EMBO/sd-character-level-ner huggingface dataset:
(D) Fraction of EdU-positive (EdU+) cells in organoids cultured for 5 days in media containing R-spondin 1 and/or noggin, as indicated. The results, presented as means and standard errors, are derived from three independent experiments, each examining five organoids per condition. Statistically significant differences: +R+N vs -R-N (P<0.001); +R-N vs -R-N (P<0.05); -R+N vs -R-N (P<0.05).
(g) YAP/TAZ directed the nuclear localization of ATF4. HLE cell were transfected with plasmid constructs coding for wild-type TAZ (1C-TAZ-WT), constitutive-active TAZ (1C-TAZ- 4SA) or constitutive-active TAZ lacking a nuclear localization signal (NLS) (1C-TAZ-mNLS) and analyzed for TAZ and ATF4 expression and localization by immunofluorescence microscopy. DAPI visualized nuclei. Scale bars, 66.2μm. Results represent three independent experiments.
B TNFα-activated bEnd.5 cells were treated with DMSO prior to incubation with antigen-stimulated mouse T cells for 30 min. VE-cadherin was immunoprecipitated from cell lysates and precipitates as well as total cell lysates were analyzed by immunoblots for indicated antigens. Quantification of pY731 blot signals of five independent experiments are shown below, with the signal intensity for the control sample (no T cells, vehicle-control) set as 100%. treatment with Blebbistatin.
Scatter plot showing the genomic distribution of FOXA2 in PANC1 cells transduced with the HNF1β-expressing lentivirus (HNF1B O.E.) and in their matched mock-infected control. The fraction of gained, unchanged and lost FOXA2 peaks overlapping HNF1β ChIP-seq peaks in transduced PANC1 cells is shown in the pie-charts on the right.
A The largest subunit of Pol V, NRPE1 (red), was visualized by immunofluorescence microscopy using its specific antibody in cells expressing FLAG‐tagged AGO4 (green). AGO4‐NRPE1 co‐localized to nucleolar dot (yellow dot, marked with white arrow, upper panel) but not in nucleoplasmic foci (lower panel).
(B) Overall structure of the S. cerevisiae Hrr251-394 K38R:Mam187-191 complex, colored as in (A). View is equivalent to Figure 2B.
(A) Scatter plot of fold changes of RNA-seq data and MeDIP-seq data. The log2 fold changes of RNA-seq expression between wild-type control and Tet2Rank-/-; Tet3aRank+/- BMMs stimulated with RANKL for 2 days are shown on the x-axis, and log2 fold changes of MeDIP-seq expression (>0) are shown on the y-axis.
(D) Phosphorylation (p) of the STAT5 protein in B220low B-ALL cells (black) and control non-leukemic B220+ B cells (grey) from the lymph node of a 11-week-old Pax5Jak2/+ mouse. The p-STAT5 level was determined by intracellular staining with an anti-STAT5 (pY694) antibody.
F. AURKA co-localize with PCM1 at the peripheral satellite clusters upon chemical dimerization of satellites with Kif5b motor domain. U2OS cells were co-transfected with GFP-PCM1-FKBP and HA-Kif5b(1-269 a.a.)-FRB and treated with 500 nM rapamycin for 1 hour followed by fixation at 6 hours. Cells that were not treated with rapamycin were processed in parallel as a control. Fixed cells were stained with antibodies against GFP, AURKA and gamma-tubulin. DNA was stained with DAPI. Cell edges are outlined. Scale bar, 10 μm. G. Quantification of pericentrosomal levels of AURKA and gamma tubulin for F. n>25 cells per experiment. Data represent mean value from two experiments per condition ± SEM (****p < 0.0001; **p < 0.01; Unpaired Student's t-test.).
I, J A schematic of the domains of p65 or FXR that were fused to GST is shown on the top. The interaction between FXR and p65 or their domains was detected by GST pull‐down followed by IB.
Western-blot analysis of CYLD and FLAG in total protein lysates from GSC#9 transfected with WT or C464A MALT1-FLAG. GAPDH served as a loading control.
