EMBO/sd-character-level-ner huggingface dataset:
F. FACS plots illustrate the gating and percentages of common lymphoid progenitors (CLP). Bar graph shows the absolute number of CLPs per 2 femurs and 2 tibias (n=5 mice for each genotype). Data information: All data are presented as mean±SEM. *p<0.05; **p<0.01, and ***p<0.001 by with one-way ANOVAs with two-tailed Student's unpaired t-test analysis for comparison of WT to PKCδ KO mice.
Spata2+/+ (WT) and Spata2-/- (KO) mice were injected intraperitoneally (i.p.) with alum (20 mg/kg bodyweight) and sacrificed 6 h latter to collect peritoneal lavages. Absolute numbers of neutrophils recruited to the peritoneum were counted by FACS (G)
a, Effect of oligomycin (Oli) and DMSO (Ctrl) on spherogenic potential of +/−KRas cells (n = 8); representative calcein staining.
C. Statistical analysis of absolute number of total nucleated cells from bone marrow B-cell subsets. Results represent the data pooled from three independent experiments and numbers represent biological replicates for each group (WT; n = 5, KO; n = 7). Bars and error bars indicate mean ± SD.
(A) Macrophages transduced with non-specific scrambled shRNA (shNS), or BECN1 shRNA (shBECN1) were infected with HIV for 10 days. Cells were lysed and analyzed for BECN1 and ACTB content by Western blotting. Left, a representative blot is shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4.
(d) Cdk5 mediates the MPP+-induced EndoB1 phosphorylation at Thr 145 and the MPP+-induced increase in the LC3-II level in neurons.
(C,D) Quantification of the nuclear morphologies (C) or γH2AX-positive DNA damage foci (D) from MCF7, MCF7 p53 KO or T47D cells that were treated with palbociclib (1μM) for 0, 1, 4, or 7 days and then analysed 48hr after drug washout. Either 100 cells (nuclear morphology) or 50 cells (γH2AX) were scored per condition per experiment and bar graphs represent mean data + SEM from 3 experiments.
(A) ROS burst in WT and rgi5x after elicitation with 100 nM flg22. Shown is the kinetic of ROS production over 40 min -/+ SE, n=8 biological replicates. RLU = Relative light units. Similar results were obtained in 3 independent experiments.
B. HAT1-catalyzed histone H3K122 succinylation was analyzed by mixing purified HAT1, histone H3 or histone H3 mutant (K122R), and succinyl-CoA in the in vitro succinylation assays. Heat-inactivated HAT1 was used as a negative control. Western blot analysis was performed with indicated antibodies.
Proposed model. CRL2-operated "double-end" inspections safeguard the mitochondrial localization of MIC19.
A. Representative image of CENP-B box FISH and mFISH stained RPE-1 metaphase spread cells. Chromosome 3 homologs are indicated by white arrows with single CENP-B box chromosomes signal magnified in insets. Scale bar represents 5 µm.
(c,d) Multiple proteases are expressed across lung cell types. (c) Distribution of expression (y axis) for ACE2, PCSKs and TMPRSS2 across lung cell types (x axis). White dot: median expression. (d) Proportion of cells (y axis) expressing ACE2, PCSK family or TMPRSS2 across lung cell types (x axis), ordered by compartment.
Mean number of both TAF and non-TAF in neonatal rat cardiomyocytes at days 0, 3, 5, 10 days following treatment for 24h with H2O2. Data are mean ±S.E.M of n=3. >50 cells were quantified per condition.
U2OS-LacO cells transiently expressing EGFP-LacI-Bub1-K together with VSV-Sgo1 or a control vector Cell lysates were immunoblotted (L). * represents non-specific bands.
(F) Scatter dot plots representing normalized total area of the Zwilch and Spindly signals, normalized to the reversine-untreated control, in the indicated number of cells from the experiment shown in panels C-D. Red lines indicate mean and standard deviation. Statistical analysis was performed with a nonparametric t-test comparing two unpaired groups (Mann-Whitney test). Symbols indicate: n.s. = p > 0.05, ∗ = p ≤ 0.05, ∗∗ = p ≤ 0.01, ∗∗∗ = p ≤ 0.001, ∗∗∗∗ = p ≤ 0.000.
