EMBO/sd-character-level-ner huggingface dataset:
K RT-qPCR of Myf6 expression in Myf6-KO (n=2 technical replicates), WT (n=3 biological replicates) and Myf6-HF (rescue) myotubes (n=3 technical replicates) (5DM). "Rescue" myotubes were generated from Myf6-KO myoblasts infected with a retrovirus containing Myf6-HF. two-tailed t-test, error bars = +/- SD
(H) Immunoblot showing the levels of the MAVS protein in siCtrl- or siRNF34-1-transfected PBMCs. α-Tubulin was used as a loading control. Cell-based studies were performed independently at least three times with comparable results.
Confocalimages of yellow fluorescent protein complementation. PAT1‐Nc was transiently co‐expressed with either SUMM2‐Nn or At4g12010 in N. benthamiana. Confocalmicroscopy on leaf disks was conducted 2 days post‐infiltration. Merged pictures show overlay of brightfield, chlorophyll and eYFP. The scale bar corresponds to 25 μm.
(D) Quantification of the degree of down-regulation of Arm-GFP and E-cad-GFP at the junction between mitotic cells and their interphase neighbours (n > 10 independent samples per cell cycle stage). Mean +/- 1 S.D. shown.
(A) Confocal fluorescence microscopy of 293T cells transfected with 0.5 μg of pQCXIP-FLAG-Human IFITM3 mutated at indicated residues and immunostained with anti-FLAG M2 antibody. Scale bars, 5 μm. The P17L, P18H, Δ22-24, P18L/L23P and P18H/Δ19-23 mutations were introduced into the human IFITM3 background.
(A) Left: Representative images of S9.6 immunofluorescence of U2OS cells depleted of BRCA2 (siBRCA2), DDX5 (siDDX5) or control cells (siC) after transfection with either an empty plasmid or a plasmid expressing DDX5. The merged images show the signal of S9.6, nucleolin (nucleoli) antibodies and DAPI staining. Scale bar indicates 25 µm. Right: Quantification of S9.6 average nuclear intensity of U2OS cells depleted of BRCA2 (siBRCA2), DDX5 (siDDX5) or control cells (siC) after transfection with either an empty plasmid or a plasmid expressing DDX5. The red line in the plot indicates the median and each symbol represents the value of a single cell. The statistical significance of the difference was calculated with Mann-Whitney U-test and the p-values show the significant difference. The data represent at least 235 cells per condition from three independent experiments.
Quantification of the immunoblot data in (E). Immunoblot signals were normalized to anti-FLAG signal. Error bars represent mean +/- standard deviation. A two-tailed one sample t-test was used to calculate p-values (italics) associated with group means difference from a hypothetical value of 1.0 (represented by dashed line).
A. Brain homogenates from LAG3 KO and WT mice were immunoblotted for the presence of murine LAG3. Western Blot does not show a specific band other than for activated murine T cells.
Schematic representation of EMX2 and HOXB9 expression in the embryonic nervous system.
(G) U2OS PIF1-KO cells expressing PIF1 WT or E307Q, L319P mutants were treated with the indicated concentrations of HU for 72 hr, and cell viability assays were performed. Data information: Error bars represent the standard deviation (SD) of at least three independent experiments. Signiﬁcance of the differences was assayed by Two-tailed non-paired parameters were applied in Student's t-test. The P value is indicated as *P < 0.05, **P < 0.01, ***P < 0.001 and n.s. (not significant) P>0.05.
C. C4-2 cells were stably infected with the lenti-virus expressing empty vector (EV) or SPOP mutants and harvested for western blot analysis with the indicated antibodies.
Retina sprout length. Sprout length from tip to base in P6 retinas; error bars: SD; unpaired T test, *p<0.05; n=3-5 retinas, one retina/mouse.
(B) Two Nmnat3 constructs: Nmnat3 (full) with a mitochondrial-targeting sequence (MTS), and Nmnat3(v1) without MTS.