Ki67 immunostaining (C) and histogram of the number of Ki67+ cells per HF (D) in adult back skin sections from Prox1CreERT2+/+; LSL-ROSA26-iDTRKI/KI mice injected with vehicles (Control), Prox1CreERT2+/T; LSL-ROSA26-iDTRKI/KI mice treated with CSA and vehicle; and Prox1CreERT2+/T; LSL-ROSA26-iDTRKI/KI treated with tamoxifen, CSA and intradermal DT, starting from early Telogen (P49) and analyzed at the end of the treatments (P58). n= 3 - 4 skin samples per mouse, n= 3 - 4 mice.
A: Representative transmission electron microscopy images of mitochondrial structures in Detroit 551 control, WS5A and CP2A NSCs (scale bar, 400 nm).
(A) Schematic representation of human Cyclin B1 and Cyclin B2 protein domain organization.
B. Schematic representation of the analysis workflow for the pannels (G-J). The top and bottom quartiles of mRNAs, ranked by stability during the MZT were determined for each species. The codon composition of each group was compared and correlated with the codon optimality defined in zebrafish (CSC).
Representative images of hematoxylin and eosin (H&E) staining of ear sections from control, DKO* and DKO*K15 mice.
(G) Immunodetection of complex V structural subunits on Western blots of total cell lysates separated by SDS-PAGE, from three independent replicates of WT and ∆4-CYB cells. The graph shows the densitometric quantification of the signals corresponding to each subunit normalized to that of the β-Actin. The mean of the three control (WT) samples was set to 1.0 and all the measurements were referenced to that value. The values plotted in the graphs are the mean ± SD (n=3). There were no differences in the steady-state levels of the tested subunits (2-way ANOVA with Sidak's multiple comparisons test).
(B) Gel picture of Ctcflos transcripts expressed in differentiated brite adipocytes amplified by polymerase chain reaction (PCR) using transcript specific primers.
2D gel analysis of fork progression in wild type and rad9∆ cells through a 70-kb region of chromosome VI for which all active origins downstream of ARS607 have been deleted. The position of probes and the time after release from HU are indicated. Arrows point to Y arcs (fork signals) with the strongest intensity.
A. Zoom-in view of the Oct6-Oct6 homodimer interface in the molecular models based on crystal structures of two POU homodimers on MORE DNA. Oct6 POUS, orange; POUHD of the other monomer, blue. Important residues are labelled and Met (Oct6) in position 151 which was identified to guide the DNA-binding preference is marked with a star. Individual helixes of POU domains are numbered. Colour representation as in Fig. 1B, 1C. For clarity, the second monomer of Oct4/Oct6 is shown in dark blue.
K, Mice learned to drink water when continuous noise was present but avoided drinking when the noise was interrupted by silent gaps. 5 OtofI515T/I515T mice (pink, mean ±SEM red) avoided drinking less efficiently than 2 Otof+/+ mice (grey, mean ±SEM black) for shorter gap durations. See also Figs S2/S3.
A. HEK 293T cells were transfected with plasmids as indicated for 24 hr and treated with DMSO or 200 nM ISRIB for 2 hr followed by analysis of the protein level of CHOP, p-eIF2α, total eIF2α, and Endou-Flag using Western blot. The α-tubulin served as an internal control. Protein levels relative to each internal control are presented in each lane.
Abro1+/+, Abro1−/−, BMDMs transduced with lentiviruses expressing GFP, ABRO1-GFP or BRCC3-GFP were treated with LPS and nigericin. Immunoblot analysis of NLRP3 ubiquitination (detected by mouse anti-NLRP3 antibody) in cell lysates immunoprecipitated with rabbit anti-NLRP3 antibody
C Representative immunofluorescence microscopy staining of Msi1 of small intestinal tissue of young mTerc+/+mice. Dashed line outlines a crypt. Arrowheads and numbers indicate ISPC positions in the crypts. Scale bar: 20 μm.D Quantification of Msi1 staining intensity of ISPCs at indicated positions in basal crypts of young mTerc+/+mice (n = 150 crypts from three mice). Each dot presents one cell. Red lines: mean values ± SEM. Unpaired two‐tailed Student's t‐test.
