EMBO/sd-character-level-ner huggingface dataset:
Side-by-side comparison of CNFY and nigritoxin. Nigritoxin is a toxin of crustaceans and insects. The translocation domain of nigritoxin (PDB entry 5M41, (Labreuche et al, 2017)) and domain D1 of CNFY show partial structural similarity (highlighted areas). This similarity was identified with DALI (Holm & Rosenström, 2010) which was also used to align both structures.
Recombinant AthPEPCK1 activity was measured at increasing concentrations of Tyr-Asp I0.5 values are indicated on each graph. Measurements were performed in the decarboxylation direction, as described in the Methods section. Data were adjusted to a modified Hill equation. The value of 1 corresponds to the activity of 4.3 ± 0.2 U mg-1. Data are mean ± SEM of 4 independent measurements.
E. eQTL analysis demonstrating the correlation between rs4971059 genotype and expression of TRIM46. The panel showed results from breast cancer tissues obtained from the mastectomy of the patients. In the boxplot, the central lines, the box limits, and the whiskers represented medians, 25th/75th percentile, and min/max, respectively (FDR=0.00147).
Western blot analysis of whole cell extract for the indicated conditions. Quantitative analysis of Rod levels using LiCor technology is indicated below. The asterisk indicates an unspecific band.
(E) Nocturnal ambulatory activity of Ndufs3 smKO and aged matched wild-type littermates from 1 and 2 months old male mice. P values were calculated by Student's t test. P values were calculated by Student's t test to determine the level of statistical difference. ; *p<0.05, **p<0.01 and ***p<0.0001.
(D) Immunoblot analysis of BAT cells stimulated with NE for 5 minutes in the presence of Wrtm, H89 or ESI-09 for the indicated proteins.
(e) Enhanced apoptosis in the granular layer of cerebella in Miz1ΔPOZNes mice. The upper panel shows representative TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labelling) staining of cerebella of age-matched control and Miz1ΔPOZNes mice. The lower panel shows a quantification of staining observed in four control and five Miz1ΔPOZNes mice. Error bars show s.e.m. P-value was calculated using an unpaired two-tailed Student's t-test.
EGFP-Rab7a wild-type (wt), Q79L (constitutively active mutant), and T22N (dominant-negative mutant) were transiently expressed in Vero cells. The cells were then infected with SARS-CoV-2 at an MOI of ~0.3. Using flow cytometry, cell populations with levels of EGFP-Rab7a expression varying by roughly one-log increments were selected, and the proportion of infected cells within each population was quantified at 8 hpi. Data were normalized to that of the cell population with the lowest EGFP-Rab7a intensity. Unpaired t-test with Welch's correction was applied. *, p < 0.05; **, p < 0.01. n = 5-6 biological replicates.
G) Muscle performance was assessed by measuring the total distance and time ran on a treadmill exhaustion test (n=6 mice per group).
B Upper panel, alignment of pore regions of ApCatSper 1-4. Amino acids of the Ca2+ selectivity‐filter motif are highlighted. Lower panel, alignment of S4 voltage‐sensor segments of ApCatSper 1-4 and of D. melanogaster ShakerB Kv channel. Positively charged amino acids are highlighted. Numbers indicate start and end position of amino acids of the selected region.
C. Cell lysates from MCF7 cells maintained under the conditions indicated were fractionated by sucrose density gradient centrifugation. Polysomal fractions were subjected to immunoprecipitation with RPS19 antibody, and precipitated were analyzed by quantitative LC-MS/MS. The heat map represents normalize spectral abundance factors (NSAF).
C. Sparsely cultured RPE cells transfected with the indicated siRNAs were immunoprecipitated with an anti-AMOTL2 antibody and analyzed by Western blotting for the indicated proteins. WCL, whole cell lysates.
Violin plot showed the relative expression of 47 inflammation-associated genes based on sample groups and cell clusters.