(B) qRT-PCR data comparing fold change in eGFP transcript levels relative to ITR2 amplicons from retinal samples infected with all four capsid variants.
A) Partial amino acid sequences of the hMPV F (blue) and hRSV F(red) antigenic site II (Lopez et al., 1998;McLellan et al., 2011b;Toiron et al., 1996). Partial sequences of the F-415 and F-416 chimeras are color coded to indicate the origin of their antigenic site II residues. Amino acids shared by hMPV F and hRSV F are colored purple. The remaining sequences of F-415 and F-416 are derived from hMPV F.
Plot of change in fluorescence from baseline to peak fluorescence for Munc18-1 G544D (H) Data are means ± SEM (*p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001 by one-way one-way ANOVA and Dunnett's multiple comparison test; n = 7-23; exact n and p values are shown in Appendix Table S1). Note, that compound 10 is fluorescent at a similar wavelength than pHluorin, so experiments at concentrations higher than 1 µM were not possible.
O. Purified recombinant His-Erk2 protein incubated with the purified PBK in the presence or absence of ATP (100 μM ) or menin inhibitor (1 μM or 0.1 μM), as indicated. After SDS-PAGE, the phosphorylation of Erk2 was detected with the pERK1/2 antibody. Anti-ERK1/2 antibody showed that equal amount of Erk2 was used for the kinase assay.
Figure 5. SLFN11 inhibits homologous recombination repair. (A-B) SLFN11 suppresses SCE. Representative metaphase spreads showing SCEs from wild type and SLFN11-deficient SF268 cells (red arrows) (A). SCEs were scored for 50 metaphase spreads for each cell line (B). Each point represents the total number of SCEs in a single metaphase spread, and black bars indicate the average value for all spreads. Statistical significance was determined using the Mann-Whitney test (***P < 0.0001).
D-E. Bar graphs showing the number of Jmjd2a peaks displaying at least 1 bp overlap with (D) an H3K4me3 peak. Jmjd2a peaks were classified as TSS-associated ('TSS') if overlapping a region of +/- 1kb of a TSS.
(A) XO8 GSCs and DFCs were differentially labeled with PKH67 (green) and PKH26 (red), respectively, and mixed before plated on laminine-coated plates. The cells were treated with 50 nM MG132 and subjected to fluorescent microscopy. Scale bar, 100 μM. (B) Quantitation of (A). Cell numbers from three independent experiments were normalized to those of control cells treated with DMSO and presented as means +S.D. (*p=0.0035, n=3). Student t-test (two-sided, one type) were used for statistical analysis.
Quantification of the inhibitory effect of BO-110 (BO, 0.8 mg/kg, 2 doses/week I.P. administration, 11 weeks) on the growth of melanoma PDXs. Red arrows mark the initiation of treatment. Shown are mean tumor size in mm3 ± SD in biological triplicates. Statistical significance was determined by Two-Way-ANOVA. P = 0.0009.
C Conformational changes of the alkaline groove between T4L fusion Ca2+-free MICU1-MICU2 and partial Ca2+-bound MICU1-MICU2 heterodimers. Inset, KRKK residues in the alkaline groove rotate upon Ca2+ binding.
(H) Immunoblotting and quantification of total and Afadin S1795 phosphorylation in adipose tissue depots from 12-week old C57BL/6 male mice fed with either chow (CD) or high-fat diet (HFD) for 6-weeks injected with vehicle or insulin (n=6).
C. Top 10 biological process gene ontology terms as determined using DAVID for genes regulated by BAZ2A in ESC+2i and ESC+serum.
(A) lncPSCA predominantly locates in the nuclear fraction of gastric cancer cells. In detail, the cytosolic and nuclear fractions of HGC-27 or MGC80-3 cells were separately isolated. RNA was isolated from either the cytosolic fraction or the nuclear fraction. Expression of lncPSCA in the cytosolc and nuclear RNA was measured. Data show one representative example of three biological replicates.
A Immunofluorescence images showing 53BP1 and γH2AX foci in A549 cells after 2-Gy radiation and A549 cells pre-treated with 6 μM RK-33, 12 h before radiation. Overlap of 53BP1 and γH2AX is seen in the merged picture of the co-immunofluorescence staining. Scale bar is 2 μm.
