EMBO/sd-character-level-ner huggingface dataset:
qPCR analysis for adiponectin (Adipoq), peroxisome proliferator-activated receptor gamma (Pparγ2), and fatty acid synthase (FAS) in RNA isolated from depot-derived cell lines after in vitro differentiation. Data are shown as mean ± SEM of 3 cell lines/group.
C1, C2, C3, C4) Dot plots showing DRD2, RGS9-2, R7BP and Gβ5 protein levels measured in striatal detergent-resistant-membrane (DRM) preparations from Tor1a+/- (+/-) and WT (+/+) mice (DRD2: Tor1a+/+ N=16, Tor1a+/- N=13, t test P=0.0129; RGS9-2: Tor1a+/+ N=7, Tor1a+/- N=6, t test *P=0.0396; R7BP: Tor1a+/+ N=6, Tor1a+/- N=6, t test ***P=0.0002; Gβ5: Tor1a+/+ N=9, Tor1a+/- N=9, t test P=0.8461)
Selected abscission-related gene expression levels in (B) WT and proIDA::CDF4 lines by using qPCR analysis. The expression of these selected genes in the wild-type plant is given as 1. The relative expression level represents only the level of expression of the gene relative to the wild type. ACTIN2 was used as the internal control. Three independent experiments were conducted. Values are given as mean ± SD, n=3. *p<0.05 by Student's t test.
G) Representative plots of β-Gal 488 fluorescence distribution in YC and OC FAPs and MuSCs and IMR90-SEN cells (in red) compared to their Fluorescence Minus One (FMO) negative control (in black).
(D) Sequence alignment of human CA7 and CA2 protein sequences generated using the Clustal O (1.2.1) multiple sequence alignment. Residues forming a ridge at the CA7 protein surface in the CA7 3D structure are highlighted in the CA7 sequence (bold/underlined). R223 is marked in turquoise and H96 and H98 (mutated to gain a catalytically loss-of-function mutant) are highlighted in green. The row below sequence alignment indicates structural features of CA7 based on the UniProt database (B = beta strand, H = helix and, T = turn).
C. Single myeloid blasts from 4 different Myc/bcl2+ DN2-derived leukemias were flow-sorted from transplanted mice and grown on irradiated OP9:OP9DL1 stroma. The clones were analyzed at two different time points. FACS plots of two representative clones, one with strong (top) and one with weak (bottom) lineage switching potential are shown.
A The binding of fluorescently (GFP) labelled MICU1 and mutants to EMRE peptide shown by MST in the presence of EGTA. B The binding of fluorescently (GFP) labelled MICU1 and mutants to EMRE peptide were analysed with MST in the presence of Ca2+.
WT mixed glial cultures were co-treated with MPSIIIA GAG (4 μg/ml) and/or the TLR4 inhibitor CLI-095 (1 μg/ml) for 24 hours. The intracellular production of IL-1β was measured (n=3 independent experiments each with 3 inter-experimental replicates). Data are expressed as mean ± STDEV and were tested by one-way ANOVA with Tukey's post-test; ***P<0.001. Symbols above bars are versus MPSIIIA GAG + vehicle.
(M) Average plot (top) and heatmap (bottom) of H3K27ac reads in HSCs in the early and late phases within accessibility-decreased (left: Green dot in Fig 3E), -unchanged (center: Blue dot in Fig 3E), or -increased regions (right: Brown dot in Fig 3E) in the late phase.
Representative images showing ANG immunohistochemical (IHC) staining in normal control and UC or CD sample.
(A) OCR of wt and gas-1 mutant nematodes (normalized to nematode size as given by the COPAS Biosort (Time of Flight -TOF)). One representative curve shown (mean ± SEM; n=3) ****p value< 0.0001; Kruskal-Wallis Test, Dunn's post hoc correction.
B) Western blot showing the percentage of restoration of dystrophin protein in mdx mice following antisense oligonucleotides administration. M is molecular ladder. WT gastrocnemius represents the standard curve using protein extracts from gastrocnemius muscle. NT is saline treated mdx mice.
c, Immunoblots of subcellular fractions isolated from HEK293 cells stably expressing GFP-DFCP1. Cyto, cytosol; micro, microsome; mito, mitochondria; PNS, post-nuclear supernatant.
