EMBO/sd-character-level-ner huggingface dataset:
A, Representative histograms and quantification of mean fluorescence intensity (MFI; A) in OT-II WT and CCR5‑/‑ lymphoblasts expanded in IL-2 or IL-15, as specified. Data shown as mean ± SEM (n ≥3).
Schematic of the viral surface in the mature particle, with E and M in side view, color coded as in Fig 1. The breathing behavior within and between E dimers, transiently exposing the fusion loop and regions normally buried at the dimer-dimer interface, is indicated by curved lines. A vertical arrow points to the hinge between domains I and II, a region that supports E protein breathing. ii). Dissociation of E dimers in the acidic milieu of an endosome, exposing the FLs and allowing their insertion into the endosomal membrane. iii). Upon fusion loop insertion, the E proteins form "extended intermediate" trimers bridging the two membranes. Curved blue arrows indicate the subsequent re-location of domain III, in blue, to the sides of the trimer to initiate the "hairpin" conformation of the individual subunits of the post-fusion trimer. iv). Upon relocation of domain III, the upstream part of the stem becomes anchored to the the
D, Co-IP analysis for H1299 cells transfected with a Flag-tagged p53 or an empty plasmid (Cont.) treated with a USP7-specific inhibitor P5091.
Figure 3. Differential lysine acetylation and protein expression in Arabidopsis leaves after inhibitor treatment. Vacuum-infiltration of leaf strips with solutions containing either of the two deacetylase inhibitors trichostatin A (B, D) versus a buffer control for 4 hours leads to differential accumulation of lysine acetylation sites. Volcano plots depict lysine acetylation site ratios (A, B)for inhibitor treatment vs. control, with p-values determined using the LIMMA package. Orange, protein with nuclear localization according to SUBA4 database. Blue, proteins with lysine acetylation sites identified. Dashed lines indicate significance thresholds of either uncorrected p-values < 5 % or Benjamini-Hochberg corrected FDR < 5 %. A missing line indicates that the significance threshold was not reached by any of the data points.
FRET-FLIM analysis of GFP:OST1 or GFP:SnRK2.4 and the effect of ABI1 fused to the mCherry fluorophore in the presence of RCAR1 and ABA. GFP lifetimes were determined after transient expression of the Arabidopsis proteins in leaves of Nicotiana benthamiana.   Representative false colour images of GFP:SnRK2 lifetimes measured in leaf tissues expressing OST1 or SnRK2.4 in combination with mCherry:ABI1 and RCAR1 without exogenous ABA. The bar marks 20 µm and the nucleus (n) and cytosol (c) are indicated.
HCC4006 cells were (C) both transfected with siRNA and transduced by adenoviruses; then treated with increasing doses of erlotinib. The surviving cell fraction was determined by an MTS assay after 72 h and compared to untreated cells.
B, Representative immunofluorescences showing cardiac Troponin T (cTnT, green) and nuclei (Hoechst, blue) staining of in vitro-generated cardiomyocytes derived from wild-type iPSCs transiently transfected with either control mimics, miR-203 mimics or miR-203 mimics + Dnmt3a/b cDNAs. Pictures were taken at day 15 of differentiation. Scale bars, 68 μm. The cTnT-positive area in these cardiomyocytes is shown in the right histogram. Data are represented as mean ± s.d. (n=2 independent experiments with 6 replicates each).
E. Quantification of in vitro matrigel invasion assay of PANC-1 siCNT cells (siCNT) and hMENA/hMENA∆v6 silenced cells (sihMENA(t)) toward rGAS6 as chemo-attractant (siCNT + rGAS6 and sihMENA(t) + rGAS6), showing that the knock‐down of hMENA(t) reduced cancer cell invasion toward GAS6. The number of invading cells were counted in 6 random fields. Data are presented as the mean ± SD of three biological replicates. Statistical analysis was performed with one-way ANOVA P<0.0001, followed by Bonferroni's multiple comparison test. **P<0.01.
B Antiproliferative activities of XMU-MP-5 and crizotinib against EML4-ALK Ba/F3 and parental Ba/F3 cells, respectively. Cells were treated with increasing concentration of each drug for 48 hours and then analyzed by MTS assay. Each concentration was performed in triplicate. Data were presented as Mean ± SEM from three independent experiments (n = 3) .