E: Cells with the indicated genotypes were synchronised in G1 with α-factor at 25°C and then released in fresh medium at 34°C (t=0). Cells were collected at the indicated time points for FACS analysis of DNA contents.
(C) Chart shows normalised read counts for asmt. A significant higher number of asmt reads is detected in the opn4 dko than in the wild-type anterior brain. Note that asmt mRNA is detected in the posterior brain because the pineal stalk is most likely included in this part. Data information: blue markers indicate wild-type, grey markers indicate opn4 dko and red bar indicates mean. Biological replicates are indicated with round, triangular, and square markers (n=3). Asterisks indicate significance (0.01<p(✱)<0.05, 0.001<p(✱✱)<0.01, p(✱✱✱)<0.001, ns = not significant).
Diagram showing the procedure of reprogramming infected with shRNA for Cbs. RT-qPCR analysis of Cbs expression in MEFs infected with shNC and shCbs. n = 3. Immunofluorescence of Sall4 in shNC- and shCbs-infected cells with and without R406 treatment on d12. n = 5. Scale bar, 100 μm.
(I) RT-qPCR of ZIKV RNA in infected hNSCs transfected with siRNAs targeting LC3, BECN or ATG9A 48 h post infection. Mean ± SEM of 3 biological replicates. *p < 0.05 by Student's t test.
C Flow cytometry analysis of dead cardiomyocytes (CD45-, zombie+) 24 hours after MI. Student`s t-test; n = 3 mice in both groups; *P = 0.0072.
Flow cytometry analysis of HeLa and TRIM16KO cells stained with Annexin-V/Propidium Iodide (double staining), untreated or treated with (D) H2O2 (400 µM, 2h)
D-F. Immunoblotting of DRG homogenates shows that nerve injury-dependent nuclear HDAC3 dephosphorylation is reduced by the calcium scavenger EGTA upon in vivo delivery on the injured sciatic nerve (Axo=Axotomy). Cytoplasmic pERK levels are used as control of axotomy-dependent signalling. (E-F). Data is expressed as mean fold change of band intensity levels ± s.e.m. N= 3 biological replicates. (**p<0.01, ***p<0.001) indicate a significant difference (ANOVA followed by Bonferroni test).
Donor GFP+ mice were treated with NaCl, G-CSF or CoPP daily. At the 5th day of treatment we transplanted 5x106 of isolated PBMC to the lethally irradiated GFP- recipient mice, together with 105 GFP- BM-derived competitor cells. After 18 or 20 weeks we performed secondary transplantation of primary recipients' BM to lethally irradiated secondary recipients and followed the chimerism for additional 14 weeks. The majority of primary recipients transplanted with G-CSF and CoPP-mobilized PBMC have detectable GFP chimerism among BM KLS cells.
Network diagram of cross-links observed between Trs31 and Rab1/Ypt1. Many cross-links are observed at the C-terminal region of Rab1/Ypt1. Cross-links involving residues present in the atomic model are colored black, while cross-links between unmodeled residues are colored pink.
C A schematic representation of model polypeptides derived from amyloid precursor protein (APP) that were used in the study. The C-terminal 99 amino acids of APP (C99) were fused in frame with the signal sequence derived either from preprolactin (PPL) or APP. Lysine and cysteine residues and amino acids within the preprolactin signal sequence mutated in the PPLssKO-C99 construct are indicated whilst the TMD and signal sequences are shown in dark and light grey, respectively.
(E) As in (C), but in the presence of ATP. Periods in which a fluorescently labeled SecA molecule is bound are indicated by grey shading. (F) As in (D), but with ATP (257 traces).
C Doubling times of yeast strains cultures, grown at 25 ºC in YPD medium. Data are presented as mean +/- SD (n = 6 for Sc, n = 3 for ScNI, Sc[Ca], Sc[Sp] and Sc[At]; technical replicates). *P<0.05 (Brown-Forsythe and Welch ANOVA tests, with Dunnett's T3 multiple comparisons tests).