NAD+/NADH ratio (J in C2C12 myocytes transfected with siRNA or plasmid for mGPDH 24 h after differentiation
(E) Immunoprecipitation analysis of siCtrl- or siRNF34-1-transfected cells infected with VSV for the indicated times. Anti-MAVS immunoprecipitates were analyzed using immunoblotting with an anti-MAVS or anti-Ub-K27 antibody. The WCL was immunoblotted with an anti-MAVS or anti-Ub-K27 antibody. Cell-based studies were performed independently at least three times with comparable results.
Western blotting analysis of the PLP-150Q/Cas9 mouse corpus callosum tissues using the antibody to Ser259 (pMYRF), phosphor-PRKG2 or MBP. Note that reduction of mouse PRKG2 by CRISPR/Cas9 leads to the decreased MYRF phosphorylation and the increased expression of MBP. The ratios of pMYRF to MYRF or MBP to GAPDH obtained from 3 independent experiments were presented under the blots. Student's t-test; pMYRF: ***P=0.00026; MBP; **P=0.0036. Data are presented as mean ±SEM. fMYRF: full-length MYRF, nMYRF: N-terminal MYRF.
Entry of SARS-CoV-2 and SARS-CoV S pseudotyped viruses is potently inhibited by four SARS-CoV S mouse polyclonal immune plasma.
(H, I) Western blotting and densitometric analyses for LC3-II/LC3-I ratio in CTNSWT, CTNS‑/-, and CTNSPatient cells cultured in the presence or in the absence of BafA1 (25 nM) and DMKG (2 mM) for 4 hrs, respectively (n = 3).
D Cell lysate from DCL1KO cells at 3 hpm was incubated with radiolabeled double‐stranded 27‐nt RNAs and then with (+) or without (−) ATP and the ATP regeneration system, the HSP70 inhibitor PES, and the HSP90 inhibitor 17‐AAG. Loaded RNA was analyzed as in (B). The intensities of the bands relative to the sample without ATP and any inhibitors (1st column) are shown on the top.
(A) The schematic of the Drosophila Ash1 protein organization. Ash1 is 2226 amino acid long and contains eight domains (indicated by colored rectangles). The SET domain together with the AWS (Associated With SET) and the post-SET domains are necessary and sufficient for Ash1 histone methyltransferase (HMTase) activity. The functions of the BAH (Bromo Adjacent Homology), PHD (Plant homeodomain) and AT-hook domains are unknown. The positions of ash122 and ash121 point mutations are indicated by arrows.
(D-G) Female C57BL/6J and ADX mice were put in normoxia or hypoxia for 6h or 24h, n=6/group, two independent experiments. (D, E) Confirmation of RNA-seq data via RT-qPCR [6h (D) or 24h (E)]. (F, G) Plasma GC concentration [6h (F) or 24h (G)]. Data information: All bars represent mean ± SEM. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. ****P<0.0001, ***P<0.001, **P<0.01, *P≤0.05.
(A) Western blotting analysis of cellular extracts from HepG2 cells transfected with FLAG-JFK or JFK mutants.
(B) Changes in lncRNA expression from HUVECs exposed to hypoxia (0.2 % O2 for 12 h or 24 h), determined by ribo-minus RNA deep sequencing (data acquired from GSE107033 ; NTRAS is highlighted (n = 2 independent biological replicates).
Summary quantification of Transferrin receptor levels in non-starved fibroblasts transduced with the indicated lentiviruses, normalized to actin (ACTB) and expressed as % of controls (n=6 biological replicates).
Cell-free plate-binding assays. A purified tagged-protein was attached to a plastic plate and a purified recombinant protein fused to alkaline phosphatase (AP) was overlaid. Bound protein was quantified by measuring AP activity. (E, upper panel) LRP4ect-Flag bound to overlaid MuSKect-mycAP in a dose-dependent manner of CTGF-full-myc, but not of CTGF-ΔCT-myc. (E, lower panel) LRP4ect-Flag bound to overlaid agrin-mycAP independent of CTGF-full-myc. Rspo2-mycAP and Rspo2-myc were used as Control-mycAP and control-myc, respectively. Mean and SD (n = 9 wells; 3 wells in 3 independent experiments) are indicated. p-value < 0.05 by two-way repeated measures ANOVA for the three panels in (E). p < 0.05 by post-hoc Tukey test is indicated by a single letter representing each group.
