EMBO/sd-character-level-ner huggingface dataset:
(A) WT and atg1Δ cells grown in YEPD medium were transferred to SD-N +50 mM MES-KOH (pH 6.2). After 120 hours, cultures were diluted 5.0×105 fold and plated onto YEPD agar. The plates were incubated at 30°C for four days. Insets indicate the plate overlaid with TTC agar to examine the respiratory competency of formed colonies.
TCGA data were analyzed to reveal the effect of high mRNA levels of key FAO enzymes on the overall survival of patients with melanoma. Statistical significance of survival was evaluated with a Log-rank (Mantel-Cox) Test (n=449, 450 and 459 for HADHA, HADHB and ECHS1 respectively).
Superposition of Sir4 H‑BRCT (orange) onto the Dbf4-Rad53-CDC7 complex (cyan, grey, blue) (PDB 5T2S) in two orientations rotated by ~180° around a vertical axis. Helices are displayed as barrels and protein-protein interfaces between Dbf4 and FHA1 of Rad53 are highlighted with dashed circles in black (interface I) and blue (interface II).
A. Schematic diagram of the I-PpoI system for inducing DNA breaks in the nuclear human genome. Addition of 4-OHT to U-2-OS-pEP15 cells stably expressing the I-PpoI endonuclease fused to the estrogen receptor (ER) induces nuclear translocation of the fusion protein and cleavage cleavage of FokI recognition sites in nuclear DNA resulting, leading to DSB induction.
Schematic drawing of FACS-based pooled shRNA screen of molecules that affect the YAP/TEAD signaling pathway in 8×GTIIC-EmGFP 293T cells.
(F) Quantification of the highlighted genes enriched in either the somata or processes at the transcript or protein level. (Upper row: Scatterplots of transcript level; n=2; crossbar represents mean. Lower row: Boxplot of protein levels; n=4).
(h) TNF-α and IL-6 levels in faecal samples from mice on the indicated diet demonstrated no colitis in all mouse groups. IL-6 and TNF-α protein production levels, as determined by performing enzyme-linked immunosorbent assays. Data information: All data shown are representative of at least three independent biological replicates.Error bars indicate SD (n=3). ****P-value < 0.0001 ***P-value < 0.001; **P-value < 0.01; *P-value < 0.05; NS: no significance (One-way ANOVA).
(F) Xenopus egg extract were supplemented with 5 µM RanQ69L, RCC1, Xenopus Nup50 wild-type and RCC1 binding mutants as well as a combination of 5 µM Nup50 and 5 µM RCC1. After 90 min, annulate lamellae were isolated by centrifugation and quantified by western blotting with mAB414 antibody. Quantitation shows the relative Nup62 signal as a mean from three independent experiments, normalized to the buffer control. Individual data points are indicated.
A. qPCR analysis of PAQR3 expression in a CHD7-mutation positive patient compared to parental controls set (N=4; ****p<0.0001; Student's t-test). Fold change was calculated according to the 2(−ΔΔCt) method, using HPRT1 and RPS1 as housekeeping genes for normalization. All data were expressed as mean fold change ± SD across replicates, relative to control parents set to 1 (dotted line), N is the number of experimental repeats.
(C) GST-GSDMD, His-tagged nucleocapsid and control GST-3C protease (GST-3Cpro) were purified from E. coli BL21, followed by a GST-pulldown assay. Input and precipitates were visualized by Coomassie blue staining.
B. Left: averaged Nanoparticle Tracking Analysis displaying the size distribution of EVs isolated from media of MDA-MB-231 cells expressing Control (pcDNA3) or FLAG-RASSF1C plasmid. Inserts: transmission electron microscopy images of single EVs. Scale bars represent 200 nm. Right: quantification of total secreted EVs (96 h, top) or at indicated times (below), as measured by NTA. Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, **** p ≤ 0.0001.
Overexpression of LOC113230 inhibited cell migration in SW-1116 and HCT116 cells. Cell migration was detected by transwell assays. Scale bar represents 100 μM.
Solubilized mitochondria from MITRAC12FLAG- or ACAD9FLAG-expressing cells were subjected to anti-FLAG immunoisolation and native elution. Eluates were analysed by 2D-BN/SDS-PAGE and western blot analysis. Total 0.8 % (MITRAC12FLAG isolation), 0.35 % (ACAD9FLAG isolation), Eluate 100 %.