(C) Scatter plot of gene expression differences between Pax5Jak2/+ and Pax5+/- Cdkn2ab+/- B-ALL cells of tumors that were isolated from lymph nodes prior to RNA-sequencing. Genes with an expression difference of > 3-fold, an adjusted P value of < 0.05 and a TPM value of > 5 (in at least one tumor cell type) are colored in blue and red, corresponding to upregulation or downregulation in Pax5Jak2/+ B-ALL cells
qRT-PCR for different ISGs relative to Rps29 using epidermal RNA from 5 day- or 9 day-old (B) K5-R1/R2 and control (CTRL) mice.
H, I Luciferase activity in WT and BECN1 KO 293T cells transfected with an ISRE (H) or IFN-β (I) promoter-driven luciferase reporter after infection with SeV for indicated time points.
E-H) Bar plots show percentage of viable cells after treatment with 0.75 mM H2O2 (E), 0.06 µM paclitaxel (F), 0.15 µM doxorubicin (G), 2.5 mM cyclophosphamide (H). Data represent mean ± SE of three biological experiments. Samples are compared using Kruskal Wallis test followed by Dunnett's test for multiple pairwise comparisons. Corrected p values are indicated as follows *p < 0.05.
H. XL-MS analysis of the 6-subunit hGID complex (RanBP9, WDR26, RMND5a, MAEA, TWA1 and ARMC8β). Cross-links within the different complex subunits are indicated by green lines, and cross-links within the same subunit by purple lines. The predicted domain boundaries within the different subunits are colored as follows: LisH domain in light orange, CTLH domain in dark orange, RING domains in blue, TWA1's CRA domain in light blue and RanBP9's CRA domain in light grey, WD40 in dark cyan, ARMC8β in dark red, and the SPRY domain in light magenta.
D. MM099MITF-SOX10-PAX3 expressing inducible MITF-SOX10-PAX3 genes was treated or not with Doxycycline (1μg/ml) for 24h and protein lysates were immuno-blotted for the indicated protein. The numbers below the gel lanes represent relative protein level, which was determined from the band intensity using ImageJ software, and normalized relative to VINCULIN.
Subcellular localization analysis of S100A9 and S100A8 in MoLC, MoDC and MoDC-TGF-β. S100A9 mean fluorescence intensities (MFI) were normalized to MoLC and represented in the upper graph. The same was done for S100A9 cytoplasmic/nuclear MFI and shown in the lower graph. Scale bar: 5µm. Graphs show normalized percentages ± SD of data from four different donors for MoLC (n=4) and MoDC (n=4) and three different donors for TGF-β-treated MoDC (n=3). When applicable, student t-test was performed to determine statistical significance **P<0.01).
Alterations in ATG gene expression after phagocytosis of opsonized E. coli. ATG3 (2.05±0.27), ATG4 (2.20±0.27), ATG5 (2.89±0.42), ATG6 (2.04±0.40), ATG7 (1.98±0.30) and LC3B (2.46±0.39) gene expression (fold) in E. coli‐phagocytosing neutrophils compared with control cells. Dotted line represents mRNA expression levels of control cells. Data are representative of six independent experiments and are presented as mean relative expression±SD Wilcoxon matched‐pairs test, *p<0.05.
HUVECs transfected with CCP5 and/or CEP41 siRNAs were scratched and incubated to evaluate wound closure. The extent of wound closure in co-transfected cells with CCP5 and CEP41 siRNAs was compared with that in control or CEP41 siRNA-transfected cells at the indicated time points (A). Scale bars, 600 μm. Quantification of the extent of wound closure in (A) is presented graphically by measuring the distance between the dotted lines at each time point in (B). Data are shown as mean ± SD of three independent experiments (n ≥ 3 scratches per experimental condition).
(E) siRNA knockdown of Parkin was performed in SH-SY5Y cells followed by 25 μM AA for 2 hours prior to fixation and immunostaining with antibodies specific to TOM20 (green), Tollip (red) and Cytochrome c (blue). We observed Tollip colocalisation with TOM20+ve/PDH-ve MDVs (denoted by arrowheads), which was still maintained following Parkin siRNA knockdown.
Tumorgrowth curves for control (blue, n = 5) and GS493‐treated (red, n = 5) MLN4924 mice. Note that after day 24, all mice in the control group were sacrificed due to the tumor size. Error bars represent SEM (n = 5).