(C) A heatmap showing the partial correlation between the expression of UPR branch pathway genes with SCNA levels controlling for the effect of the gene copy number change using data from GISTIC2.0. Rows depict genes from the UPR branch pathways from REACTOME and columns depict the 32 tumor types. Cells are colored in red or blue if the gene showed significant correlation with SCNA level in that tumor type (partial correlation test setting copy numbers for genes as control, after Benjamini-Hochberg multiple hypothesis correction, FDR < 0.05). Color intensity corresponds to the partial correlation coefficient between gene expression and SCNA level. The left side bar indicates pathway membership of the genes. The bottom panel shows the variances of SCNA scores for each tumor type and the number of normal tissue samples available for partial correlation analysis.
C) Schematic representation of TSP1 monomer and the TSP1 proteolytic fragments (N-term, C-term) and recombinant domains (P123-1, E123-1, E123CaG-1, Ca-1) used in the study
(C, D) Expression of GGGGCC-nLuc-3xFLAG (C) and +2CGG-nLuc-3xFLAG (D) RAN translation reporters in HEK293T cells treated with 2 μM TG (for stress induction) analyzed by immunoblot (n=3 biological replicates). To evaluate effects of SRPK1 inhibition cells were pre-treated with DMSO or SRPIN340 before reporter transfection. Data information: Error bars represent mean +/- SD. Two-tailed Student's t test with Welch's correction. ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001 and ∗∗∗∗p < 0.0001.
Immuno-EM of SipB-transfected COS-2 cells. COS-2 cells were transfected with a plasmid expressing SipB-YFP, and 24 h after transfection, cells were fixed and prepared for immuno-EM using an antibody specific for GFP and a gold-labeled anti-rabbit antibody. SipB was seen localized to structures made up of closely apposed membranes that were often in close proximity to mitochondria (A). Mitochondria were often seen apparently fusing to the SipB-induced membranous structure (B, see arrows in inset on top; C, inset to the right). Mitochondria were often seen contained with the SipB-induced membrane structures (D). Bars, 250 nm.
The expression of the stemness markers SOX2 and NESTIN was evaluated by western-blot and immunofluorescence (SOX2 in red NESTIN in green) in MPZ (+, 20 μM, 16 hours) and vehicle (-, DMSO, 16 hours) treated GSC#9. GAPDH served as a loading control. Scale bar: 10 μm.
(B) Vector copy number (VCN) in peripheral blood eight weeks post-transplantation (mean ± SD, each dot represents an individual mouse).
(C) Schematic representation of the PP2A holoenzyme that is composed of a catalytic subunit (PP2Ac), a scaffold protein (PR65), and a variable regulatory B subunit that interacts with the complex via PR65-α/β HEAT domains (Huntington/elongation/A subunit/TOR). CIP2A interacts with PP2A holoenzyme and modulates its activity toward specific substrates. The gene names for the identified autophagy-regulating candidates and the corresponding proteins (bold) are indicated.
(H) ArfGAP1 WT or ArfGAP1 KO HEK293A cells were starved of amino acids (-AA) for 2 hours, and stimulated with 4mM glutamine (+Gln) or asparagine (+Asn) for 2 hours. Lysates were analyzed for mTORC1 activity as in (B), and phosphorylation of S6 at Serine 235/236 (pS6) was also analyzed. ArfGAP1 and actin were probed for as controls.
(A) Crystal structure of the human AR LBD core dimer based on PDB 5JJM (1 monomer in grey and 1 monomer in pink). W752, located at the interface of the AR LBD dimer, is involved in hydrogen bond formation with T756 of the neighboring LBD and thereby stabilizes the interface. R752 disrupt this stabilization by steric hindrance and charge repulsion. The side chains of both W and R are shown at position 752. A close-up of the LBD-LBD interface is given. The ligand (DHT) is depicted as spheres.
H, I WT and lincRNA-EPS-/- iBMMs were infected with VSV (MOI 0.1) for 6 h or 10 h (H) or transfected with polyI:C (1 μg/mL) for 4 h or 8 h (I), phosphorylation and total protein expression were analyzed by Western blot with α-tubulin and β-Actin as loading controls.