(B-D) Behaviors of MPTP-PD mice assessed by pole (B), beam (C) at 3-6 weeks post-MPTP injection, and locomotor activity (total distance & average speed, D) tests at 6 weeks post-MPTP injection. n= 20 GSK-650394-treated MPTP-PD mice, 14 vehicle-treated MPTP-PD mice, and 8 MPTP-untreated non-PD mice. Data are represented as mean ± SEM. Significantly different at p=0.0012#, 0.0001*, 3.09E-08##, 8.21E-08** in graph B and p=0.0009#, 0.0035*, 1.03E-06##, 0.00003** in graph C and p=0.0001*, 0.0284**, 0.0101# (total distance), 1.49E-08*, 0.0005**, 0.0001# (average speed) in graph D.
D ChIP assays to detect ub-H2B binding at E-box, TSS and gene body of tim and Pdp1ε in not RNAi (timG4/+;Udcr2/UnotRNAi) and control (timG4/+;Udcr2/+) (n=3). Student's t-test, *P < 0.05, **P < 0.01, ***P < 0.001. Statistical difference is measured using two-way ANOVA, P<0.001, significant effect of genotypes were found for tim E-box (P<0.01), Pdp1ε E-box (P<0.05), tim TSS (P<0.05) and Pdp1ε TSS (P<0.001) and tim gene body (P<0.01). G4, GAL4; U, UAS.
F) Box-plots representing the distance (µm) between the centres of two fluorescent signals from the indicated fusion proteins The distance between each pair of fluorescent proteins is represented by a dot. Between 4-10 different gonads were analyzed for each condition.
H, LDA (sphere forming assay) with METneg and METhigh subpopulations sorted from BT308NS, measuring GSC frequency after irradiation in the absence (5 Gy) or in the presence (5 Gy + JNJ) of JNJ38877605. Vehicle: non-irradiated vehicle-treated cells. *: 2 test, P=0.0002.
(G) Luciferase assay using 3xSd-Luciferase reporter in S2 cells, transfected with single or combination of Yki isoforms. Error bars represent SD, n=6. * p-value<0.05; **** p-value<0.0001 (unpaired two-tailed t-tests).
(A) Functional complementation of the mepK deletion of BW25113 ΔmepK pHV63(ycbB) was performed with the pHV30 vector or recombinant plasmids encoding mepA, mepK, mepS or derivatives encoding catalytically inactive endopeptidases under the control of the PrhaBAD promoter. (B) The complementation assay was repeated for BW25113 Δ7EDs pHV63(ycbB), which was obtained by deletion of all chromosomal endopeptidase genes except mepM. Induction of ycbB and of endopeptidase (ED) genes was performed with 0.2% L-arabinose and 1% L-rhamnose, respectively. BHI agar plates contained chloramphenicol (20 µg/ml) to counter-select loss of pHV63(ycbB).
(D) Quantification of mCherry+/GFP‐ (mCherry‐LC3) red puncta per cell (a measure of acidic autophagosomes) is shown. Data are mean±s.e.m. (n=3; 100 cells were analyzed per experiment and group). *P0.05 versus WT group.
Relative bacterial counts (CFU) compared to the medium control (100%) in human lung epithelial A549 cells 1 h after infection with MTB, pre-incubated with recombinant MTB-reactive IgA1, IgA2 or IgG1 antibodies and non-reactive isotype control as indicated. (C) Representative results for individual HBHA-reactive memory B cell antibodies from TB patients and HCW.
IFN-α release evaluated by ELISA in supernatants of BMDCs obtained from C57BL/6 or KO mice and incubated for 20 h with wild-type or fdsc-αDEC phage particles. LPS or CpG-ODN were used as controls. MyD88−/− and Tlr9−/− but not Tlr4−/− BMDCs were unable to produce IFN-α after fdsc-αDEC stimulation. Bars represent mean values ± SD. Cumulative results are shown of three independent experiments assayed in duplicate. Comparative analyses were performed using Student's t-test for unpaired samples.
RNA sequencing (F, left: heatmap) and GO analysis (F, right) of untreated MECP2-KO organoids vs PHA 543613 (N = 4 samples each of ~10-15 pooled organoids) indicated that treatment upregulated expression of genes in synapse-relevant pathways.
H. Schematic depicting the experimental setup of the in vivo tumor growth of pre-treated cells. PeTa cells were pre-treated in vitro with 100 nM GSK-LSD1 for 1, 3 or 6 days, or DMSO treated for 6 days prior injection.
G. Contact zone length, quantified as the percentage of the perimeter of a mitochondrion in close contact (<20 nm) with ER, extracted from EM images.
