EMBO/sd-character-level-ner huggingface dataset:
A) Flow cytometry histograms showing stable expression of the indicated IFITMs in HEK293T cells.
F. HEK 293T cells lysates were subjected to m7GTP-agarose pull-downs as in (C) in the presence or absence of RNase A (10 µg/mL). RNA was extracted from parallel lysates and RNA content was analyzed by agarose gel electrophoresis.
3D) nt and PINK1 knockdown (kd) SH-SY5Y cells were stained with the photo-reactive dye MTR and either irradiated for 45 min or left untreated. 24 h and 48 h after irradiation the LAMP-2 and actin content were determined by western blotting. A representative blot 48 h after irradiation is shown on the right. The relative LAMP-2 content of untreated cells was set as 1. Cells with stable PINK1 knockdown exhibited after 48 h a reduced Lamp-2/actin ratio compared to the control (nt) cells; n = 5, p<0.001.
Lipolysis rates after stimulation with 1 nM isoproterenol as measured by glycerol release from adipocytes after six days of adipogenic differentiation. Data are shown as mean ± SEM of 3-7 replicates and normalized by lipid content of the cells. The entire experiment was repeated twice.
F. Molecular docking of Dvl binding motif (DBM) or KY-02061 to Dvl PDZ domain were analyzed by in silico experiments. The superimposed structure of DBM (green) and KY-02061 (yellow) on the surface of Dvl PDZ domain (gray) was visualized.
We utilized exome sequencing data from 24 MSI CRCs and corresponding normals and whole genome sequencing data from 12 MSI CRCs and corresponding normals. The tumor data was filtered against the corresponding normals as well as outside controls to remove germline variants. Only the areas targeted by the exome sequencing kit were included in the analysis. Insertions and deletions were then filtered out, leaving the somatic missense, nonsense, synonymous and non-coding mutations in the region targeted by the exome sequencing kit. On this set of variants a) hot spot analysis was performed, and b) MutSigCV was utilized, resulting in a ranking of genes Genes with mutations in one or two tumors only were excluded. The top 73 genes were validated by MiSeq sequencing in a validation set of 93 additional MSI CRCs. The data was filtered against > 60,000 outside controls to remove germline variants. Insertions and deletions were left out, resulting in a set of somatic missense, nonsense, and synonymous changes with MAF < 5 x 10-5. On this set of variants, OncodriveFML was utilized. Genes with mutations in only one tumor were excluded, resulting in a ranking of 57 candidate driver genes. Further functional studied were carried out for SMARCB1 and STK38L
(C) Venn diagram from cross analysis of down-regulated genes obtained from RNA-seq analysis in JFK-overexpressing and ING5-depleted HepG2 cells with genes targeted by ING5 from ChIP-seq. GO enrichment analysis of 140 potential target genes using DAVID is shown.
Mice were injected with Ctrl MC38 cells or Ifn-DKO cells and treated with 5-FU or PBS. (F) Pictures of tumors and spleens from a representative experiment. Image panels were cropped from the same picture.
Immunoblotting of subcellular fractions of GID1 and mutations expressed in rice protoplasts. Total (T), soluble (S) and nuclear (N) protein fractions were isolated from protoplasts for 12 hours after transformation. Equal amounts of proteins from each sample were loaded.
A) Bar graph showing the relative change in OCT-measured volume between the outer nuclear layer and the RPE layer following intervention with test articles. Anti-VEGF-A and anti-ANG-2 were given at 5 mg/kg and anti-VEGF-A/ANG-2 at 1, 5, and 10 mg/kg (low, mid, and high dose).B) Representative OCT images converted to heat maps with the scaling grade given on the right of the figure delineating fluid filled areas of the retina. Baseline (D46) and 14 days treatments of IgG control, anti-VEGF-A, anti-ANG-2, and bispecific anti-VEGF-A/ANG-2 at the end of the experiment (D60) are shown. For the region of interest, the corresponding FA image at D60 is also shown as comparator.