B-D. Examples of Min protein patterns emerging from nearly homogeneous initial conditions in E. coli cells of different sizes. Lateral dimensions (in µm) from top to bottom: 2x6.5, 2x8.8, and 5.2x8.8 respectively. The gray-scale images show cytosolic near-infrared fluorescence emitted by the protein eqFP670 at the first (left) and last (right) time points. The color montages show the sfGFP-MinD intensity (indicated by the color scale at the bottom right) over time. The scale bar in panel B corresponds to 5 μm. Red arrows show the oscillation mode at the respective time point.
D. Box plot showing rotarod performance data for CWH43WT/WT, CWH43WT/M533, CWH43M533/M533 and CWH43M533/A530 mice at 7 months of age. Data shown are the mean, 1st quartile, 3rd quartile, minimum and maximum for each group of mice. Statistical significance was determined using the unpaired t-test. When compared to wild type CWH43WT/WT mice (n=10), balance time on the rotarod was decreased significantly among heterozygous CWH43WT/M533 mice (*P=0.04, n=8), homozygous CWH43M533/M533 mice (*P=0.03, n=7), and compound heterozygous CWH43M533/A530 mice (*P=0.03, n=4).
C-E. Ccdc108 depletion affects centriolar distribution of IFT-B proteins during centriole migration in MCCs. Embryos were co-injected with GFP-IFTs (C: Ift74; D: Ift80; E: Ift88; green), Cetn4-RFP (purple) and each morpholino, and imaged at stage 18. HA tagged Ccdc108 proteins were co-expressed to test for the rescue of phenotypic defects. Xenopus embryos were subjected to immunoblotting to evaluate the protein expression levels. α-tubulin (α-Tub) served as loading control. Quantitative plots show that Ccdc108-depleted MCCs showed a significant decrease of centriolar distribution of IFT-B proteins (Ift74, Ift80 and Ift88), and Ccdc108-IFT interaction deficient mutants are unable to rescue the decreased centriolar accumulation of IFT-B proteins. >40 MCCs from 6 embryos for each condition. Data information: Quantitative data from three independent experiments were scored. Unpaired two-tailed t-test was performed (*** p<0.001). Mean ± s.d. values are also presented.
Model of ubiquitin-dependent BRCA1 recruitment to DSB sites. BRCA1 localizes at DSB sites via two redundant ubiquitin (ub)-dependent processes. The first mode is mediated by the ANK-BRCT domain of BARD1, also known as BUDR, which recognizes H4K20me0 nucleosomes modified with H2A-K13/15ub, the product of RNF168. Our work is consistent with a role for the E3 ligase activity (green) for promoting this binding event. The second mode on BRCA1 recruitment is dependent on the BRCT domains of BRCA1 binding to BRCA1-A whose RAP80 subunit recognizes Ly63-linked ub chains (ubK63), most likely on histone H1.
(c) Effect of p53 on the maturation of LC3. Immunoblots are shown for wild-type (WT) or p53−/− HCT116 (n = 3).
Schematic illustration of key enzymes in glycolysis and tricarboxylic acid (TCA) cycle.
(J) Relative mRNA expression levels of key autophagy genes such as Lamp1, Lc3b and p62 were detected in controls and 3,4-DC treated U2OS cells. Data is depicted as a heatmap showing means of at least three independent experiments (*** = p < 0.001 versus WT/Ctr and # = p < 0.05, ## = p < 0.01, as compared to WT treated with 3,4-DC).
CRH-Cre male mice received stereotaxic delivery of AAV-EF1a-DIO-Kir2.1-P2A-dTomato or control AAV-Flex-mCherry vectors at 7-8 weeks of age and were maintained on chow diet for 7 weeks before switching to HFD. measurements of fat mass (B, **p=0.0006, unpaired Student's t test) and lean mass (C, p=0.3728, unpaired Student's t test) at 15 weeks after viral delivery.