Immunohistochemistry (IHC) staining of p-AKT from TNBC primary tumor (n = 20) with high or low micropeptide CIP2A-BP expression. Lower panels show higher-magnification images of insets in upper panels. Right panel is the quantification of IHC staining p-AKT.
(G, H) Western blot (G) and quantitative analysis (H) of dystrophin expression in body-wide muscles from mdx mice treated with PMO at 12.5 mg/kg/week for 3 weeks mixed with MOTS-c (500 μg) intravenously (n=3; *p<0.05). 0.5 µg, 1 µg, 2.5 µg, 5 µg and 10 µg total protein from C57BL/6 and 50 µg of muscle samples from untreated and treated mdx mice were loaded. α-actinin was used as the loading control. Fold change refers to PMO-M relative to PMO alone.
(E) Pharmacological inhibition of MALT1 proteolytic activity prevents CARD14-induced gene expression in HaCaT keratinocytes. CARD14 expression was induced by doxycycline (dox) treatment in the absence or presence of different concentrations of mepazine as indicated. The next morning, cell culture medium was refreshed and IL-8 and MCP-1 concentration in the cell supernatant was measured 8 h later by ELISA. TNF stimulation (MALT1-independent) was used as a negative control. Values are the mean of triplicates ± s.e. Data are representative of two independent experiments. Significance levels, *P<0.05, **P<0.001, ***P<0.001 by student t test.
eWAT was collected from lean (C) and obese (HFD 16 weeks) (D) WT or CD169-DTR mice after 12 days DT-mediated ATM depletion. Representative pictures of dissected eWAT are shown on the left, the corresponding eWAT weights expressed as mean ± SD of more than 12 samples are shown in the right, with statistical significance calculated using the Student's t-test (**P < 0.01 and ****P < 0.0001). The zoomed-in area shows clear, oily lipid accumulation in the absence of ATMs (lower left part).
Percentage of BIR products among repair outcomes by 6 hr are shown. (mean ± SD; n = 3). Data information: Welch's unpaired t-test was used to determine the p-value in all panels.
Images of wings from flies with the indicated genotypes. Arrows mark the ectopic veins at L5 and arrowheads mark the classical notched wing. Scale bars, 500 μm.
D. Number of distal caQTL in 1 Mb windows versus genomic location mapped in ESCs (maroon) and EpiLCs (teal).
(A) Gating strategy, phenotype and frequency of circulating plasmablasts (CD19+CD27++CD38+) isolated by flow cytometric cell sorting from 3 TB patients (TB7, TB24, TB33) in comparison to one representative HD. Boxes indicate sort gates. The plasmablast frequency is indicated.
Activation of dynamin-2 with Ryngo 1-23 or expression of constitutively active dynamin-2 (S764A mutant, expression confirmed by the grayscale image) restored phagocytosis of IgG-3-μm beads (n = 34-51 cells), but had no effect on the phagocytosis of IgG-6-μm beads, n = 36-72 cells (E); ***P<0.001 EtOH Ctrl vs rapalog Ctrl, ###P<0.001 rapalog Ctrl vs rapalog Ryngo/Dyn2S764A.
H. Blood glucose levels of control and RbpjiΔEC mice on HFD during 2-DG uptake assay. n=5, data represent mean ± SEM, unpaired t-test.
(A) The relative fold change of carbon metabolites with or without HU treatment for 60 min. Error bars represent standard deviations (SD) from six independent experiments.
F. Protrusion and retraction speed of cells treated with the indicated PMOs or siRNAs was assessed as in (D). Graphs show average normalized values from n=10-13 cells imaged for 1 hr. Bars: mean ± s.e.m..
A Experimental SAXS profiles of monomeric BSP and its subconstructs such as BSP12, BSP123, BSP1234, BSP45, BSP345 in 10 mM Ca2+ (green) and 10 mM EDTA (red) are fitted to the crystal structures directly (black, 10 mM Ca2+; blue, 10 mM EDTA) or to the rigid-body models refined using Xplor-NIH against SAXS profiles (magenta, 10 mM Ca2+; cyan, 10 mM EDTA). The residual is defined as Icalc/Iexp.
