EMBO/sd-character-level-ner huggingface dataset:
D. Violin plots of fractional distance analysis showing the average distribution of endosomes in cells from panel (E) and fig. EV3A. Graph represents mean ±s.d. of n=15 cells per condition from 3 independent experiments. Dashed lines represent median and solid lines represent interquartile range. Cartoons representing the overexpression and control LE/Ly phenotype. Significance two-tailed student t-test. **** P<0.0001
B MEF-Cuedc2-/- cells were transfected with increasing amounts of FLAG-CUEDC2 (mouse) plasmids (1 μg and 2 μg). At 24 hours after transfection, the cells were treated with the proteasome inhibitor MG-132 (10 μM). Cells were cultured for additional 6 hours and subjected to immunoblotting.
A UV-visible absorption spectra of recombinant DJA6 and DJA5. Recombinant DJA6 after elution from Ni-NTA Sepharose beads followed by concentration is shown on the right.
The graph shows the mitotic numbers during 72 hours of regeneration in feeding conditions for cct3A RNAi and controls. Error bars are s.d. from the mean and n.s. indicates not significant using two-tailed Student's test with equal sample variance; n ≥ 8 planarian per time point.
(B) Lysosomes from livers of fed rats, untreated or treated with paraquat (+PQ), were processed as in (A). Graph shows changes in LAMP‐2A distribution induced by the PQ treatment, expressed as times the value in untreated animals and are the mean of three experiments.
BMDM cells were stimulated with C.albicans (5×106), Curdlan, and α-mannan for 24h. Glucose uptake, pyruvate level, lactate production, and ATP level were determined using assay kit.
In vivo lineage tracing of upper (Blimp1Cre) and lower (Dlk1CreER) dermal fibroblasts during wound healing. Experimental strategy for in vivo lineage tracing.
The spectrum of neutralizing activities elicited by PiCoVacc was investigated in mice (D) and rats (E). Neutralization assays against the other 9 isolated SARS-CoV-2 strains were performed using mouse and rat serums collected 3 weeks post vaccination. Points represent individual animals and humans; dotted lines indicate the limit of detection; horizontal lines indicate the geometric mean titer (GMT) of EC50 for each group.
Relative expression of xbp1 and atf6 related to gfp control at 72 hours and 13 days of regeneration during either starving or feeding conditions in cct3A(RNAi) animals. The graph shows that cct3A RNAi down-regulates xbp1 and atf6 specifically during starvation at 72hR. n = 3 replicates (5 planarians each) per time point.
Localization of SPATC1L (red) and CAPZB (green) in testicular sperm. Overlay with bright field image is shown at right. The white arrow indicates the spatial overlap between SPATC1L and CAPZB. Scale bar = 5 μm.
Mapping of the SPATC1L binding site on RIα by in vitro binding assay using purified GST-SPATC1L and His-RIα proteins consisting of regions 1-6. Purified GST protein only was used as a control. Binding was confirmed by immunoprecipitation using an anti-SPATC1L antibody followed by immunoblot analyses of RIα, detected using an anti-His antibody. In, input; Sup, supernatant; IP, immunoprecipitated protein.
SARS2-Mac2 binds to Paip1. SARS2-Mac2 but not Δ16-SARS2-Mac2 interacts with Paip1M.
(C) Scatter plot of INHBB and PMEPA1 gene expression levels in all MB groups. Colored dots represent each patient samples and colors represent the MB groups (WNT in blue, SHH in red, Group 3 in yellow and Group 4 in green). The p-values were determined by Spearman rank correlation test *p < 0.05, **p < 0.01, ***p < 0.001.
DNase-Seq tag density plots showing all peaks detected in replicate 1 of TB IL-2 and TB IL-2nil (32694) ordered by increasing fold change of tag count for TB IL-2 compared to TB IL-2nil. The sequence tag density is also shown in parallel at the same sites for the DNase-Seq analyses of CD4 naïve T cells (TN), TB IL-2 DMSO and TB IL-2 Ruxolitinib and ATAC samples from in vivo derived Th2 (Shih et al., 2016), Th1 and Th17 cells. The location of the 1000 IL-2 pDHSs is shown to the right.