A,B WT, WT with GABA, WT with GABA and 10 mM GSH and WT with GABA and 200 nM rapamycin were tested for intracellular ROS levels under (A) pexophagy and (B) mitophagy conditions. After 24 h incubation, cells were stained with DHR−123 and propidium iodide for 1 h. Living cells were analyzed for DHR−123 fluorescence by flow cytometry. Data represent mean + s.d. (n = 3). *P < 0.005, **P < 0.01
Difference in deuterium uptake by sE404r and sE419r trimers (D404-D419). Left panel, deuteration difference for each peptide reported against the 1-p value obtained via Student's t-test between the two different constructs. In the right panel, peptides are reported as short horizontal lines, with length and position corresponding to the peptide length and location along the protein sequence (x-axis) and with their deuteration delta on the y-axis. In both panels, red (positive) and blue (negative) indicate changes above the Student's t-test threshold, and in grey those not reaching this threshold. Four peptides, termed HDX-a, HDX-b, HDX-c and HDX-d, were identified as showing a strong increase in deuteration in sE404r compared to sE419r. The same pattern was observed in the comparison between sE404r and sE428r, whereas no difference deemed "significant" by the same test was seen when comparing sE419r with sE428r (see Fig EV3).
F Kaplan-Meier survival analysis of overall survival of mice injected i.v. with SUM159PT gNFIB shCTRL (n = 10), SUM159PT gNFIB sh1 ERO1A (n = 12), or SUM159PT gNFIB sh2 ERO1A (n = 13) cells, two-tailed log-rank test.
(E and F) Patients were divided into four subgroups according to different TNM stages. The difference among different subgroups was statistically significant by overall Log-rank comparisons (OS: P<0.001, DFS: P<0.001). Pairwise Log-rank comparisons showed that subgroups III or IV exhibited poorer survival rates than that of subgroups IB and II (OS: P<0.01, DFS: P<0.001).
l-m, Comparison of the lower bound of TCR-beta repertoire (l) and richness (m) of naïve CD8 T cells among three participants.
C. β-catenin-mediated reporter activity in HEK293T cells expressing the indicated RNF43 constructs. Cells were treated with control medium (no Wnt3a) or Wnt3a-conditioned medium (Wnt3a) overnight. Average β-catenin-mediated reporter activities ±s.d. in n = 2 independent wells are shown.
F Comparison of oxygen consumption rates (pmol O2/s, normalized for cell numbers by Hoechst staining) of basal, proton leak, maximum and non-mitochondrial respiration in WT and MIC60 KO cells obtained from 3 independent experiments. The data is normalized to basal respiration from HAP1 WT. Bar and error bar represent mean ± SEM from 3 independent experiments. *P = 0.01 for basal (using one sample t-test), ***P = 0.0004 for maximum respiration and *P = 0.012 for non-mitochondrial respiration (using unpaired Student's t-test).
E) The figure shows the CFU counts of the P. gingivalis strains with MoDCs that lack DC-SIGN (si-DC-SIGN). The analysis of readings used One-way ANOVA analysis of different groups and Tukey's test for multiple comparisons (* p<0.001).
B. Carfilzomib, Bortezomib and MLN9708 promote the secretion of inflammatory related cytokines in M2 macrophages derived from PBMCs. After induced by IL-4 (20 ng/ml) for 24hours to differentiate into M2 macrophages, PBMCs derived macrophages were stimulated by Carfilzomib, Bortezomib (500 nM) or MLN9708 (500 nM). The secretion of IL-1β, IL-6 and TNFα were detected through ELISA experiments 24 hours after stimulation. Data from three experiments are presented as the mean ± SD. T test was used for statistical analysis of differences between groups. *p < 0.05, **p < 0.01, ***p < 0.001 (student's t-test).
A Chemical structure of RK-33.B A predicted molecular model of RK-33 docked into the ATP-binding cleft of DDX3. RK-33 is displayed in pink, the surface of the DEADc domain is in green, and the surface of the HELICc domain is in red.C Hydrogen bond interactions between RK-33 and DDX3. Alpha helices are displayed in green, and β-sheets are shown in maroon.
F. The GAL-Mia40 strain was much more resistant to Q97-GFP expression than WT cells, indicating that high Mia40 levels can suppress polyQ toxicity.