The SARS-CoV-2 spike protein S consists of the two subunits S1 and S2 and binds through S1 to ACE2 on host cells, which is required for viral fusion with host cells (A) (A) TMPRSS2 may cleave S in trans and allow fusion of SARS-CoV-2 with the host cell plasma membrane. In contrast, ADAM17 may either cleave S in trans at the plasma membrane or may cleave it once the fusion peptide of S has inserted into the host plasma membrane after endocytosis, which is conceptually similar to a cleavage in cis. After ADAM17 cleavage fusion of SARS-CoV-2 with the host cell is likely to happen after endocytosis. Inhibition of ADAM17 reduces viral uptake and fusion.
Immunisation with cGAMP-VLPs enhances VLP-specific CD4 T cell responses. BMMCs from C57BL/6 mice were pulsed overnight with cGAMP-VLPs and used to stimulate cells from spleens of immunised mice. Cells were co-cultured for six hours prior to evaluation of CD4 T cell responses by ICS. The percentage of total CD4 T cells producing each cytokine is shown in (B)
E, F. Knockdown of EXOSC10 increased RNA foci in HeLa cells expressing (G4C2) 80 repeats visualized by in situ hybridization targeting sense RNA foci. In total 25 (Ct) and 24 (EXO10#5) images were analyzed in 3 independent experiments. G. Knockdown of EXOSC10 increased RNA foci intensity in HeLa cells expressing (G4C2) 80 repeats. Each dot represents average cellular RNA foci intensity (Arbitrary unit) of RNA foci-positive cells in each randomly taken image. In total 25 (Ct) and 24 (EXO10#5) images were analyzed in 3 independent experiments.
F. A scheme illustrating the step in the Hog1 MAPK cascade at which osmostress acts to enhance Hog1 phosphorylation.
(E) Representative electron of MEFs . Full arrowheads designate the limits of the zone of intimate contact between ER and mitochondria 20 nm). Scale bar: 100 nm. Data represent percentage of ERmitochondrial contacts per mitochondria perimeter. Error bars represent ±SD from 40 images MEFs Data information: For graph the P values was determined by a Mann-Whitney U test. ns = not significant, *P < 0.05, **P < 0.01
(G,H) Mature iMGL were immunostained for (G) PU1 and CD11b and (H) Iba1 and TREM2. Scale bar 20µm.
(d) Quantification of total tumour numbers per gut in sacrificed Apc Pten and Apc Pten MycT58A mice. Overexpression of proteolytically stabilised MYC did not increase the number of tumours in Apc Pten mice (Mann Whitney, n = 9 vs 19).
A-GAfter iPSC‐based reprogramming of fibroblasts, we generated DAn from PD patients (n = 10) and gender‐ and age‐matched healthy controls (n = 4) using a 30‐day differentiation protocol. Blind to researcher, resulting iPSC‐derived DAn showed similar properties and maturation state in PD and controls. Specifically, studied iPSC‐derived DAn encompassed 30‐day ventromedial (vm)‐DAn‐enriched cultures of morphologically mature DAn showing typical bipolar morphology, lacking PD neural phenotypes, mostly of the A9 subtype, and showing properties of tyrosine hydroxylase (TH)+ mature neurons. Representative immunocytochemistry analyses of vmDAn from PD patients and controls showed that (A) TUJ1‐positive cells expressing neural tubulin III (TUJ1) co‐expressed TH (Scale bar, 25 μm); (B) co‐expressed the A9 subtype marker of inward rectifier K+ channel GIRK2 (Scale bar, 25 μm); (C) co‐expressed the A9 subtype marker of transcription factor Forkhead Box A2 (FOXA2) (Scale bar, 12.5 μm).
(B, C) Puromycin-treated cells with UBQLN4 siRNA contain increased number of ALIS. At 72 h after transfection of the two distinct siRNA duplexes for UBQLN4 (UBQLN4 siRNA#1 and #2) or control siRNA (5 nM each), the cells were treated with 5 µg/mL puromycin for 2 h, and then subjected to immunostaining with an anti-polyubiquitin FK2 antibody (shown in green, B) as in (A). The number of ALIS was determined. The quantified data in (C) represent mean ± SEM. n = 76 cells for control siRNA, n = 89 cells for UBQLN4 siRNA#1, and n = 81 cells for UBQLN4 siRNA #2. P‐values were calculated by Welch's t-test between the siRNA‐transfected and the respective control condition (*P < 0.01).