SCNAs determined by sWGS in 4 tumor subparts (T1 - T4) and the CSF sample, collected from patient G1. Amplifications are shown in dark blue, deletions in orange, and copy number neutral regions are in dark grey. sWGS from plasma and urine samples collected at the same time as the CSF sample showed no SCNAs
Transcription (bottom) and translation (top) profiles for lacZ. Profiles are shown for cells in the absence and presence of IPTG (1 mM). Position of genetic parts and gene is shown below the profiles. RBS is omitted from the genetic design due to its size. (E) Measured promoter strength in RNAP/s units, RBS initiation rate in ribosomes/s units, and the transcriptional terminator and translation termination efficiency for lacZ. Data shown for cells in the absence and presence of IPTG (1 mM).
Representative recording of Continuous measurement of oxygen consumption rate (OCR) in isolated mitochondria from BAT of WT fl/fl and QKI KO fl/fl:AP2-Cre mice on NCD; Oxygen consumption was performed under basal conditions, following the addition of 0. 25 mg mitochondria (Mit), 5 mM substrate glycerol-3-phosphate (G3P), 2 mM GDP, and 450 mM ADP, 2 μg/ml oligomycin, and 1.5 μM FCCP. Quantification of experimental data. (n=3 biological replicates, per group)
(F) Treadmill performance was significantly improved in the KO-NDUFS3 mice when compared to the KO-GFP, from 2 months onwards. P values were calculated using Log-rank (Mantel-Cox) Test; p=0.0016 (KO-NDUFS3 vs KO-GFP); p=0.0014 (KO-GFP vs WTFlx); n-indicates the number of animals used per group.
(a) EGF enhances nuclear LC3-II content in hepatocytes. Immunofluorescence (IF) depicting nuclear LC3-II in RALA hepatocytes in presence or absence of EGF (10 min). Native/inverted images are shown. Scale bar, 5 μm. Bars represent mean±s.e.m. ***P0.001 compared with control (Con); Student's t-test, 50 cells from two experiments.
Western blot of NIH-3T3 cells expressing sgCtrl or sgP5CS-2 and treated with TGFβ or mock for 48h in the presence or absence of 0.15 mM proline.
A 293FT cells were transfected with 3xFlag-Usp27x (pFCMV7.1 vector backbone) together with a construct driving expression of untagged BimEL or 3xHA-BimEL(both pMIG vector backbone). Cells were lysed, and 3xHA-BimEL was immunoprecipitated with anti-HA-antibodies. IP products were tested by Western blotting for the presence of Bim and FLAG-Usp27x probing with antibodies against Bim or against the FLAG-peptide. See also Appendix Fig. S1B. Western blots show representative of n≥3 independent experiments.
(F) T47D-MTVL cells transfected with control or HP1y siRNAs, were incubated with 10 nM R5020 for 6h. RNA was extracted, and cDNA was generated and used as a template for real-time PCR with BCAS1, KRT23, IGFBP5, and GAPDH specific primers. The histograms show the mean ± SD of 3 experiments performed in duplicate. The levels of HP1y and tubulin were analyzed by western blotting using specific antibodies. * P-value < 0.05.
Northern blotting shows that the flam-piRNA precursors in the Flag-Gasz complex (Flag) accumulated upon Zuc depletion (Zuc KD).
(a) AMPK phosphorylates the Ulk1 S/T domain in vitro. Top: schematic representation of Ulk1 domain structure and deletion constructs used to map phosphorylation sites. The mouse Ulk1 protein consists of an N-terminal kinase domain (KD; 1-278), serine/threonine-rich domain (S/T domain, 279-828), and C-terminal domain (CTD, 829-1051). Bottom: the indicated Flag-Ulk1 deletion mutants were immunopurified from transfected HEK293 cells and were used for in vitro AMPK assay as a substrate. Phosphorylation was examined by 32P-autoradiogram and protein level was determined by western blot.
Representative pictures of adipocyte-specific QKI-deficient mice under NCD or HFD conditions.
(C) Domain composition of GRK2 and the corresponding location of the mutations (RGS, regulator of G protein signaling domain; PH, pleckstrin homology domain).
