EMBO/sd-character-level-ner huggingface dataset:
(A) K-fibers are connected to MTOCs and extend to spindle poles. Oocytes 6 hours after NEBD were fixed following cold treatment. Microtubules (α-tubulin, green), MTOCs (pericentrin, magenta), kinetochores (ACA, red) and DNA (Hoechst333342) are shown. Five oocytes from 2 independent experiments were analyzed. Scale bar, 10 μm.
(F) Representative model of a cross section of a centriole's proximal region. Colored arrows indicate the different structural features identified.
B. Up- (red) and down- (blue) regulated genes identified in A549 cells following treatment with 100 IU/mL IFN-α2 for 6h: ISGs were defined as induced by IFN-α2 with FC>2, p-value ≤ 0.001.
(g) Immunoprecipitation of LETM1-GFP with anti-LETM1 failed to pull down MCUR1-Flag in transiently transfected COS7 cells.
A) Scheme of the procedure before DNA spreading. Cells were treated for 1.5 hours with 20uM MRe11 inhibitor (Mirin), before sequential addition of IdU and CldU for 20 minutes each.
(E) The 614 KAP1 common binding sites (see Fig EV2D) were interrogated for their nearest gene and this gene list was converted to DAVID IDs and used for gene ontology analysis. 4 gene clusters were significantly enriched (p-value <0.05, drawn on the plot as a dotted line): zinc finger proteins (p=1.1 x 10-19), fibronectin folding (p=0.016), protein phosphatase (p=0.033), and synapse (p=0.047). Venn diagrams on the right show numbers of KAP1-bound loci, ZNFs and KZNFs and the overlap.
C) Pulldown assays were performed by using purified GST- LC3 (A, B and C) isoforms, each incubated together with empty vector (EV) or HA-TFGwtLIR or HA-TFGmutLIR3 transfected HeLa cell lysates respectively. Ponceau staining reports GST-LC3 isoforms and GST-GFP used as a negative control. WB analyses show HA-TFGwtLIR or HA-TFGmutLIR3 in the pulldown and in total extracts (Input). Densitometry analyses of HA-tagged TFG normalized over GST-tagged LC3 isoforms (Ponceau) were performed and reported (right). Data are mean value ± SEM. Statistical analysis was performed by multiple t-test. *, P<0.05; ns, not significant. (n=3 independent experiments).
(D) HEK293T cells were transfected with HA-cGAS (WT or C474S mutant) (200 ng), Flag-STING (200 ng) and Myc-ZDHHC18 (200 ng) expression plasmids for 24 h before luciferase reporter assays. Data information: Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; **, P˂0.005; ***, P˂0.001 (D
B. Top graph: analysis of Golgi P4M-YFP intensity normalized to the cytoplasm in control and NPC1I1061T patient fibroblasts and NPC1I1061T fibroblasts lacking either ACBD3 ('sgACBD3'), PI4KIIα ('sgPI4KIIα') or PI4KIIIβ ('sgPI4KIIIβ'). Control: n=9; NPC1I1061T: n=12; NPC1I1061T + sgACBD3: n=9; NPC1I1061T + sgPI4KIIα: n=5; NPC1I1061T + sgPI4KIIIβ: n=8. Bottom graph: analysis of P4M-YFP intensity in endomembrane compartments normalized to the cytoplasm in NPC1I1061T patient fibroblasts. NPC1I1061T: n=406; NPC1I1061T + sgACBD3: n=172.
(D) LN229 cells stably transduced with indicated shRNAs targeting NEDD4L or a scrambled shRNA were detached by trypsinization (see Methods) and subjected to western blotting. The ratio of mono-ubiquitinated to native Merlin in each lane was quantified by Image J and is shown under the blot.
(B) Lung histology in B6.K18-hACE2IP-THV mice, vaccinated with LV::S after SARS-CoV-2 inoculation. H&E (rows 1 and 3) (scale bar: 500 μm) and NCoV-2-specific IHC (rows 2 and 4) (scale bar: 50 μm) staining of whole lung sections (scale bar: 50 μm) from the primed (i.m.), boosted (i.n.) and challenged B6.K18-hACE2IP-THV mice compared with their sham controls. H&E and NCoV-2-specific IHC were performed on contiguous sections. The IHC fields correspond to the rectangles in the corresponding H&E images above them. A representative NCoV-2-specific IHC on a lung section from a non-infected (NI) mouse is also shown.
