EMBO/sd-character-level-ner huggingface dataset:
G) Quantification of total Sgo2 signal on spreads in early or late CSF arrest (16 hours or 30 hours after GVBD, respectively) relative to CREST per kinetochore pair (per single kinetochore in anaphase II) (left dot plot), and Sgo2 signal averaged per oocyte (right dot plot) at the indicated stages. The number of kinetochore pairs and oocytes analyzed is indicated. The scheme of measurements is shown on the right. Meta: metaphase, ana: anaphase.
(C Statistical analysis of Ki67 activity in ADC lung sections of vehicle (Veh) and phenformin (Phen) groups. The numbers of tumors analyzed over vehicle and phenfortmin groups were 25, 22 for Ki67 Results were shown as mean ± SEM. Significance was calculated by two-tailed unpaired Student's t-test with Welch's correction. ****p<0.0001 (C)
D, E The mRNA levels of PD-1, NFATc1, or the mRNA and protein levels of granzyme B in lung infiltrating CD8+ T cells were examined at day 26 (mean of triplicates ± SD, and the mRNA samples were prepared from at least 3 mice per group).
(L) Average of tumor weights (harvested at same time) from mice treated (i.p.) with IgG1, lexatumumab, ROCK1i, lexatumumab + ROCK1i and anti-CD8+ lexatumumab + ROCK1i (n=4-6, 50μg Lexatumumab, 2mg/kg ROCK1i, 6 doses). ROCK1i indicates GSK269962A and was administered to animals via intra-tumor injections. Various treatments were started when tumors were ~100mm3 size.
Immunofluorescence analysis for 5mC in d6 PGCLCs.Nuclei were stained with Hoechst (blue). Scale bar: 50 μm.
Western blotting was performed before and after Siwi KD using the anti-Ago3 antibody. Total BmN4 lysate (Total), supernatant (Sup) and pellet (Pellet) fractions upon centrifugation were used.
(B) The effect of YYR motif mutations on KLF4 PARylation. Constructs of KLF4-Zinc 1-YKH/AAA mutation, KLF4-Zinc 2-YYR/AAA mutation and KLF4-Zinc-2-Y451A mutation were co-transfected with Myc-PARP1 into 293T cells, respectively, and then pulled-down using M2 agarose followed by measuring KLF4 PARylation with anti-PAR antibody.
Accumulation of ELVs with a minimal distance to the ribbon of less than 200 nm in 1/2-DKOs (one-way ANOVA followed by Tukey's post-hoc test; ***p = 0.0002).
HeLa cells were transfected with GFP-LC3, treated with DMSO or 10 μM MG132 for 8 hours and immunostained with anti-p62 antibody. Scale bar=10 µm.
A. Schematic design of the chronic BCAA feeding experiments (n = 6 in each group).
(b) Intravascular rolling and firm adherence as well as transmigration of neutrophils and classical monocytes (cMOs) to the inflamed perivascular tissue as assessed 6 h after intrascrotal injection of TNF in postcapillary venules of the cremaster muscle of WT mice, quantitative data are shown (mean±SEM for n=6 mice per group; #p<0.05 vs. saline; *p<0.05 vs. drug vehicle; One-way ANOVA).
A. Schematic design of the hypogonadism experiments in the mouse model (n = 6 in each group).
HMDM were stimulated as in (A), or with 10 ng/ml LPS for 6 h and pro-IL-1β levels in the cytosol measured by western blot. Blot is representative of three independent donors.
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).
(a) Brains of the 'rescued' mice (Becn1−/−; Becn1EGFP/+) and of control Becn1+/+ littermates were lysed and subjected to immune isolation using an anti-GFP antibody. Proteins bound to anti-GFP antibody were isolated, detected and identified by SDS-PAGE, Coomassie brilliant blue staining and mass spectrometry. Seven bands pulled down by anti-GFP antibody specifically from 'rescued' mice lysate are numbered (this is a copy of image from our previous report with modification).
(d) HEK293 cells were co-transfected with vectors encoding for ULK1-HA, ULK1-Myc and AMBRA1WT or AMBRA1AA respectively. Protein complexes were immunoprecipitated and analysed as in a. Quantification is shown on the right. n = 3 extracts prepared from independent experiments. Data are presented as means±s.d. and significance is P = 0.014.
