3, P7: KI67; P10, P14: MCM2). Data information: ; dotted lines mark GZ borders; scale bars G) = 50 µm. H Confocal image of proliferating astrocytes at P10 (ACSBG1+, cyan; MCM2+, magenta) that did not express NESTIN (white). I, J Quantification of total proliferating astrocytes (ACSBG1+/KI67+ for P3/P7; ACSBG1+/MCM2+ for P10/P14) per area at distinct timepoints per total DG (I) or hilus, GZ and ML (J). Data information: All data are represented as mean ± SEM; number of experimental animals throughout figure: n = 5 (P3) and n = 6 (P7, P10, P14), I) indicated by red dots; scale bars ,H = 10 µm, K Confocal images of proliferating rNSC-derived astrocytes (GFP+/ACSBG1+/MCM2+; arrowheads) at P10. Data information: scale bars K) = 10 µm
Figure 3A. The discriminant microbial taxa of the ileum, cecum, and colon of ten adult CtM Hanwoo are shown, determined to the genus level by the linear discriminant analysis (LDA) effect size (LEfSe) method. The LDA scores represent the degree of consistent difference in the relative abundance between groups. For orphan sequences (i.e., unassigned at the genus level), a high-rank lineage is provided (f, family; o, order). B. The intestinal branched-chain amino acid (BCAA) levels in the adult male and CtM Hanwoo (n = 10 in each group). BCAA levels in the luminal contents of the ileum, cecum, and colon were quantified by an enzymatic method using a BCAA assay kit. The lines, boxes, and whiskers in the box plot diagrams represent the median, first and third quartiles, and min-to-max distribution of replicate values, respectively. The scattered dots in the box plot diagrams represent the individual replicates.
Figure 6(A) Schematic representation of experiments (B) Time line of experiment (C) Representative immunofluorescence images showing CENP-A and CENP-C reloading in the indicated conditions. Cells with centromeric CENP-A/CENP-C are marked with a red dashed contour line while a yellow contour lines mark cell without centromeric CENP-A. The centromere position is marked using immunofluorescence staining for CENP-B. White dashed lines contour DAPI stained nucleus of representative cells. (D) Bar plot showing the percentage of cells with CENP-A and CENP-C co-localization after a CENP-A/COFF/ON cycle in the indicated conditions. Error bars show SD from 5 independent experiments. (E) Box plot of CUT&RUN qPCR for CENP-A (green) or CENP-C (orange). Box plot shows median, 25th and 75th percentiles, whiskers show minimum and maximum values. Results from 3 independent experiments including combined data from qPCR reactions using alpha-satellite primers and primers binding at the centromere of chromosome 4. Enrichment is measured relative to the IgG control and normalized to Alu repeats.
Figure 1Left panels. The structures of the N-terminal regions from Drosophila Delta (A) and Serrate (B) are shown in a cartoon representation (rainbow coloured from blue at N-terminus to red at C-terminus). These have been overlaid on their mammalian equivalents DLL-4 (A) and Jagged-1 (B) in the context of their complexes (PDB entries 4xlw and 5uk5 respectively) with Notch-1 (cartoon representation, coloured grey). The structure of isolated Drosophila Notch is also depicted in each panel (cartoon, rainbow coloured) superposed on the respective copy of mammalian Notch-1 (cartoon, grey) for each complex. The overlays demonstrate the high degree of conservation in domain structures and arrangements between the Drosophila and mammalian homologues. Right panels. A close-up view of the C2 domains of each ligand overlaid with their mammalian equivalent. These demonstrate conservation of overall fold but large differences in the apical loops, particularly in the β1-2 and β5-6 loops. Isolated structure of N-terminal Delta, with residues deleted in ∆β1-2 highlighted as red Van Der Waals spheres. Purified Drosophila Delta and Serrate NE3 proteins bind to liposomes (D) Binding is reduced in Delta∆β1-2, but not to the Serrate equivalent using liposomes composed of PC:PS:PE-fluoroscein (80:15:5). Notch binding to Drosophila Delta NE3 (E) WT and ∆β1-2 (Delta∆β1-2) variants both bind to Notch, unlike variant with F204A substitution in DSL domain. Comparisons were performed with a two-tailed unpaired t-test. Values are shown as scattered data points with the dark lines representing the means. ns, no significant difference, **P < 0.01; ***P < 0.0001.