(G) Table summarising the EV protein analyses in Figs 4 and 5 (normalised to cell lysate protein levels). Data analysed by the Kruskal-Wallis test: *P < 0.05. Significantly decreased levels are in blue and increased levels are in red.
D. Western blot of SPH in RIPA lysates from 14-month-old female WT, Grn-/-, Trem2-/-, and Double-/- mice. Actin was used as loading control. E. Quantification of SPH protein levels in D normalized to WT (n=3). F Data information: Data represent mean ± SEM. For statistical analysis one-way ANOVA with Tukey's post hoc test of Grn-/-, Trem2-/- and Double-/- was used. Statistical significance was set at **, p < 0.01; ***, p < 0.001; ****, p < 0.0001, and ns, not significant.
A. Integrative analyses of differentially (FDR < 0.05) expressed transcripts from naïve and activated Dot1L-deficient B cells (left panel) with H3K79me2 ChIP values from WT naïve and activated B cells (right panel).
D. Co-expression of GEMC1 and Multicilin results in similar levels of FOXJ1 expression (measured by RT-QPCR) as Multicilin alone in HEK293T cells. The mean and standard deviation of 4 individual experiments in HEK293T cells are graphed.
B: Prion-infected tga20 COCS (45 dpi) immunostained with NeuN and LAMP1. Control: NBH-exposed COCS. Nuclei: DAPI. Prion infection induced LAMP1 upregulation in neurons (quantification: Appendix Fig. S4A) (n=3 individual biological replicates).
(D) Expression levels of selected genes from the clusters shown in panels B and C. G, gallbladder; L, liver; I, intestine; O, organoid; T, tissue.
(F) Co-immunoprecipitation from HeLa cells transiently transfected with V5-epitope-tagged HSP27 (P182L or S155Q/P182L mutant) using anti-V5 beads (n=2). Right: the location of Ser155 (red) in the crystal structure of peptide-bound cHSP27 (PDB: 4mjh) and in silico creation of the S155Q mutation (purple) showing a clash with the bound peptide. The peptide is shown in white sticks.S155Q disrupts binding of all IxI/V motifs.
The response of tethered fliM∆N ΔcheZ cells (strain EW635), induced for CheY expression from a plasmid (200 µM IPTG) Lines and shaded regions are the mean time spent in clockwise rotation ± SEM. The arrow marks the estimated time at which the stimulant arrived to, or left (as indicated), the flow chamber. N is the number of cells. α-Methyl-DL-aspartate (MeAsp) and leucine were used at 1 mM, benzoate (pH 7.0) at 50 mM. D, negative stimuli.
(F) Western blot of CathB levels and the cytosolic protein GAPDH in the cellular and cytosolic fractions of wt and ASMko BMDMs extracted with digitonin (left). Mean ± SEM pro-CathB and CathB levels in the cytosolic fractions (right) (n=2 cultures per genotype, Student´s t-test).
G. Spectrum of diversification in wild type and h3.3. GC = gene conversion; PM = point mutation; Amb = ambiguous; Other = deletions or duplications.
(e) Metabolic stress-induced decrease of clonogenic survival was attenuated in the absence of p53. HCT116 cells subjected to metabolic stress as in d were monitored for clonogenic survival.
d Similar representation as in (c) for the terms "Tyrosine-protein kinase", "Serine/threonine-protein kinase" and "Receptor".
(B-C) EVL protein expression in sparse/migrating wild-type (WT) and EVL-/- mouse brain endothelial cells (MBEC) and mouse lung endothelial cells (MLEC). Actin was used as loading control. Western blots are representative of three independent experiments.
C) IL3 and JUN mRNA expression levels after two hours of stimulation with PMA/I normalised as in B. The standard error is shown from 5 independent experiments.
D: Cell lysates from control or ELDR overexpressing NOKs, control or Cal27 and JHU029 cells treated with two different ELDR siRNAs were subjected to Western blot analysis for PCNA expression using specific antibodies. The membrane was reprobed with an antibody against Actin as internal control for normalization. The bottom panel shows a quantitative representation of Western blot band intensities. n = 3 biological replicates. Data are represented as the mean ± SD,
I. Bar plots showing fold changes measured by isoform specific RT-qPCR of PTC+ and PTC- isoform from genes indicated on the bottom in WT and CASC3-KO HCT116 cells. Relative levels from each replicate are shown by white circles. Error bars indicate standard error of means.