(G) Western blotting to examine the KD efficiency of SLBP. GAPDH was used as a loading control. The white line delineates the boundary where irrelevant lanes have been removed from the same blot
Representative image of IR‐ (10 Gy; 1‐h recovery) and MMS‐ (1 mM for 1‐h; 24‐h recovery) induced NSMCE2 and γH2AX foci in MEFs. Scale bar, 2.5 μm.
A. Quantitative analysis of developmental expression of Lrig1 mRNA in rat hippocampus by real-time RT-PCR. The results are shown as mean SEM of n=3 independent assays. The levels of Lrig1 mRNA were normalized using the expression of the housekeeping gene Tbp (TATA binding protein). The insert shows the expression of Lrig1 in embryonic E17.5 rat hippocampus examined by RT-PCR. Control sample without reverse transcriptase (-RT) is also shown.
(B) Macrophages were transduced with non-specific scrambled shRNA (shNS), or TLR8 shRNA (shTLR8) and analyzed for TLR8 expression. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4.
During adaptor-mediated basal autophagy, an ULK1-inpependent ATG13-ATG101 complex interacts with ATG9A at p62/SQSTM1 clusters and promotes the ATG9A-mediated turnover of these clusters. Upon loss of the ULK1-indpendent ATG13-ATG101 complex, or disruption of the ATG13-ATG101-ATG9A interaction, the p62/SQSTM1 clusters accumulate, resulting in an accumulation of ATG9A at p62/SQSTM1 clusters.
The PTCx NMD reporter consists of a fusion between GFP (in green) and LacZ (in blue) genes; a PTC is present downstream of the GFP coding region, making the transcript an NMD substrate.
B Western blot analysis of cells expressing conditional Clb2m (+) or Clb2mΔCdk (Δ) fusions to the indicated proteins, before (−) and 5 h after (+) β‐estradiol treatment. Tub1 served as a loading control. c, control cells.
The PA transfer activity of PTPIP51 (PTPIP51_ΔTM and PTPIP51_TPR) was monitored by a FRET-based lipid transfer assay. A schematic cartoon of the FRET-based in vitro lipid transfer assay is presented on the left. a.u.: arbitrary unit.
B. Cells expressing a KV10.1*mVenus fusion under the control of the endogenous promoter to render a mild overexpression were fixed and immunostained for pericentrin. Venus fluorescence colocalized with pericentrin-positive structures. Scale bar: 5µm.
(D) Representative immunofluorescence images of HeLa cells transfected with GFP-Cyclin B2-WT or GFP-Cyclin B2-4A. After 36 h of transfection, cells were treated with nocodazole for 2 h. Then cells were fixed and co-stained for ACA (red) and DNA (blue). (E) Scatter graphs illustrating kinetochore intensity of GFP-Cyclin B2-WT/4A treated as in D. Bars represent the mean kinetochore intensity (±SD) normalized to the values of GFP-Cyclin B2-WT. Each dot represents one cell (≥30 cells from three independent experiments).
B. HeLa-Flag-Bclaf1 cells transfected with siCtrl or sip65 were treated with TNF (10 ng/ml) for 2 hours. The nuclear fraction was isolated and subjected to immunoprecipitation with an anti-Flag or control IgG antibody, followed by western blotting analysis.
E13-16 images and analysis of ECE2 OX in the developing mouse cortex reveal ectopic positioning of Sox2+ (D) progenitors and Ctip2+ deep- (D) and Satb2+ upper layer neurons (E) (Scalebars = 100 µm; electroporated cells shown in green). F, Quantification at 3dpe, counting the proportion of brains with normal vs. abnormal positioning of Sox2+ neural progenitors and Ctip2+ and Satb2+ neurons and that of brains with intact vs. disrupted basal membrane (n=5 CTRL and 8 ECE2 OX brains; exact binomial test: ****P < 0.0001). Ventricle marked by V.
F. Cignal-RARE system luciferase assay testing cyp26c1 MO on RA acid levels in zebrafishembryos (n = 5 replicates). Embryos were separated in groups of 20-30 and luciferase assayed. RLU, Relative Light Units.
