EMBO/sd-character-level-ner huggingface dataset:
ApoEVs isolated after IgG1 and lexatumumab (D) treatment (MDA-MB-436) were run on western and blotted against CD63 and PD-L1.
time constant of the exponential component obtained from fits to Cm-data following 200 ms depolarization
H Representative reconstructions of control and β-catex3 neurons. Scale bar= 20µm
Ubiquitylation of CMG-MCM-7 was reconstituted with the indicated factors as described in Materials and Methods. 'Neddylation' indicates addition of the C. elegans ULA-1_RFL-1 E1 enzyme, the UBC-12 E2 enzyme, the DCN-1 E3 enzyme and NED-8.
(C) Wild‐type, rho0, Δnpr2, and Δatg7 cells were exposed to amino‐acid starvation medium supplemented with galactose. Additionally, wild‐type cells were treated with rapamycin during starvation (left panel). Phosphorylated (Atg13‐P) and dephosphorylated (Atg13) Atg13 was monitored at indicated time points by whole cell extraction and western blot analysis using α‐Atg13 and α‐Cdc11 antibodies.
a) Summed 2D projections of PLA interactions (left) and co-localisation (right) (n=3) between PIN1 and PIN4 laterally bisected 2D-projected heat map. Treatments as indicated. b) Quantification of positive PLA interactions. n.t (no treatment) and 10µM NPA, n=4; 10µM IAA and 10µM IAA+ 10µM NPA; n=3. Error bars indicate standard deviation.
(D) The progeny virus RNA in cultured supernatants of ZIKV and the mutants were detected by qRT-PCR in three technical replicates. Two-way ANOVA and Dunnett's multiple comparison test was used for statistical analysis. The error bars represent the standard deviation. *** p<0.001, **** p<0.0001.
(M) After indicated treatments with KMTR2 (DR5 agonist) and ZDEVD (caspase-3 preferred inhibitor) , cells were allowed to grow 24 hrs, followed by cell viability analysis.
(A) Close-up view of the ribbon diagram of the modelled GRAM domain of GRAMD1b (GRAM1b) showing amino acid side chains of R189 and other amino acids, lying in the ~4-14 Å vicinity of R189, that were mutated in mini-mutagenesis screen as shown in (B).
D) Deletion of NPL3 decreases telomeric R-loops. The indicated strains were crosslinked and subjected to DRIP. DNA-RNA hybrids were immunoprecipitated using the S9.6 antibody. R-loop levels were determined by quantitative PCR on indicated telomeres. Data represents mean % input +/- SEM n=3. Specificity of S9.6 antibody was determined treating a fraction of the samples with RNase H.
Densitometric analysis of immunoblots from C show reduced PICK1:GluA2 Co-IP following incubation with Tat-P4-(C5)2 but not Tat-C5. Bar graphs show mean with error-bars as SEM. (One-way ANOVA followed by Dunnett´s multiple comparisons test, *** p≤0.001, n = 4/group)
Kaplan-Meier survival curves stratified by the patient MICA-129 genotype for all patients (n = 446). The survival curve is displayed for the first 66 months; 7.6% of the patients were followed longer. Effects on overall survival were determined by Cox regression with covariate adjustment as indicated in Table2. The HR indicates the risk per MICA-129Met allele carried by the patients (additive risk model). The numbers of patients carrying the three genotypes and the number of events (in brackets) are indicated.
(F) Top: 2D gel electrophoresis of the Lk distributions of the YEp13 minichromosome produced in the presence of TOP2 or Top2-∆83. Plots compare the relative intensity of the Lk distributions (divided into ten sections). Bottom: 2D gel electrophoresis of the same samples upon nicking the DNA in order to reveal the occurrence of knots. Graph: Pkn of YEp13 (mean ± SD from three independent experiments).
80.4% of the 15-20-nt RNAs corresponding to transposon sequences were antisense to transposon mRNAs.
E. Quantification of last 10 seconds of fluorescence recovery (90-100 seconds) in B and D. Bars represent mean ± SEM. Statistical significance was calculated according to the Mann-Whitney U test. N = 12, 11 and 11 spines for EGFP-GSK3α baseline, cLTD and washout groups and 20, 11 and 9 spines for EGFP-GSK3β baseline, cLTD and washout groups, respectively.