(Left) Western blot analysis of large scale HALO-NEDP1 pulldowns from HEK 293 NEDP1 KO lysates. (Right) Diagram of mass spectrometry sample preparation.
Identification of the potential LncRNAs repressed by Snail from CRC metastatic tissue by using bioinformatics approach to analyze the promoter regions of lowly expressed LncRNAs, and 26 LncRNAs were discovered due to their promoter regions containing multiple copies of E-box elements, among which LOC113230 contained 7 E-boxes in its proximal promoter region.*: previously reported LncRNAs in cancers. P-value by Student's t‐test.
E. PCM1 siRNA-treated U2OS cells were transfected with two types of plasmids (EGFP- and mCherry-tagged) that produce PCM1-WT* and PCM1-S372A*. Immunoprecipitation and subsequent immunoblotting were performed with the indicated antibodies. Quantification data is shown on the right. Statistical analysis was performed using two-tailed unpaired student's t-tests. *p<0.05, **p<0.01, n.s. not significant.
(C) EUC1 overexpression is toxic at elevated temperatures and upon exposure to the membrane fluidizing drug benzylalcohol. For (C, D, F), serial dilutions of the indicated strains were spotted and grown on YPD control (or selective media) plates or under conditions as indicated. See also Fig. EV4A-B.
(B) Quantification of AQR position in WT and knock-in animals that harbor mig-2S139 point mutations. N = 100 - 111. ***, P < 0.001 by Fisher's exact test.
A. Simplified scheme of upstream regulation of the TCA cycle. Arrows indicate activation and bar indicates repression. TCA = Tricarboxylic acid cycle, PDC = Pyruvate dehydrogenase complex, PDK = Pyruvate dehydrogenase kinase.
Schematic of the chemical genomics screen; each strain's KO library was robotically plated on 1536 solid agar plates and each KO colony size was used as a proxy for fitness in each condition.
(B) Network of the genes dysregulated in TG-PBS and significantly rescued in TG-Ova-(GA)10.
(D) Representative images of EdU (red) and DAPI (blue) staining at 5 dpa. (E) The graph represents the mean +/- SD of EdU+ cells over the total number of cells in the spinal cord of 5 to 12 tadpoles. Each data point represents a tadpole, with an average of 9 sections analysed per animal.
GSEA showing significant enrichment of four distinct signatures of mammary stem cells within data sets from MDA231-LM2 cells either expressing MKK7-JNK or treated with JNKi. Mammary stem cell signatures are indicated as follows: a, up in mammary stem cells b, up in fetal mammary stem cells ; c, up in adult mammary stem cells and d, up in mammary repopulating units
B. Volcano plots showing differential protein expression 1hr and 24hr after ALKAL2 +/- lorlatinib stimulation as indicated. Dashed lines indicate differential expression thresholds. Differentially expressed proteins indicated in blue. Most pronounced responding proteins indicated in black and labelled.
G. Immunofluorescence staining of CLIMP63 (green) and lysosomes (TMEM192-HA, red) in RCS chondrocytes with indicated genotypes (ctrl=wild type) upon FGF18 treatment (50 ng/mL for 16h). BafA1 (100 nM; 4 hours) was used to inhibit lysosomal degradation; scale bar 20 μm. Insets show magnification of CLIMP63 accumulation into lysosomes; scale bar 2 μm. Quantification of CLIMP63 fluorescence intensity into TMEM192-HA decorated lysosomes. Mean +/- standard error of the mean (sem) of N=3 biological replicates. n=10 cells/experiment were analyzed. Analysis of variance one way (ANOVA) p=1.55e-7; Tukey's post hoc test ***p<0.0005; NS not significant. H. EATR assay in RCS with indicated genotypes (ctrl=wild type) showing % of cells with acidified ER by FACS analysis. FGF18 was used at 50 ng/mL for 16 hours. Mean +/- standard error of the mean (sem) of N=4 biological replicates/treatment/genotype. Analysis of variance one way (ANOVA) p<0.0001; Tukey's post hoc test ***p<0.0005; NS not significant.