(E) Phylogenetic tree based on 31 biallelic SNPs in pyk1 and in 500bp up- and down-stream regions. Strains carrying the common A-allele are in orange, while strains carrying the unusual T-allele are in blue Strains JB22 and JB50 (underlined and bold) refer to heterothallic and homothallic versions of the laboratory strain, respectively. The pie chart shows the relative allele frequencies at the genomic locus across all wild strains. Genotype calls at the locus were checked manually and were conclusive, i.e. no strain produced reads with both alleles.
E. AP staining of the primary cultured teratomacells derived from trisomic and wild-type ES cells. Ts6, Ts8, or Ts11 ESC teratomacells grew ES-like colonies that were stained positive for AP. Scale bar, 200 μm.
Figure 6: Prmt1 regulates similar and overlapping transcriptional programs mediated by β-catenin in LSK-MLL-ENL cells. (A) Heatmap analysis and Venn diagram showing the commonly regulated genes after the loss of function of Prmt1 and β-catenin in Hoxa9-/- LSK-MLL-ENL cells.
B. Home cage-activity test. Spontaneous locomotor activity of mice chronically fed chow with or without 0.24% (w/w) lithium carbonate for two months was monitored for 6 days in the home cage.
A mRNA of IFNAR1, but not IFNAR2 or STAT1, was stabilized by RBM47 ectopic expression in 293T cells with or without IFN-α stimulation. Cells were treated with IFN-α or PBS for 6 h, and the relative gene expression levels were determined using qRT-PCR.The PCR results are represented as the means ± SD of n = 3 biological replicates. Data information: The data shown are representative of n = 3 independent experiments. NS, non-significant; **P ≤ 0.01, and ***P ≤ 0.001 (Student's t-test). The data shown are representative of three independent experiments.
(e) Macrophages were incubated with iRBCL 24 h before addition of LPS. Paired t-test was performed to determine statistical significance. Each symbol represents the value obtained for cells from an independent donor in an independent experiment. (e) n=3. Asterisks indicate significance (*p<0.05, **p<0.01 and ***p<0.001) when values were compared RBCL (e).
Western blot analysis of ubiquitin and the autophagy marker LC3 in RIPA, and p62 in RIPA and urea total brain lysates from 4.5-month-old mice with the indicated genotype. Calnexin used as a loading control. (n = 3 biological replicates per genotype). Quantification of B. Protein expression was normalized to levels in wild type animals. Data represent the mean ± SD.
C. HEK293T cells were transfected with indicated siRNAs, followed by pCMV-FL-miR30 (P) reporter with either pSUPER-control or pSUPER-miR30 constructs. RL was co-transfected as internal control. FL/RL luminescence ratio was calculated. Data are presented as mean SD (n = 3), P‐value was calculated using Student's t‐test.
(G) The anti-aggregation activity of tryptophan single mutant (W169S) and double mutant (W169S/W172S) was examined by CHO-induced MDH aggregation assay. Light scattering values were monitored.
qRT-PCR analyses of normalized miR-9 expression, expressed as fold over the untreated condition, in FaDu cells serum starved and then stimulated with 20 ng/ml of Epidermal growth factor (EGF) for up to four hours. Data represent the mean (±SD) of three independent experiments performed in duplicate and one-way ANOVA test was used to verify the statistical significance.
Human to mouse stroma substitution. CD34/CD31 staining for respectively human (h) and mouse (m) blood vessels in original human specimens and paired Ren13 and 28-PDOX are shown (20X). Ren-PDOX OT referred to tumor generated from first implantation of human specimen in mice. Insets show human and mouse kidney as positive/negative controls of staining (20X).
(A) Strategy of conditional knockdown of COUP-TFII in adult mice. A LacZ knock-in allele is inserted into the genomic COUP-TFII locus after the second LoxP site.