(d) Neurodegeneration of Pdf clock neurons was assessed using confocal microscopy in adult flies at day 7. Flies expressing Htt93Qex1 driven by Pdf-GAL4 (n = 16 brain hemispheres) showed loss of s-LNVs compared to Canton S (CS) control flies (n = 13), which was ameliorated by coexpression of mGpx1 (****P 0.0001; n = 16). Comparisons were performed by Kruskal-Wallis one-way ANOVA.
F Percentage of promoters with the indicated DNA motifs under the ChIP-seq peak (±100 bp from the peak summit) within each regulatory class (no DEG, UP or DOWN) for either MycERWT (left) or MycERHEA (right). p-values calculated with Fisher's exact test.
A Experimental scheme of retroviral injection paradigm. Adult mice were stereotactically co-injected with the MMLV CAG-dnLEF-IRES-GFP (dnLEF) and CAG-RFP (control) and were sacrificed 17dpi.
(G - H) Quantification of the expression patterns in developing embryos, projected along the A-P axis for MED4 (G) and for pain (H) for the different promoter variants, respectively. The errors bars are standard deviations from 3-4 biological replicates measurements (different embryos). The fluorescence background measured in a wild-type embryo is shown as yellow dotted lines. The fluorescence patterns for pain recapitulate the typical hb_ant enhancer activity, characterized by a gradient of reporter expression (black arrow in H) with a sharp drop at around A-P=50%, which was expected for a developmental gene. An exemplary AP profile for the hb_ant enhancer is shown as grey empty triangles (the background was adjusted at about 3000 a.u for better comparison). In contrast, the constructs containing the constitutive MED4 gene promoter lead to a stronger and more homogeneous expression with an only slightly enhanced expression level at the anterior tip (black arrow in G).
A-F. Representative photographs of immunofluorescent staining for α-SMA (red) and human β2M (green) on cultured human AT-MSCs (A), murine primary dermal fibroblasts (mFB) (B), mFB treated with 2 ng/ml recombinant human TGF-β1 (C), and co-cultures of mFB with AT-MSCs (D) or TGF-β1 siRNA transfected AT-MSCs (E) or control siRNA transfected AT-MSCs (F) after 48 h culture. Nuclei were counterstained with DAPI (blue). G. Quantification of α-SMA immunofluorescence shown in (A-F)
A. Schematic illustration of FUS‑NTD‑GST truncation constructs. Amino acid numbers are indicated
ROC curves showing the ability to determine infectivity (as assayed by viral culture in Vero E6-TMPRSS2 cells) using the CT values of WHO-E, Wölfel-sgE, and Mills-sgE for each of the samples for which these values were determined. For each test, the true-positive rate (chance of correctly predicting samples to be culturable at a given or lower CT) was plotted against the false-positive rate (chance of incorrectly predicting samples to be culturable at a given or lower CT) as a step function line. The lines show performance of the tests as the (CT) threshold for a positive result is increased; the lines are solid for detectable values and dashed when a primer set returned an undetectable value. Each line is labelled with the lowest CT value that surpassed a 95% sensitivity threshold (the horizontal dotted line) for that marker.
Immunoblot analysis of Fasn in TA muscle of 3-month-old HSA-Cre and control mice.
(G) Multiplex IF analyses revealed that transfection with the SEMA7A_WT or SEMA7A_R148W construct decreased the levels of canalicular membrane Bsep and Mrp2 expression in mouse primary hepatocytes in collagen sandwich cultures in a dose-dependent manner (0, 0.2, 1.0 μg per well of 6-well plate; 1.5 ml culture medium per well). Scale bar, 50 µm. Together, the Sema7aR145W mutation can reduce hepatic Bsep and Mrp2 protein expression and lead to intrahepatic BA accumulation and cholestasis (Appendix Table S16). Subsequently, cholestasis triggered an adaptive response in the liver by down-regulating the expression of BA synthetic enzymes of Cyp7a1 and Cyp8b1 and up-regulating the expression of BA efflux transporters Mrp3, Mrp4 and Ostα/β.