G. The enriched biological process of upregulated MOS-regulated decay genes in MOSAsn95Lys oocytes, obtained via Gene Ontology (GO) analysis. The transcripts numbers of each biological process were labeled on the right.
A Quantification of TMRM fluorescence by flow cytometry in U2OS:GFP‐parkin cells treated with 25 μM antimycin A (anti A), 25 μM antimycin A and 10 μM oligomycin (anti A + oligo), and 20 μM CCCP (CCCP) for the indicated time, represented as a fraction of fluorescence intensity compared to DMSO‐treated cells. Error bars represent the mean ± s.e.m. (n = 3 experiments).
A, Immunoblots of H358 and A549 cells treated with vehicle (DMSO), AZD 4547 (5 µM) and BI2536 (5 nM), alone or in combination for 24h.
D Relative mRNA levels of FGF7. Bars represent mean FGF7 mRNA levels normalized to GAPDH mRNA and SEM from samples of 5 individual 45 days or 120-day-old mice. The data are presented as fold over values obtained with wild-type P45 samples. *P-value < 0.01.
A. Fold enrichment values on all repeat masker classes and on Refseq genes, on the basis of all uniquely aligned reads, shown as mean and s.d., n=6 biological replicates. Dashed line represents an IP/Input ratio of 1, taken as a reference.
D. Representative IHC staining of IDH2 in normal prostate glands and GL 3 - 5 PCa glands. Scale bar = 100µm.
Figure 1 - Expression kinetics from a synthetic model system for ERK signal duration. A: HEK293 with a stably transfected ∆RAF1:ER fusion protein were treated with ER antagonist 4-hydroxytamoxifen (4OHT, ON scenario in B). To generate pulses, ERK signalling was turned off using the MEK inhibitor U0126 (ON/OFF scenario in B). To distinguish between primary and secondary response genes, translation was blocked with cycloheximide (CYHX) in parallel to 4OHT stimulation (ON/CYHX scenario in B). In addition, we used actinomycinD (ActD) to determine mRNA half-lives via transcriptional shut-down and 4-thiouridine (4SU) to determine mRNA half-lives via metabolic labelling.
A, B Survival rate of (A) control and (B) Gr28bMi adult raised on control and the indicated concentrations of saponin-containing cornmeal diet (n = 4).
A, C E, Confocal images of neuronal processes of fixed neurons transfected with MtDsRed and SYN-GFP and C, myc-Miro1 (Miro OE) or E, myc-Miro1ΔEF (Miro ΔEF). Neurons are either non-treated (NT), TTX treated (1 M, 48h), PTX treated (100 M, 48h), or DMSO treated (1:2000, as PTX). Scale bar, 10 m. B, D F, Fraction of SYN-GFP clusters co-localising with mitochondria in cultures in B, control conditions, DMSO 28.7% 3.9, TTX 16.6% 3.1, PTX 50.0% 7.2, ANOVA **p0.001, n=8-9 neurons, D, with the expression of myc-Miro1, DMSO 33.9% 4.7, TTX 35.9% 5.4, PTX 46.7% 4.0, ANOVA, *p0.05, n=8-9, F, with the expression of myc-Miro1ΔEF, ANOVA p0.05, n=9-12. Experiments performed in E16 mouse hippocampal neuronal cultures at DIV 10-12. Error bars represent SEM.
G-H ELISA assays of IL-2 and IFN-γ in CD3+ T cells with the indicated treatments. (n = 3)
Ptpn2fl/fl, Lck-Cre;Ptpn2fl/fl, or Lck-Cre;Ptpn2fl/fl;Lck+/- HER-2 CAR-T cells were incubated with 24JK-HER-2 or 24JK sarcoma cells and the proportion of CD8+IFNγ+ versus CD8+IFNγ+TNF+ CAR-T cells determined by flow cytometry.
F) Solid phase transfection of nontargeting (scrambled), MKI67 targeting gRNA complexes into Cas9 expressing RPE-1TP53 -/- cells. Cells were fixed after 72 hours, stained with Ki67 antibody (red), and Hoechst (blue) to mark DNA and imaged. Scale bar, 50μm. G) Quantification of experiments in Fig 2F. Data derived from 3 independent experiments. P value (scrambled vs MKI67) < 2e-16, Mann-Whitney U test.