Electron microscopy of macrophages 10 h after infection with HSV-1. (a) Arrows indicate membrane-coiled structures emerging from the nucleus of an infected cell. (b-d) Four-layered membrane structures formed by coiling of the nuclear membrane. (e,f) Glucose-6-phosphatase (black deposits) on autophagosome-like structures emerging from the nuclear envelope or free in the cytoplasm, and viral capsids in the cytoplasm engulfed in the lumen of an autophagosome-like compartment. N, nucleus; VP, viral particles. Scale bars, 1 μm (a), 0.25 μm (b-d,f) or 0.4 μm (e). Images are representative of three independent experiments with at least 100 cell profiles in each.
(E) Western blot analysis of CLPPprotein levels in heart (He), quadriceps (Quad), liver (Li), kidney (Ki), lung (Lu), brain (Br), spleen (Sp) and pancreas (Pa). TUBULIN and ACTIN are used as a loading control. The arrowhead indicates positions of CLPP, and the star indicates position of cross-reacting bands.
(B) Localization of Ykt6 relative to Atg1 during growth and nitrogen starvation conditions. Cells expressing GFP-tagged Ykt6 under the control of the PHO5 promoter and genomically 3xmCherry-tagged Atg1 were grown in SDC or SD-N for 2 h, and analyzed by fluorescence microscopy. Individual slices are shown. Scale bar, 5 µm. Scale bar of inset is 0.6 µm. Right, percentage of Ykt6 puncta co-localizing with Atg1. Error bars represent standard deviation of three independent experiments. Cells (n≥200) and Atg1 dots (n≥100) were quantified. Arrows indicate Ykt6 positive dots colocalizing with Atg1 (B)
D Bar-graph showing the Gene Set Enrichment Analysis (GSEA) of genes differentially expressed between Primary A and Primary-B melanomas (primary melanoma signature), performed combining GO gene sets (GO) and Gene set enrichment analysis (GSEA) of the primary-melanoma signature.
(H) Senescent nevusmelanocytes (n) stain less intensely for lamin B1 as compared with nonsenescent melanocytes in epidermis (e). White dotted line shows the basement membrane between the dermis and epidermis. Bottom panels (Epi and Nevus) are expanded from white boxed areas on top. Confocal microscopy for DAPI (blue), MelanA (red), and lamin B1 (green) stained tissue. Bars, 20 µm. (I) Quantitation of results from H for three different nevi. Epifluorescence images of lamin B1- and MelanA-stained nevi were obtained and epidermal or nevusMelanA-positive cells were scored for the presence (positive) of a characteristic lamin B1 "ring." At least 50 MelanA-expressing epidermalmelanocytes and at least 100 nevusmelanocytes were scored. Average of three different nevi ± SEM; P < 0.0005.
(j) The bar graph shows the top correlated transcriptional regulators, predicted by ingenuity Pathway Analysis (IPA) for the SSTR2 gene-gene correlations. The dotted line marks a correlation coefficient of zero.
(B) The sequential assembly of a novel gene regulatory network required for reprogramming. Each connection (line) represents the regulatory interaction between the indicated nine TRs during the reprogramming course. The red connections indicate functional synergy between the TRs. The light grey circles shown at 18 hrs timepoint represent the TR genes that have not yet been expressed. The O/S/K/M labeled beads placed on the gene circles denote the direct O/S/K/M binding at putative gene regulatory regions as deciphered from our ChIP-seq binding profiles. O: Oct4, S: Sox2, K: Klf4 and M: c-Myc.
A, Brdu assay for CNE1 cells stimulated with 100ng/ml INSL5 peptide in the presence of an anti-INSL5 antibody at 50 or 100ug/ml, or an isotype-matched IgG control (IgG) for 24h. Scale bars represent 20μm.