D. A representative example of an adult female posterior midgut at low (A) and high magnification (B, Region 4-Region 5) showing the initiator caspase reporter DBS-S-QF (Red, immunostaining anti-HA) after 16 hours of paraquat treatment in Oxford food at 25 Co; note the expansion of the labelling with DBS-S-QF to large intestinal cells (ECs) (compare D with A). The image on the left was acquired at low magnification with the 10x objective, while the right panel was acquired using the 40x. White dotted line outlines the gut using DAPI staining as a reference. Genotype: y1 w1118 UAS-mCD8::GFP.L QUAS-mtdTomato-3xHA Act-DBS-S-QF (BL83131)
DNA sequence tag density plots from ChIP-Seq assays of RUNX1, ETS1, STAT5 and JUND in TB IL-2, and STAT5 and JUND in TB IL-2nil ordered as in (D).
PET summation images (0-90 min) in horizontal (upper panel) and coronal view (lower panel) depicting [11C]Erlotinib distribution in one H2-c-fosLTR/Egfrwt mouse (M125). Anatomical structures are labelled with arrows (T, tumor; L, liver; H, heart; B, brain). Scale bars: 1cm Concentration-time curves of [11C]Erlotinib in bone tumors in right scapula of three H2-c-fosLTR/Egfrwt mice measured with PET. Broken line indicates threshold for in vitro effect of Erlotinib (1 µM)
A Immunoblot of endogenous BiP resolved by native-PAGE from lysates of CHO-K1 S21 wild-type (wt) or FICD-/- cells either transiently overexpressing wild-type FICD (high expression level; Hi) or mutant FICDE234G (E/G) or stably expressing recombinant wild-type FICD (low expression level; Lo). The cells in lanes 1-4 were mock transfected. Where indicated cells were exposed to cycloheximide (CHX; 100 µg/mL) for 3 h before lysis. Unmodified ('A') and AMPylated ('B') monomeric and oligomeric (II and III) forms of BiP are indicated. Immunoblots of the same samples resolved by SDS-PAGE report on FICD, total BiP and eIF2α (loading control). Data representative of four independent experiments are shown.
F WB analysis of pep-AP, TALDO1, PARP, cleaved-PARP and cleaved-caspase-3 within the tumors in C(a).
Fold change in gene expression in TB+ IL-2 cells for Jund -/- compared to Jund+/+ mice. Data from 2 replicates are shown.
(B) Amino‐acid sequence of NAF‐1. Peptide sequences identified by mass spectrometry are indicated by a double underline. The TM domain is indicated by a bold single underline. Cys residues in the cytosolic domain are denoted with asterisks (*). The CDGSH domain is highlighted in grey, and the predicted 2Fe‐2S coordinating Cys‐3‐His‐1 aa are marked in bold. A downwards arrow head (∨) represents the site in which a Flag epitope was inserted. A double‐lined arrow (⇓) indicates the Glu residue that when mutated (E37Q) causes WFS2. Predicted phosphorylation sites found using the PhosphoMotif Finder from the Human Protein Reference Database (HPRD) are indicated in bold within a box; β‐adrenergic receptor kinase substrate motif (aa 25-29), PKA and PKC kinase substrate motifs (aa 32-34 and 67-69), and casein kinase II substrate motif (aa 34-37).
G) Representative single section of CellROX-DeepRed fluorescence in ES and 2-cell-like cells (green arrow) obtained using live cell microscopy. Scale bar, 10 μm. n, indicates the number of independent replicates. Representative images from 3 independent biological replicates are shown.
(A) H1299 neo and HA‐BCL‐2b5 cells treated with control (CTRL) or NAF‐1 shRNA were either mock infected or infected with Ad‐BIK in the absence or presence of 50 μM zVAD‐fmk. Cell lysates were analysed by immunoblot.
C. Long distance (blue) and within distance (pink) between residue pairs were mapped into one of the states of the proteasome (4cr2) showing the accumulation of those into the base of the complex. Residue pairs satisfying other states are represented in yellow. The bar plot shows the distribution of all residue pairs in the complex showing that long distance links locate mainly in the base.