C Regression analysis of the correlation between TERT and TA-ERVs expression in 103 tumour samples across 11 cancer types. BRCA (breast invasive carcinoma), n = 17. cHL (classical Hodgkin lymphoma), n = 5. COADREAD (colon adenocarcinoma/rectum adenocarcinoma oesophageal carcinoma), n = 6. HGSC (high-grade serous ovarian cancer), n = 6. KIRC (kidney renal clear cell carcinoma), n = 12. LIHC (liver hepatocellular carcinoma), n = 9. LUAD (lung adenocarcinoma), n = 6. OSCC (oral squamous cell carcinoma), n = 8. PAAD (pancreatic adenocarcinoma), n = 10. PRAD (prostate adenocarcinoma), n = 6. THCA (thyroid carcinoma), n = 18.
(B) Phase-contrast images of wild-type or PABPC4KO HeLa cells depleted of PABPC1 by siRNA-mediated knockdown. Scale bar, 100 μm. (C) Total numbers of viable cells in (B) were quantified with acridine orange and propidium iodide staining and graphed as a percentage of wild-type HeLa cells. Error bars represent the SEM of three biological replicates.
Cell line-specific model calibration for two selected cell lines C32 and WM115. Left: R2, Q2, and MSPE for C32 and WM115 models built with increasing numbers of PLSR components. Middle: Relative viability as measured experimentally (z-score-scaled) or as predicted by the three-component PLSR models using tenfold cross-validation. R2 reports model fit, and Q2 reports model prediction accuracy. Right: PLSR score plots for the first two components of C32 and WM115 models. Shown PLSR models were developed using RPPA data from Supplementary Dataset S3.
Isolated cryo-EM density of SecYEG with the fitted molecular model of the translocon in front and the cytoplasmic views. SecY is displayed in rainbow pattern, SecE in purple, and SecG in green. Dashed box: A contact site between tilted SecE TMHs 1/2 and SecY TMH 8. Cryo-EM density corresponding to the ribosomal RNA helix 59 ("H59") is displaced toward the nanodisc. No contact with the lipid bilayer could be detected. Blue ribbon: Structure of the translocon-free 50S ribosomal subunit (PDB ID: 4UY8). Central cross-section through the SecYEG model. The "plug" TMH 2a occupies the central position, thus keeping the translocon sealed. The nanodisc perimeter is indicated as a dashed circle. The lateral gate of nanodisc-embedded translocon undergoes rearrangements relatively to a quiescent conformation (left, PDB ID 5AWW) and an RNC-bound detergent-solubilized state (right, PDB ID 5GAE).
(F-H) Representative micrographs (F), respective quantification (G), and immunoblot analysis (H) of wild-type (WT) and ACS1-deleted (Δacs1) yeast aged to day 3 compared to young (day 1) cells expressing GFP-Atg8p chimera as in (C)-(E). Data represent means ± SEM (n = 4).
(G) PtenΔC/ΔC mice (2-4 months) treated with Slc6a20a-ASO display normal levels of climbing in the Laboras test. n = 6 mice for WT-saline, 7 for WT-ASO, 7 for ΔC-saline, and 8 for ΔC-ASO, *P < 0.05, **P <0.01, ns, not significant, two-way ANOVA with Bonferroni's test. The error bars represent SEM.
(D) Statistical analysis for fluorescent intensity of nuclear F-actin in (A), (B) and (C). Fluorescence intensity are quantified from at least 30 cells for each group in (A) and (B). One-way ANOVA. *P < 0.05; **P < 0.01.
(B) Representative stills illustrating mitotic progression in mCherry-H2B expressed cells treated with Control siRNA or Cyclin B2 siRNA. Images were acquired at the indicated time points after the start of NEBD. The arrow indicates lagging chromosomes
a, Protein extracts from drpr null (w; drprDgr;5/drprDgr;5) pupae at puparium formation (0 h) and from the fat bodies of wild-type (Canton-S) third-instar larvae were analysed by western blotting with anti-Drpr antibody. Third-instar larvae were either fed or starved for 4 h.