(a) DNA methylation differences between stem and non-stem cells and their enrichment within DMRs of different epigenetic mutants using permutation tests (data from Stroud, Greenberg, Feng, Bernatavichute and Jacobsen 2013). Mutants are in alphabetical order according to the gene acronym. Red indicates an enrichment of methylated DNA in the respective context and blue a depletion.
(A, B) Immunoprecipitation with various lipid-coated beads using HeLa NOD1-GFP (A) and NOD2-GFP cells (B). Cell lysates of HeLa NOD1 or HeLa NOD2 cells were incubated with lipid-coated beads at room temperature for 2 h.
(C) Polymerization of 5 µM hGBP1F induced by addition of 2 mM GTP in the presence and absence of 5 µM LPS-O55:B5 was monitored by absorption spectroscopy at 350 nm. The absorbance signal was superimposed with nucleotide composition of the same solution analyzed at defined time points. Maximal hydrolysis rates (turnover numbers) were determined for hGBP1F variants in the presence and absence of 5 µM LPS-O55:B5. Graphs show mean turnover numbers ± SEM of combined data from at least three independent experiments. Significance was determined by two-way ANOVA with Tukey's multiple comparison test. n.s., not significant; ***, P ≤ 0.001; ****, P ≤ 0.0001.
B Quantification of peripheral ER structures in WT cells in which PAH1 was replaced by PAH1-HA or pah1(7A)-HA, without and with overexpression of ICE2 (SSY2841, 2842, 2843, 2844). Bars are the mean percentage of cell cortex covered by tubules (purple) or sheets (green), n = 3 biological replicates. Upper error bars are s.e.m. for the sum of tubules and sheets, lower error bars are s.e.m. for sheets. Asterisks indicate statistical significance compared with the respective control cells not overexpressing ICE2, as judged by a two-tailed Student's t-test assuming equal variance. *, P < 0.05; **, P < 0.01; n.s., not significant.
(E) RAB21 colocalizes with the WASH and retromer complexes. Transiently expressing GFP:RAB21 HeLa cells were fixed and stained for endogenous EEA1, FAM21, WASH and VPS26. Boxed region is magnified and single channels are depicted. Scale bars: 10µm or 5µm in enlarged view.
Note the accumulation of profoundly altered mitochondria in Cox15sm/sm muscles (white arrows), possibly as a result of partially digested organelles within endolysosomes. Black arrows indicate examples of normal mitochondria. In rapamycin-treated Cox15sm/sm animals only a few of these structures are present, which can be detected also in rapamycin-treated WT samples. The bar corresponds to 1136 nm (4400X)
Total oxygen consumption rates (OCR) per gram in BAT from WT fl/fl and QKI KO fl/fl:AP2-Cre mice under basal conditions were measured using a Clark electrode. (n = 3 biological replicates)
C Stable U2OS cell lines described in (B) were treated with LLOMe for 1 h and chased for indicated time. LC3 and GAPDH levels were analyzed by immunoblotting. Quantification is shown in Figure EV2B.
A. Blue native PAGE analysis of RISP and CORE1 assembled into free cIII2 and supercomplexes (SCs)
Quantification of subtelomeric DNA from ChIP experiments using strains carrying the indicated Myc‐tagged proteins (2A9 and 8B7: SPBC2A9.02‐Myc and SPBP8B7.08c‐Myc, respectively). Immunoprecipitated DNA is expressed as fraction of input DNA. An untagged strain (−) served as a negative control. Bars and error bars are averages and s.d. from three independent experiments. Statistical significance was assayed using the unpaired, two‐tailed Student's t‐test. ***P 0.001 relative to untagged strain.
F Thus, model N simulates a larger constant stable phase delay than model W when a single daily 25 mpk dose is given at ZT8 under LD 12:12.
C Histograms of the observed unwinding and rewinding velocities for Sgs1 in the presence of RPA (brown bars). The mean unwinding rate was 51 ± 3 bp/s (N = 2139). The mean rewinding rate was 66 ± 3 bp/s (N = 2091). White bars show for comparison the distributions of unwinding and rewinding velocities for Sgs1 alone
(c-e) Neutral lipids in lymphoblasts from a control (UC) and HD-affected human (e) stained with BODIPY 493/503. MAP2 staining highlights neurons. Extended study in Supplementary Figure 15b.