PC3, DU145 and V5-SLC1A3-DU145 cells were subjected to ASNase and TFB-TBOA treatment at indicated concentrations and cell proliferation was measured by IncuCyte assay.
U2OS-H2B-EGFP cells were transfected with indicated siRNAs for 48 h or were treated with PF-670462 and filmed in 5 min intervals for 24 h. Time from nuclear envelope breakdown to MAT was quantified in 100 cells. Shown is mean of the medians ± SD (n=3). Statistical significance was determined by ANOVA (**** p<0.0001).
The cell proliferation assay in HCT116 CRC cells shows growth advantage conferred by the SMARCB1 R377C mutation compared with the wild type SMARCB1 or the vector control. The error bars designate the standard deviation (SD)
E-K. Immunofluorescence in the striatal region in mice treated with 6OH-DA and rIFN-β for optineurin (E, quantified in F) and Tom20 (E), with quantification of individual mitochondrial size by mitochondrial section area (G). 8OHdG- (H-I), OxDJ1- (J-K), and DAPI-labeled nuclei. Scale bars equal 10 microns.
A. Schematic drawing of MDI protein and deletion mutants. These proteins were expressed under the nanos-gal4 driver, and tested for their ability rescue the hatching rate and mtDNA level of eggs from mdi1 females (progeny column) or for localization and recruitment of partner protein Larp to mitochondria in cultured cells (localization column). N= 3 x >100 eggs / genotype for hatching rate. The relative mtDNA level was the average of 3 biological repeats.
(A-B) Representative phase contrast, red fluorescence (indicating geminin-mCherry levels), and yellow fluorescence (indicating p53-Venus levels) images of cells in response to a low (A) or high (B) frequency Nutlin-3 dosing regimen over 40 h.
ABCC1 mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2) in lung cancer (luad & lusc studies, *p<0.0001) and colon adenocarcinoma (coad study, *p=0.005) grouped into having no alterations or putative driver missense mutations in TP53. Statistical analysis by Mann Whitney test, n is indicated in the figure. Data information: TP53 status is indicated for each cell line. Data are represented as mean ± SEM. See also Figure EV5 and Appendix Figure S5.
E β-galactosidase staining in parental A549 cells and A549 DDX3 knockdown cells displaying senescent cells identified by the blue color.
(c) Midguts dissected from animals at puparium formation that contain Uba1H33 loss-of-function mutant cell clones (lacking RFP) and analysed by fluorescence and differential interference contrast microscopy. Wild-type (+/+) control cells possess stronger RFP and heterozygous Uba1H33/wild-type (H33/+) cells have weaker RFP. Representative images are shown. (d) Quantification (μm2) from c, n = 8 (+/+), n = 11 (H33/+) and n = 11 (H33/H33) animal intestines per genotype with 1-5 cells measured per intestine.
(D) Km, Vmax, and IC50 values for tested enzymes. Vmax was calculated from curves in (A) at 100 M ATP.
D: Cells with the indicated genotypes were synchronised in G1 with α-factor at 25°C and then released in fresh medium at 34°C in presence of nocodazole (t=0). Cells were collected at the indicated time points for FACS analysis of DNA contents.
Automated microinjection was performed on organotypic slices of mouse E14.5 dorsal telencephalon using Dx-A488 along with mRNA for RFP Organotypic slices of mouse E14.5 dorsal telencephalon injected with Dextran-A488 (green) and RFP poly-A+-mRNA. After 24h in culture the progeny expresses RFP (magenta; blue: DAPI, n = 17 cells injected, 8 RFP positive). Percentage of RFP-positive and RFP-negative cells (n = 17 cells injected).
High-resolution imaging of mitochondria in live cells using the Airyscan module of Zeiss LSM880 confocal microscope. Images of IMM in living HeLa, L6, and H1975 cells, stained with 10-N-nonyl acridine orange (NAO). NAO preferentially binds phospholipids in the IMM, such as cardiolipin. Arrowheads indicate cristae in the IMM. Scale bar = 500 nm. N ≥ 3 independent experiments for each cell type.