EMBO/sd-character-level-ner huggingface dataset:
(H) Mean cfu of Pto DC3000 COR- 4 days after spray inoculation of Col-0Cas9 WT and CRISPR glv; n=12 biological replicates from 3 pooled experiments-/+ SD (Students T-Test, *p<0.05).
(A) Surface plasmon resonance (SPR) assay of the direct interaction of AG with galectin-9. Curve fittings to a 1:1 Langmuir binding model calculated with TraceDrawer are shown as smooth black lines.
E. Representative inward current traces elicited by 10μM AMPA in rat primary OPC in the absence or in the presence of 10μM DNQX
Hematoxylin and eosin staining of the distal colons of mice (Scale bars, 200μm) Histological scores. Each symbol represents an individual mouse. Small horizontal lines indicate the mean (error bars, s.e.m)
Recovery phase-specific interaction of HSATIII with the CLK1 N-terminal region. HSATIII-ChIRP/western blotting was performed on HeLa cells expressing FLAG-CLK1∆C or FLAG-CLK1∆N Asterisk: an unidentified partial fragment of FLAG-CLK1∆N.
(A) DNGR-1 KO MuTu DCs were transduced to express indicated DNGR-1 proteins, FACS-sorted and expanded. Surface (left panel) and total (right panel) DNGR-1 expression was determined by flow cytometry.
(D) Maximum projection of 2z slices of basal region of Hela cells stained with Phalloidin at 15 mins post anaphase onset, when cells were treated with DMSO or ZM447439 during flat monopolar cytokinesis, showing clearance under DMSO treatment and a failure to clear actin with ZM447439 treatment. Dotted mask shows position of DNA in actin channel. Scale bar - 10 µm.
(I) WB analysis of detergent-soluble and -insoluble DSS-cross-linked fractions of HeLa and TRIM16KO cells, untreated or treated with MG132 (10 µM, 4h) and probed with indicated antibodies.
Volcano plots showing the enrichment of RBPs which bind to REL-WT relative to REL-OPT transcripts (A) Data information: vertical dotted lines indicate a 1.5-fold enrichment while horizontal dashed lines indicate the p-value cut-off of 0.05. Points shaded in blue indicate RBPs which have a differential fold change of more than 1.5 and p<0.05.
Analysis of chromosome segregation in strains from (B). Distribution of fluorescently labeled Chromosome III was analyzed in large-budded cells 16 hours after switching the medium to Galactose. Scale bar represents 2 μm.
F, G Flow cytometric analysis of microglial debris uptake by cultured astrocytes. After knockdown of TAM family members, astrocytes were co-cultured with fluorescence-labelled apoptotic microglia. Fluorescence of internalized microglial debris in GLAST+ astrocytes was quantified by flow cytometry (n = 4 independent experiments, one-way ANOVA with repeated measures). Results are shown as ratios to the value of non-transfected astrocytes.
C. RPE-1 cells were treated with 75 ng/ml nocodazole for 4 hours. Mitotic cells were shaken off, washed 2 times with phosphate-buffered saline (PBS) and released in serum free medium. After 2 hours, cells were either directly harvested (2 hour sample) or treated with the indicated APC/C inhibitor for another 18 hours before harvesting. Left: Representative blot. Right: Quantification of MCAK/Uba2 signal ratio normalised to the untreated, 2 hour release sample Error bars show standard deviation of 3 independent experiments, asterisks the p-value of a two-tailed unpaired Student's t-test (*P < 0.05).
(Q) Western blot analysis with cell lysates of mock and CHIKV (MOI 1, 24 h) infected control and IRGM knockdown HT-29 cells transfected with indicated siRNA and probed with the indicated antibodies.
B. Immunohistochemical analyses of lamin B1-high cells. The lamin B1-high cells express Sox2 or PSA-NCAM, but not Prox1. Arrowheads indicate Prox1 negative lamin B1-high cells in the SGZ.
(i) The percentage of total cellular area occupied by lipid droplets (left) and the average number of lipid droplets per cell (right) was calculated for each of the samples by quantification of eight or nine different fields. *P 0.001; analysis of variance, P 0.01 for each person with HD versus each control individual by Tukey post hoc test. Subject identifiers are as in h.