(A) Nuclear (Nuc.) and cytoplasmic (Cyto.) fractions of U2-OS cells were analyzed at times indicated after IR exposure by SDS-PAGE western blotting. PARP1 and LDHA are fractionation controls and phospho-specific p65 signals are indicated. Representative gels from n = 3 biological replicates are shown. Right panel: quantitation of nuclear p65 and phosphorylated p65 species (n = 3). Fold changes compared to untreated samples (ut) and time points post IR are indicated on Y and X axes, respectively.
(D) A visualization of metabolic pathway enrichment results of the differential metabolic fluxes in the virus+remdesivir group vs the control group, using Fisher's exact tests (Methods). Y-axis represents the odds ratio of enrichment, the horizontal dashed line corresponds to odds ratio of 1. The dot color corresponds to the negative log10 adjusted one-sided P value from Fisher's exact tests, and dot size corresponds to the number of enriched target reactions. The datasets are ordered by P values, all pathways displayed have FDR<0.1.
A-D: Surface Plasmon Resonance analysis of the MSP domain of VAP-A binding onto immobilized unphosphorylated (A), monophosphorylated pS209 (B) and pS213 (C), and bi-phosphorylated pS209+pS213 (D) STARD3 FFAT peptides. Representative sensorgrams resulting from the interaction between the MSP domain of VAP-A injected at different concentrations and the different FFAT peptides are shown in (A), (B left), (C), and (D left). Binding curves display the SPR signal (RU) as a function of time. Some samples were measured twice (concentrations printed in bold). Signal obtained for the negative control peptide immobilized on another flowcell is systematically subtracted, as well as the bulk effect recorded with buffer only. Steady-state analysis of the interaction between pS209 (B right) and pS209+pS213 (D right) STARD3 FFAT peptide, and the MSP domain of VAP-A. Equilibrium responses (Req) extracted from the left panel in association phase were plotted as a function of the dimeric MSP domain of VAP-A concentration, and fitted with a Langmuir binding model.
From top to bottom: fluorescence pictures of the SVZ and absolute number of cells in 4D- (white bars) or 4D+ (black or red bars for all or RFP+ cells, respectively) mice scored positive for various markers as indicated. Insets in (C) are magnified (right) with arrowheads pointing label-retaining NSC (white) or astrocytes (empty).
(C-E) RNA-seq analyses were performed in 786-0 cells stably expressing shNT or shGDH1 treated with or without aa starvation for 12 h. Gene ontology cellular components (C) and KEGG enrichment (D) analysis of differentially expressed genes was performed using shNT- and shGDH1-expressing 786-0 cells. The enrichment of differentially expressed ribosomal protein-coding genes was measured by GSEA (E).
A. Validation of Rnaseh2b-/- MEF lines. RER activity (DRD:DNA) is undetectable in a Rnaseh2b-/- line consistent with complete inactivation of the Rnaseh2b gene (Reijns et al, 2012). Mean of three independent experiments; error bars, SEM, **** = p<0.0001, two-tailed t-test. Rnaseh2b-/- and Rnaseh2b+/+ control MEFs on a C57BL/6 p53-/- background.
Representative 1 mm brain coronal slices stained with TTC after 24 h of insult corresponding to animals injected with MTMyc or MTFL457.
(G) The fraction of counts that align to the CHIKV genome is shown for CHIKV-high cells. Only cell types that include >20 cells are shown.
Schematic representation of the β protein (Hedén et al, 1991). The first residue of each domain is indicated. XPZ is a proline-rich repeat region (Areschoug et al, 2002a). Known human ligand binding partners are indicated above each respective domain. IgA binds to a region denoted IgABR. Factor H binds the β75K region, but does not bind via XPZ.
A. Heatmap of 65 DAM-associated gene transcripts analyzed by NanoString in FCRLS- and CD11b-positive Grn-/- (n=6), Trem2-/- (n=5) and Double-/- (n=6) microglia in comparison to WT (n=7) microglia isolated from 6-month-old male mice. The expression corrected and housekeeping gene normalized RNA counts for each gene and sample were normalized to the mean value of WT followed by a log2 transformation.
Model illustrating GemC1 as an early regulator of multiciliogenesis through the control of transcription factors McIdas and FoxJ1.Abbreviations: MCC: multiciliated cells.
