EMBO/sd-character-level-ner huggingface dataset:
C. MTECs were cultured ex-vivo and transitioned to ALI culture condition. Quantitative real time PCR was used to measure the expression levels of GemC1, McIdas, FoxJ1 and Geminin mRNA levels at different time points during multiciliogenesis. Values indicate expression levels (+/- standard error, s.e.) relative to ALI DAY 1 (marked by *), following normalization against the house-keeping HPRT mRNA. qPCR data were analyzed by the REST-MCS beta software from at least three independent experiments.
A Scatter plots of pairwise comparisons of transcript expression in U2OS cells. Plots describe log2 fold change in transcript expression in mock and polyclonal MLLT6 knockout cells treated with and without IFN-γ as indicated. Horizontal axis shows log2 fold change in transcript expression and vertical axis represents statistical significance (log10 of p-value, n=3) with candidates nominated for further validation (red).
I) Representative images of the LMNB1 staining in freshly isolated YC and OC FAPs (LMNB1 in green/DAPI in blue). Scale bar = 25 μm. J) Graph showing the relative quantification of LMNB1 fluorescence intensity normalized for nuclei number,in the staining shown in (I).
E. Quantitative qRT-PCR of selected genes in tissue MΦ from adult Irf8-/- and Irf8+/+ mice. Data are normalized to β-actin and GAPDH and expressed as ratio of the mRNA expression compared to microglia of Irf8+/+ mice or to liverCD11bhigh cells of Irf8+/+ mice and show mean ± s.e.m. Three mice per group were analyzed.
(f-h) Fluorescence images of NRK cells expressing GFP-Cx43 maintained in the presence of serum (f), absence of serum (g) or treated with lindane (h) and incubated with Alexa594-transferrin for 15 min before fixation. Top: single and merged channels and outlined area at higher magnification. Bottom: 3D reconstructions and higher magnification details of the outlined areas. Nuclei are highlighted with DAPI. Scale bars: 5 μm. Uncropped images of blots are shown in Supplementary Fig. 9.
Glycine and proline representation in protein acid hydrolysates of untreated NIH-3T3 cells and their secreted ECM, produced as in Figure 1d. Amino acids were measured by GC-MS.
(a) Reduced levels of soluble mTOR (as a function of tubulin) in stable inducible PC12 cells expressing mutant (Gln74; Q74) huntingtin compared with those expressing wild-type (Gln23; Q23) huntingtin (four independent experiments; P 0.0001; unpaired t-test).
investigating the role of nuclear calcium signaling in mRNA induction of Arc, Fosb and Npas4. i, immunohistochemical analysis of MSNs infected with rAAV-pCKIIa-GCaMP3-NLS. Infection on DIV5, fixation on DIV12. Hoe = Hoechst, D32 = anti-Darpp-32, GFP = anti-GFP, 40x magnification, scale bar = 10µm.
C) Histological analysis of pancreas from PdxCre and KC mice with different grades of PanIN lesions at 330 days of age. Anti-TIMP1, anti-MMP7, anti-TSP2 and anti-CCN2 staining of a representative KC PanIN lesion (200X, scale bars: 100μm)
B PARP cleavage was not induced by S-HAD treatment. PARP cleavage was monitored by Western blot analysis in Hela cells treated with S-HAD or cisplatin (CP) as described in (A). The blot was stripped and reprobed with ß-actin antibodies as a loading control. Molecular weight markers (kDa) are indicated on the left.
F. Immunoblot analysis of flag-OFD1 or flag-S735A in HEK293 cells stimulated with FSK as in C. The levels of α-tubulin were used as loading control. G. Quantitative analysis of the experiments shown in F. A mean value ± SD of three independent experiments is shown. Student's t test *p<0,05 versus S735A mutant (3 hours and 4 hours, +FSK) and basal values (-FSK). H
E HeLa cells transiently co-transfected with EGFP-CALCOCO1 and Myc-VAPA or -VAPB were immunostained with anti-Myc antibody. Scale bars, 5 μm.