(a) Rag acts through TORC1 to regulate S6K phosphorylation. HEK293 cells were transfected with constructs as indicated. Co-expression of of mTORKD construct (600 ng) or rapamycin treatment (rapa, 20 nM, 30 min) abolished the effect of RagAQ66L and RagCS75N on S6K phosphorylation. The protein level of mTORKD was determined by immunoblotting with anti-mTOR antibody.
(B) Top: GC-MS analysis of acid hydrolyzed and BSTFA-derivatized, 2.1 RT eluted fraction from the EPS of wild type Xcc strain. Bottom: matching spectrum from NIST database, corresponding to glucopyranose pentakis-O-trimethyl silyl (See also Fig. EV3C).
(f) Wild-type Ba/F3 cells were cytokine starved overnight and stimulated with mIL-3. Cell lysates were analysed for protein levels of phospho-FOXO3 (T32), glutamine synthetase, p27 and actin. Shown are representative blots (n=4).
C Representative images of BMMΦ and LP stimulation derived MGC of day 6 with internalized 1µm and 10µm beads and staining for immunofluorescence by phalloidin (turquoise) and quantification of bead uptake after 24 hours by FACS. Depicted are 3 independent experiments with mean; scale bar, 20 µm.
(B and B') Number of ECs over time (left), number of EBs over time (middle), and probabilities of EB loss through apoptosis (right graph). The simulation starts with 1000 EC cells in all figures In (B) a challenge at day 1 imposes a loss of 500 EC cells (black dashed vertical line). In (B') two successive challenges are imposed: one at day 1, reducing by half the number of ECs (as in B), and a second one at day 3, causing a loss of 200 cells.
Figure 6: Cognitive decline in 8-month old Fmn2 -/- mice is rescued by the HDAC inhibitor Vorinostat.. B. The time spent in the center and the corners during a 5 min open field exposure was similar amongst groups (Fmn2-/- placebo, n=9; Fmn2-/- Vorinostat, n=12).
(C) 3D reconstruction of the old APPPS1/CX3CR1+/GFP slice in co-culture with the young WT slice (10 DIV) and immunostained using GFP (green) and M3.2 (red). GFP positive old microglial cells surrounding amyloid plaques exhibit intracellular M3.2 positive immunoreactivity indicative of Aβ uptake. Overview at low magnification is shown in the left panel. Scale bar: 15 µm. A detailed plaque is shown at higher magnification in the right panels. Scale bar: 10 µm.
Analysis of competitive fitness of strains described in (A). Cor1WT strains harbored a chromosomally-integrated clonNAT selection cassette, whereas Cor1** contained a hygromycin selection cassette. Strains were cultivated in CM media containing galactose (C) or glycerol (D) as carbon source.
F. WT MEFs stably expressing NCOA4 IDR (aa 167-334) fused with tandem FKBP were treated with 10 μg/ml FAC or 20 μM Dfo for 12 h and then cultured with 0.1 nM FKBP ligand (AP20187) for 6h. The cells were fixed for imaging and immunostained with anti-myc to analyze puncta of the fusion protein. Scale bar, 10μm. G. Number of puncta in (F) are shown as means ± SEM of at least 35 cells in each condition from two biological replicates. P<0.0001 (Dfo+ligand vs FAC+ligand) and P=0.048 (FAC vs FAC+ligand) (Kruskal-Wallis ANOVA with Dunn's multiple comparison test). P values were adjusted using the Bonferroni method.
(a) NOX2 activity in Slamf1+/+ and Slamf1-/- BALB/c peritoneal macrophages stimulated for 0-100 min with E. coli F18, S. aureus or PMA, assessed with lucigenin. Data are representative of five independent experiments (mean ± s.d.).
C qRT-PCR analyses of YAP target genes (ANKRD1, CTGF and CYR61), MITF and SOX10 in wild-type YAP or YAP-5SA expressing melanoma cells compared with mock transfected cells.All
Lysates from wildtype and ∆Gid2 yeast strains expressing endogenously tagged 3xFLAG-Gid10 that were grown at 42°C for one hour, and then returned to 30°C for the indicated timepoints were run on an SDS-PAGE gel and immunoblotted with αFLAG and αPGK.
series of Ttyh1 mutants with deletions in the C-terminal cytoplasmic tail region , and (F) their effects on cell distribution assessed by intraventricular in utero electroporation at E13.5 followed by immunolabeling at E15.5 using anti-GFP antibody. Scale bar: 100 μm.