HEK293 cells were infected by lentivirus containing NF45-specfic shRNA or NF90-specfic shRNA, and then stimulated in serum for 0, 3 and 6 h. Cell lysates were prepared to analyze the expression levels of the indicated proteins by western blot.
Kaplan-Meier analysis of the correlation between expression level of LOC113230 and overall survival of colon adenocarcinoma (COAD) patients from TCGA database. P<0.001. P-value for Kaplan-Meier curves was determined using log-rank test.
qRT-PCR detection of Ccl2 mRNA in CD11c+MHCII+ cells sorted from IMQ-treated back skin (8h). (n = 5-12; 3 experiments). Data information: Data are shown as mean ± SEM. P‐values were calculated by multiple t-test with Tukey multiple comparison test. Statistical significance: ns > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001, **** P < 0.0001. See Appendix Table S3 for exact P‐values.
F PEMs were pretreated with the indicate inhibitors for 2 hours and stimulated with recombined of IFNβ1 (1 μg/mL) for another 3 hours, followed by qRT-PCR for detection of the Akt2 mRNA levels. DMSO, n=2; inhibitors, n=3. Data information: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 and ns, not significant (P > 0.05); using one-way ANOVA test Data are from two independent biological replicates Error bars , mean ± SEM).
C. Mitotic cdc20-3 cells containing PEST-CDC5 plus PEST-IME2-∆C and/or PEST-NDT80 were shifted to 36°C for 30 min and subsequently treated with estradiol (t = 0). Top, time-lapse series from the imaging of SPBs (Cnm67-RFP) and Mpc70-GFP. Frame width, 19 μm. Bottom, quantification of cells with Mpc70-GFP at SPBs. Data information: data are representative of two independent experiments.
(B) ssDNA repair efficiency of cells expressing MMS2 from the GAL1 promoter as determined from the maximal and final percentages of cells with Rad52 foci during the time course (right panel). Cells were synchronized in G1 from galactose-containing medium and maintained in galactose (a, c) or shifted to glucose (b) for 1 hour in G1; subsequently, cells were released into S phase in the presence of 0.033% MMS for 1 hour, treated with 2.5% sodium thiosulfate to inactivate the MMS, washed and released into fresh medium for different times. Cells were maintained either in galactose (a), glucose (b) or shifted to glucose 2 hour after MMS inactivation (c). The percentage of cells with foci at each point was normalized to the highest value in galactose, taken as 100 (left panel). Wild type and mms2∆ controls were analyzed in parallel Data information: The mean and SEM of independent experiments are shown. Statistically significant differences according to an unpaired two-tailed Student's t-test are shown, where one, two and three asterisks represent p-values <0.05, <0.01 and <0.001, respectively.
(E) Western blot analyses of RNF5, SCAP and IDI1 in Ctrl and HA-RNF5 OE MCF7 cells.
Gene editing of the Trim28-loci resulted in a robust loss of Trim28 protein, as evaluated by IHC where the expression of Trim28 in RFP+ cells were quantified and are displayed as mean ± SEM. Approximately 600 RFP+ cells per animal and group was evaluated. Scale bar 30 μm.
NEDD8 trimers co-immunoprecipitate with endogenous PARP-1 in NEDP1 KO cells. Lysates were prepared from U2OS NEDP1 KO cells and immunoprecipitation was performed with PARP-1-Trap or GFP-Trap as a negative control. Bound proteins were resolved by SDS-PAGE and processed for Western blot analysis with the indicated antibodies.
B) Glutamatergic touch neurons ALM and PLM expressing mec-4 were scored for number of spots in processes.
primates.Macaques were immunized three times through the intramuscular route with various doses of PiCoVacc or adjuvant only (sham) or placebo (n=4). SARS-CoV-2-specific IgG response (A) and neutralizing antibody titer (B) were measured. Points represent individual macaques; dotted lines indicate the limit of detection; horizontal lines indicate the geometric mean titer (GMT) of EC50 for each group. Protective efficacy of PiCoVacc against SARS-CoV-2 challenge at week 3 after immunization was evaluated in macaques
Four-month-old C57BL/6 male mice kept on HFD for 2 months were subjected to daily administration of phosphate-buffered saline (Con, n=4) or verapamil (Ver, 25 mg per kg body weight, i.p., n=3) for 10 days. Low-fat diet-kept mice (n=5) of same age were used as a negative control. (a,b) Levels of LC3-II from 1% Triton X-100-insoluble fraction of livers were analysed by immunoblotting (a) and quantified (b).