D) Percentage schizonts (from total number of schizonts in a well +/- s.d.) located in the different hepatocyte sub-populations by NF54, NF135, NF175 on day 3 p.i.. Each dot represents a biological replicate. For each parasite line, at least 100 schizonts were characterized from 2x 96 wells for the final percentage. The values from three biological replicates were used in a RM ANOVA test followed by a Tukey's multiple comparison test. Percentage of schizonts in Z1/hGK++/hGS- hepatocytes is not different between the three parasite strains. Percentage of schizonts in Z2/hGK+/hGS- for NF54 is significantly different from NF135 (p = 0.0015) and NF175 (p = 0.0015). Percentage of schizonts in Z3/hGK-/hGS+ hepatocytes for NF54 is significantly different from NF135 (p = 0.0002) and NF175 (p = 0.0.0002). Data information: * p <0.05; ** p < 0.005; *** p <0.001; **** p <0.0001
(B) Oxygen consumption rate (OCR) of Stat3+/+ cells cultured in 2i conditions without LIF or with LIF for several passages. 200nM FCCP and 200nM Antimycin were injected and resulted in a higher mitochondrial respiration activity in cells cultured in the presence of LIF. Mean and s.e.m. of 4 replicates is shown. See also Appendix Figure S3D.
D) RNA Fluorescence in situ hybridization (FISH) demonstrated that circFNTA was predominantly localized to the cytoplasm of J82 and UMUC3 cells. DAPI was mainly localized to the cytoplasm. Scale bar, 20 μm.
B. Volcano plot presentation of the differently expressed transcripts in GRN-/- hiMGL treated with isotype compared to WT hiMGL. Genes with more than 20% significantly changed expression are marked in purple (upregulated) or blue (downregulated). Data information: Data represent mean ± SEM. For statistical analysis the unpaired, two-tailed student`s t-test was performed, Statistical significance was set at *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001, *****, p < 0.00001, and ns, not significant.
C: rotarod test. Blue and red lines refer to Pitrm1+/+ (n=9) and Pitrm1+/- (n=7) 4 mo animals, respectively. Error bars indicate ±SD. Statistical analysis was by unpaired, two-tail Student's t test. *p<0.05; ** p<0.01.
C. Proportion of cells in a given cluster from B represented by either B6 or D2 genetic background.
D. A palindromic motif 14 bp downstream CUG816 in the 5′UTR of PTEN is evolutionarily conserved. (upper panel) Phylogenetic analysis of the 5′UTR of PTEN mRNA in bonobo (Pan paniscus), killer whale (Orcinus orca), and mouse (Mus musculus). The CUG816 initiation codon of PTENε is highlighted in a blue box and the 14 bp downstream palindromic sequence is highlighted in a red box. The putative hairpin structure shown in the lower panel was predicted by the Mfold web server.
qPCR (B) of the indicated genes or proteins in parental or IκBα KO HT29 cells obtained at pre-confluence or 7 days post-confluence. Bars represent mean values ± standard deviation of 3 technical replicates from 3 biological replicates performed.
MISTRG mice were reconstituted or not at birth with ~200.000 human CD34+ cord blood HSPCs, and subcutaneously transplanted with 10x106 U-2932 cells at six weeks of age. the average human leukocyte composition in the bone marrow of the mice is shown in B.
(D) The nature of conserved KAP1 binding sites between human ESCs [11] and 293Ts (ENCODE) (see Fig EV2D) is shown (left pie chart) compared to their abundance in the genome (right pie chart).
(D) RNA from adult male heads (n = 50 heads per genotype) of indicated genotypes was subjected to real-time qPCR.
Limited proteolysis. Recombinant purified proteins were incubated with increasing concentrations of trypsin. Remaining protein levels were analyzed by quantitative immunoblotting. Data are means ± SEM (* p < 0.05, **p < 0.01, ****p < 0.0001, by 2-way ANOVA and Dunnett's multiple-comparison test; n = 4 independent experiments; exact p values are shown in Appendix Table S1).
I. Ectopic Sugarbabe expression in the fat body partially restores the pupal volume of CG>ERK7 larvae (I) (N=4 replicates of 10 pupae/replicate for each genotype).