E. Increased CXCL10 and CCL5 protein (detected by ELISA) is secreted by Rnaseh2b-/- MEFs. (B, D, E) Mean data from three experiments for six independent Rnaseh2b-/- MEF lines versus four independent Rnaseh2b+/+ MEF lines. Error bars, SEM. * = p<0.05, ** = p<0.01, Mann-Whitney U test.
(B) One hour 35S pulse-labeling of mitochondrial proteins in HeLa cells silenced for LETM1 (siR1) or DRP1 (siD), or co-silenced for LETM1 and DRP1 (siR1D) for 144 h. Coomassie stained gels are used as loading controls and polypeptide assignments are indicated to the right
G. Morphological differences of cortical microglia from WT, Grn-/-, Trem2-/- and Double-/- mice shown by branch volume, sphericity score, branch length and the number of branch nodes. Statistical analysis of group difference for the morphological scores "Branch volume" (auc = 0.72), "Sphericity score" (auc = 0.82), "Branch length" (auc = 0.69) and "Number of branch nodes" (auc = 0.80) was performed using the Wilcoxon rank sum test with continuity correction and Bonferroni post-hoc correction for multiple testing in R (version 4.0.3). Two images per mouse (n=3 per genotype, female) were analyzed, each data point represents one microglia cell. Median and interquartile range are displayed.
C. Number and percentage of unusual alternative splicing genes (UASGs, FDR <0.05) in LincGET-depleted 2C compared to Control-LNA L2C. ExS, exon skipping. A5S, alternative 5' Splicing. InR, intron retention.
(B) Absolute numbers of IFN-γ+ NK cells in one of the 4 draining lymph nodes before and after LPS administration in mice in which NK cell entry in the lymph node was blocked or not by anti-CD62L treatment.
H: Close-up view of the structure near the Phospho-FFAT motif highlighting critical residues (in stick model) of human VAP-A present in the binding interface. Data information: Phosphorous, nitrogen, oxygen, and sulfur atoms are colored in orange, blue, red, and yellow, respectively. Carbon atoms are shown in green and grey/pink in the MSP domain and the FFAT motif, respectively. The numbers of the peptide residues are noted in subscript.
(A) BLM-induced mice were treated every other day beginning on day 10 with 10 nmol/dose FA-TLR7-54 or TLR7-54.
A. Schematic of mass-spec (MS) proteome profiling. Cortex and OB were isolated from Daam2 Het and KO mice (N=3 each) and digested for peptide library generation. Total numbers of detected and differentially expressed proteins in each brain region are indicated in pie charts. Venn diagram shows differentially expressed genes in each region and genes differentially expressed in both.
B-E. Co-colonization of N1 WT (B and D, n=4 mice) or N1 Δbte2 (C, n=4) with E1 WT (B and C) or E1 overexpressing Bti2a (E1 pBti2a, D). FecalCFU was monitored over time (B-D) and E1 CFU compared to N1 WT-E1 WT group at four-weeks post co-colonization (E).
(B) Control or PRR7 transfected HEK293 cells were treated with cycloheximide for the indicated time points and c-Jun protein levels were measured by Western blotting. PRR7 expression significantly stabilized c-Jun levels at 120 min (110.0 ± 7.5% vs control 68.7 ± 7.9%) and 240 minutes (83.6 ± 5.2% vs control 43.7 ± 3.4%). Values for c-Jun were normalized to their respective 0 min time point (n=4 gels for each group performed blind). T-tests between similar time points were used to analyze results.
I. EMSA was performed using either Cy3-labeled wild type or mutant miR-199a-3p, and Cx43-enriched membranes prepared from C33a parental cells (Cx43+). Cx43- membranes were used to control unspecific binding.
C-E. Co-treatment with olaparib and Wnt inhibitor regulates expression of senescence associated genes. E) Expression of senescence-associated genes was analyzed in the tumors from all four treatment groups (treated for 56 hours) by qRT-PCR. Each data point represents an individual tumor and horizontal lines represent mean. p-values for the significant changes as calculated by Mann-Whitney U test are shown. Each lane represents an individual tumor.
B. Effect of oligo#5 on pre-mRNA splicing of the reporter gene, stably transfected into HeLa cells.
Ribosome fractionation of mESCs transduced with Rptor shRNA (two targets mixed) in 2iL.