Based on the FACS results, the expression of Oct4GFP and E-cadherin was summarized in Oct4GFP+E-cadherin+ cells (B) and in Oct4GFP-E-cadherin- cells (C).
M238P cells were transfected separately with miR-143-3p, miR-145-5p or a negative control (miR-neg) mimics and RNA content was analyzed using whole genome microarrays (dataset 1, n = 2). (A) Heatmap showing the genes differentially expressed after individual miRNA mimic overexpression.
(C) Euc1 Slx5-binding mutations (SBM1/SBM2) reduce/abolish ub-HSs and recruitment of Slx5 to ub-HSs. ChIP-qPCR for ub-K48 (top) or Slx5 (using Slx5 antibody, bottom) in euc1∆ ubx5∆ cells expressing the indicated constructs from plasmids under the control of the EUC1 promoter. Data represent means ± SD (n = 3). See also Appendix Fig. S7E-G.
(D) Line graph showing the change in the average normalized FUNCAT intensity representing the quantity of newly synthesized proteins at various time points following DHPG and NMDA treatments. Data presented as mean +/- SEM. Data points in all groups were normalized to the average of the basal group. ***p<0.001 n= 21-54 neurons per group from 3 independent platings.
(A) A cartoon and corresponding immunofluorescence image depicting the Drosophila germarium. Terminal filament cells (TFC) and cap cells (CapC) create a niche for female germline stem cells (GSC), which divide asymmetrically to self-renew and produce a cystoblast (CB). The CB undergoes four mitotic divisions to create differentiating cystocytes (CC). The germline (gray) is supported by somatic (green) escort cells (EC) and follicle stem cells (FSC) that produce follicle cells that surround developing egg chambers. The spectrosome (Spec, red) is a specialized organelle in the early-stage germline, such as GSCs and CBs. The spectrosome structure is round while fusome is branched, which branches over the mitotic divisions in further differentiated germ cells, connecting the CCs within a cyst.
(C) Co‐immunoprecipitation of NAF‐1‐Flag and HA‐BCL‐2b5. Lysates from H1299 HA‐BCL‐2b5 cells infected with Ad‐NAF‐1‐Flag were collected and treated as in (A).
Kaplan-Meier analysis of CD45.2 C57BL/6J mice injected i.v. with murine MLL-AF9-transformed AML blasts (day 0) and treated with ara-C and/or HU days 20-24. n = 5 per treatment group, except for vehicle (n = 4).
D Ratio of toxicity and viability of U87 spheroids (3D) treated as indicated (NEN 1.2 µM, Domperidone (Domp), Imipramine (Imi), Amitriptyline (Ami), Desipramine (Desi), each 30 µM, Clomipramine (Clomi 20 µM, Cyclodextrin (CD) 0.75%). Data information: , data are presented as mean (SD) (N=3) and were analyzed by a one-way ANOVA with Tukey post-hoc test or a two-way ANOVA with Tukey post-hoc test * p< 0.05; ** p< 0.01;*** p< 0.001; **** p < 0.0001.
Rotavirus RNAs have a 5′ cap but not a 3′ poly(A) tail. Its NSP3 protein (instead of PABP) binds to the 3′ end of the viral mRNA and interacts with eIF-4G directly to maintain the closed-loop RNA for the initiation of viral RNA translation and to block host mRNA circularization (Piron et al, 1998)."
B, Cells were treated as in A, but over an extended series of time points. RNA was isolated and subjected to qRT-PCR against the indicated transcripts. Three independent experiments are represented as mean ± SEM.
1205Lu cells were exposed to 3T3-F442A EV (3T3-EV) and treated, or not, with Mdivi-1. Cell migration was then evaluated in Boyden chamber assays (left panel; n=6). Right panel, 3T3-F442A EV were added to 1205Lu cells, which were immediately treated, or not, with Mdivi-1. Cell motility was then tracked by video microscopy (n = 40 cells per group) (right panel).
E: Heat map showing depletion of shRNAs targeting Cdc and Cdk genes in all day 20 samples.
1205Lu cells exposed to 3T3-F442A EV were stained with a MitoTracker probe. Then, cells were fixed and stained with BODIPY before observation by confocal microscopy. A zoomed crop of the area containing mitochondria and lipid droplets in a membrane protrusion is shown (scale bar: 5µm).