C. Nuclear enriched protein fractions obtained from sham-operated livers and liver 48 h post PH were analyzed by Western blot for YAP expression. Sp1 was used as a loading control. Image is representative of a single experiment with n = 3 animals per group.
Quantitative gene expression by RT-qPCR of IL8 mRNA from human colonic enteroids (over 40 enteroids per individual sample per well) exposed to control (vehicle) or TNF α. with or without FKK9 (n = 5; 3 removed due to poor response and tissue integrity). Data shown as mean fold change relative to vehicle control (con) for each paired sample (n = 3 replicates). Each paired sample data set represents biopsies from an individual patient. *, ## p < 0.05, Pair-wise one way ANOVA with Tukey's post hoc test.
cTAZ attenuated heterodimerization between STAT1 and STAT2 induced by IFN-α. Following transfection, cells were treated with or without IFN-α (50 ng/ml) for 1 hour and subjected to IP assays using Flag antibody.
F. A proposed model based on the above results showing that standalone hTrmt13 binds either to tRNA or synthesized DNA, while the complex of hTrmt13 and TFs (e.g., USF1) excludes the binding with tRNA but not DNA.
I. Cells of the newly made strains were grown on galactose for 1 or 7 days, respectively. Cells were lysed before the distribution of Rnq1 in the soluble and pellet fractions was quantified. Shown are mean values and standard deviations of three independent replicates.
A) Snapshots of the divergence of the velocity field from a representative movie. Note the areas of positive divergence in the nests, areas of positive and negative divergence in the LECs, and an increase of magnitude on the differences between them over time. Scale bar = 40 µm.
(A) Schematic illustration of STXBP4 protein, where the identified 9-amino acid sequence of STXBP4-WW domain was aligned across the indicated species.
quantification (B) of Parkin levels in spinal cord homogenates. Protein levels are normalized by β-actin. Results are expressed as mean ± SEM and relative to Non Tg control at 30 days; n= 8 (4 males and 4 females). Paired Wilcoxon's test at 90 days, **p= 0.0078; paired Student's t test at 120 days, **p= 0.0054. Paired Wilcoxon's test for 30 and 60 days showed no statistically significant differences. Parkin levels are decreased in SOD1-G93A at 90 and 120 days compared to Non Tg.
WT or Sirt5-deficient MEF cells (Sirt5 +/+ or Sirt5 -/-) were infected with or without VSV-GFP viruses for 12 h, and viral infectivity was detected by western blot analysis (Q)
Adhesion of WT, ∆bac and ∆bac + pLZ.bac complemented A909 strains to human CC1- or CC5-expressing CHO transfectants, or empty vector control cells. Mean and SD from n = 5 independent replicates is displayed.
(C) Endogenous Tollip and LAMP1 colocalise in SH-SY5Y cells treated with AO for 2 hours. Antibodies specific to LAMP1 (green) and Tollip (red) were used.
(D) Digitonin permeabilized BMK Bax-/-/Bak-/- cells expressing SMAC-mCherry in the mitochondria intermembrane space (50 μL, 500,000 total cells) were incubated with 25 nM of Bax and 2 nM cBid for the indicated time at 37°C in a 96-well plate. The samples were centrifuged for 10 min and separated into supernatant and pellet fractions. SMAC-mCherry release was calculated as the fraction of total (supernatant + pellet) mCherry fluorescence coming from the supernatant fraction. The data was normalized to the percent SMAC-mCherry release of wt Bax and cBid at 60 min. Each symbol represents the normalized SMAC-mCherry release for one single replicate (n = 3 or more independent replicates). Where applicable the data was fit with the [Agonist] vs. response - Variable slope equation in Graphpad Prism 8.0.1. The dotted lines represent the 95% confidence interval of the fit.
(G) Schematic diagrams showing the domains of ENKD1 and CP110 that mediate their interaction.
Histological analyses of lymphatic vessel density by Lyve1 (blue) and Prox1 (purple) in representative lymph nodes of animals in (D) processed at the endpoint of the experiment (4 doses of BO-110 or vehicle control). N= 6 mice per experimental condition.