D Western blot analysis of SDS-PAGE of total lysates from liver, skeletal muscle and brain from the indicated genotypes, each lane showing the results for one animal. The graph shows the densitometric quantification of the signals obtained in the liver. Data are presented as mean ± SEM (n=2 WT; n=2 het; n=3 KO). The asterisks represent the significance levels calculated by two-way ANOVA with Sidak's multiple comparisons: ***P = 0.0002 and ****P < 0.0001 (WT vs KO)
Population analysis. Pre-enriched iNKT cells from WT BALB/c mice (NKT1, Red; NKT2, Black) were stained with Indo-1. As a measure of intracellular [Ca2+], the ratio of Indo (Violet) and Indo (Blue) was analyzed by flow cytometry. Timing of the addition of cross-linker, goat anti-Armenian hamster IgG (H+L), and extracellular calcium (mM) was as indicated;
E. Model for SPATA2 function in TNF-α signaling. SPATA2 interacts with CYLD and HOIP under steady-state conditions, and TNF-α-stimulation results in their recruitment to the TNF-RSC. SPATA2-dependent recruitment of CYLD impacts activation of TNF-α-induced NK-B signaling and necroptosis.
(A) PCA of gene expression dynamics during PGCLC differentiation. 4 biological replicates are shown. n = top 500 most variable genes. PGCLCs were sorted for SSEA1 and CD61 expression and further divided into XGFP+ and XGFP-. Axes indicate the variance. Arrows indicate hypothetical trajectory. Shapes indicate the biological clone (clone A11 = square, clone E9 = rhombus).
(A) (i) Representative optical neutralization (ON) images showing rhabdomere structure of the indicated genotypes. Rearing conditions and the age of the flies are indicated on top. (*CD- Constant Dark). (ii) TEM images showing a single ommatidium from the photoreceptors of rdgB9 and rdgB9;dEsytKO mutants reared in 12 hr L/D cycle ( / ) for 2 days. Scale bar: 1µm (asterisk indicates degenerated rhabdomere).
Yeast three-hybrid assays showing that CBF1 represses the interaction of the Pfr-phyB with PIF5 (B) in yeast cells. AD-PIF4, phyB-BD and CBF1 were expressed in the yeast strain Y190 as indicated. The β-galactosidase activities were measured by liquid culture assays using ONPG as the substrate. Error bars represent SD of three independent yeast clones.
F Model prediction and experimental validation of proliferation upon single or combined inhibitor treatment with AKT VIII and U0126 upon 5 U/ml Epo stimulation. Maximum proliferation was scaled to 1. Proliferation was measured as cell numbers, counted with a hemocytometer after 96 hours by trypan blue exclusion assay. Solid lines represent model trajectories. Experimental data is represented as mean ± standard deviation. N=3
(A) Schematic representation of the experimental procedure. Catheters pre-colonized with S. aureus were allowed to form biofilms in an in vivo context by subcutaneous implantation in mice. 24 h post-implantation mice were treated with a single subcutaneous injection of different mycoplasma strains and the effectiveness of each treatment was followed by positron tomography with [18F]-FDG-MicroPET.
(B) Structural comparison between free and HsAtg4B‐bound LC3. Crystal structure of free LC3(1-120) (PDB code 1UGM) is superimposed on the HsAtg4B‐bound LC3. HsAtg4B‐bound LC3 is coloured green, and free LC3 is coloured grey.
C Summary of the datasets obtained from SFB-TAP and BioID2 results, including the number of high-confidence interacting proteins (HCIPs). BDFR, Bayesian false discovery rate.
RT-qPCR showing the mRNA level of SRSF2 in APLNR+ cells and day 5-differentiated cells without or with 2.5 nM PLB treatment. The SRSF2 expression was normalized to that in APLNR+ cells. The ACTB gene was used as a control. P-values were determined by an unpaired two-tailed Student's t-test.
G. HCC4006 cells were transduced with control (AdCont) or RHOB-overexpressing adenoviruses (AdRHOB) at an increasing multiplicity of infection (MOI), then erlotinib IC50 values were determined after 72 h by an MTS assay and a correlation analysis was performed.