Profiles of the converted red fluorescence at side become skewer (steeper near the front) over time. The dotted line represents the axis of symmetry of the intensity profile of the photoconverted fluorophores at t = 0.
F ChIP analysis of Abo1-GFP over the dh and imr regions in wild type and swi6Δ cells. Data are the mean of three independent experiments and error bars represent ±SEM. P-values, calculated using a two-tailed unpaired t-test, indicated no significant differences (P > 0.05) for wild type and swi6Δ cells.
4E-BP1 siRNA and corresponding control transfected TNBC cells were cultured with or without TGF-β. The indicated proteins were determined by immunoblotting analysis.
(G) Fluorescence microscopy shows BCG- and MTB-reactivity of representative anti-HBHA antibodies compared to a non-reactive isotype control antibody. Scale bar 10 μm (top/bottom).
western blot analyses of the expression of osteogenic markers. Cells were treated with Smurf1 or control siRNAs, and cultured in osteogenic medium for 5 days. Results are shown as mean ± SEM; n=3; *: p<0.05, **: p<0.01 and ***: p<0.001 by ANOVA with Tukey's post hoc test
Analyses of HER2, HER3 and pHER3 in the cells used in (D). Numbers below the blots show the quantitation of the signal of each band, referred to SKBR3 cells (intensity of band in SKBR3 cells=1). pHER3 levels were analyzed by a specific anti-pHER3 antibody.
Sequence alignment of the RBD sequences from the SARS-CoV-2, GD/1/2019 and GX/P2V/2017. Red triangles indicate the two residue substitutions at the binding sites of both GD/1/2019 RBD and GX/P2V/2017 RBD. Blue triangles indicate the five other residue substitutions at the binding site of GX/P2V/2017 RBD. Identical residues are highlighted in red background, and similar residues are labelled in red and boxed in blue lines. The green Arabic numerals 1-3 indicate cysteine residues that pair to form disulfide bonds.
d, Limiting dilution transplantation, TIC frequency. Genetic model: +KRas (black) versus -KRas (grey) ex vitro (n = 4) or ex vivo (n = 2). Pharmacological downregulation: control (black) versus treated spheres (grey; AZD8330 plus BEZ235 (AZD+BEZ)) (n = 2). Ctrl, control.
(A) Co-immunoprecipitation of endogenous SLP2, PARL and YME1L in mitochondria isolated from human FITR293T cells using either SLP2- or PARL-specific antibodies. IgG was used as a negative control. In, input (10%).
C The frequency of CDK12 amplification in HER2-amplified- and HER2-nonamplified breast cancer. The bar graphs indicate the frequency of HER2 and CDK12 co-amplified cases among the patients with HER2 gene amplification (left). Tables show the percentage of CDK12 amplification in the indicated cohorts (right). Amp, amplification; non-amp, non-amplification.
(H) FACS-based analysis of EGFR surface expression: IRF2BP1 and IRF2BP2 were knocked down for 48 hours in HeLa cells, cells were serum starved for 16 hours, stained with fluorescent anti-EGFR antibodies and analyzed by flow cytometry. Shown are means of 3 independent experiments +/-SEM.
(A) Comparison of migration and invasion abilities between T- and B- lines. PC3 T- and B-line cells were incubated for migration (16h) and invasion (24h) assay. 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).
C. sEVs were eluted from the beads with a glycine buffer and analyzed by NTA. Representative NTA traces were shown.
H Volcano plot showing DEGs in the bulk RNA-seq analysis (n=3 biological replicates). Green dots represent down-regulated genes. Red dots represent up-regulated genes.