(d) USP33 regulates RALB ubiquitylation at Lys 47. (e) The GTP-GDP status of RALB affects RALB ubiquitylation at Lys 47. For c-e, 6xHis-tagged ubiquitin and the indicated RALB mutants were introduced into HEK293T cells expressing GFP shRNA or USP33 shRNA. Ubiquitylated RALB was purified by Co2+ metal affinity chromatography and detected by antibodies specific to RALB. WT, wild type.
Representative Western blot for Fam134 proteins in single knockout mouse embryonic fibroblasts (MEFs).
D Endogenous interaction between MAVS and SIRT5. Anti-MAVS antibody was used for immunoprecipitation, and normal mouse IgG was used as a control. Data information: IP, immunoprecipitation; TCL, total cell lysates.
16-days old MCF10A spheroids grown in matrigel/collagen mix were stimulated for 24h with either macrophage-conditioned or control medium. Representative images of MCF10A spheroids categorized into 4 groups according to the filling of the lumen with cell nuclei (clear, partially filled, almost filled and filled). Spheroids stained for DNA (Hoechst 33342 in blue) and F-actin (Phalloidin in red).
A. Heat map depicting all human AML samples from the Haferlach study (Haferlach et al., 2010) whose transcriptomes resembled DN2-leukemia by a Spearman's rank correlation coefficient ≥ 0.5. The top 100 up- and downregulated gene signature of Myc/Bcl2+DN2-derived myeloid blasts was applied (see also Figure 3B).
Percentage of pH3-positive cells in the carcinomas of the indicated genotypes (left panel). Representative images of pH3 immunohistochemistry (right panel). Red arrowheads: pH3-positive cells.
B, The lysates from control (pCS2), Endouc-expressing (Endouc), and EndoucK242A-expressing (EndoucK242A) cells were applied to PPA. The resulting fractions from 1-10 collected from sucrose gradient were subsequently subjected to RT-qPCR assay to quantify (B) exogenous huORFchop-tagged luc (luc mRNA) The distribution of relative abundance of luc and CHOP transcripts contained in each fraction was determined.
E) Localization analysis of GFP-fused CENPC-CT and CENPC643-864 lacking the CM upstream region (green) on mitotic chromosomes in CENP-C knockout DT40 cells. CENP-T (red) was used as a centromere marker. DNA was stained using DAPI (blue). Scale bar indicates 10 μm.
E 100 nM CXCL12 and Gal-3 were added to Jurkat T cells, and their co-localization was assessed on the cell surface by PLA. Control experiments were performed as indicated (representative example of n = 3). White scale bar: 10 µm.
Quantitation of the single strand annealing (SSA) reporter assay in U2OS cells. All cells were treated with DMSO; where indicated, both PFM03 (50 μM) and PFM39 (50 μM) MRE11 inhibitors were added. Averages shown; n = 4, error bars, SEM. Insert, western blot analysis of NBS1 and CtIP protein levels upon depletion with siRNA.
B) Side views of the CA-CCpep-CNNT and CA-CCCT complexes. The RG loopCENP-A binding site in each complex is indicated by a dotted circle.
F RNA-binding protein immunoprecipitation assay of piRs-3-I2 and piRs-3-I3 in Piwi1 immunoprecipitates from brain tissue extracts (n=6 biological replicates). Normal mouse IgG was used as a negative control.
I) Representative image of PDE4A expression in CD25+/CD54+ and CD25-/CD54- IL-15 activated NK cells. Scale bar: 10 µm.
(A) Average number of LGG-1::GFP-containing puncta in N2 wild-type animals (WT) fed either control bacteria or bacteria expressing daf-2 (as a control) or rab-10 dsRNA for two generations. p < 0.0001 for either daf-2 or rab-10 RNAi treatment compared to control RNAi treatment, unpaired, two-tailed t-test. n, total number of seam cells observed. Error bars: ±SEM. See Figure 1 for details. Please see Table S1 for quantification of all data.(B) Average number of LGG-1::GFP-containing puncta in rab-10(ok1494) mutants compared to N2 wild-type animals (WT), p < 0.0001, unpaired, two-tailed t-test. n, total number of seam cells observed. Error bars: ±SEM. Please see Figure 1 for details. Please see Table S1 for quantification of all data.