(A) Overall survival analysis of mice bearing Daoy cell line expressing SOX9 with doxycycline (dox) -inducible FBW7α ( Daoy-SOX9/T-FBW7α). The dox-preconditioned or the control cells (105cells) were orthotopically xenografted to the cerebellum of 6-weeks old Athymic Nude-Foxn1nu mice, which were continuously fed with either the dox-containing chow (red line) or the regular chow food (green line), respectively. Micexenografted with dox-preconditioned Daoy-SOX9/T-FBW7α and fed continuously with dox-containing chow (red line) survived longer (p= 0.0285) than the control group (green line)
H. Micron IV infrared and fluorescein in vivo imaging of naïve mouse fundus and following laser-induced CNV at D0, D3, D7, D14.
(B) Intensity profiles showing abundance and relative distribution of structural subunits from CI (upper graphs), CIII (middle graphs), and CIV (bottom graphs). The identities of MRC complexes and SCs are as in Figure 1.
(J-K) Sirt5 KO mice are more sensitive to Paraquat-induced nigrostriatal dopaminergic degeneration. Female Sirt5 KO and WT littermates were treated with paraquat as in (G-I). The brain sections were stained to detect tyrosine hydroxylase (TH) positive dopaminergic neurons in the SNc region, as described in 'Materials and Methods'. Representative immunohistochemistry images (original magnification, 100×; scale bar, 100 μm) and the corresponding quantifications are shown in (J) and (K), respectively. The results are average ± SD. *p<0.05, n.s.: not significant (two-tailed unpaired t-test).
A and B. Proliferation curves of SKBr3 cell line knocked-down for YAP (A) or p53 (B). si-GFP oligos are used as negative control.Cell viability analysis in A and B was determined by trypan blue dye exclusion staining, in C was determined by ATPlite luminescence analysis. All the values are means + s.d. of six replicates from three independent experiments.
TCLs from MEFi were analyzed by immunoblotting for β-catenin, PPARγ, ATGL, MGLL and β-tubulin. Results are representative of three independent experiments.
(b) Secondary siRNA screening analysis was performed on candidate RAB GTPases selected from the primary screen using 3 individual deconvoluted siRNAs. Data are mean ± SD (n> 5 different fields/experiment).
(C) Histopathological evaluations in lungs from four groups of macaques at day 29. Lung tissue was collected and stained with hematoxylin and eosin.
Protein levels of LC3 I/II in METTL3-knockdown SMMC-7721 (B), Bel-7402 (C) cells under hypoxia condition for 48h.
(A) Diagram showing the experimental procedure for the evaluation of the effect of Palbociclib on the autoinflammatory disease in Trex1-/- mice.
(A) ARPE-19 cells infected with either adenovirus expressing TFE3-WT-Myc or TFE3-S321A-Myc for 16h. Cells were fixed, permeabilized and stained with antibodies against Myc. Scale bar, 10 µm. Quantification of the percentage of ARPE-19 cells with nuclear TFE3-Myc (means ± SD of 3 independent experiments, students t-test, ****p < 0.0001; n>400 cells per condition).
Effect of recombinant HPV16 E6 protein on the proliferation of HT3 cells. Each point represents mean ± SEM (n = 5). ***P = 0.0001 compared with control (Ctrl) on day 4. HT3 cells were cultured in serum-reduced medium in the presence or absence of recombinant HPV16 E6 (400 nM).
B. The Pearson correlation analysis of RNA-seq results of human oocyte samples from control and U0126 group (n=2 sample for each group). Scale bar indicates the range of the correlation coefficients (r) displayed.
E. Gelatine zymography assay shows downregulation of MMP-9 metalloprotease in MDA-MB-231 cells over‑expressing RASSF1C.
F IFNβ1 luciferase assays of HEK293T cells with transfection of AKT2/AKT2-T309A/S474A and TBK1 (n=3) or infection of VSV (n=3). Data information: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 and ns, not significant (P > 0.05); using a one-way ANOVA test Data are from three independent experiments Error bars , mean ± SEM
(e) Auto-correlation analysis of detrended Venus::HES5 spatial profile in (c) with multiple peaks indicating spatial periodicity; significant peaks (red arrowhead) lie outside gray area indicating 95% significance based on bootstrap approach (see Materials and Methods) and non-significant peaks (black arrowhead).