(E) Analysis of OTUD1 protein levels in colorectal adenocarcinoma patients with different clinical stages from tissue microarray CoI05-118e.
(F) Principal component analysis (PCA) of the measured proteins in CTNSWT, CTNS-/-, and CTNSPatient (n = 3).
(A) Epifluorescence microscopy of live cells containing a subgenomic replicon with a GFP-tagged NS5A. Huh7-Lunet cells were transfected with replicon RNA and seeded onto carbon-patterned sapphire discs. Twenty-four hours later cells were analyzed by fluorescence microscopy and immediately processed for EM. (a) Fluorescence image; (b) enlarged fluorescence image of the cell of interest; (c) merge of bright field and fluorescence images. Coordinates etched onto the surface of the sapphire disc were used to record the position of the selected cells. White squares in a and c enclose the cell shown in b. (B) EM micrograph of the cell boxed in panel Ab overlapped with the fluorescence image. Areas marked with a green dotted line indicate regions of intense fluorescence. Note that the images do not match perfectly because the fluorescence image corresponds to the complete cell whereas the EM image represents one 60 nm ultrathin section of the same cell. (C) Higher magnification images of the two different regions, labeled 1 and 2 in panel B, corresponding to regions with intense fluorescence (1) or a region corresponding to the intersection of high to low fluorescence (2). Region 1 (top panel) corresponds to a DMV-containing area residing in close proximity of the ER; region 2 (bottom panel) corresponds to a LD-enriched area containing DMVs in very close proximity. Areas marked with white squares in the left images are magnified in the corresponding right panels. LD, lipid droplet; ER, endoplasmic reticulum; DMV, double membrane vesicle; m, mitochondrium; if, intermediate filaments.
Models depicting the relationship between binding sites and functional status for Rad54 and Rdh54 bound to a mitotic Rad51-ssDNA presynaptic complex.
A Schematic representation of the luciferase-reporter constructs used to assay miR-1236 activity against a CDS target site in FOXL2 mRNA. The 231-bp human FOXL2 segments harboring either the C402 (WT) or the G402 (mutant) nucleotide were inserted in-frame into the CDS of the luciferase gene in the pGL3 control vector.
Endogenous Fis1 is modified by His-SUMO-2 stably expressed in HEK293 cells. His-pulldown (His-PD) and lysate samples were blotted as indicated.
Protein degradation in indicated yeast strains monitored by pulse-chase experiments for the lysine-less CPY*-K0-HA Values for each time point are reported as means ± standard deviation
Total eFluor780+ events in the BAL of influenza-infected mice described in A, B 10 days p.i. (n = 3 mice from each group).
D Quantified UbG76V-GFP protein levels relative to actin control for each indicated lane for the blot in (B). ****P<0.0001, ANOVA with Dunnett's posthoc comparison to wild type. N=3 trials. Error bars indicate SEM.
E Proposed model for the regulation of pexophagy and mitophagy by GABA. Elevated GABA activates Tor1 in starvation conditions and inhibits pexophagy and mitophagy by activating Sch9.
Confocal laser scanning fluorescence microscopy (CLSM) images showing DNA staining (blue in the merged images), rDNA FISH (green) and NCL immunofluorescence (red) in untreated HeLa cells or in cells treated with α‐amanitin (50 μg/ml), AMD (50 ng/ml) or the Pol III inhibitor ML‐60218 (200 μM) for 5 h.
Structure similarity between SARS-CoV-2 RBD and SARS-CoV RBD.RBD is shown in a space-filled model with colored surface. ACE2 is shown as gray tube model. The three glycosylation sites in SARS-CoV are labeled. Note that N357ST in SARS-CoV is changed to N370SA in SARS-CoV-2, which is different from the NXS/T pattern required for glycosylation, and hence this site is more likely to be unglycosylated. The two possible cross-reactive regions are marked with yellow circles.