(I) The induction of Ac-MTs is blocked in HIV-1-VSV-luc (Virus) infected, but not in uninfected (NI) or Mock infected CHME3 depleted of EB1, but not CLIP170 at 6 h.p.i. Tyrosinated MTs (Tyr-MTs) are not affected. Representative fields are shown. Similar results were obtained in three independent experiments. Scale bar, 50 μm.
E MBP‐ALFY3255-3526 conjugated to amylose resin was incubated with GST or the indicated GABARAP mutants. The pulled‐down complexes were subjected to SDS-PAGE and visualized by immunoblotting with anti‐MBP and anti‐GABARAP antibodies. Data are representative of three independent experiments.
(a,b) The occupancy of dUTX on the promoter regions of apoptosis and Atg genes was detected by chromatin immunoprecipitation (ChIP). SL2 cells overexpressing HA-dUTX were chromatin-immunoprecipitated with anti-HA and anti-GFP (IgG control) antibodies following ecdysone treatment. qPCR was used to assess the binding to the promoters of dark, dronc, drice and rpr (a)
D. Agarose/formaldehyde gel separation of neotranscribed rRNAs collected from LacZ and PNRC1-expressing cells pulsed for 15 minutes with 3H-uridine and chased for the reported time points (minutes). Samples were loaded according to the amount of incorporated 3H, quantified by liquid scintillation. FU was included as a control of a blocked rRNA processing.
(B- C57BL/6 mice received 10,000 γ-radiation attenuated WT, CSPSIINFEKL or UIS4SIINFEKL sporozoites, either intravenously (n=6-8 mice per group) or (E- intradermally (n=4 mice per group). Additional control mice did not receive sporozoites (n=6-8 intravenously, n=4 intradermally). Spleens and livers were harvested either at day 14 (n=5 livers and n=6 spleens for intravenous immunisation) or day 42 (n=8 for intravenous immunisation), and IFN-γ-secreting lymphocytes following restimulation ex vivo with SIINFEKL peptide were quantified. Flow cytometry plots show representative percentages of CD8+ T cells co-stained with IFN-γ and CD11a (B, E).
E, F Apoptosis in WM115 cells with or without 48 h JUN knockdown after 96-h treatment with increasing doses of vemurafenib
A non-significant increase in T regulatory cell ICOS expression was also noted (I).
(D) Deletion of residues 342-356 of IFT54 increases its interaction with kinesin-II. Cell extracts from wild type (WT), ift54 expressing HA-tagged full-length (FL) IFT54 or IFT54Δ342-356 mutant were subjected to immunoprecipitation with anti-HA antibody followed by immunoblotting with the indicated antibodies. The normalized ratios of FLA8 and FLA10 in the immunoprecipitates (IFT54 versus the mutant) are 1:3.90 and 1:3.13, respectively.
[B] Quantification of total leaf area per plant (square centimeter, cm2). Values correspond to the means ± SE of three biological replicates. Different letters denote significant differences at p < 0.05, Tukey's multiple comparison test within each group of the same DAT.
A Dose-response viability curves in presence of increasing concentrations of IMT1 for one-week, viable cells were counted and normalized to DMSO-treated controls. Data are expressed as mean ± SD of n=3 independent experiments with four technical replicates. IC50 values were calculated with non-linear least square fit, RKO: 521.8 nM, MiaPaCa-2: 291.4 nM and HeLa: 29.9 nM.
Western blot of NIH-3T3 cells treated with TGFβ (2 ng/mL for all experiments) or mock for 48h in the presence of 0.5% FBS.
(a, b). Drp1WT and Drp1S616D, but not Drp1S616A, rescue PINK1-null induced crushed thorax in Drosophila. Representative thorax images of PINK1WT and PINK1-deficiency (PINK1KO) Drosophila expressing either mhc-gal4 (Mhc/+), mhc-gal4 driven human Drp1wt (Mhc>hDrp1WT) or mhc-gal4 driven human Drp1S616A (Mhc>hDrp1S616A) or mhc-gal4 driven human Drp1S616D (Mhc>hDrp1S616D) are shown. Images were taken either under light microscopy (a, upper panels, yellow arrowhead indicates the collapsed throax) or SEM (b, lower panels). Quantitation of crushed thorax is shown (b). > 200 flies for each experiment are analyzed. Scale bar=200µm. One-way ANOVA followed with Tukey's test. ***p<0.001. Data was presented as mean ± SEM of three independent experiments. For each condition, >200 flies were quantified.