(F) opn4 dko larvae show significant more displacement in large-angle turns at the onset of the dark interval than wild-type on the 5th, 6th and 7th dpf Data information: boxplot divides the data in quartiles: the box indicates the interquartile range, with the horizontal line in the box denoting the median of the data set, the whiskers extend to the minimum and maximum, and meet the box at the median of the lower (quartile 1) and median of the upper (quartile 3) half of the dataset. Black dots indicate biological replicates n=18, the red dot indicates the mean, red error bars indicate the confidence interval (95%), asterisks indicate significance (0.01<p(✱)<0.05, 0.001<p(✱✱)<0.01, p(✱✱✱)<0.001, ns = not significant).
H1299 cells transfected with the indicated shRNA in normal medium or after 12h glucose starvation (A) Representative FACS analysis of apoptosis. Data are presented as mean ± s.e.m. from 3 independent experiments; *p < 0.05 compared to NC glucose starvation (A) (Student's t-test).
Quantification of H.a. Noco2 sporulation in the indicated plants 7 days post inoculation (dpi) with 105 spores per ml water. Error bars represent mean ± SD (n=4). Two independent experiments were carried out with similar results.
Correspondence between Nuc/Cyto ratios induced by each tile in NucLibB and its hnRNPK IP/Input ratio. Coloring indicates local point density. Spearman's correlation R and P-value are indicated.
Schematic representations of the various assembly and disassembly sub-complexes observed in this study in L. pneumophila, P. aeruginosa and S. oneidensis (wild type and mutant strains), respectively. The blue shaded area in (A) represents an intact IM sub-complex in the vicinity of a PL sub-complex. Note that the boundaries between the different parts in these schematics are tentative.
(A)In vivo imaging of the mitochondrial network was performed in muscles expressing Fis1K148R. Adult muscles were transfected with plasmids encoding mitochondrially targeted yellow fluorescent protein (mtM13‐YFP) and Fis1K148R. Twelve days later muscles were observed in vivo with confocal microscopy. TMRM was injected into the muscles to monitor mitochondria, which retain membrane potential. Mitochondrial network was greatly altered but mitochondrial membrane potential was conserved.
Blood glucose levels of InsA-peptide immunized mice (n=3) and CI (n=7) mice were assessed at indicated days post immunization. Dots represent individual mice. Mean ± SD, statistical significance was calculated by using repeated measure ANOVA test, all comparisons were not significant.
Representative images of vDNA foci detected by click chemistry to PML at 1, 3, 6 and 8 dpi in P6 SCG neurons infected with HSV-1EdC in the presence or absence of IFNα (600 IU/ml). Z-stack images of individual vDNA foci were acquired. Scale bar, 20μm. Zoom scale bar, 1 μm. Percent colocalization of vDNA foci detected by click chemistry to PML at 1, 3, 6 and 8 dpi in SCG neurons infected with HSV-1EdC in the presence or absence of IFNα (600 IU/ml). Each point represents the percentage of 20 vDNA foci that colocalized to PML from 3 biological replicates.
a, b, VEC and siAtg5 cells cultured with oleate (OL) or in MCDM were examined for their rates of TG synthesis (a) and β-oxidation (b) as compared to cells in regular medium alone (*P  0.03, **P  0.004 with VEC cells in the same medium, n = 34).
Western blot analysis of the apoptosis marker c-PARP, c-caspase 3 and PCNA in lysates (20 µg) from GBM cells treated with 24OHC (0 - 20 μM) for 72 h.
Representative fluorescence polarization binding curves are shown for LNS2SS2- and LNS2SS2A+ interacting with Nxph1 with or without Ca2+ added.
(K). The percentage of vesicles with different diameters was measured after 100 nM AngII stimulation or incubation with 400 nM Compound 7. Compound 7 significantly decreased vesicle size under AngII stimulation. (L). The percentage of pre-spike foot (PSF) (left panel) and stand-alone foot (SAF) (right panel) were calculated after incubation with the indicated concentrations of Compound 7. Data information: Data were analyzed using one-way ANOVA and displayed as the mean ± s.e.m. P<0.05; ##, P<0.01; ###, P<0.001: cells pre-incubated with PTP-MEG2 inhibitors compared with control vehicles. N.S. means no significant difference. Data were from 6 8 (L) independent experiments. # indicates P<0.05 and ### indicates P<0.001 compared with control group.