HEK293T cells were transfected with empty FLAG-tag vector as a control or FLAG-Nup50 N-terminal fragment (aa 1-120 of the human sequence). 24 h post transfection cells were lysed, FLAG-tagged proteins immuno-isolated and analyzed by western blotting (B), with 10% of the inputs loaded. The quantification of the western blot (B, lower panel) shows the mean signal intensity normalized on the input of at least two independent experiments. Data points from individual experiments are indicated.
The plots illustrate the average expression levels of the indicated mRNAs (mean ± SD of two replicates) in tumor samples classified as ATRA-sensitive (Sens) and ATRA-resistant (Res) according to the response of Ki67. *Significantly different (P-value < 0.05, Student's t-test).
NEDD8 trimers bind to GFP-PARP-1. NEDP1 U2OS KO cells were transfected with GFP or with GFP-PARP-1 and 24 hours later cell lysates were collected. Immunoprecipitation was then performed with GFP-Trap, and bound proteins were resolved by SDS-PAGE and processed for Western blot analysis with the indicated antibodies. GFP-PARP-1 but not GFP alone can co-immunoprecipitate NEDD8 trimers from NEDP1 KO cells.
E and F Cholesterol levels of HCT116 cells (E) and HepG2 cells (F) treated with or without 30μm terbinafine for 72 hours.
Silver staining images showed ASS1 as a novel LOC113230 interacting protein. The LOC113230 interacting proteins were identified by incubation biotin labeled LOC113230 with cytoplasmic extracts prepared from SW-1116 cells and the co-eluted proteins were identified by Mass spectrometry. NC, Negative control.
IHC staining and quantification showing pRSK2 (n=4), pCREB (n=7 wt, 6∆Ob) and c-Fos (n=5) positive cells (%) in OS from H2-c-fosLTR/Egfrwt and H2-c-fosLTR/Egfr∆Ob littermates. Scale bars: 100µm
H. Schematic representation of the Kap114p domain configuration using the same color code as shown in F.
D) RT-qPCR analysis of expression of CaSR in human spinal tissue. n=3, Student's t-test.
(B) Digitonized mitochondria (digitonin-to-protein ratio of 2:1) were analyzed by BN-PAGE, followed by CI in gel activity (IGA) assays and Coomassie staining. The SC I+III2+IV1 band (b1) was excised from the control (143B) lane and the SC I+III2 bands (b2 to b4) were excised from the COX1∆ and COX2∆ lanes. Their protein compositions were subsequently analyzed by nano-LC/ESI-MS (see also Figure EV2). The relative position of the molecular weight marker is indicated on the left.
E-F The qPCR analysis of 45S pre-rRNA from HEK293 cells treated with indicated shRNAs (E) and plasmids (F) for 24 h. Western blots show the expression levels of NF45, NF90, FLAG-NF45 and FLAG-NF90. (n = 3)
(d-e) 2µM mCherry-p62 and/or GFP-NBR1 were incubated in presence of 5µM GST-4xUb. Representative micrographs (d) and quantification of particle number for each channel (e) are shown. Averages and SDs from at least three independent experiments are shown
(A) Control shRNA or UVRAG shRNA cells were transfected with BAX plasmid, and apoptosis was assayed (n=3, *P0.05).
Fluorescence Recovery After Photobleaching (FRAP) experiment on AcGFP-Siwi and AcGFP-Siwi-D670A. Red dotted lines represent recovery traces of Siwi-D670A foci (n=36) and black dotted lines represent recovery traces of Siwi foci (n=36). Solid lines represent locally estimated scatterplot smoothing (LOESS) curve and the grey areas represent 95% confidence level interval. Fluorescence intensity is quantified with the softWoRx software and normalized to minimum and maximum in a 0-1 scaling.
G, H. The capacity of CD8+ cells for effector function in MC38 tumors was further assessed by measuring (G) production of TNFα by ICS and (H) intracellular straining of the cytotoxic mediator granzyme B followed by flow cytometry.