Differential gene regulation between vaccine groups.Figure 4a) Top genes differentially regulated between vaccine groups 4 hours post-vaccination. Note, only genes differentially expressed in either study group (concomitant 4CMenB or control vaccines alone) were included in intergroup analysis. The plotted lines are the LOESS (locally estimated scatterplot smoothing) regression curves with the 95% confidence intervals in grey. The FDR was derived by comparing fold-changes in gene expression in the control group with the test group, from baseline to the time point designated, and is reported if statistically significant (FDR <0.05). P-values were obtained from the moderated t-statistic, after adjustment for multiple testing (Benjamini and Hochberg's method). Pre-vaccination samples n= 125, 4 hour samples n= 28, 24 hour samples n = 31, 3 day sample n= 30, 7 day samples n= 36. The expression E value, are the gene expression value derived from the voom-limma workflow (Law et al., 2014). Note, only genes differentially expressed in either study group (concomitant 4CMenB or control vaccines alone) were included in intergroup analysis. The plotted lines are the LOESS (locally estimated scatterplot smoothing) regression curves with the 95% confidence intervals in grey. The FDR was derived by comparing fold-changes in gene expression in the control group with the test group, from baseline to the time point designated, and is reported if statistically significant (FDR <0.05). b) Same as (a) but top genes differentially regulated between vaccine groups 24 hours post-vaccination. Note, only genes differentially expressed in either study group (concomitant 4CMenB or control vaccines alone) were included in intergroup analysis. The plotted lines are the LOESS (locally estimated scatterplot smoothing) regression curves with the 95% confidence intervals in grey. The FDR was derived by comparing fold-changes in gene expression in the control group with the test group, from baseline to the time point designated, and is reported if statistically significant (FDR <0.05). P-values were obtained from the moderated t-statistic, after adjustment for multiple testing (Benjamini and Hochberg's method). c) Same as (a) but top genes differentially regulated between vaccine groups 3 days post-vaccination. Note, only genes differentially expressed in either study group (concomitant 4CMenB or control vaccines alone) were included in intergroup analysis. The plotted lines are the LOESS (locally estimated scatterplot smoothing) regression curves with the 95% confidence intervals in grey. The FDR was derived by comparing fold-changes in gene expression in the control group with the test group, from baseline to the time point designated, and is reported if statistically significant (FDR <0.05). P-values were obtained from the moderated t-statistic, after adjustment for multiple testing (Benjamini and Hochberg's method). d) Same as (a) but top genes differentially regulated between vaccine groups 7 days post-vaccination.
TAK1/MKK7/JNK complex is recruited to phagosomes of M2 (IL-4) macrophages in a K63 polyubiquitylation-dependent manner.Figure 3(A) Immunoblot (IB) analysis showing the recruitment of TAK1, MKK7, JNK and TAB1/TAB2 to the phagosome in M2(IL-4) macrophages, while MKK4 is not recruited. Rab7a, a phagosomal marker, was used as a loading control for phagosomes and vimentin was used as a loading control for total cell lysates. The white line in the JNK blot shows other bands were cut out. (B) Quantitation of three independent IB experiments by imageJ of non-saturated blots for TAK1, MKK7, TAB1 and TAB2 expression on phagosomes of resting M0 macrophages and M2(IL-4) macrophages. Error bars represent SEM. *p<0.01, **p<0.001 (Student's T-test) (C) IB showing enrichment of K63 polyubiquitylated proteins on the phagosome of M2(IL-4) macrophages compared to M0 macrophages. Treatment with the UBC13 inhibitor NSC697923 reduces recruitment of TAB1, TAB2, TAK1 and MKK7 to the phagosome of M2(IL-4) macrophages, indicating a K63-polyubiquitylation dependent translocation for these proteins.
Figure 5Representative clinical pictures of murine wounds at 0, 3, 5, 7 and 10 days after wounding. Enhanced wound healing in LPS primed MSCs group as opposed to all other groups. Statistical analysis of 20 wound areas per group at the indicated time points, expressed as percentage of the initial wound size (day 0), for PBS control, non-primed MSCs, LPS primed MSCs, non-primed scrambled siRNA-treated (Scr) MSCs, LPS primed Scr MSCs and LPS primed TLR4 silenced MSCs. Results are mean ± SD of five biological replicates representing 1 of 3 independent experiments. Statistical analysis was performed using one way ANOVA.