(F) Working model for the recruitment and regulation of Ykt6 during autophagy. Ykt6 arrives either after prenylation of via COPI-coated vesicles at the ER, where it binds the Dsl1 complex. Ykt6 is packaged into COPII-coated vesicles, which deliver Ykt6 independently from Atg9 vesicles to the PAS. Atg1-Atg13 kinase controls Ykt6 activity until autophagosomes are completely closed.
(C) Average growth rates of tumors from the first treatment to the end point from same experimental groups of mice as indicated in B. P value was calculated by two-tailed Student's t-test and is indicated within the graph P =0.001. Data are shown as mean ± SEM.
A Identification of parental origin of the chromosomes was distinguishable based on H2B-mCherry fluorescent intensities (paternal chromosomes exhibit lower intensities; n = 20 oocytes). Bars and error bars denote means ± SD. The z-projection image shows major satellite-mClover (centromeres, green) and H2B-mCherry (chromosomes, red). Time from anaphase onset is shown in h:min. Scale bar = 4 μm. The 3D-reconstructed image shows maternal (magenta) and paternal (cyan) chromosomes. Spots indicate centromeres.
In the absence of Notch signaling, the BRM complex maintains the accessibility of Notch-responsive enhancers to allow Su(H) recruitment by promoting nucleosome turnover. When Notch signaling is activated, the nucleosome turnover at Notch-responsive enhancers increases, increasing the accessibility of the chromatin and allowing more Su(H) to bind. The BRM complex is essential for the process to occur. Target genes are activated via co-activators.
Hematoxylin and Eosin (HE) staining of representative transverse sections of GC muscles from 3-month-old HSA-Cre and control mice. The black arrows indicate fibers with centrally located nuclei and yellow arrows indicate mononuclear cell infiltration. Scale bars: 40 μm
G) P493-6 cells stably expressing NTC or shSPI1 or shPHF12 were injected subcutaneously into nude mice (n=5 for each group). Photo (G) of tumors collected at the end of the experiment (day 25).
C GFP‐Atg11, GFP‐Atg11 hrr25‐ts, and GFP‐Atg11 atg1‐D211A cells were analyzed for GFP‐Atg11 dot formation. Quantification of at least 70 cells in three individual experiments is shown. Error bars represent standard deviation. Scale bar, 3 μm.
Relative force measurements after normalization of absolute tetanic force to GC muscle weight from 3-month-old HSA-Cre and control male mice.
(G, H) Immunofluorescence staining of Rab35 (green) and DAPI (blue) (G) showing that Rab35 fluorescence intensity is reduced in hippocampal area (CA1) of GC-treated aniamls (H) (n=15 slices/condition; unpaired student's t-test, ***p=0.0003). Data information: All numeric data represent mean ± SEM
(d) PtdIns(3) P production in RAW264.7 cells stably expressing SLAM or a mock construct, transfected with eGFP-tagged p40 PX and treated with beads coated with E. coli outer membrane extract. Data are from three combined experiments (a) or are representative of at least three independent experiments (b,d) or two independent experiments (c) with at least 100 beads or bacteria per experiment (error bars, s.d.).
(A) Electron micrographs of immunogold-labeled Tau (arrows) in multivesicular bodies (yellow dashed lines) of rat hippocampus (scale bar: 250nm)
WT (Prom1+/+) and KO (Prom1-/-) mice were fasted for 4 hours and subjected to immobilization test. (O) Serum epinephrine level of mice after a 30 minutes-immobilization was determined (n = 3/control group, 7 or 8/immobilized group).
(E) IFIT-1 reporter activity from PMA-treated THP-1-IFIT-1 shSAMHD1 cells lacking STING, MAVS or matching gRNA control (Ctrl) cell line transduced for 24 h with DRV-treated HIV-1 GFP (1×1010 genomes/ml).
(k) The line plot illustrates smoothed expression levels of the indicated genes across the human AT2 pseudotime trajectory.