Representative traces demonstrating the spontaneous activity of the mHb neurons in a cell-attached mode from TMEM16A cKO mice compared to the one from littermate controls. D. A summary bar graph showing the frequencies of spontaneous firing of the mHb neurons in TMEM16A cKO (4 mice) and littermate controls (The numbers inside each bar indicate the numbers of recorded cells from 4 mice each, paired Student t-test, data are presented as mean values ± s.e.m.).
(F) Left panel: ZINB-WaVE (Risso et al, 2018, 2019) was used to statistically separate gene expression variability into parts linked to AP position and parts independent thereof. Scatter plot of ZINB-WaVE loadings separates known dorsal and ventral marker genes on ZINB-WaVE component 1. Right panel: Genes encoding homeodomain TFs and genes encoding Ig domain molecules (see color code) show high loadings on ZINB-WaVE component 1 and 3, demonstrating high variability independent of AP position.
(k-m) Analysis of the IgH/c-Myc translocation frequency in spleen B cell derived from WT (Samhd1+/+) or Samhd1 KO (Samhd1-/-) mice. (k) Schematic illustration of the experimental design for the translocation assay. (l) Southern blot analysis of PCR-amplified fragments with a Myc-specific probe from two independent experiments. (m) Frequency of IgH/c-Myc chromosomal translocations derived from two independent experiments (mean ± sd; Fisher's exact test).
(c) Pseudo-color look-up table applied to mean nuclear Venus::HES5 intensity within motorneuron (MN) and interneuron (IN) domains, corresponding to segmented image in (a). (d) Dimension of microclusters in DV axis for MN and IN domains; microclusters counted contained cells with high and similar levels of HES5 (Materials and Methods); bars show mean ±SD; data consists of 34 microclusters measured from 5 sections and 3 independent experiments; 2-tailed Mann-Whitney test. **** p<0.0001.
C. Significantly enriched Hallmark gene sets in low STAT3 versus high STAT3 groups. Dotted line: adj. p-value = -log10(0.05). Red = up-regulated, blue = down-regulated.
K-means clustering of 5 major groups of genes in Ronin fl/del, Ronin del/del (day 4) and Ronin del/del (day 8) transcriptomes.
Protein level of p-STAT3 and STAT3 in colonic epithelial cells was detected by using Western Blot (one mouse per lane). The relative expression of p-STAT3 was calculated.
Luminex analytes from WT CHIKV-infected joint cell lysates are categorized based on fold change states no difference (ND)) at 2 dpi relative to mock, and 6 dpi relative to 2 dpi. The numbers in the heatmap represent Log2 fold changes of analytes or genes. Analytes in complete or partial agreement with corresponding gene expression values derived from RNA-sequencing (RNA-seq) data appeared predominantly in the (D) up then ND state (Mock to 2 dpi, then 2 dpi to 6 dpi, respectively). † indicates analyte involvement in the canonical pathways. Differences in analyte concentrations during attenuated CHIKV infection are indicated in the checkbox. Yellow represents lower while green represents higher concentrations relative to WT CHIKV.
(b) Representative 3D rendering of genotypes indicated in (a). Anterior (A), Dorsal (D), Left (L).
B) Immunoblots show decreased MYC protein level in differentiated keratinocytes and Mettl14 KO cells.
B Knockout of DCAF12 rescues degradation of MAGE-A proteins in A375 cells. DCAF12 KO A375 cells were treated with complete media or EBSS before quantitative TMT proteomics. Note MAGE-A genes are not significantly altered by EBSS in DCAF12 KO cells.
(A) BH3‐only BIK displaces a subset of BCL‐2 complexes at the ER. Purified LM from H1299 HA‐BCL‐2b5 cells either mock infected or infected with Ad‐BIKb5 was subjected to cross‐linking with BMH and visualized by immunoblot. Asterisks (*) denote BCL‐2 cross‐linked products, which are displaced by BIK. Bold arrow denotes region containing cross‐linked NAF‐1/BCL‐2.
mRNA expression of inflammation markers relative to LysM-Cre/Nrp1+/+ in mouse RPE-choroid-sclera complexes at D7 for Il1b (E); n = 6 (LysM-Cre/Nrp1+/+), n = 10 (LysM-Cre/Nrp1fl/fl), Il6 (F); n = 3 (LysM-Cre/Nrp1+/+), n = 4 (LysM-Cre/Nrp1fl/fl), Vegfa
C, Long-range RMD is dependent on POLD3 when one DSB is close to a repeat. mES cells carrying the RMD-GFP reporter were transfected with nontargeting siRNA (Ctrl) or a pool of POLD3 siRNAs (siPOLD3) 24 hours before for the first time, and with transfection of sgRNAs/Cas9 the second time. The graphs show the frequency of GFP+ cells normalized to the transfection efficiency. The distance between the sgRNA targeting sites and the repeats is indicated.