(B) Immunoprecipitation and western blotting showing that DDX43 associated with Vret and Ago3.
Hypothetical schema showing normal endothelial cell (left), in which the apparent competitive binding of DAG and VEAL2 to the C1 domain of PRKCB restricts the activation of PRKCB and phosphorylation of junctional proteins. The controlled turnover of junctional proteins dictates the basal endothelial permeability and maintains homeostasis. Under hyperglycemic conditions (right), excessive glucose increases DAG levels in endothelial cells. Increased DAG levels further outcompetes VEAL2 and hyperactivates PRKCB, enabling increased translocation to membrane. During this condition, junctional protein turnover and degradation is unchecked and leads to hyperpermeability. VEGF- Vascular endothelial growth factor, VEGFR2- Vascular endothelial growth factor receptor 2, PLCγ- Phospholipase C gamma, PIP2- Phosphatidylinositol-4,5-bisphosphate, DAG- Diacylglycerol, PRKCB- Protein kinase C beta, VEAL2- Vascular Endothelial Associated LncRNA 2.
(h,i) Effect of nutrients and pHi on binding of ARL8 and KIF2 to polymerized microtubules. HeLa cells treated as in (f) and (g), followed by isolation of polymerized microtubule fraction and western blotting. The asterisk indicates a nonspecific band. For all panels values are means ± s.e.m. of three independent experiments carried out in triplicate. All comparisons are with the control within each treatment condition, *P0.05, **P0.01, ***P0.005 Student's t-test; n.s. not significant. Uncropped images of blots are shown in Supplementary Fig. S7.
Circos plots of ChIP-seq data showing genome-wide enrichment of dCas9 in ring stage parasites. The 14 chromosomes are represented circularly by the outer grey bars, with chromosome number indicated in roman numerals and chromosome distances indicated in Arabic numerals (Mbp). Enrichment for intron- or promoter-targeted dCas9 (normalized to non-targeted dCas9) is shown as average reads per million (RPM) over bins of 1,000 nt. The maximum y-axis value is 1,200 RPM for the promoter-targeted dCas9 (rings represent increments of 200) and 400 RPM for the intron-targeted dCas9 (rings represent increments of 66.7). var genes are represented by red bars. An asterisk indicates an unintended binding event.
Impact of TMPRSS2 on IFITMs levels. B. TMPRSS2 does not decrease IFITM amounts measured by flow cytometry. 293T cells were transfected with the indicated IFITM plasmids, with or without TMPRSS2, and analyzed 18h later.
(B) Violin plots of Vero-E6 cells labeled for Spike protein. The Multi-wavelength Cell Scoring algorithm in MetaXpress was used to determine the integrated fluorescent signal in individual cells as a measure of the amount of Spike protein within each cell. The plots show the population distribution of the integrated signal for all of the treatments. The Boxes in the plot show the interquartile range (IQR) with the top and bottom edges marking the 75th and 25th percentiles, respectively. The horizontal line in the box is the median value, and the whiskers are defined to be 1.5 IQR. The ordinate is a log scale. The effect of the treatment is assessed quantitatively by changes in the median signal level, and qualitatively by observing changes in the modes. The dashed line is 3 standard deviations above the mean signal in the Mock samples and is used as a cut-off to quantify the number of cells that are positive or negative for the Spike signal. The statistics table below the plots shows the number of cells counted in each treatment group, and the median of the population.
F: Schematic diagram of a genetic cross between parasite lines NTH∆PP and LAP3/mCherry and the resultant ookinete population after mosquito transmission and drug selection (oocysts, liver and blood stage parasites not shown). Colours represent NTH::GFP (green), LAP3::mCherry (red) and their co-localisation (orange). Spots in ookinetes depict crystalloids. The red cross indicates that sporozoite formation is blocked. Self-fertilization events are omitted.