A) Heatmaps and cumulative distributions showing ZEB1 genomic distribution in the high-grade PDAC cell line PANC1. For comparison, the acetylation and methylation levels at the same regions are also shown in the low-grade PDAC cell line CFPAC1.
B Senescence curve of a representative est2∆ clone (upper panel). DNA samples were prepared at the indicated time points to analyze telomere length by Southern blot (middle panel) and t-circles production by RCA assay performed in the absence of dCTP and dATP.(lower panel). The graph shows signal intensities of the dots measured with the Fiji software (arbitrary units).
C. Significant transposons fold changes (p<0.05) were pooled and shown in a boxplot (grey). Note that the median value (black bar) is above 0. Arrow indicates the P-element (P-ele). Fold changes of individual transposons are shown in a barplot. Red bars, upregulated transposons. Blue bars, downregulated transposons.
Comparison of the 72-h measured relative viability AUC for 8/10 cell lines treated with SB590885 versus PLX4720
(C) Complexes from HEK293A cells transiently expressing the indicated mCherry constructs were immunoprecipitated using RFP-Trap before analysis by immunoblotting.
(C) Western Blot of whole cell lysate of adult mousebrain slices treated with proteasome inhibitor MG132 (10 M) and MEK inhibitor PD98059 (10 M) for 4 h. Proteasome block increases the levels of phosphorylated Munc18-1 and ERK1/2, which can be prevented by MEK inhibition. Blots were stained for pMunc18S241, Munc18, pERK1/2 and ERK1/2.(D) Quantification of (C). ERK phosphorylation of Munc18-1 in adult mousebrain slices expressed as ratio pM18S241 divided by total Munc18-1 levels. Vehicle (DMSO) was set to 1 (DMSO: 100 ± 0.8%; MG132: 375 ± 14.2%; MG132 + PD98059: 24 ± 3%, n = 3, ** p<0.01).
[b] (top) Cartoon schematic illustrates SyGCaMP6f targeting and action. (bottom) Image shows typical punctate SyGCaMP6f expression at DIV15. Scale bar, 20 µm.
E Venn diagram showing the overlapped DEGs in osprr73 mutants (pink circle) with previously identified salt-responsive genes which derived from China rice data center (black circle). Heatmap showing 6 common genes, the colored bar represents log2 (fold change).
F. Viability of primary human PMNs following incubation with 1.25% filtered culture supernatants and a dose response of the indicated dominant-negative (DN) toxins using the viability dye CellTiter. Emut1Dmut = LukEmut1LukDmut, Amut1Bmut = HlgAmut1HlgBmut, Cmut1Bmut = HlgCmut1HlgBmut, Smut1Fmut = LukS-PVmut1LukF-PVmut. Bars indicate Mean ± SEM, with n = 3 donors.
(D) Pulldown assay with in vitro-translated Mam187-191 (wild-type and alanine mutants) and Hrr251-394 K38R. Mam1 mutations also disrupt Hrr25 binding when the two are co-expressed in E. coli (Figure EV6B). Bottom: Sporeviability of MAM1 mutant strains (see Table EV2 for strains; strains tested are KC549, KC560, KC566, KC552, KC554, KC556, and KC558; 46-48 tetrads were dissected for each strain). "--" indicates that this mutation was not tested for sporeviability.
C) Graphical representation is the change in fluorescence (ΔF) normalized to basal fluorescence (F), ΔF/F. The final 10 seconds of baseline recording and 10 seconds of the depolarization phase are shown, arrow indicates start of depolarization. Non-linear regression was performed in GraphPad Prism7 using the plateau followed by one phase decay model. The decay constant (k) for GFP was 0.4971 s-1, while for GA50 it was 219.5 s-1. Similarly the tau (τ) values were 2.012 seconds for GFP and 0.00455 seconds for GA50, respectively. Data presented as mean ± SEM for each imaged timepoint. Statistical significance was determined using the Sidak-Bonferroni method, ****p < 0.0001, n=20 puncta regions from 4 biological replicates.
D. S staining of infected U2OS-ACE2 cells analyzed by immunofluorescence. The Hoechst dye stains the nuclei. Scale bar: 40 µm.