N Relative RUNX2 expression levels between K-control and knockdown groups. Data information: Data represent the means ± SEM. n = 3 for all experiments. Unpaired t-tests for N , *P < .05, **P < .01, ***P < .001.
(D) flg22-induced PP2C38 band shift was compromised in map4k4 mutants. PP2C38-HA were expressed in Col-0 and map4k4 protoplasts and treated with 1µM flg22 for 30 min.
H. Left panel: Schematic outline of the analysis of microRNA-sequencing data. Right panel: Expression of microRNA module 2 amongst experimental groups. Kruskal-Wallis test. Wildtype vehicle: n = 9; CamkIIδc TG-vehicle n = 7; CamkIIδc TG-Vorinostat n = 10; In the boxplots in H, the center line indicates the median, while the upper and lower lines represent the 75th and 25th percentiles, respectively. The whiskers represent the smallest and largest values in the 1.5× interquartile range.
B. Boxplots showing differential gene expression (AC versus DMZ) and associated ATAC-seq signals (Two biological replicates). The central band within the boxplot represents the median and the whiskers show 1.5 times the range between the first and third quartile (IQR).
(N) Lifespan assay of wt, gas-1(fc21), gas-1(fc21); cest-2.2 O/E and cest-2.2(lf); gas-1(fc21); cest-2.2 O/E mutant nematodes. Data information: the median lifespan ± SEM is reported underneath the graphs and additional information (e.g. n numbers)
C. The number of PGCs labeled with PkH26 (red) that migrated to the genital ridge in a frozen section, the number of PGCs labeled with PkH26 (red) was counted using Image J software. Scale bar: 70 µm (Data are shown as mean ± SEM, n = 6 independent experiments, ** p < 0.01, **** p < 0.0001, one-way ANOVA.).
(D) Total levels of p62 in these cells were quantified in 20 cells from three independent experiments using the Zeiss LSM 510 Meta software and the average normalized to the average p62 level in control (mock transfected) cells. Error bars = SEM.
(A) Heatmap of the transcriptomic dysregulation caused after treatment with lurbinectedin in five different cell lines of SCLC -DMS-53 (green rectangle), NCI-H510A (Brown rectangle) and NCI-H82 (Yellow Rectangle) with a False Discovery Rate < 0.05 (2998 common Differentially Expressed Genes, DEGs) shows that the vast majority of genes are downregulated (n=3 biological replicates). Color legends correspond to the three cell lines and ctl (basal - Pink rectangles), as well as samples treated with lurbinectedin (Red rectangles).
(E) Native filter assay analysis of TBS (p=0.7124), Triton-X (p=0.3170), SDS (p=0.4833) and formic acid (FA) (p=0.8144) fractions from APP23p40+/+ (n=8) and APP23p40-/- (n=8) mouse brain homogenates. Mean ± s.e.m., statistical analysis: two-tailed unpaired t-test between the same fractions.
(A-D) Panels (A) to (D) show the gene function prediction performance of the single-plant network versus sampled SRA networks for GO categories related to abiotic stimulus responses, development, biotic stimulus responses and hormone responses, respectively. Categories are shown in the context of the GO hierarchy and colored according to how well the single-plant network performs in comparison with 500 sampled SRA networks (see Materials and Methods). Solid arrows represent direct parent-child relationships in GO, dashed arrows represent indirect relationships. Grey nodes depict untested GO categories. White nodes depict GO categories for which there was insufficient information to score the performance of the single-plant network versus the sampled networks, i.e. categories for which the single-plant network and more than half of the sampled networks did not give rise to any predictions at q ≤ 10e-2.
Lyzs-Cre and p38γ/δLyzs-KO mice were fed a ND or a HFD for 10 weeks. (A) Representative H&amp;amp;E and oil red stained liver sections (Scale Bar: 50μm)
(B) Immunofluorescence micrographs showing the distribution of ZO1-containing tight junctions and cilia in the epithelium and VE-cadherin-containing adherens junctions in the endothelium of the Airway Chip in the absence (Control) or presence (+ Virus) of infection with GFP-labeled influenza PR8 (H1N1) virus (MOI = 0.1) for 48 h (blue, DAPI-stained nuclei; bar, 50 μm).
olorectal tumor outcomes in WT (n=7), IL-33KO (n=4) and ST2KO (n=3) mice at the completion of the AOM/DSS carcinogenesis protocol. C) representative images of H&E-stained distal colon in each group (scale bar: 100 μm).