Glycogen metabolism enzymes are autophagy regulators in skeletal muscle.Fig 7(A) Primary cultured muscles with control lacZ RNAi, treated for 12 hrs with Rap+CQ. Note the formation of large GFP-Atg8a vesicles throughout the muscles. (B) GFP-Atg8a vesicles are reduced in primary cultured muscles with GlyS RNAi, treated for 12 hrs with Rap+CQ. Knockdown of Pfk (C) or CG9485 (D) causes increased accumulation of GFP-Atg8a vesicles in primary cultured muscles treated for 12 hrs with Rap+CQ. (E) Quantification for A-D of the mean ratio of GFP-Atg8a punctae area to total muscle area per well (n = 4). SEM is indicated with *p<.05; **p<.01. (F) Control white RNAi muscles accumulate large autophagosomes at 1 mg/ml CQ. (G) RNAi knockdown of CG9485 increases autophagosome accumulation in the muscle. (H) RNAi knockdown of AGBE reduces autophagic vesicle accumulation in the muscle. (I) Quantification of the GFP-Atg8a punctae area in muscles from white, CG9485, and AGBE knockdowns.n = 6 larval muscles with SEM indicated and *p<.05. (J) Western blot analysis of endogenous Atg8a from third instar muscle lysate. Dmef2-Gal4 driven knockdown of AGBE but not CG9485 inhibits Atg8a lipidation, indicating reduced autophagy levels.
CPAP-Tubulin interaction is a cancer target.Figure 1(A) Proof-of-principle experiment. Time-lapse images show overexpression of Myc-tagged CPAP-WT (i) or CPAPΔT (ii) has no effect on two centrosome-containing MCF10A cells (-Dox, two centrosomes). The cells were imaged from interphase to Cytokinesis. Bar graph at right quantifies mitotic duration of cells overexpressing CPAP-WT and CPAPΔT. We define mitotic duration as time consumed from the onset of cell rounding until cytokinesis. Number of cells (n) analyzed in each condition is indicated at the top of each bar. Number of independent experiments (N), (N)=3. Error bars, mean ± SEM. Unpaired t-test. CPAP-WT (iii) or CPAPΔT (iv) expressing extra centrosome-containing MCF10A cells (+Dox, extra centrosomes). Note compared to CPAP-WT expressing centrosomes (iii) CPAPΔT expressing centrosomes nucleate enhanced levels of microtubule asters already at prophase-like stage (iv). White arrows indicate centrosomal dots. Red arrows indicate centrosomes nucleating microtubule asters causing multipolar spindles. Scale bar, 2µm. Bar graph at right quantifies mitotic duration and percentage of cells exhibiting prolonged mitosis in cells expressing CPAP-WT and CPAPΔT. (N)=3. Error bars, mean ± SEM. Unpaired t-test ***P < 0.0001 (B-D) Fixed cell images showing the expression of CPAP-WT (top panel) and CPAPΔT (bottom panel) in extra centrosome containing MCF10A (+Dox, extra centrosomes), MDA-MB-231 and H1975T790M cells. Note, in CPAP-WT expressing cells, clustered extra centrosomes remain inactive with no or reduced microtubule nucleation. On the other hand, CPAPΔT expression enhances microtubule nucleation in extra centrosomes (arrows) and preventing them from clustering at G2-like interphase and mitosis. Cells were stained with CPAP (GFP), microtubules (α-tubulin, red), Cep152 (magenta). Scale bar, 2µm (E) Bar graph quantifies percentages of mitotic cells exhibiting multipolar spindles upon CPAP-WT or CPAPΔT expression. (N)=3. Error bars, mean ± SEM. Unpaired t-test **P < 0.001 (F) Subcutaneous xenograft tumor volume measurements of MDA-MB-231 cells expressing CPAP-WT (red) as control or CPAPΔT (blue) in nude mice. (i) Bar graph at right shows total tumor volume reduction at day 22. (ii) Each condition used 4 mice each containing 4 xenograft tumors. Error bars, mean ± SEM with n = 16 for CPAP-WT and n = 16 for CPAPΔT. Unpaired t-test ***P < 0.0001.