The assembly of V-ATPase V1-V0 holoenzymes in NDST3 KO RPE1 cells over-expressing HDAC6 or EGFP as a control. Representative immunoblots for ATP6V0D, ATP6V1A, ATP6V1C1, LAMP1 and GAPDH are shown in (P).
E Temporal course of plasma VEGF at the early and late stage of COVID-19 infection by cytokine assay. Data shown are the levels of plasma VEGF in patients with (n=8) and without (n=10) disease progression at the early stage (one to three days after laboratory-confirmed for COVID-19) and late stage (more than three days after laboratory-confirmed for COVID-19).
B. Scatterplot showing the changes in H3K27me3 upon BAZ2A depletion in ESC+2i and ESC+serum. ESCs were subjected to two consecutive treatments with siRNA-control and siRNA-Baz2a, each one lasting for 4 days. Mean of normalized H3K27me3 read counts in ESC+2i and ESC+serum treated with siRNA-control or siRNA-Baz2a over all TSSs (+/- 1kb) were calculated. Log2-fold changes of (siRNA-Baz2a/siRNA-control) are plotted relative to the mean of normalized H3K27me3 occupancies. The red line represents the mean of H3K27me3 fold-changes.
C 15N-Filtered Diffusion Ordered Spectroscopy-NMR measurements to PAP8. Exponential decay curves of PAP8 in absence or in presence of MBP-PAP5 are shown in red and black respectively. The units on the y-axis are normalized values of the integrals of the signal measured in the amide proton region.
D Changes (Δ g) in inguinal WAT (iWAT) mass of mice in (C). n=5. *P<0.05, **P<0.01 relative to GFP by Student's t-test. N.S., not significant. E Changes (Δ g) in epididymal WAT (eWAT) mass of mice in (C). n=5. *P<0.05, **P<0.01, ***P<0.001 relative to GFP by Student's t-test. N.S., not significant.
(C) LN229 cells stably transduced with indicated shRNAs targeting NEDD4L or a scrambled shRNA were treated with DMSO or thapsigargin (TG) 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.
Scoring of EMX2 and EZH2 mRNA staining intensity in human GBM tumour samples. Scoring system: - 0-0.5 foci/nuclei, + 0.51-0.75 foci/nuclei, ++ 0.76-1 foci/nuclei and +++ >1 foci/nuclei
H, I Effect of cold stress on the interaction of OST1 and EGR2. Arabidopsis protoplasts expressing EGR2-Myc/HF-OST1 and EGR2-Myc/HF were treated at 4°C for 0 and 2 h. Total proteins were immunoprecipated by anti-HA agarose beads. The co-immunoprecipitated products were detected by anti-HA and anti-Myc antibodies, respectively. Representative pictures are shown in (H), and relative interaction is shown in (I). Data information: In H) Relative band intensities are shown. In I): each bar represents the mean ± SEM of three independent experiments (**P < 0.01, two-tailed t-test).
Shown are the schematics and responses for th acetate sensors For the acetate sensor, the response of the sensor is shown in unmodified E. coli MG1655 with glnL intact (open diamonds). The dynamics of induction are shown (right graph) where cells are induced at the time indicated by the dashed line (see text). Representative cytometry florescence distributions for Figure 1h are shown i
(D) Q-PCR validation of Aldh1l1 at sedentary and after exercise for 50 min (n = 6, means ± SEM, * p < 0.05, two-tailed student's t-test).
C, D RT-PCR analysis using primers specific to the ST7 exon 11 (C) and ABI2 exon 8 (D) splicing reporters, respectively, of samples where FLAG‐tagged Matrin3 and its mutants have been overexpressed. Quantification of at least three replicates for each condition is shown as a histogram of the percentage of exon inclusion. *P 0.01 compared with control sample (−).