D In vivo ookinete differentiation in midgut of the infected mosquitos. Right panel indicates the parasite smear stained with Giemsa solution. Values are means ± SEM (n=3 biological replicates), two-tailed t test, **, P<0.01. Scale bar = 5 μm.
(I and J) Western blotting on extracts from mouse intestinal epithelial tissue demonstrated increased p62 and LC3‐II protein expression 2 (I) and 4 (J) days post β‐catenin deletion in β‐catenin−/lox‐villin‐creERT2 mice compared to control β‐catenin+/lox‐villin‐creERT2 mice.Source data for this figure is available on the online supplementary information page.
(F) IL-1β levels in supernatants of starved tandem HeLa cells reconstituted with flag-pro-IL-1β and myc-Caspase 1 as in E.
(D-F) p62 aggregates are detected in neurons (arrows; D) and oligodendrocytes (arrows; E) but absent from astrocytes (F) in Epg5−/− mice.
B. Cell cycle distribution of trisomic and wild-type ES cell lines. The percentage of cells in G1, S, and G2/M phases was determined via flow cytometry. Error bars, ±S.D. n=3. * P < 0.05, ** P < 0.01.
HEp-2 cells were incubated with 20 µg/ml of whole cell extract of Y. pseudotuberculosis expressing CNFY, the toxin variant mut1: CNFYI535L/P536A/V537G or mut2: CNFYI535L/P536A/­V537G/F539L/­D541A/K542A or no CNFY protein (empty vector). The cell nuclei were stained with DAPI (blue) and the actin cytoskeleton was stained using FITC-phalloidin (green). The results indicated the formation of polynucleated cells and stress fibers only in cells treated with CNFY and CNFYI535L/­P536/V537G. The white scale bar is 20 µm.
D LC3 immuno-EM analysis of HC and DM platelets. Arrows indicate immunogold-labeled LC3 clusters. No clusters were found in HC platelets. Representative areas of clusters of gold labeling in DM patients (DM1-3) are presented. Shown in the insets are enlargements of the gold clusters adjacent to mitochondria-like structures.
A) Gene ontology enrichment analysis showing immune system process (GO:0002376) pathways for genes with >1.5 fold-change expression between IL-15 and IL-2. The color of the nodes is determined by the significance of the enriched term assessed by 2-sided hypergeometric test with Bonferroni's step-down method for P value correction.
J. Confocal images of control and U18-treated GFP11-SAC1 HEK293 cells (top) and control and NPC1I1061T patient fibroblasts immunolabeled with anti-SAC1 antibody (bottom). Insets show an enlarged view of SAC1 centered on a perinuclear region. K. Quantification analyses of GFP11-SAC1 (top; Control: n=10; U18: n=10) and anti-SAC1 (bottom; Control: n=7; NPC1I1061T: n=8) mean fluorescence intensities in Golgi normalized to the cytoplasm.
(C) Western blot showing that Hel2(1-315) is defective in RQC but not in NGD. The arrest products derived from the R(CGN)12 reporter in ltn1∆ cells expressing truncated Hel2 mutant protein were detected with an anti-GFP antibody.
Growth of B16 melanoma xenografts in siblings of Ifnar1+/+, Ifnar1+/- or Ifnar1-/- mice. Treatment started 10 days after tumor cell implantation. BO-110 was administered at 0.8 mg/kg, every third day for 2 weeks. N= 6 mice per condition. Graphs show the mean tumor size ± SD at each time point. Statistical significance was determined by Two-Way ANOVA.
HeLa cells with or without transient expression of H2B-GFP or EGFP-TOP2A were exposed to nocodazole for 3 hr. Mitotic cells were cytospun onto coverslips and Lysates of asynchronous cells were immunoblotted (D). * represents non-specific bands.
(F) Identification of the domains of CP110 mediating its interaction with ENKD1.
The human breast cancer cell lines MDA-MB-231 and MDA-MB-231-V5-SLC1A3 cells were intravenously injected into pretreated NSG mice. Once mice showed breathing problems, they were sacrificed, and lung and liver were collected and blindly scored for metastasis lesions. The p-value was calculated by one-tailed unpaired t test in Prism7. Data are presented as mean ± SEM (n=8). Data information: The pretreatment started 2 days before the injection of cancer cells. And mice were either injected with 60 U ASNase or saline per day. The p-value was calculated by two-tailed unpaired t test in Prism7, unless otherwise stated. *p<0.05, **p<0.01, ***p<0.001.