Model for the role of mitochondrial function in autophagy regulation under amino‐acid starvation.Figure 7Model for the role of mitochondrial function in autophagy regulation under amino‐acid starvation. Amino‐acid starvation induces the two regulatory arms of the autophagic response, ATG8 induction and autophagic flux. Autophagic flux is regulated in an Atg1, PKA, and TORC1‐dependent manner, while ATG8 induction is regulated by PKA. Mitochondrial respiratory deficiency induces PKA activity and, thereby, suppresses both arms of the autophagic response.
JQ1 treatment inhibits apoptosis in the rd10 mouse retina.Fig. 2JQ1 treatment inhibits apoptosis in the rd10 mouse retina. Intravitreal injection of JQ1 (or vehicle) was performed at PN14, as described in Fig. 1. Eyeballs were collected at PN18, PN21, PN24, PN27, and PN30. Cryosections were prepared and used for TUNEL staining. a Representative TUNEL (green) images showing an inhibitory effect of JQ1 in rd10 retinas. Scale bar 50 μm. Blue: DAPI staining of nuclei. For images of PN21 and PN27, see Additional file 1: Figure S2. b Quantification of TUNEL-positive cells (per 500 μm ONL length): mean ± SEM, n = 6 mice; **P < 0.01, *P < 0.05 compared to rd10 vehicle control. c Caspase-3/7 activity assay showing an inhibitory effect of JQ1 on retinal cell apoptosis. For the assay, homogenates were prepared from retinas collected and pooled from six mice at PN24. **P < 0.01 compared to rd10 vehicle control, n = 3 independent assay experiments. d For TUNEL/IBA1 and TUNEL/Recoverin co-staining (PN24 retinas), a TMR red kit (Roche) was used so that TUNEL-positive nuclei appear red. The data show that TUNEL-positive nuclei do not overlap with IBA1-positive cells; instead, they are localized within recoverin-positive (photoreceptor) cells. Scale bar 50 μ
is associated with poor prognosis of NPC patients A-C, Kaplan-Meier curves showing the overall survival (OS) curves of NPC patients with low or high INSL5 concentration (A), low (≤4000 copy/ml) or high (>4000 copy/ml) EBV DNA copy number (B), and the combination of INSL5 concentration with EBV DNA copy number (C).Figure 2A-C, Kaplan-Meier curves showing the overall survival (OS) curves of NPC patients with low or high INSL5 concentration (A), low (≤4000 copy/ml) or high (>4000 copy/ml) EBV DNA copy number (B), and the combination of INSL5 concentration with EBV DNA copy number (C). D-F, Kaplan-Meier curves showing the disease-free survival (DFS) curves of NPC patients with low or high INSL5 concentration (D), low or high EBV DNA copy number (E), and the combination of INSL5 concentration with EBV DNA copy number (F). G, Nomogram, including plasma INSL5 level, plasma EBV DNA, body mass index (BMI), pretreatment hs-CRP, T stage, N stage and age for five-year overall survival (OS) in patients with nasopharyngeal carcinoma. H, Nomogram, including age, plasma INSL5 level, serum lactate dehydrogenase level, plasma EBV DNA and VCA-IgA titer, for three- and five-year disease-free survival (DFS) in patients with nasopharyngeal carcinoma
Figure 2A BGL3 is recruited to DNA damage sites. U2OS cells were subjected to laser micro-irradiation to generate DSBs in a line pattern. The relocation kinetics of BGL3 to DSBs was monitored by RNA fluorescence in situ hybridization (FISH) in a time course as indicated. BGL3 intensities at the laser line were normalized into a numerical value using Nikon NIS-Elements AR software (version 4.40.00). Data are presented as mean ±SD of four biological replicates. B Chromosome aberrations induced by BGL3 depletion. Wild-type or BGL3 depleted BJ-5ta cells were used in the metaphase spread analysis for spontaneous DNA breaks. Representative image (left panel) and the percentage of cells containing at least one DNA break (right panel). Data are presented as mean ± SD of three biological replicates. Two-tailed Student's t test, ** P<0.01. C MCF-7 cells were treated as indicated, and cell response to ionizing radiation were analyzed by colony formation assays (left panel). Data are presented as mean ± SEM of four independent experiments, analyzed by two-way analysis of variance (ANOVA), **P < 0.01. Knock-down efficiency of BGL3 siRNA was examined by qRT-PCR and normalized to β-Actin (middle panel), data are presented as mean ± SD of three biological replicates. Two-tailed Student's t test, **P < 0.01. Knock-down efficiency of CtIP siRNA was examined by blotting (right panel). D MCF-7 cells were transfected with the indicated siRNAs. Cell sensitivity to camptothecin (CPT), hydroxyurea (HU), etoposide (ETO), or ionizing radiation was determined by MTS assays. Data are presented as mean ± SD of three biological replicates. Two-tailed Student's t test, *P < 0.05, **P < 0.01, NS: no significant difference. E BGL3 deficiency inhibits DNA damage repair. Quantification of γ-H2AX foci at indicated times after irradiation (2Gy) are presented. Data shown are results of three independent experiments (100 cells for each experiment), presented as mean ± SD, two-tailed Student's t test, *P < 0.05, **P < 0.01, NS: no significant difference.