B tGnd1‐GFP is stabilized in ubr1Δ san1Δ cells. S. cerevisiae wt and ubr1Δ san1Δ mutant cells expressing tGnd1‐GFP were grown at 30°C. Cycloheximide was added, and protein levels were determined at the indicated time points by Western blot using GFP‐specific antibodies. Zwf1 levels are given as a loading control.
Top: Schematic of the co-culture system used to assess vesicle transfer in transfected cells. Donor cell were transfected with the indicated GFP-fusion proteins and then labeled with DiD. Acceptor cells were transfected with a H2B-mCherry plasmid. After 24 h, the cells were detached, replated in 1:1 ratio and cultured for 4 h. Cells were then fixed and stained with HCS CellMask™ Blue. Bottom: Representative confocal images of co-cultured donor and acceptor CAD cells. Yellow arrows point to DiD-labeled vesicles inside acceptor cells.
D. Western blot of PTEN variants in WT (lane 1) and N-terminal extended PTEN isoforms-/- (lane 2) Hela cells with a PTEN monoclonal antibody
C (left) Immunoblotting of SLC7A5 in MeWo cells transfected with non-targeting (NT) or SLC7A5-specific siRNAs for 48 hr. (right) GC-MS-based quantification of intracellular essential amino acid levels in MeWo cells mock or si-SLC7A5-transfected for 24 hr and then treated with LDHAi for 48 hr. Data information: Statistical analysis was performed by ordinary one-way Anova for the comparison of more than two groups. Data are shown as the mean ± SD, n = 3. ns: not significant, *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001
C) The ratio of spliced to unspliced p120-MS2bs RNA was determined by RT-qPCR from cells expressing the indicated MS2 fusion proteins. Average values and standard deviations of seven biological replicates are shown.
E Responsiveness to pilocarpine (PC) of WT (n=6) and Fxr2 KO mice (n=6). (two-tailed Student's t-test). Data are presented as mean ± SEM.
C: Comparative structural analysis of representative 2D class averages of Dam1WTc (upper row) and Dam1WTc-Bim1 (lower row). Densities exclusive to Dam1WTc (arrow) indicate the topology of Bim1 (scale bar; 10 nm).
D Visualization of interaction between PBL27 and MAPKKK5K375M, 6xA by BiFC analysis in Arabidopsis protoplasts. Venus fluorescence indicates interaction between PBL27 and MAPKKK5K375M, 6xA. Scale bar=10µm.
cell type annotations visualized by UMAP. B) The sample specific UMAP visualization of two samples.
B. Binding kinetics of UVR8 pre-monomerized by UV-B versus the COP1 WD40 domain obtained by grating-coupled interferometry (GCI). Sensorgrams of UVR8 injected are shown in red, with their respective 1:1 binding model fits in black. The following amounts were typically used: ligand - COP1 (2000 pg/mm2); analyte - UVR8 +UV-B (highest concentration 2 μM). ka = association rate constant, kd = dissociation rate constant, Kd = dissociation constant.
Left panel: MT-HCT116 cell extracts were fractionated as cytosolic and nuclear portions and subjected to IB analyses, respectively. Right panel: The cytosolic and nuclear fractions were immunoprecipitated with anti-β-catenin antibody and subjected to IB analyses
(a) Immunofluorescence images showing anti-RPA-1-positive foci in response to 5-FU after depleting the indicated genes by RNAi or empty vector control RNAi (L4440; scale bars, 5 μm).
B, C Typical examples (left) and current-voltage relationships (right) of (B) IKur and (C) IK,ACh in VM and AMCMs.Data information: Data are presented as mean ± SEM. In (A), *P < 0.05 by unpaired t-test. In (B, C), *P < 0.05 by two-way repeated measures ANOVA followed by pairwise comparison using the Student-Newman-Keuls test for (B) and Mann-Whitney rank-sum test for (C). In (B), P = 0.778, 0.350, 0.03, 0.02, 0.002, 0.001, < 0.001 and < 0.001, respectively, for comparison between VM and AM within membrane potentials of −20, −10, 0, 10, 20, 30, 40 and 50 mV. In (C), P = 0.01, 0.01, 0.01, 0.01, 0.03, 0.397, 0.397, 0.397, 0.671, 0.207, 0.207, 0.09, 0.01, 0.039 and 0.015, respectively, for comparison between VM and AM within membrane potentials of −120, −110, −100, −90, −80, −70, −60, −50, −40, −30, −20, −10, 0, 10 and 20 mV. CMs = cardiomyocytes; hESC-atrial (AM) and hESC-ventricular (VM) CMs; IK,ACh = acetylcholine-activated potassium current; IKur = potassium ultra-rapid delayed rectifier current. 4-AP = 4-aminopyridine; CCh = carbachol.