I. MFN2 and OPA1 immunoblots and quantification in Ifnb+/+ and Ifnb-/- CN cultures and quantification. Vinculin was used as a loading control. Error bars are SEM from 3 independent experiments.
d) Above: Ptma expression presented by a t-SNE plot and its trajectory analysis over the disease course. Ptma expression correlates with proliferation of rMGs at d7 during CNV in Cx3cr1CreERT2:Rosa26-tdTomato mice. Below: Representative immunofluorescence of proliferating EdU+(white) Iba1+ (red, Tomato) microglia at sites of CNV on d7 (arrow) next to an EdU-Tomato+Iba1- cell (asterisks) after EdU treatment from d0 to d6. Arrowhead points towards an intravascular myeloid EdU-Tomato-Iba1+ cell. Typical pictures from three mice obtained from one independent experiment are shown. Scale bar represents 25 µm.
(E) Consolidated quantification of actin intensity at the poles of cells at 6 mins post anaphase onset under different conditions as in (A). Despite reduced elongation, actin is cleared from the poles in both Control and RACGAP1 depletion. Data represented as mean±SD. siControl-n=44, 0.98±0.051, siRACGAP1-n=48, 0.99±0.041. Unpaired Welch's t-test comparing siControl and siRACGAP1 shows no significant difference between them, p=0.5199. One sample t test comparing siControl and siRACGAP1 to theoretical mean 1 (implying no change in actin compared to metaphase levels), shows significance for both treatments, with *p=0.0195 for siControl and *p=0.0392 for siRACGAP1. With means lower than 1 (red dashed line) for both treatments, it suggests significant clearance of actin from poles.
F. Distribution of caQTL hotspot targets in relation to nearest transcription start site in ESCs as percentage of total targets.
(A) Lesion sizes (left) were determined 5 days after C. higginsianum (Ch) inoculation. Invasion rates (right) of Ch on Arabidopsis leaves were determined 3 days after spore inoculation. An average of 3 replicates is shown (±SD) (left) and (±SE) (right). (■, p < 0.05 in two-tailed tests between the indicated samples. *, p < 0.05 in two-tailed tests compared to the corresponding WT values. Two independent experiments were combined for statistical analysis.)
(D) Bone metastasis-free survival in WT C57BL/6 mice subsequent to IC inoculation of RM1 BD Irf- BV (n = 9) and RM1 BD Irf7 OE (n = 7) cells (**p = 0.0028 by log-rank (Mantel-Cox) test).
G) qPCR (fold change) of PGC1α mRNA normalized by β-actin mRNA. Results are expressed as mean ± SEM and fold change of Non Tg at 30 days; n= 6 (3 males and 3 females) for 30 and 120 days, n= 4 (2 males and 2 females) for 60 days and n= 5 (3 males and 2 females) for 90 days. *p= 0.035 at 90 days and ***p= 0.0007 at 120 days. Paired Student's t test (for 60, 90 and 120 days) and paired Wilcoxon's test (for 30 days) were used for comparisons.
A, DNA replication measured by EdU incorporation. RPF-PCNA reporter cells were transfected with indicated siRNAs and pulsed with EdU for 20 min. S-phase cells positive for RFP-PCNA were analysed. n > 150. Error bars, SD; n= 3 biological replicas.
F, G. Quantitative real-time PCR analyses of the relative expression levels of the interferon inducible genes Irf7 and Oas1 within liver of Tie2-GFP (n=4) or Tie2-IFNα (n=4) mice euthanized 30 days post-transplant. The basal expression of Irf7 estimated in liver of control mice (i.e. Tie2-GFP injected with saline), was set to 1 and utilized to calculate the fold increase values observed. Mean values are shown; error bars=S.E.M.; p-values were calculated by Mann-Whitney test.
(H) Luciferase Reporter Assay from HEK-293Ts co-transfected with DLL4 3'UTR reporter plasmid and either scr or miR-30c. Data presented is relative to an internal firefly control (n=3). Data information: data are presented as mean ± SD. *P<0.05, **P<0.01, ***P<0.001 (Unpaired Student's t-test). All repeats are biological.