Staining of 20μm brain sections shows plaque formation with 6E10 antibody and DAB 6 weeks post-injection with (G) lentiviralAβ1-42 + 3 weeks DMSO treatment and (H) IP injection with 5 mg/kg Bosutinib 3 weeks post-lentiviral expression (3 weeks treatment) clears plaques in WT mice (N = 7).(I) Lentiviral Aβ1-42 + DMSO and (J) IP injection with 5 mg/kg Bosutinib 3 weeks post-lentiviral expression (3 weeks treatment) in parkin−/−mice (N = 7).
(g,h) Lungneutrophil infiltration (g) in IAV-infected Ripk2−/− mice treated with rapamycin, Ripk2−/− mice and WT mice (t.p., total protein). *P 0.05, **P 0.01, ***P 0.001 (Mann-Whitney test (b); one-way ANOVA with Tukey's post-hoc test (d,g,h)).
(A) Ten-fold serial dilutions of the indicated strains were spotted on YPD containing the indicated concentrations of hydroxyurea (HU) and were incubated for 2-3 days.
(F) Quantification of the percentage of co-transfected cells presenting aggregates upon expression of the indicated kinase, from the experiments like in E. (G) Quantification of the percentage of cells presenting nuclear aggregates from the experiments like in E.
Dose-response curves showing the modulation of R837-induced (5 μg/ml; 18 h) IL-12 secretion by prior treatment of BMDCs with the indicated synthetic lipids for 1 h.Chemical structures and ΔEC50 values of the synthetic OxPL variant lipids analyzed in (A), presented relative to EC.
E, Metabolites were purified from five (CNE1 cell line and HK1 cell line) or seven (CNE2 cell line) independent samples of two vector and INSL5 overexpressed cell lines and analyzed by liquid chromatography-mass spectrometry (LC-MS). Red: glycolytic intermediate metabolites. Green: tricarboxylic acid cycle (TCA cycle) intermediate metabolites. PPP: pentose phosphate pathway. The color scale bar represents Z-score of the metabolites' level.
C Transmission electron microscopy of larval epidermis overexpressing Atg16B shows autophagosomes in direct contact with plasma membrane (magenta arrows) and at the sites of cell-cell junctions (orange arrows). The lower panel shows a higher magnification of Atg16B image in Fig 3D.
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 loadings plot of PLS-DA of genus abundances in F. VIP score cut off of 1(n=4-5 mice per group).
1.3 Å-resolution crystal structure of Gid1065-284 substrate-binding domain (pink cartoon) in complex with Art22-8 degron (grey sticks, C-terminal Trp was attached to accurately measure peptide concentration). The grey mesh represents electron density corresponding to the Art2 peptide.
(A) Trypan blue counting was used to analyze growth curves for P493-6 cells that expressed NTC or SPI1 shRNA or PHF12 shRNA. ** P<0.01 as compared between indicated groups. (mean ± SD, n = 4 biological replicates, Student's t‐test)
(C) Co-IP of endogenous EZH2 with eIF4G2 or PABP1 from C4-2 cell lysate pre-treated with RNaseA in 37oC for 30 min. The effectiveness of RNaseA treatment was monitored by RT-PCR analysis of the presence of GAPDH mRNA.
A. Putative miR-10b binding sites within 5'UTRs of candidate splicing factors mRNAs.
Figure 1. Comparison of genome structures recovered from five synchronized stages over the cell cycle. (F) Principal Component Analysis (PCA) of the distance matrix in (E).
Release of IL- (ELISA) fro THP-1 cells (n=3) Data information I one representative of 'n' (given in brackets for each panel) independent experiments is shown (mean+SD) Student's t-tes
Drp1-KO MEFs which carry shRNAs (Oma1 or scramble) and ectopic Mfn1, were stained with TMRE. The arrows indicate cells that lost the mitochondrial membrane potential in (C). Scale bar, 10 µm. The percentage of cells that maintained the membrane potential is shown. Values are average ± SD (n = 3). 100-150 cells were analyzed in each experiment.