(D) and (E) liposomes containing RNA isolated from EVs released from BMMs infected with WT M.tb were also added to cells 5 hr prior to infection. Data shown are the mean ± SD of three independent infections and all data shown are representative of at least three independent experiments. Scale bar, 5 μM n.s., not significant
G, H Stabilisation of a second copy of DDmyc-PKAc1 leads to the observation of mainly one parasite per vacuole in cells treated with Shld-1 (100 parasites were counted in three independent replicates).Data information: In C and G, data are presented as mean ± SEM. Scale bars = 2 μm (C and G), 3 mm (A and E).
time course and temperature dependence of uptake. (A) Standard uptake reactions were performed in the presence or absence of the ATP-regenerating system. After the indicated times at 27°C, the vacuoles were reisolated, washed, treated with protease, and luciferaseuptake activity was assayed.
(G) GFP-Parkin-expressing HeLa cells with various pathogenic mutations (Fig. 1 C) were treated with CCCP and subjected to immunoblotting. Asterisks show ubiquitylation of GFP-Parkin. Vertical black lines indicate that intervening lanes have been spliced out. IB, immunoblot; IP, immunoprecipitation.
Profile plots showing the Log2 LFQ intensity (I) and representative immunofluorescence (J) for collagen I (red) expression in wild-type and Fam134 knockout MEFs. Scale bar: 10μm. Inset scale bar: 5μm. Nuclei were stained with Hoechst 33342.
B. Proportional Venn diagrams indicating the number of up- (left) and down- (right) regulated genes in MM047CDK7i-R and MM074CDK7i-R compared to the parental MM047 and MM074, respectively. The number of genes overlapping between the data sets is indicated. 261 genes were found up-regulated and 241 down-regulated in MM047CDK7i-R and MM074CDK7i-R. Hypergeometric p-value is indicated.
B. Overview of experimental approach to identify dmDis3l2CM-associate RNA by high-throughput sequencing. See text for details.
(D) Scheme of arginine biosynthesis pathway, with protein localisation based on PomBase annotations (Lock et al, 2019).
Caspase-1 and IL-1β concentration in EV lysates. Each bar represents a mean of n= 2 technical replicates, vertical lines indicate SD. **, p < 0.01; ***, p < 0.001; n.s. not significant (two-tailed t-test).
(C) Quantifications of %G1, %S and %G2/M at different time points, in control and dopamine perturbed backgrounds, color coding scheme to represent the cell cycle phase as shown through FUCCI reporter is below the graph. Across development, at 48h AEL (domeMESO-Gal4; UAS-FUCCI/+, n=34, domeMESO-Gal4; UAS-FUCCI; THRNAi, n= 13, domeMESO-Gal4; UAS-FUCCI; DdcRNAi, n= 15, domeMESO-Gal4; UAS-FUCCI; Dop2RRNAi, n= 19, domeMESO-Gal4; UAS-FUCCI; DATRNAi, n= 17), at 72h AEL (domeMESO-Gal4; UAS-FUCCI/+, n=38, domeMESO-Gal4; UAS-FUCCI; THRNAi, n= 22, domeMESO-Gal4; UAS-FUCCI; DdcRNAi, n= 29, domeMESO-Gal4; UAS-FUCCI; Dop2RRNAi, n= 47, domeMESO-Gal4; UAS-FUCCI; DATRNAi, n= 29) and at 96h AEL (domeMESO-Gal4; UAS-FUCCI/+, n=55, domeMESO-Gal4; UAS-FUCCI; THRNAi, n= 14, domeMESO-Gal4; UAS-FUCCI; DdcRNAi, n= 19, domeMESO-Gal4; UAS-FUCCI; Dop2RRNAi, domeMESO-Gal4; UAS-FUCCI; DATRNAi, n= 19) Data information: FUCCI (fluorescent ubiquitination-based cell cycle indicator) reporter shows G1 phase cells in green, S phase cells in red and G2/M phase cells in yellow. AEL indicates After Egg Laying. The quantifications in in C represents mean. The statistical analysis applied is Two-way Anova with Tukey's multiple comparisons test. The domeMESO-Gal4; UAS-FUCCI control comparison temporally in C is analysed using One-way ANOVA with Tukey's multiple comparisons test. 'n' represents the number of lymph gland lobes analyzed, *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001.
(F) Immunofluorescence images of PDAC tissues from KPC mice treated with vehicle (control), and 2mg and 5mg of tamoxifen, scale bar 50 μm. (G) Quantification of LOX-L2 for images in F. n ≥ 4 mice per condition, and n> 10 sections per animal