(G) Co-immunoprecipitation and immunoblot analysis of extracts of 293T cells transfected with plasmids expressing Flag-caspase-1 and indicated HA-tagged WT ubiquitin (Ub) or mutants (K6-, K11-, K27-, K29-, K33-, K48- and K63-Only), together with empty vector or Myc-USP8, followed by MG132 (10 mM) treatment for 6 hrs.
B. Western blot analysis of nucleolin in DRG neurons from wildtype (WT) and GAR+/- mice cultured in Boyden chambers. Tuj1 was used as a loading control. The higher nucleolin band in GAR+/- corresponds to WT nucleolin and lower band to nucleolin with a 41 aa deletion (corresponding to about 4 kDa reduction in protein size).
I) Activation of pAKT (Magenta) was examined in Icos1ø and Icos1 treated-animals within or around vascular (CD31+, green) and pericytes (NG2+ cells, yellow) of the BBB. High-resolution confocal images (insets) reveal the prevalence of activated pAKT (magenta) co-stain (cyan arrows) in pericytes (yellow) of the BBB along vasculature (green, or dotted outline) versus reactive neuroglia (NG2+pAKT-) in the parenchyma (red arrows) in Icos1ø vs. Icos1 treated animals. Scale bar is 10 µm.
(B) Immunoblots of CHO cell extracts resolved by 15% SDS-PAGE do not show increased levels of LC3-II in CT60 cells compared to wild-type CHO-KI cells or CT60 cells stably transfected with NPC1-YFP. No difference is noted with 10 μM U18666A, a drug that mimics npc1 loss of function. Rapamycin treatment (1 μM) of CHO-KI cells demonstrates robust activation of autophagy with increased LC3-II levels.
(B) UMAP plots of ACTA2 and ITGB1 expression of fibroblasts in human wounds. Raw scRNA-data are derived from (Davis et al. 2020, Data ref: Davis et al, 2020).
(A) Significantly deregulated canonical pathways in Cx3cr1-Rheb1Δ/Δ versus Rheb1fl/fl GL261 tumours, as identified by the IPA software from differentially regulated genes and divided in three categories: Adaptive immunity, Cytokine signalling, and Innate immunity. Size of bubbles is indicative of ratio of differentially regulated genes. The x-axis represents -log10(p-value) with a threshold of p≤0.05 applied.
acetylated lysine (C), and ΔΨm (D) in CD48- HSCs and CD48+ progenitor cells (HPCs) in the late phase after the administration of 5-FU.
The model depicts inter-regulatory balance between PP2A and HuR in controlling pro-inflammatory and anti-inflammatory response via altering Ago2 phosphorylation-dephosphorylation cycle and exosomal export of miRNAs in mammalian macrophage cells. Left half of the model shows Lipopolysaccharide (LPS) induced PP2A upregulation via TLR4 pathway during late hours of treatment which results in Ago2 dephosphorylation. Right half of the scheme represents Leishmania induced PP2A increase mediated by membrane glycolipid Lipophosphoglycan (LPG). Interestingly, the RNA binding protein HuR plays a central role in both the contexts. Inhibitory effect of HuR on PP2A ensures phosphorylated form of Ago2 to dominate which in turn facilitates miRNA unbinding to Ago2 and miRNA export via exosome thereby promoting pro-inflammatory cytokine response. On the contrary, Ld induced downregulation of HuR via a zinc-metallopotease, GP63 which results in PP2A upregulation that facilitates anti-inflammatory response necessary for the parasite survival and proliferation.
Effects of mocetinostat on cleaved caspase expression and susceptibility to gemcitabine in the patient-derived pancreatic cancer cells. Note that hPaca1 behaves similar to Panc1, but mocetinostat had no significant effect in hPaca2. Scale bar 20 μm. n = 3, mean ± SEM, Dunnett's multiple comparisons test (P-values in the graphs are *P = 0.01-0.05, **P = 0.001-0.01, ***P < 0.001, and ****P < 0.0001; for exact P-values, see Supplementary Table S4).
(A Conceptual mathematical modeling schematics depict TNF-induced necroptosis signaling via RIPK1/3 (RIP) and phosphorylation of MLKL (pMLKL). RIP is counteracted by a putative (A) constitutive NFκB-dependent survival factor X.