(I) Effect of ANO8-YFP on myc-STIM1 and Orai1-HA at the ER/PM junction. Data information: The first number in parenthesis indicates the number of similar experiments performed and the second number is the number of cells analyzed. All results are given as mean±s.e.m of the indicated number of experiments or cells analyzed.
(A) WT (BY4741), tgl1∆, yeh1∆ ,and yeh2∆ cells expressing GFP−Atg8 were grown to mid-log phase in YPD and shifted to SD-N for the indicated time periods. Cells were lysed and subjected to SDS−PAGE, followed by western blot analysis using anti-GFP antibodies. Quantification of the GFP/GFP−Atg8 ratio is presented on the right. Error bars represent the s.e.m. of three independent experiments. *P < 0.05 (Student's t-test).
C. Intracellular survival of ΔactA-(pADc-GFP) and ΔactA-(pADc-inlK) in MVP-GFP transfected Jeg3 cells. Statistical analyses were performed on the results of 3 independent experiments using the Student's t test. P values of <0.05 were considered statistically different and are labeled here as *.
N: The correlation of given stimulus intensities to fEPSP slope revealed a highly significant deficit of NexCre cTKO (red) compared to LM (grey), (unpaired Student's t-test, ***p < 0.0001).
C-E. Comparison of Sec61 complex conformations in the ss-bound (pale green) with the apo (dark green) Sec complex from this study (C), with the apo Sec complex from Itskanov (PDB 6N3Q, D) and with ss-opened ribosome-bound Sec61 complex (PDB 3JC2, E). Alignments of structures were based on TMs 7-9. The black arrows indicate the movement of Sec61α TM helices of the Sec61 complex. The plug is indicated by "P".
(E, F) SNF1 is required for efficient recruitment of Rfa1, but not Psf2, to HU-stalled replication forks. Cells were grown and synchronized in G1 by α-factor before release into the fresh medium supplemented with 200 mM HU for the indicated time. Cell extracts were prepared and subjected to MYC-ChIP of Rfa1-13MYC (E) or Psf2-13MYC (F). The amounts of DNA in the precipitates were quantified by qPCR. Error bars represent SD from three biological repeats.
Combined IF and DNA FISH for GFP (IF) and telomeres (FISH) in SaOS2 and HuO9 cells. Cells were forward transfected with Polη-GFP, and then after 24 hours transfected with 20nM siRAD54#2. Cells were stained for GFP and telomeres 48 hours after siRNA transfection. Scale bars = 10 µm Quantification of data in F. GFP negative cells were excluded from analysis. Cells were considered positive if they showed 1 or more colocalization events between GFP (Polη) and telomeres. At least 50 GFP positive cells were counted per condition per repeat, n=3. Values shown are mean±sd. Values were compared using standard two-way ANOVA followed by Sidak's multiple comparison test.
K. Overexpression of MIA40 rescues ∆ψm of ρ0 puf3∆ cells. Single copy plasmid expressing Mia40 driven by the MIA40 promoter was transformed into the indicated strains.
A. Schematics of the live-cell imaging experiments. The embryo imaged from pronuclei until blastocyst stage and transferred to pseudo-pregnant females
(d) ITM, ARM and ASM of 30-d-old female flies with pan-neuronal expression of UAS-Odc-1 compared with their genetic controls (n = 7-8 independent experiments; F = 17.49 for ITM, F = 1.58 for ARM, F = 24.61 for ASM; one-way ANOVA with Bonferroni correction).
(d) Comparison of the ORF1b of the SARS-CoV-2 and SARS-CoV genomes with the 9-bp deletion region shown enlarged.