D Heatmap of force-dependent in-situ affinities AcKa of NKG2D binding with different ligands.
D. Interaction of AAR2 and PRP8 in human cells. HA‑tagged PRP8 (aa1755-2335) was co-expressed in HEK293 cells with either wildtype AAR2, AAR2(S284A) or AAR2(S284E) mutant versions. Immunoprecipitation of PRP8 led to a co-precipitation of wild typeAAR2 and phospho-null AAR2(S284A). In contrast, the phospho-mimicry AAR2(S284E) version did not bind PRP8.
(b) MEFs as in a were treated with CCCP (30 μM) for the indicated times and then subjected to immunoblot analysis.
LMS (red) and HMS (black) gene expression quantification in Epi cells by random-primed RT-qPCR relative to RPL11 and represented as log2 fold change to CTR. Each dot corresponds to an independent replicate, bars represent Mean ± Standard Deviation values.
(a, b) MCF-7 cells were cultured for 24 h following siRNA with or without FBS before western blot analysis (a) and cell-viability assays (b).
DC3.2-Rab39a cells (Rab39a KO with dox-inducible Rab39a) were incubated overnight with or without 1 µg/ml dox to induce Rab39a expression. 1x105 cells were then fed with Ova-Fe and exposed to reporter T cells as in (A). Error bars show SD of duplicate wells. None of the bead concentrations are p < 0.05 for Rab39a siRNA vs β2m using two-way ANOVA. Representative plot of 3 independent experiments
F) Comparing activity of USP1WT and USP1ΔL1L3 on a peptide substrate i.e. LRGG-AMC (100µM). USP1ΔL1L3 cleaves the peptide substrate more efficiently compared to USP1WT (n=2, technical replicates).
(M) Hif1α protein level was detected by Western blotting in YY1iKO vs Ctrl ASCs. β-actin was used as the loading control.
Histology and IHC study on postmortem lung sections from rhesus macaques infected with live SARS-CoV. All animals were euthanized 7 days after viral challenge, and anti-SARS-CoV monoclonal antibody was used to identify SARS antigens in the tissue. Representative data from lung sections were shown. Histology samples include: a. Control group. b. High-dose group. c. Placebo group. The arrowheads point to alveoli space filled with proteinaceous fluid. IHC samples include: d. Control group. e. High-dose group. f. Placebo group. Arrows point to cells that were positive for SARS antigen expression.
At 2 days post-fertilization (dpf),Lyz:dsRed or mpx:GFPlarvae were transferred into DMSO ctrl or FK506 (1 μg/ml) containing 0.5 × E2. At 3 dpf, zebrafishlarvae were microinjected with AFeGFPconidia into the hindbrain and mortality, and fungal burden and neutrophil recruitment were assessed.A, B Absolute neutrophil numbers in treated and untreated mpx:GFPlarvae were quantified by direct counting of fluorescent neutrophils in non-infected whole fish (n = 11-13 per group). There were no significant differences.
A-I. Dye release time courses from liposomes as a percentage of maximal release. E. Two different sets of reactions, where wild type GSDMD (dark to light orange) and the mutant GSDMDI104N (dark to light blue) were independently incubated at the concentrations of 260, 130 and 65 nM with 5 nM caspase-1 and 400 μM 6-carboxifluorescein-loaded liposomes. The time point of 60 minutes is highlighted by a vertical dashed line.
(D) CASPASE 3 (red) staining in shScr, sh1 and sh2 at day 5 of neuroectodermal differentiation. Nuclei were counterstained with DAPI. Scale bar, 20 µM.
B Schematic representation of the exon 1 nucleotide sequence of zebrafish grk2 gene targeted by the ZFN.
Average number of 2W1S-specific cells recovered/mouse after sorting 3 replicate samples of Il7rf/f compared to CD4creERT2 x Il7rf/f . Errors bars indicate the standard deviation.
PL45 stably expressing Dox-inducible TGIF1 were treated with vehicle or Dox for 48 hr and analyzed for binding of TGIF1 to the Twist1 promoter by ChIP and agarose gel.