E, Overlay of normalized (at 705 nm) difference spectra plus a difference spectrum of the photosensory domain in the presence of the bacterial HO BphO
quantification of Tau levels (E) in hippocampal synaptosomes reveal that GC increases total Tau levels in animals expressing EGFP, but not Rab35 (n=5-6 animals/group, 2 replicates, 2-way ANOVA, GC x Rab35 interaction F1, 39=10,51 p=0.002; Sidak posthoc analysis *p=0.0168)
Control of epidermal autophagy by TOR signalling. (C) Quantification of Atg8a puncta in an area of 10000 µm2, n=6-8 larvae each genotype. We assumed unequal sample size and unequal variances and calculations were performed. Values are presented as box plots. Box plot elements are: center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers.
E Double-marker immunofluorescence and quantitative analyses of ACE2 intensity level in type II pneumocytic TTF1-positive and CD31-positive endothelia in lungs from young and old humans (n = 4-7 individuals per group). Scale bar, 100 µm. a.u. = arbitrary units.
(c Empirical cumulative density plots depict the distribution of correlation coefficients for (c) Myofibroblast markers (red points) with DLCO in comparison to all background proteins (black line).
(B) Real-time quantitative PCR of IP3R and SERCA2 transcripts in B cells. Data are presented as mean ± SD from three independent Pacs1+/+ and Pacs1-/- pairs of mice.
Figure 3: Hippocampal FMN2 is essential for extinction learning and cognitive flexibility.B. Fmn2 mRNA levels were determined in the hippocampus of mice injected with either scrambled or Fmn2 siRNA via qPCR (n= 4/group). Fmn2 levels are reduced in mice injected with Fmn2 siRNAi when compared to the scrambled control group (*P < 0.05). Error bars indicate SEM.
Representative flow cytometry analysis of surface ECAD (Left), MFI of surface ECAD (Middle), and percentage of surface ECAD negative cells (Right) in murine PDA cells, after treatment with DMSO, 2.5μM Ionomycin (IONO), and 10ng/ml TGFβ for 72h. Representative of 3 independent murine PDA cell lines run in triplicate. Statistical analysis by ANOVA (****, p<0.0001; non-significant (NS); ±SD).
Processing areas of Alu RNAs on the secondary Alu RNA structure. Secondary structure of Alu RNA adapted from Hadjiargyrou and colleagues (Hadjiargyrou & Delihas, 2013). As in our previous studies (Cheng et al., 2020; Zovoilis et al., 2016), we depict the SINE RNA processing areas (highlighted in pink) based on short RNA-seq data and mapping of the 5'ends of Alu RNA fragments. X mark the cleavage sites of Alu RNA that correspond to enriched processing areas (the high densities of 5'end fragments distribution) at the heatmap of Figure 1B. The rectangle depicts the critical region that binds and suppresses RNA Pol II based on (Mariner et al., 2008) that may be affected due to processing points.
D. Immunohistochemical analysis of FadA in log and stationary phases. Fn12230 (Fn), fadA-deletion mutant US1 (∆fadA) and spontaneous mutant lam in log and stationary phase were fixed before being placed onto glass slides and stained by mAb 7H7 at 1:800 dilution, followed by incubation of HRP-conjugated anti-mouse IgG and developed by DAB. The large FadA aggregates are detected specifically in wild-type Fn 12230 in the stationary but not in log phase. FadA was detected on lam, but without secreted aggregates. No FadA was detected in US1. The imagines were taken using 40X objective. Scale bar equals 20 μm.
A Schematic outline of the intraductal injection approach used to generate ILC xenograft models. ILC cells are transduced with RFP-luciferase expressing lentiviruses and injected into 3rd thoracic and the 4th inguinal milk ducts, highlighted in red, of 10-week-old NSG females. Tumor growth is monitored by bioluminescence imaging.
(F) Supernatants collected 18 h after infection were assessed for cytokine levels by ELISA. Data are presented as the mean±SD of at least three separate experiments, each performed in triplicate. ***p<0.001, vs. SC (A and C); WT mice (D and F). UI, uninfected; SC, solvent control (0.1% DMSO).