Figure 4A PLX4032 dose-response curves of parental and resistant cells after YAP/TAZ knockdown. Cells were transfected with either control (siCon) or YAP plus TAZ (siYT#1) siRNAs for 72 hr, and then treated with PLX4032 at the indicated concentrations for additional 72 hr. Relative cell viability, compared with DMSO control, was measured by CCK8 assay. Sigmoidal dose-response curves were fitted to data, and significance of the difference in IC50 values were determined by extra sum-of-squares F test. B Time-course analyses of cell viability after YAP/TAZ siRNA #1 knockdown. Cells were transfected with the indicated siRNAs for 48 hr, and then treated with PLX4032 (2 &amp;amp;#x3BC;M) for the indicated times. Relative cell viability, compared with initial cell viability, was measured by CCK8 assay. Significance of the difference between control and YAP/TAZ depletion for parental or resistant cells were determined by t-test. C Immunofluorescence micrographs identifying BrdU-incorporated cells. WM3248 cells were transfected with the indicated siRNAs for 48 hr, and then treated with PLX4032 (2 μM) or DMSO for additional 24 hr before 45 min BrdU labeling.D Quantification of the experiment presented in (C). E Immunoblotting for the indicated proteins after transfection of siRNAs. Resistant SKMEL28 and WM3248 cells were transfected with the indicated siRNAs for 48 hr, and then treated with PLX4032 (2 μM) or DMSO for additional 24 hr. F Cell viability assay of resistant SKMEL28 cells treated with PLX4032 (PLX, 2 μM), Erlotinib (Erl, 2.5 μM), MK-2206 (2.5 μM), or their combinations. Relative cell viability compare with DMSO control was analyzed by CCK8 assay after drug treatment for 72 hr. G Cell viability analyses of resistant SKMEL28 cells. Cells were transfected with the indicated siRNAs for 5 days. Relative cell viability, compared with that of control siRNA-transfected cells, was measured by CCK8 assay.
Figure 5(A) Experimental set‑up. BMDCs cultured at low density (2x103 cells/cm2) were stimulated with poly(I:C) and IFN‑α was added at various time points. IFNAR signaling was interrupted using anti‑IFNAR1 blocking antibody at the indicated time point. BMDC activation was measured 24h after poly(I:C) stimulation by flow cytometry. (B) Representative dot plots showing CD86 and CD40 expression by low‑density BMDCs stimulated with poly(I:C) for different periods of IFN‑α exposure. (C) Quantification of CD86 and CD40 upregulation by BMDCs expressed as a fold change in gMFI over unstimulated controls. Data are pooled from 2 independent experiments. Black lines indicate mean values. Dotted lines represent a fold change equal to 1. (**p<0.01, ***p<0.001, ****p<0.0001, one‑way ANOVA).
BET2 is upregulated in the rd10 mouse retina compared to B6 WT control.Fig. 6 BET2 is upregulated in the rd10 mouse retina compared to B6 WT control. a-c Western blots of retinal homogenates collected from B6 or rd10 mice at PN14, P21, or PN24 (>6 mice at each time point). Quantification: normalization to β-actin and WT at each time point; mean ± SEM; n = 3 independent Western blot experiments; *P < 0.05, **P < 0.01 compared to WT control. d Immunostaining of BET2, BET3, and BET4 on paraffin-embedded retinal sections collected at PN24. Arrow points to dots of condensed staining. Scale bar 50 μm