Mice were treated as described in Fig.1A. LP cells were isolated from each mouse. The proportions of IL-22+ cells in CD3-RORγt+, CD3-RORγt-, CD3+RORγt- and CD3+RORγt+ were determined by flow cytometry.
H. North-western blot assay showing direct association between the indicated bacterially expressed, purified GST-fusion proteins and in vitro transcribed, biotinylated RNA probes based on the sequence of the B4 SINE depicted in (G). Top panels, binding of a 256nt probe corresponding to the CACACA-containing B4 SINE sequence, was compared to an identical B4 SINE deleted of its CACACA by truncation of its 3' portion (B4 SINE-Δ3'). RNA probes hybridized on the membranes were detected by their Cy3 fluorescence. Total GST-fusion protein loading was visualized by Ponceau S staining. Representative of two independent experiments.
Alcian blue (cartilage) (I) staining of scramble and Fam134bmo medaka fish. Graph shows quantification of Ethmoid plate (EP), Palatoquadrate (PQ), Ceratohyal (CH), Paired Prootics (PO), Ceretobranchials 1 to 5 (CB1 to CB5) cartilage length (I) in Fam134bmo and scramble fish. Values were expressed as % relative to the scramble (100% red dotted line). Mean +/- standard error of the mean (sem) of n=9 fish/genotype. Student unpaired T-Test *p<0.05; **p<0.005; ***p<0.0005. NS not significant.
A, B Indicated VHH antibodies (1 µM) were incubated at room temperature or at 90°C for 5 min and centrifuged for 20 min at 20 000 g. The supernatants were diluted 50-fold (20 nM) and analyzed for RBD-binding by BLI.
Immunostained horizontal sections show the expression of human P301Ltau in ECneurons in absence of endogenous mousetau (ECrTgTau-Mapt0/0). Fluorescence in situ hybridization of humantau mRNA combined with immunofluorescent labeling (Immuno-FISH) of humantau protein (huTau) verifies P301Ltau transgene expression in the EC. Scale bars 50 μm.
(C) Representative immunoblots describing changes in the phospho-AMPK and total-AMPK levels at various time points after DHPG treatment in cortical synaptoneurosomes in the presence or absence of anisomycin. Note in each case phospho and total AMPK levels were normalized individually to their respective tubulin levels before calculating the phospho/total ratio of AMPK.
D, E MAGE-A3/6 protein levels are actively degraded upon nutrient deprivation. HeLa cells were treated for the indicated times with complete media (DMEM + 10% FBS) or EBSS containing 100 µg/mL translation inhibitor cycloheximide (CHX). Protein degradation rates are shown (E). Quantitation represents average of n=3 with standard deviation shown. Data information: Asterisks indicate ** p<0.01. ns indicates p>0.05 using 2-way ANOVA.
Morphological analyses of epididymal sperm in WT, He and KO mice. Epididymal sperm were observed under an inverted microscope. The arrows indicate separated tails, black arrowheads indicate separated heads and white arrowheads indicate folded heads. Scale bar = 50 μm.
A Co‐localization of endogenous TBC1D5 and VPS35 with mCherry‐ATG9A, in steady state and autophagy induced by mTOR inhibitor KU0063794 (6 h).
A Schematic representation of the integrated mini virus (A1 J-Lat Tat-GFP) utilized in the primary screen of small molecules. Expression of the GFP reporter is under control of the HIV-1 LTR promoter in this cell line.
F) γH2A.X analysis showing a significant (p = 0.065 [**]) increase in the number of cells with DNA double-strand breaks in the K15+ bulge following extended organ culture experiments. Mann Whitney U test performed using N of 5-6 HFs from 2 patients. Values plotted represent the mean number of positive cells counted per HF analysed. Error bars are standard error.