Enzymatic activity of phosphofructokinase in whole tibialis anterior muscle cytosolic homogenates is expressed as mean fold change ± SEM from age-matched WT at 65 days of age *P = 0.016 (WT n = 6, SOD1G86Rn = 7) and 105 days of age ***P < 0.0001 (n = 5/genotype), two-way ANOVA followed by Fisher's LSD post hoc test. Data shown are representative of two independent experiments having similar results.
(B) Immunoblotting (IB) analysis of wild type (WT) and PAQR3-deficient MEFs after GS for different time as indicated.
(G) PC3 cells were pre-treated with 10μM PAG for 16 hrs, and incubated for migration (16h) and invasion assay (24h) in the presence of 10μM PAG. Data information: Data shown represent the means ± SD (n=3 biological replicates). Student's t-test was used for the statistical analysis (*P<0.05; **P<0.01; ***P<0.001).
(B-D) The effect of miR-515-5p overexpression on NRAS, FZD4, CDC42BPA, PIK3C2B and MARK4 mRNA levels in MCF7 (B), MDA-MB-231(C), A549 and H1299 (D) was determined by qPCR 48 h following transfection of the indicated cell line with non-targeting control miR (NC) or miR-515-5p. Data is displayed as the normalised mean ± SEM. P values were calculated by t-test between miRNA conditions and their respective NC conditions (*, P<0.05; **, P<0.01; ***, P<0.001).
(C) day 20±2 cerebral organoids derived from controls, patients and EML1-heKOs stained for the neuronal marker MAPT and the adherens junction marker NCAD, counterstained with DAPI. Ectopic neural rosettes and neuronal heterotopia are highlighted with dotted yellow lines. (D) Quantification of VZ areas with ectopic neural rosettes (3 batches, 3 organoids analyzed per batch, significance based on Kruskal-Wallis-test, P=0.0001, Dunn's post hoc test for multiple comparisons performed to define statistical differences between genotypes, single data points are presented colored by batch). (E) Quantification of heterotopic, disorganized or organized cortical areas (3 batches, 3 organoids per batch, significance based on Kruskal-Wallis-test, P=0.0001 for "organized" and "heterotopic"; no significant difference for "disorganized", Dunn's post hoc test performed for multiple comparisons to define statistical differences between genotypes). Data information: * marks statistical significance in relation to Control 1, # in relation to Control 2. P-values: ***/###<0.001. VZ: ventricular zone; Data in graphs are represented as means ± SD. Scale bars: 50µm.
(E) Quantitative analysis of dystrophin expression in body-wide muscles from mdx mice treated with PMO-M (n=4) or PMO alone (n=3) (*p<0.05; two-tailed t test).
C Left, CD53-CD2 docking model. The HDX-MS identified regions are shown as a red rod in CD53 and as a blue arrow in CD2. The black box indicates the CD2 transmembrane region and the dashed line indicates the linker to Ig domains. Right, CD53-CD2 docking model with CD53 modeled in the closed conformation. The modeling was based on the CD81 structure, in which EC2 reorients to interact with the TM domain. Docking of CD19 Ig to CD53 EC2 is in the same manner as Left.
B) First degree of microbial neighbors of the CMA and two important clinical variables (Liver Fat and Uric Acid) are presented based the multi-omics network analysis. Full networks can be found in iNetModels (http://inetmodels.com).
Close up view of the CtUba4 active site and the CtUrm1 C-terminus (top). A superposition of the linker from apo CtUba4 structure is shown (bottom). Crucial residues are shown as ball-and-stick model and the tentative positions of Cys202 Cys305 are indicated.