(a) Schematic showing three levels of repression. A small guide RNA (sgRNA) directs deactivated Cas9 (dCas9) to block transcription from a promoter. sRNA binds to the mRNA and promotes degradation by recruiting Hfq. The mf-Lon protease targets a tag (blue) added to the protein. The protease is also targeted to itself to reduce toxicity (Methods)
A. qRT-PCR analysis of RNA samples from normal human skin (NS) and AK for activin βA (INHBA), normalized to hypoxanthine phosphoribosyltransferase (HPRT). Expression levels in one of the normal skin samples were set to 1. Scatter plots are shown. NS: N=4; AK: N=21. ns = non-significant (Mann-Whitney test).
A-C: GFP-MOSPD2 (A and C expressing cells were transfected wit Flag-STARD3NL ∆FFAT (C), and labelled using anti-Flag (magenta) and anti-Lamp1 (late endosomes/lysosomes marker; red) antibodies. The subpanels on the right are higher magnification (3.5x) images of the area outlined in white. The Overlay panel shows merged green and magenta images. Scale bars: 10 µm
(B) Interaction of SCOC with UVRAG is unaffected by FEZ1-GFP. As in (A), co‐immunoprecipitation was preformed in HEK293 cells transfected with FLAG-SCOC, Myc-UVRAG and FEZ1-GFP. Myc-UVRAG was detected as in (A), FEZ1-GFP was detected with anti‐GFP antibody.
C Schematic model for PI(4,5) P2 induced FAK activation in focal adhesions. Locally increased concentration of FAK upon focal adhesion targeting promotes formation of FERM mediated FAK dimers. Binding of FAK dimers via their KAKTLRK basic region (dark blue) to PI(4,5) P2 rich membranes in focal adhesions causes dissociation of the autoinhibitory interaction between the FERM and Kinase (KIN) domains (step 1). The released kinase domains reorient to interact via their own basic residues with the membrane (step 2). This aligns a large surface (F-K', K-K' and F'-K in Fig.2a) for formation of the symmetric dimer and exposes the autophosphorylation site for efficient trans-autophosphorylation across the symmetric dimer (step 3). Src is recruited to the autophosphorylation site and phosphorylates Y576 and Y577 in the activation loop (A-loop) of FAK to induce catalytic activation of FAK (step 4). Possibly an additional mechanism is involved in removing the kinase domain from the membrane to expose the Src phosphorylation sites, thereby potentiating the activating step 4 (see text).
Immunoblots and quantification of indicated proteins in DC fibroblasts treated with DMSO and with 2 μM ATM inhibitor, KU-55933 for 48 hours. Mean (± SD) quantification values of three DC lines with and without ATMi treatment are shown. P values on the basis of Student's t test.
D-E. Representative pictures of Peyer's Patches (D) and quantification of lymphatic vessel density (E) in Casp8WT, Casp8ECko and Casp8ECko/MLKLko mice injected with TNF-α (n=7 WT, 5 ECko, 15 ECko/MLKLko. Peyer's Patches are pooled from 3-5 mice per genotype). Scale bars: 200µm. Data information: All data is shown as mean ± SEM. * P<0.05, *** P <0.001, **** P <0.0001; ns: not significant.
(c) Staining with CTIP2 and TBR1 antibodies shows TCF20 knockdown decreases the colocalization of CTIP2 and TBR1 with GFP in E13.5-E16.5 brains. White arrows represent CTIP2, GFP double-positive cells. White arrow heads represent TBR1, GFP double-positive cells. (d, e) Statistical analysis of CTIP2, GFP and TBR1, GFP double-positive cell ratio in GFP positive cells. n=3 brains. Data information: Error bars represent the means ± S.E.M. Two tailed unpaired T-tests were used to analyze the data, n.s. (no significant difference), p<0.05(*), p<0.01(**), p<0.001(***). Scale bar: (d) 50 μm
(F) Representative images of organoid formation from indicated ISCs were shown (upper panel). Scale bar, 200 μm. Organoid formation ratios was shown as means ± S.D. ** p<0.01 by two-tailed Student's t-test. (lower panel). n=6 for each group. GW501516 (10 μM) were added directly into organoid culture medium.