A The overall fold of SiaB/SiaC complex. The two SiaB molecules are shown as cartoons in light blue and pink, respectively. The two SiaC molecules are all shown as cartoons in yellow. ADP and TPO68 are shown as spheres in atomic colors (C, cyan; N, blue; O, red; P, orange). B Detailed interactions between SiaB and SiaC. The interacting residues are showing as sticks. The C-atoms of SiaB and SiaC residues are colored in light blue and yellow, respectively. H-bonds are indicated by black dashed lines.
D) Chromosome spreads at the indicated stages of meiosis, stained for endogenous Mps1 (red), centromeres with CREST serum (green) and DNA with Hoechst (blue). For early and late anaphase II spreads oocytes were chemically activated with Strontium and fixed 25min or 1h later, respectively.
D 2a2iL-RH6 cells form teratomas that consist of three embryonic germ layer-derived tissues. (i) Rosette structures (ectoderm), (ii) cartilage (mesoderm), and (iii) primitive gut (endoderm; scale bar 50 µm).
(c) Top: coimmunoprecipitation (co-IP) of LAMP-2A (L2A) with anti-LRRK2 from lysosomes incubated with LRRK2proteins as in a. Co-immunoprecipitated fractions were immunoblotted for LAMP-2A and LRRK2. Input: immunoblot for LAMP-2A before the affinity purification. Bottom: amount of LAMP-2A coimmunoprecipitated, expressed as a multiple of the value with WT LRRK2 (n = 3 or 4 independent experiments).
Figure 6. MGC formation is dependent on iNOS induced DNA damage A BMMΦ from wt and iNOS-/- mice were stimulated with LP for 6 days and quantified for MGC formation by hemacolor staining. Depicted are means ± SEM of 3 independent experiments.
(p) The indicated proteins from the plasma analysis were selected based on their common direction of correlation with patient lung function in two independent patient cohorts with distinct clinical characteristics.
Figure 2. MGC present dysregulation in inos expression A BMMΦ were stimulated with live BCG (MOI 15), with heat fixed (HI) BCG, or with LP, 1µg/ml of mono-, di- or tri-acylated lipomannan from M.bovis BCG for 6 days. Then, cells were stained for intracellular iNOS and quantification by flow cytometry. Depicted are means ± SEM from 3 independent experiments.
Model 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.
Comparisons of physicochemical properties between soluble proteins and aggregators. Hydrophobicity (gravy scores) (B) and isoelectric points (C) are shown as combined violin- and boxplots (p-values are for non-parametric Wilcoxon test).
Representative epi-immunofluorescent microscope images of L6 cells immuno-stained against LC3B and LAMP1 after iron treatment (250 µM, 24 h) followed by 3 h withdrawal.
(F). Heat map of relative miRNA expression of various miRNAs in HEK-293FT cells transfected with expression vectors of the top 5 genes from the screen, or the ctrl (GFP) vector. Red color represents suppressed expression compared with ctrl (GFP). n=3.
(A) Heat map showing a subset of mRNAs of genes immunoprecipitated by anti-EZH2 antibody in LNCaP and C4-2 prostate cancer cell lines, which was generated based on the distinct RIP-seq reads on specific gene exons. The units of the heatmap values were reads per kilobase million (RPKM).
(A) Axial T1-weighted images of the right thighs obtained in patients immediately before (upper panel) and 18 months after MAB infusion. Please note the progression of fatty degeneration and atrophy except for Pt 05 where no evident modifications can be detected. (B) Representative percentile of MRI quantitative parameters in transplanted patients compared to untreated patients. SIR (left image) and MVI (right image) of the quadriceps. Red line: Pt 01; dotted green line: Pt 02; dotted purple line: Pt 03; dotted dark blue line: Pt 05; dotted light blue line: Pt 06). Empty dots correspond to pre-treatment measures. Orange dots correspond to post-transplantation measurement. The black line corresponds to the median, while gray dotted lines to 75°, 90° and 95° percentile. Please note the modification of the trend of Pt 05 after treatment.
(d) HE cells were transduced with shScrambled (shScr) or shLSD1 with or without UK5099 (10 µM) the day after the sort and day 3 CD43+/GPA+ cell frequencies ± SEM relative to shScr are presented (n=3 biological replicates 1-2 technical replicates each, one-way ANOVA test). Data information: ns, not significant, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001
(c) The levels of endogenous Rps3p (top) and Rpl3p (middle) were analysed by immunblotting in wild-type and atg7Δ cells. Ponceau staining (bottom) controlled for equal loading. Uncropped images of blots are shown in Supplementary Information, Fig. S6. Starv, starvation.