(B) rs1432689 genotypes are correlated to SPINK6 expression in human lung tissues and esophagus mucosa from GTEx database. Sample sizes for each genotype are shown in the x-axis. The y-axis shows the normalized expression of SPINK6 (Norm. expression) in the indicated trusses. Median and interquartile range are represented by a white line and dark box respectively. Data distribution is colored with light blue; a wider section of the violin plot indicates the data on the section have a higher frequency. Linear regression was used for data analysis.
During mitotic progression, β-catenin binds to Plk1 PBD in a phosphorylation-independent manner and localizes at the midbody/contractile ring of telophase cells (β-catenin p-S60 is surrounded by actomyosin contractile ring during early telophase). The Ser60 residue of β-catenin is phosphorylated by bound Plk1, which recruits Ect2 to the midbody and facilitates the formation of the β-catenin-Plk1-Ect2 complex. The resulting complex induces RhoA activation and mediates the progression of cleavage furrow ingression and subsequent cytokinesis steps.
Representative photographs of GAS and SOL muscles dissected from WT and DKO mice (n=5). Scale bar: 1cm.
A. Miro1 induces EYFP-Parkin translocation in the presence of PINK1 shRNA. PC6 cells were transfected with EYFP-Parkin and Miro1 or treated for 3h with A&O (both 10 µM) in the presence of scrambled shRNA or PINK1 shRNA. Miro1 induced Parkin translocation also in the presence of PINK1 shRNA while A&O treatment did not. ****P < 0.0001 compared with the respective control group, n = 5-6 dishes, 20 fields per dish, one-way ANOVA
Meta-gene plot showing average ISWI enrichment (y-axis = ChIP/Input) in clonal ISWI-3HA parasites at 12 hpi from 1.5 kb upstream of the translation start site ("Start") to 1.5 kb downstream of the translation stop site ("Stop") for all genes, which are grouped into quartiles based on their transcript levels (RPKM) at 12 hpi. Dark red represents genes with the highest transcript levels ("1st"), light red represents genes with the second highest transcript levels ("2nd"), orange represents genes with the third highest transcript levels ("3rd"), and yellow represents genes with the lowest transcript levels ("4th"). One replicate was used for the ISWI ChIP-seq and the transcription data are an average from the two replicates of the untreated ISWI-3HA clone used for the differential expression analysis.
I. Representative pictures of CD45 and NIMPR14 staining at late disease stages (n= 5 WT, 5 ECko), showing accumulation of CD45+ and NIMPR14+ cells (black arrowheads) in Casp8ECko intestine at sites of impaired epithelial barrier integrity and tissue necrosis (red asterisks). Scale bars: 100µm.
(A, B) C57BL/6 mice were left untreated (NT) or were intraperitoneally treated with indicated amounts of AG for 3 d in the absence or presence of the MMP inhibitor marimastat (10 mg/kg) given intraperitoneally prior to AG stimulation. Lung sections stained with H&E (A) and quantification of lung lesion burden from H&E stained sections (B). Data information: Data in (A) are representative of n=3 independent experiments. Data in (B) are means + SD of indicated numbers of mice from one of n=3 independent experiments and each symbol represents data from 1 mouse. One-way ANOVA followed by Dunnett's post hoc test (B) was used for statistical analysis. ns, not significant; ****, p<0.0001. Scale bar, 200 μm.
(E) Contour plot showing the first and second principal components of a PCA for the MD trajectories for the WT (left) and P182L peptide (right). The larger spread in the P182L peptide suggests a larger sampling of the conformational landscape.
(H) HeLa cells transiently transfected with HA-Parkin were subjected to mitochondrial stress by treatment with 25 μM antimycin A (AA) for 2 hours, then fixed and stained with antibodies specific to HA, PDH and TOM20. TOM20+ve/PDH-ve MDVs were quantified in cells that were either expressing or not expressing HA-Parkin (n = 12-14 cells per condition from 3 independent experiments).