Figure 3 - From integrated proteomic subtypes to drug sensitivity prediction (A) Heat map of standardized, log2-transformed and median-centred giBAQ protein quantification (z-scores) across the combined CRC65/CPTAC dataset. Cell lines/patients are displayed as columns and proteins are shown as rows. Black bars to the left of the heat map indicate the presence of the respective protein in the CMS classifier. Annotation bars on top of the heat map visualise the membership of the different cell lines/patients in five annotation categories. (B) Elastic net regression was used to model drug sensitivity as a function of protein profile with the CCLE, CTRP, GDSC and Cetuximab datasets as input. The resulting models were used to predict the drug sensitivity of cell lines/patients (see also Appendix). In the heat map of standardized predicted AUC values (z-scores), cell lines/patients are displayed as columns with the same annotations and ordering as in (A), while drugs or combinations thereof are shown as rows. Coloured bars to the left of the heat map indicate drugs, which are more effective in a respective subtype (see main text and Appendix for details). See also Figures EV2-4.
A The MAPKKK5-GFP protein was detected in the membrane fraction. The total (T), soluble (S), and microsomal membrane (M) fractions purified from Nb leaves expressing MAPKKK5-GFP were used for immunoblots with antibodies against GFP, PM-localized aquaporin PIP1 and cytosolic ascorbate peroxidase EAP1.
(C) Yield of purified EVs from BMMs infected with various M.tb CDC 1551 strains based on Nanosight analysis. Data shown are the mean ± SD (n = 3 per group) and all data shown are representative of three independent experiments.
Figure 5: GFP-Aub iCLIP in GSCs and targeting by piRNAs, in Cbl mRNAs (A) GFP-Aub crosslinks in cultured GSCs (Ma et al, 2017), in Cbl mRNAs. Thin boxes are 5'- and 3'UTRs, lines are introns, and thick boxes are exons. The coverage of Cbl mRNAs with iCLIP reads is shown in blue. Significant crosslink clusters are shown in red. (B, C) Sequences of crosslinked regions in 5'UTR (B) and 3'UTR (C) of CblL mRNA. The nucleotides (nt) in significant crosslink clusters are in red. The sequence, occurrence and origin of anti-sense piRNAs from ovarian and embryonic libraries are indicated. Mismatched nt are in blue.
(C) Confocal microscopy showing Parkin ubiquitination in HCV-infected cells. HCV-infected cells prestained with MitoTracker (Mito) were immunostained with anti-Parkin and ubiquitin (Ub) antibodies. In the zoomed images, the arrows (white spots) indicate the merge of Mito (green), Parkin (red), and Ub (blue). Nuclei are demarcated with white dot circles. Fluorescence image of HCV E2 verifies HCV-infected cells (light gray).
t-SNE maps highlighting the expression of SARS-CoV-2 entry receptors ACE2 Transcript counts are given in a Log2 scale.
(F) Staining for Tbr2 in E15 WT and hFOXM1-cKI mice. Scale bar, 50μm. (G) Graph shows the number of Tbr2+ cells in 4x104 μm2 in enlarged SVZ (WT n=6; hFOXM1-cKI n=9; two-tailed unpaired t-test, P=0.0003). (
A. Structure of the FATE1 protein. Two predicted coiled-coil domains (CC1 and CC2) and a C-terminal transmembrane region (TM) are present. Purple, Mff-homology region. The position of L151 is indicated.
SDS-PAGE and Western blot analysis with the indicated antibodies of total yeast lysates from WT cells and the indicated mutants
(E) Simulated charge displacements associated with K+ binding to outward, transporter translocation, and K+ dissociation from inward-facing GltPh in units of e0; SDs determined by bootstrap sampling range from 7.10-3- 8·10-3 e0.
A) Bar graph demonstrating platelet aggregation induced by complexes of heparin, VEGF-A165, and anti-VEGF-A (IgG1) in vitro using washed human platelets. Introduction of modification of the Fc-region in RG7716 does not allow platelet aggregation to happen as compared to anti-VEGF-A as wild type IgG1. All three components are needed as heparin/anti-VEGF-A alone does not activate platelet aggregation. Error bars show SEM of three independent experiments and **** denotes significance using ANOVA (P < 0.0001) and Dunnett's multiple t-test comparing to IgG control with P < 0.0001 of Heparin/VEGF-A/anti-VEGF-A against IgG control.