(D). Temperature unfold CD spectra for (G4C2)4 RNA alone (which shows a characteristic G-Q structure with minima at 237 nm, maxima at 264 nm and no additional signal), or in the presence of 2 μM DB1246, DB1247 or DB1273. A characteristic induced CD spectrum, in the 350 nm - 550 nm region, is observed only in the presence of each small molecule, confirming that each of these three compounds are binding to (G4C2)4 RNA G-Qs. Data in A represent mean ± s.d., n=1 with 3 technical replica. Data in C represent mean ± s.d., n=3 independent experiments. Data in D represent mean ± s.d., n=3 independent experiments.
C qPCR analysis of up- and down-regulated genes Pooled RNA was prepared from sorted B220+GFP+ spleen B cells of MaxKO-cd19 (n=4), MycKO-cd19 (n=4), or DKO-cd19 (n=4) and control HET-cd19 (n=4) mice activated Genes were randomly selected and qPCR was performed using specific primers for cd72, med13l, card11, ssh2, cdc7, mrpl12, rpl39, and cysc. max and c-myc were included as controls and actin was used for normalization.
I Populations of worms with different extent of lysosome permeabilization were analyzed. Graph represents percentage of worms with less than 5, 5 to 20 or more than 20 permeabilized lysosomes in the region of hypodermis corresponding to 100 µm of body length.
B. Salt stability of Smc5/Smc6-Twin-Strep interactions with Nse5/6 and Nse6(1-179). Immobilized Smc5/Smc6-Twin-Strep was mixed with Nse5/6 or Nse6(1-179)-CPD-His ('in'). Beads were washed with buffers containing the indicated salt concentrations. Bead fractions were analysed by SDS-Page and Coomassie staining. Pulldown efficiencies were estimated from the intensity of Coomassie gel bands.
C. Confirmation of sensor localization to different cellular compartments. Green, HyPer7; blue, DAPI stain
C) EMSA results of the binding affinities of CENP-C fragments indicated in (B) to the CENP-A nucleosome. All fragments were phosphorylated by CDK1.
(A) The rescue of the effects of 15 µM IPZ on MI spindles was examined in mouse oocytes expressing histone H2B-mCherry from microinjected mRNA, co-stained with SiR-tubulin and noninjected or injected with mRNAs coding for RanQ69L or hTPX2. Maximum intensity z-stack projections from confocal live-cell movies 30 min after GVBD, at metaphase I and anaphase I. Time in hh: mm is relative to GVBD. Scale bars, 10 µm.
A schematic illustration of the co-transcriptional RNAPII-spliceosome complex. plaNET-seq mainly detects splicing intermediates corresponding to 5' splicing site (5'SS) co-purified with engaged RNAPII complex.
(F) C5b-9 (MAC) surface levels on HIV-1-infected cells (strain NLAD8). Results are expressed as MFI of staining on infected (Gag+) cells. Each dot represents a single donor of CD4 T cells. n=6 donors of CD4 T cells. Data information: Error bars indicate SEM. *P<0.05, **P<0.01, Wilcoxon test. Only significant comparisons are depicted.
E. Plot of the total fluorescence/integrated density (in arbitrary units (A.U.)) of Chm7-GFP within (and outside of) the SINC. Error bars represent SD deviation of the mean from > 50 SINC or non-SINC accumulations pooled from 3 independent replicates. p values from un-paired student's T-tests with Welch's correction. **** is p ≤ 0.0001.
(e) Predicted structure of the RBD of SARS-like CoV Rp3. Template: 2ghw.1.A, GMQE:0.81, QMEAN:-1.50.
D. A549 cells were treated with 125nM dBRD9-A (+) or DMSO (-) for 6h prior stimulation with 1000 IU/mL of IFN-α2 for 16h. Following lysis, western blot was used to detect levels of the indicated proteins. Data are representative of at least two biological replicates.
CDependence of regulatory volume decrease (RVD) of HEK cells on LRRC8 genes. Cells were exposed to hypotonic medium starting at t = 0, and intracellular calcein fluorescence was followed over ˜1 h as semiquantitative measure of cell volume. Data are presented as mean values ± SEM from sixteen wells.