(D) The protein abundance of NANOG was upregulated in KL tumors compared with K and KP mice. Scale bar, 50 μm.
(B) Hemolysis assay (n=4) of 1 μg/ml purified PLY in the presence of increasing concentrations of MRC-1 peptides, P2, scrambled P2, P3 and control peptide CP2(1-1000 μM). Data represent mean ± s.e.m. * denotes P < 0.05 by one-way ANOVA with Dunnett's post hoc test for multiple comparisons. Exact P values are shown in Appendix Table S4.
(A) Intra-architectural mutations: both change of motif strength and motif position within the same construct. The Mec2 motif composition is shown here as an example.
Similarity plot based on the full-length genome sequence of nCoV-2019 WIV04. Full-length genome sequences of SARS-CoV BJ01, bat SARSr-CoV WIV1, bat coronavirus RaTG13 and ZC45 were used as reference sequences.
(A) Gene expression level of stromal activation markers COL1A1, ACTA2, SPARC, FN1 and FAP in PS-1 cells which were exposed for 72 hrs to CM from control (CM of PS-1 cells ), epithelial (blue) or mesenchymal (red) PDAC cell lines using qPCR. Values were normalized to control and n=6 per group, 3 biological replicates for each cell line. Data information: data are represented as mean±SD, Student's t-test.
(B) H1299 cells stably expressing GFP-LC3 were fractionated into HM (containing mitochondria), and LM (containing ER). Fractions were analysed for the presence of MCL‐1, BCL‐2, Beclin‐1, the mitochondrial marker mtHSP70 and the ER marker calreticulin.
I-K. Analysis of Treg cells isolated from mice shown in (D). (I) Total Treg cell numbers (mean +SEM) isolated from CNS and dLN. (J) Ratio of Treg and Th17cells isolated from the CNS. Data are representative FACS plots, gated on VD-CD90+CD4+cells with mean frequencies per group. (K) Quantification of Treg/Th17 cell ratio (mean +SEM) within CNS and dLN.Cells were restimulated with MOG for 6 h and (I-N) in the presence of PMA/Ionomycin for 4 h.
Mice were superinfected as described in Fig 3A (C) Absolute neutrophil counts in the lungs following administration of αIL-17 or IgG isotype control antibody, as determined by flow cytometry Data information Dat are representative of two independent experiments with 3-4 in (C mice per group All data are represented as mean ± S.E.M. Statistical significance was determined wit unpaired-students t-test in (C
(A and B) BMDMs were infected with Mtb-WT, Mtb-Δeis or Mtb-c-eis at different MOIs (0.1, 1 and 10) for 18 h (A) or for the indicated periods of time (B; MOI = 10). Supernatants were assessed by ELISA for levels of TNF-α and IL-6. Data (A and B) are presented as the mean±SD of five experiments.
A: Ubc9 D100A enzymatic activity can be recovered by limited amount of DTT. 21 nM Aos1/Uba2 and 75 nM Ubc9 were incubated with H2O2 for 30 min prior addition of 65 nM each YFP-SUMO1 and CFP-RanGAPtail diluted in DTT-free buffer. The final DTT concentration in the reaction was 6 µM. Prior to addition of ATP, extra amount of DTT was added at indicated final concentration.
(B) Immunofluorescence (IF) visualization of NLRP3 (green) and nuclei (blue) in skin fibroblasts from a representative patient and control. Scale bar: 30µm
Western blot showing total TDP-43 levels, quantification in B, ratio paired-t-test.
(H, I) Autophagosome number is reduced, but autophagic flux is not significantly altered in starved Rpn1 vs. white RNAi muscles expressing GFP-mCherry-Atg8. (J) Flux measurement is shown on the right as the ratio of mCherry punctae to GFP-mCherry (n = 6). SEM is indicated.