EAE was induced by immunization of naive B6 mice with MOG (35-55), and the mice were randomly divided into five groups. BMDCs transduced with either lentiviral vector encoding GFP and NLRC3 (LV-NLRC3) or only GFP (LV-Ctrl) were administered i.v. 4 times, once every 4 days, starting at day 10 after EAE induction. cytokine response (D) to MOG (35-55) in splenocytes taken from DCs-treated mice 26 days after EAE induction.
E: Actin and myosin distribution in a computational amoeboid cell (upper row), along with the resulting traction force patterns and maps for 4 different times (lower row). The edge velocity of the protrusions was approximately 5.6 μm/min.
A, B. Expression of sugarbabe is downregulated in fat bodies upon knockdown of PWP1 (A) and ectopic expression of ERK7 (B) (N=3 replicates of 10 fat bodies/replicate for each genotype).
B. FATE1 mRNA expression is increased in H295R/TRSF-1 cells by Dox treatment. The efficiency of FATE1 knockdown by specific (siFATE1) vs. control (siC) siRNA nucleofection is shown (mean ± SEM; n=4 with 3 replicates/experiment).
(I) Representative confocal microscopy images of immunostaining for CD127, ST2, CD3 and insulin in islet grafts. Scale bar = 50 µm.
(A) Female C57BL/6J mice were put in normoxia or hypoxia for 6h or 24h, injected i.p. with PBS or DEX (10 mg/kg) and livers were isolated after 2h for genome-wide transcriptomics via RNA-seq. N=3 per group for a single RNA-seq.
(G) HIV-1-infected CD4 T cells (strain NLAD8) were cultured with the indicated antibody and NHS or HIHS to determine complement-mediated cytotoxicity. After 24h, the percentage of infected (Gag+) cells in each condition was determined by flow cytometry. One representative experiment is shown.
(a) The gene structure of Rae1. The black-arrowed boxes indicate exons. A transposable element, P{GawB}NP3499, located ∼400 bp upstream of the first exon of Rae1 was used to generate imprecise excision mutants of Rae1. PCR analysis indicates that ∼900 bp and a ∼1.5-k bp DNA fragment in the Rae1 promoter region are missing in Rae1EX28 and Rae1EXB12, respectively. (b) Western blot analysis on Rae1 protein in the brain lysate of wild-type, Df(2R) 5764/+, Rae1EX28/+, or late second instar Rae1EX28, Rae1EX28/Df(2R) 5764(/Df) and Rae1EXB12 /Df(2R) 5764 larvae. β-tubulin was used as the loading control. Full-length blots are presented in Supplementary Figure 9. (c) Quantification of Rae1 protein levels in the Rae1 heterozygous and homozygous mutant brains. Rae1 protein levels were first normalized to β-tubulin protein levels and are presented as percentage of wild-type level. *P 0.05, **P 0.001. Error bars denote s.e.m.
(e) Electron microscopy images show large structures (asterisks) that are often enwrapped with double membranes in the HEK 293T cells co-transfected with Atg14L-EGFP and Beclin 1-AsRed: concentric membrane 'rings' (panel 1); two large structures (3-5 μm in diameter, panel 2) containing material with high electron density (inset, enwrapping double membranes); numerous autophagosomes (arrows, panel 3) in the cytoplasm; immuno-electron microscopy image of a Atg14L-Beclin 1 structure (labelled with anti-GFP antibody and developed by DAB, panel 4) enwrapped with concentric membrane 'rings'. M, mitochondria; N, nucleus. Scale bar, 500 nm.
Design of the experiment. Gestating Lgr5-DTReGFP females were vehicle- or LGK974-treated by oral gavage between E13-E15 or E15-E17. Small intestines of treated embryos were analyzed at E18.5.
(B) Proteins significantly different between supplementation and control studies. Red and blue colors denote the increased and decreased plasma level in supplementation study compared to control study, respectively. * Denotes significance (one-way ANOVA; FDR <0 .05).
(G) Graph represents Spindly levels at aligned KTs for cells Spindly levels were determined relative to CID and all values were normalized to the mean fluorescence intensity quantified in control PoloWT-EGFP expressing cells, which was set to 100% (n≥633 KTs from at least 35 cells for each condition, n=2 independent experiments). Data information: Statistical analysis was calculated using an unpaired t-test (Mann-Whitney). p values: ****, <0.0001. Data are shown as mean ± SD. Scale bar: 5 μm.