F Visualization of the interaction between PBL27 and MAPKKK5K375M by bimolecular fluorescence complementation (BiFC) analysis in Nb leaves. The results were photographed at 38 hpi. Venus fluorescence indicates the interaction between PBL27 and MAPKKK5K375M. Scale bar=50µm.
e. Dot plot representation of top 30 receptor-ligand interactions based on molecule co-expression and reference-based cell subsets. Mean relative expression of both interaction partners (dot colour) and interaction p-value (dot size) shown. P-values are derived from one-sided permutation tests and refer to the enrichment of the interacting ligand-receptor pair in each of the interacting pairs of cell types.
(a,b) Transcript levels of HS memory genes HSP18.2 and APX2 in ein3-1 non-heat stressed (NHS, NHS+187), 44°C heat stressed SA187-colonized (HS+187), thermoprimed (LAT) as well as thermoprimed SA187-colonized plants (LAT+187) at 1 h, 24 h, 48 h, 72 h and 96 h of recovery at 22°C . Data information: For transcript level analysis, the data were normalized to tubulin as reference gene and the respective 22°C NHS, NHS+187 control plants, that were harvested at the same time points. All treatments are compared with direct 44°C HS treatment for statistical significance. All plots represent the means of 3 biological replicates. Error bars indicate SE. Asterisks indicate a statistical difference based on the Student's t-test *P ≤ 0.05; **P ≤ 0.01; **P ≤ 0.001 for differences between NP in comparison to NP+187, P and P+187 treatments.
Different doses of the IFNβ antibody were added to the media of the siRNA-transfected MCF7 (left) or T47D (right) cells right before the media were transferred to the wild type cells. The wild type MCF7 or T47D cells were then cultured in these media for 48 hours, and the expressions of ISGs were measured by qPCR. Each sample has 3 replicates. Error bars represent mean ± SD.
(C) Representative IF images of Msk1 in the whole brain sagittal sections of wild-type (top) and Msk1-/- mice (bottom) at 6 months old. The areas within the white squares are magnified in the right panels in each genotype. Scale bar = 2 mm in whole brain images; 50 μm in the magnified images. Data information: BS: brainstem, CBM: cerebellum
A Control animals (+/w; UAS-sec5IR/+), n= 19, and those with salivary gland-specific knockdown of sec5 (fkh-GAL4/w; UAS-sec5IR/+), n=20, were analyzed by histology for the presence of salivary gland material (red dotted circle) 24 hours after puparium formation.B Quantification of data from (A). Data are represented as means. Statistical significance was determined using a Chi-square test.C Control animals (+/w; UAS-sec15IR/+), n= 20, and those with salivary gland-specific expression sec15 (fkh-GAL4/w; UAS-sec15IR/+), n= 20, were analyzed by histology for the presence of salivary gland material (red dotted circle) 24 hours after puparium formation.D Quantification of data from (C). Data are represented as means. Statistical significance was determined using a Chi-square test.E Control animals (+/w; UAS-sec3IR/+), n= 20, and those with salivary gland-specific expression sec3 (fkh-GAL4/w; UAS-sec3IR/+), n= 20, were analyzed by histology for the presence of salivary gland material (red dotted circle) 24 hours after puparium formation.F Quantification of data from (E). Data are represented as means. Statistical significance was determined using a Chi-square test.G Control animals (+/w; UAS-sec8IR/+), n= 20, and those with salivary gland-specific knockdown of sec8 (fkh-GAL4/w; UAS-sec8IR/+), n=19, were analyzed by histology for the presence of salivary gland material (red dotted circle) 24 hours after puparium formation.H Quantification of data from (G). Data are represented as means. Statistical significance was determined using a Chi-square test.I Control animals (+/w; UAS-exo84IR/+), n= 19, and those with salivary gland-specific knockdown of exo84 (fkh-GAL4/w; UAS-exo84IR/+), n=20, were analyzed by histology for the presence of salivary gland material (red dotted circle) 24 hours after puparium formation.J Quantification of data from (I). Data are represented as means. Statistical significance was determined using a Chi-square test.