(b) Boxplots display principal component two across ILD patients (orange) and control samples (purple) for the three study cohorts. The boxes represent the interquartile range, the horizontal line in the box is the median, and the whiskers represent 1.5 times the interquartile range (Chicago cohort: ILD n = 9, controls n = 8; Nashville cohort: ILD n = 20, controls n = 10; Munich cohort: ILD n = 3, controls n = 11).
D MICAL2PV interacts with N-GTPase, EF hand and C-terminal domains of Miro2, but not with the C-GTPase domain. A schematic representation of protein domain organization in Miro2 and its truncation mutants was shown in (panel a). H1299 cells were co-transfected with Flag-MICAL2PV and different Myc-tagged Miro2 mutants. Transfected cells were lysed, and immunoprecipitation was performed using an anti-Myc antibody and subjected to Western blotting with different antibodies as indicated (panel b). It should be noted that the upper band (marked by "*") migrating closely above the Flag-M2 band in the top section of panel b is a non-specific species because it is present in anti-Myc immunoprecipitates of cells only expressing the vector control, not expressing any Myc-Miro2 (lane 1).
B   In the boxplots, the central line shows the median. Statistical significance was assessed using Wilcoxon test. Boxplots of the distribution of the values of: B. length C. pI D. hydrophobicity E. disorder content and F. helicity for sequences that are functional (green) and non-functional (red
C 5meC enrichment analysis of the IAP, Xist, H19 loci in MEFs upon ATO treatment at 0.3 μg/mL for 4 or 7 days as measured by MeDIP-qPCR.
SHAPE analysis of the complete sfRNAs of ZIKV (D) Nucleotides with SHAPE reactivity greater than 0.85 are labeled in red, and moderately reactive site (0.4-0.85) are labeled in cyan. Unlabeled sites have low or no SHAPE reactivity (<0.4). The SHAPE reactivity were also annotated onto the corresponding secondary structures in (B) Nucleotides which SHAPE reactivity was not determined are labeled in gray in (B)
(E) ATG38-2GFP ATG17-2mCherry cells in wild-type and atg14Δ were cultured at 30°C with or without rapamycin. After 180 min, cells were analyzed by fluorescence microscopy. Bar, 5 µm.
(G) Immunoblot analysis of the protein content of p16, p21, p53 and DCR in normal (n=4 placentas) and in IUGR-complicated placentas (n=4 placentas). Each lane represents one independent placenta.
C-H Antibiotic-treated C57BL/6 male mice were transplanted with fecal microbiota from wildtype or Vil-Ogt KO mice and then induced with DSS for colitis (WT n = 5, KO n = 7). (C) Daily changes in body weight
p-JNK (F; n = 5 animals/group) and IRS-1pSer312 (G; n = 6 animals/group) levels (normalized by total JNK and total IRS-1, respectively) in skeletal muscle of mice 7 days after i.c.v. injection of vehicle or AβOs. In (F), *P = 0.0464; in (G), *P = 0.0081; Student's t-test.
G-H Probability density of mRNA distributions measured by smFISH for 20 ng/ml TNF for 1h (blue) versus 1h TNF + 4h pretreatment with 300nM A-485 (green) (G) and 1h TNF (blue) versus 1h TNF+62.5nM JQ1 cotreatment (yellow) (H) for Tnfaip3 (left) and Tnf (right).
The 2D plots of the first three principal components (PCs), labeled based on the clusters obtained by K-means clustering algorithm.
A Experimental scheme for birthdating of adult-born neurons and recombination. For morphology analysis, CAG-RFP was stereotactically injected into the DG (C-F), for marker expression analysis, BrdU was injected i.p. every 24 hours for three days (B). Tamoxifen was applied i.p. every 12 hours for five days from day 10 to day 14. Mice were sacrificed 3 days post Tamoxifen (dpT) and 13dpT, which corresponds to 17dpi and 27dpi, respectively.
A. Mean EAE clinical scores (+SEM).Data consist of (A) n=10 WT, n=4 IL-1R1-/- PBS, n = 4 WT, n=4 IL-1R1ΔT and n=5 IL-1R1-/- PC61 treated mice.
Quantification of LC3B puncta size from (F). Experiments were performed three times, and one representative experiment is presented here.