(C) Average cross-sectional area of mitochondrio (n=3mice/group Bar graphs represent mean±SD. Statistics for graph One-way ANOVA followed by Tukey"s
F. Representative images of SCNT embryos at 115 h after injection of different siRNA as indicated. These images are representative examples of the quantification shown in Fig 5G. n ≥ 3. Scale bar, 50 μm. G. Injection of siRNA-6B improved the preimplantation development rate of SCNT embryos. Both cumulus cells, Sertoli cells, and C57 MEF cells were used as donor cells. The bovine intraspecies SCNT embryos derived from bovine ear fibroblast cells. Shown is the percentage of embryos that reached the indicated stages. ♂ and ♀ indicated the male and female, respectively. Error bars, s.d., n ≥ 3. H
I-J, Assessment of TAM suppression of T cells was assayed by evaluation of inhibition of T cell proliferation. TAMs were isolated by magnetic bead separation using F480 microbeads and co-cultured at a 1:1 ratio with CFSE labelled CD8+ T cells. CFSE dilution was analysed by flow cytometry to measure proliferation. Percentages of CFSElo T cells were analysed by Kruskal-Wallis with Dunn's multiple comparisons test. Representative histograms are shown (right panel). Experiments were repeated twice for each tumour cell line (n=3 mice/group) *P <0.05 **P <0.01 ***P <0.001.
Ribopuromycylation assay showing global translation profile of HeLa cells overexpressing FLAG-HA-Ago1 or FLAG-HA-Ago1x. Densitometric analysis of four independent experiments is shown as bar graph (mean ± S.E.). Puromycin densities were normalized to ponceau S stain densities. *, P < 0.029 (Mann-Whitney test).
High resolution confocal images show colocalization (arrow heads) of small NE Tau clusters with nuclear pore proteins (NPC marker, POM121). Scale bars=10 μm.
E HeLa cells were treated with control (CTRL), Drp1, or Mfn1 siRNA for 72 h. Whole cell lysates were immunoblotted for Drp1 or Mfn1 to show the efficiency of depletion. GAPDH was used as loading control. siRNA-treated cells were infected with S. flexneri for 4 h 40 min, then fixed for microscopy and stained for endogenous SEPT7 for quantitative confocal microscopy. Graph represents the mean % ± SEM of Shigella inside SEPT7 cages from at least 4 independent experiments per treatment. Student's t-test, ** = p <0.01; *** = p<0.001.
A. Representative images of cells of A. tumefaciens C58 strains ΔtssB, ΔtssLΔtssB, and ΔtdeiΔtssB cells each expressing TssB-GFP from pTrc200. Upper panel: phase contrast images; Lower panel: green fluorescence images. Examples of GFP streaks were indicated by white arrowheads. Scale bar: 2 μm.
B, C Extracts of A549 cells (B) or human PBMCs (C) incubated with EBSS for various time points (above lanes) were subjected to immunoprecipitation with anti-Beclin-1 and immunoblot analysis with indicated antibodies (shown on the left).
mTORC2 in adipose tissue is not required for cold-induced lipid droplet mobilization. (A) Representative H&amp;amp;E staining of sWAT sections from AdRiKO and control mice (n=5/group).
(C,D) Cryo-EM maps of RAG TCC (C) at 3.8 Å and Paired STC (D) at 2.9 Å shown in both top and front views with protein colored white, target DNA colored red, and signal DNA colored blue. Insets highlight the different connectivity between signal and target DNA in the TCC and STC.
Three-four months old BL/6 mice were treated with an acute dose of LPS (4 µg/g body) or vehicle (saline). Microglia (pool of 2 mice per group per replicate; 1 female and 1 male) were FACS-sorted 24 hours later. Representative multicolour flow cytometry analysis showing the percentage of the mean ± SEM of 5 independent experiments of Ly6C and CD206 expressing cells in CD11b+CD45int cells from saline or LPS-injected mice.