WT or LRRK2 KO RAW264.7 macrophages, RAW264.7 macrophages pre-treated with 1 μM GSK2578215A (GSK inh) and WT or Rab8A KO RAW264.7 macrophages were treated with 1 mM LLOMe for 30 min. ubiquitin K63 positive vesicle numbers were analysed by immunofluorescence and high content imaging. Scale bar = 20 μm. Right panels show quantification of number of positive vesicles per cell. Data show the mean ± SEM of three to four biological replicates. ns=non-significant, *p≤0.05, **p≤0.01 by One-way ANOVA followed by Sidak's multiple comparisons test.
(A) The studied patient harbored compound heterozygous mutations in COX6A2 gene (Inoue et al, 2019).
A Immortalized MEFs were infected with retroviruses expressing the indicated shRNAs, followed by selection with puromycin for 72 h. Cell extracts were prepared 48 h later and analysed by Western blotting as indicated. SMC1 was used as a loading control. *non‐specific band.B Quantification of the frequency of end‐to‐end chromosome‐type fusions of cells treated as in (A) represented as a percentage of fusions observed after TRF2 depletion. A minimum of 2,000 chromosomes were scored for each sample. Error bars represent SD of three independent experiments. The P‐value was calculated using an unpaired two‐tailed t‐test. NS, P > 0.05.
C. Fold induction (log) of SASP genes in Rb∆K7 vs control littermates. Genes that overlap between the GSEA and G:profiler are highlighted in green. Yellow indicates genes that are transcriptionally regulated in epithelial SASP. Cxcl12, chemokine (C-X-C motif) ligand 12, has not been previously implicated in SASP in epithelial cells or fibroblasts, but is induced in Rb∆K7 islets. Log ratio is the difference between the mean of RbΔK7 samples and the mean of control samples of the log2 normalized values.
Fold induction of IFN stimulated genes (CXCL10 and IFIT2) each overlaid with SARS-CoV-2 E (qRT-PCR).
A. Domain organization of Sec63. The sequence of the acidic patch on the C-terminus - divided into C1 and C2 regions - is shown in the lower panel. The two phosphorylated threonines (T652 and T654) are marked in the C2 region. The J domain of Sec63 is indicated by "J".
M The phosphorylation of CREB and FST expression were detected by Western Blotting in Ba/F3-FLT3/ITD cells treated with CREB inhibitor 666-15 for one day. ^: non-specific staining of p-ATF1 protein due to the conserved motif.
Immunoblot analysis of total lysates from fibroblasts (fbs) and of in vitro-synthesized proteins (i.v.p). fl: in vitro-translated full-length XRCC4 protein; ret.: reticulocyte lysate used for in vitro protein synthesis; 225*: in vitro-translated XRCC4 R225* truncated protein; Ct: lysate of control fbs; and II-1 and II-2: lysates of fbs from patient II-1 and II-2. α-XRCC4 (Abcam, 1:1,000) and α-GAPDH antibodies were used.
(D) Immunohistochemical staining of OTUD1 in colorectal adenocarcinoma and its matched adjacent normal tissue (The scale bars represent 1000 μm).
(H) Cross-linked SDS-PAGE analysis of recombinant mTLR4 (extracellular domain)/mMD-2 complexed with GM3 18:0, GM3 species enhancing mTLR4 activation.
(e) Immunoblot analysis (left) of ER proteins in Atg5f/f B cells left untreated (UT) or treated with lysosomal protease inhibitors (10 μM leupeptin and E-64d) for the final 8 h of the third day of LPS-induced differentiation (Leu + E-64d (8 h)). Right, quantification of band intensity (presented as in Fig. 1c). *P 0.05, **P 0.01 and ***P 0.001 (Student's t-test).
(B) Long-term growth transformed B cell cultures infected with recombinant EBV mutants were seeded at a starting concentration of 2 x 105 cells per ml.
C. Cloverleaf scheme of the mt-tRNAMet sequence. Nucleosides that were exchanged in the mutational analysis shown in the following panels are marked with arrows and the nucleotide positions in the tRNA are given.