A, B Schematic of UBE2S~Ub (A) and UBE2C~Ub interactions (B) with the APC/C. UBE2S~Ub uses its C-terminal extension to bind to a groove formed by APC2 and APC4. The UBE2SHTH interacts with APC2 and the APC11 RING domain positions the substrate-linked Ub for chain elongation. UBE2C~Ub is positioned by the APC11RING and APC2 winged-helix B (WHB) domains during substrate ubiquitination (Brown et al., 2015; Brown et al., 2016).
(D) Images of beads binding to EmGFP-Tm1-I (green) and DIG labelled in vitro transcribed RNA fragments (magenta).(E, F) Mean DIG-Cy5 fluorescence measured on beads capturing the RNA fragment, with or without UV cross-linking, indicated below the charts. P values of pairwise Mann-Whitney U tests are indicated. In panel F, none of the non-cross-linked samples differ significantly from the no RNA control (p>0.05). Numbers below the plots indicate the number of beads analysed.
(e) HeLa cells were transfected or not with vector encoding AMBRA1 and treated with 35 μM cycloheximide (CHX) for 6 and 8 h before extraction. ULK1, actin and AMBRA1 were analysed by western blotting. Quantification is shown below. n = 3 extracts prepared from independent experiments. Data are presented as means±s.d. and significance is P = 0.049 and P = 0.02.
E. Highlight of the primary sequence differences between SPICE and VCP. The 11 mutations distinguishing the two viral regulators are shown on the surface of SPICE in purple. The contact surface of C3b on the regulator in the C3b-SPICE (CCP1-4) complex is shown in green on the right panel.
(D) IGV graph showing location of MYC binding peaks on ALKBH5 and FTO from published ChIP-seq datasets (Walz et al, 2014; Data ref: Eilers M, 2014). In this dataset, high levels of MYC were induced with 1µg/ml doxycycline for 30h and ChIPed by MYC antibody. Red triangle indicates the E-box.
(G) Percentage of rectal prolapse of 5-month-old mice COPS8fl/fl and COPS8ΔIEC. Data are represented as mean ± SEM from seven biological replicates per genotype. **P<0.01, NS- non-significant using one-way ANOVA.
(F) Proposed model for the regulation and role of Taf12 phosphorylation during the early and late steps following nutrient starvation in S. pombe. Question marks represent unknown regulatory pathways. See Discussion for details.
L-M. MCU expression levels correlate with HIF1α (L) and HIF1α-regulated genes (M). A linear model (lm) to test the power of MCU expression levels predicting the expression of HIF1α and HIF1α-regulated genes was calculated and plotted for each of the 532 samples of the TCGA database (see Figure 1). Equation and R2 values of the linear regression and significance indicating deviation from 0 are shown. The area of 95% prediction limit is shaded below and above the linear regression line. The HIF1α-regulated gene set was compiled from Broad Institute GSEA database (http://www.broadinstitute.org/gsea/msigdb/cards/V$HIF1_Q5.html, merged sets of V$HIF1_Q3 and V$HIF1_Q5).
(F) Quantitative scoring of EGFL7 staining in glioma specimens yielded about 25-40% EGFL7-positive blood vessels (n = 13 astrocytoma WHO° grade II, n = 25 astrocytoma WHO° grade III, n = 24 GBMs WHO° grade IV)
Quantification of relative nuclear mCherry TDP-43 on total fraction, ratio paired-t-test.
A. thalian leaf piece (K) ROS production (0-45 min, n=6) Data information represent data (mean+SEM) combined from 'n' (given in brackets for each panel) technical or biological replicate plant leave
Comparison among Hsf1 (~60KDa), denatured HSF1, Poly A polymerase (~56KDa) and no protein (just TAP buffer) with regard to Alu RNA processing (estimating relative full length RNA remaining) (two replicates). The full gels are available as Source Data For Figure 8. Relative full length RNA remaining was calculated using ImageJ area under the curve software over time. Error bars represent standard deviation from the mean.
(A and B) BMDMs were infected with Mtb-WT, Mtb-Δeis, or Mtb-c-eis (MOI = 1) for the indicated periods of time, and then subjected to Western blot analysis using Abs raised to p-ERK1/2, p-p38, p-JNK, and β-actin. Data shown are representative of three independent experiments that all yielded similar results (A). Expression of phospho-MAPK/β-actin protein in cytoplasmic extracts of BMDMs was quantified densitometrically (B).