C-D IF staining of NIH3T3 cells after IR (1Gy) and 1 hour chase. Cells were pulsed with EdU 30 min prior to fixation, stained with antibodies against γH2AX and 53BP1, and counterstained with DAPI. Representative images can be found in Fig EV5C. (C) Quantitation of the number of 53BP1 foci per nucleus, and (D) mean volume of 53BP1 foci (mean ± SEM of >30 cells per condition and cell cycle stage).
G-H, Joint analysis of kit mutant nonCM scRNA-seq data from 0, 2, 7, and 14 dpi with LIGER. G, All nonCM visualized on tSNE. H, Bar plots showing comparison of nonCM cell type contribution between wildtype and kit mutant at each time point.
Transmission Electron Microscopy (TEM) fungal inoculated tomato leaves.Representative TEM images from four independent experiments. (A, G); Healthy non-inoculated leaf tissue. (B-F) Tomato leaves inoculated with the OA deficient A2 strain. (H,I) Tomato leaves inoculated with wild type S. sclerotiorum. Arrows, autolysosomal/autophagosomal-like structures; C, chloroplast; V, vacuole; N, nucleus; Circle, active dismantlement of chloroplast; Rectangle, chromatin condensation within the nucleus. Black scale bars = 2 µm, white scale bars = 1 µm. Sections were examined with a Phillips Morgagni 268 transmission electron microscope at an accelerating voltage of 80 kV. Digital images were recorded with a MegaViewIII digital camera operated with iTEM software.
C Hypothetical conformational movements of PEN-2 and PS1 TMD2 for the presentation of C99 to the active site from the convex side are shown by dashed red arrows.
(B) IceLogo representation of the N-termini substrates of GNAT2 vs all that of other GNATs. To construct the dataset, all GNAT2 substrates with NTA yield threshold >30 % were selected in the positive set. The negative set corresponded to the compilation of all substrates with a threshold >30 % of all other seven GNATs. The color symbol is associated to the default choice, which the software proposes for each class of amino acid: Green is for the class of small hydrophilic uncharged residues including S, T, G. Acidic residues including D or E are colored in red. Positively- charged residues including K, R and H are displayed in blue. N or Q are in purple. Hydrophobic residues (A, I, M, V, L, W, Y, F, P) are shown in black.
The enriched DNA motif is identified by the motif-discovery algorithm MEME in AP2-O3 binding sites.
(C) Representative polysome profiles obtained from HeLa cells untreated or treated with 10 µM of (PR)20 for 16h. The presence of halfmers is indicated (arrows).
(D, E) Mapping of the Smaug interaction domain in SMO. Extracts from Cl8 cells transfected with Myc-SmaugWT and various regions of SMO fused to either HA (D) or to GFP (E) were immunoprecipitated with αMyc (D) or αGFP (E) and analyzed by western blotting with αMyc (lower panel in D and upper panel in E), αHA (D, upper panel) or αGFP (E, lower panel). In: Input; Sup: supernatant. See also Fig EV1D-F.
Extended network motif based on (a) and including an additional repressive interaction from X onto Y used to explore changes in fluctuations as well as Y levels (indicative of Her6 downregulation).
Co-localization (Col) is indicated by white dots. STING translocated to the autophagosomes in the absence of EGFR. , the cells were labeled with LC3 (Autophagosome marker, Red) antibody. (D) No STING was detected in the autophagosomes even after 3h after stimulation if EGFR was not inhibited.
(E) Males and sterile hermaphrodites (via FUdR treatment) show the formation of spherical structures in the BWM that resemble mature exophers. MOM - mitochondrial outer membrane.
(a) Representative confocal images of segment A3 muscle 6/7 synapses stained for both DVGLUT (green) and FasII (red), in wild-type, Rae1EX28, Rae1EX28; atg1/+, Rae1EX28; atg2/+ and Rae1EX28; atg18/+ wandering larvae. Scale bar represents 10 μm. (b) Quantification of the number of boutons in wild-type, atg1/+, atg2/+, atg18/+, Rae1EX28, Rae1EX28; atg1/+, Rae1EX28; atg2/+ and Rae1EX28; atg18/+ larval NMJs (segment A3 muscle 6/7; n = 12, 12, 12, 12, 12, 16, 12 and 21, respectively).