B FACS analysis (propidium iodide (PI)) of USP9X high and low expressing DLBCL cells shown in (A) to determine cell survival. Cells were treated with taxol and collected at the specified time points. PI negative cells are indicated relative to time point 0 (n=3 ± SD).
K) Quantification of the proportion of Cas9-positive cells (left) and mCherry-positive cells (right) in the VZ plus SVZ that are GFP-positive 24 h after control (Con, white) or gGFP (black) Cas9 plasmid (left) or protein (right) electroporation. Data are the mean of 3 independent experiments each (3 embryos per condition in total, from 3 litters).(D, H, K) Controls were set to 100% and the gGFP conditions expressed relative to control (D, 11%; H, 24%; K left, 40% K right, 28%). Error bars indicate SD; *, P<0.05; **, P<0.01; ***, P<0.001.
F Oxygen consumption rate of male mice treated as in (C), determined as in (C) (n=9/10). *P=0.044 (9 h), *P=0.013 (12 h) in repeated measures 2x2 ANOVA with Holm-Sidak posttests (Cited4-/- vs. Cited4+/+)
E. Flow cytometry analysis of MΦ populations in the liver or kidney in adult mice lacking Ccr2 or Nr4a1. Each symbol represents one mouse. Data are summarized from three independent experiments and represent mean ± s.e.m. Significant differences were determined by an unpaired t test. n.s.: not significant. *P < 0.05, **P < 0.01.
(d) Spleens from an L2A-cKO mouse and its control littermate (left), and flow cytometry of peripheral T cells from such mice (right). Numbers in quadrants (right) indicate percent CD4−CD8+ T cells (top left) or CD4+CD8− T cells (bottom right).
D. Protein lysates from parental (left), GCS-KO (middle), and LCS-KO (right) HeLa cells, CTRL or GOLPH3-OE were processed for SDS-PAGE and WB with the indicated antibodies. Data are representative of at least 3 independent experiments.
Immunoblotting analysis of expression of the indicated proteins in TNBC cells cultured with or without TGF-β.
(A) Immunoblotting against the HA tag or the GAPDH of proteins extracted from HEK293 cells transfected for 24 hours with 100 C4G2 repeats embedded in the human antisense C9ORF72 and fused in all three possible frames with a HA tag.
(B) Gene expression analysis of the indicated stress-induced genes in YSC5106 WT, nat4∆, H4R3K and double mutant strains. Expression levels were normalized to RPP0, whose expression remains unchanged.
Representative image ), cf and qRT-PCR quantification of intracellular Shigella in HeLa cells pre-treated with arsenite in the presence or not of amitriptyline, and corresponding controls
Lymphocytes from the Peyer's patches of C57BL/6 and Vα14 mice were stained with anti-CD3 and CD1d (PBS57) tetramer. Percentage of lymphocytes that were CD3+CD1d-tetramer+ iNKT cells among the Peyer's patches of C57BL/6, Vα14, and Jα18-/- mice are shown. Mann-Whitney test. Error bars are SD. C57BL/6 n=22; Vα14 n=16; Jα18-/- n=8.
Primary cortical neurons at 1 DIV were fixed and labeled with MAP-2 (green), β-III-tubulin (red) and WGA (white). The inset shows a magnified image of the area depicted in the merged panel. Yellow arrowheads point out TNT-like structures.
A Experimental scheme. Groups of four to six-week-old C57BL/6 mice (n=5 per group) were immunized i.p. with 104-107 PFU of WNV-poly(A), PBS (negative control) or mock (untreated). On day 30 post-immunization, mice were challenged i.p. with 3× 107 PFU of WT WNV
B. Response of HyPer7 probes targeted to indicated compartments to incubation with antimycin A (AntA, red curve and data points) or ethanol as control (black curve and data points). HeLa cells were grown with galactose as carbon source. Solid line represents average, points colored in the lighter version of the respective color are the corresponding ratios measured in individual cells. Data information: As most of the data were not normal distributed, instead of a t-test, a Wilcoxon/Mann-Whitney-U-test was performed and samples were compared in pairs. ***, p ≤ 0.001
(D) Cells were treated with sodium arsenite (50 µM) for 45 min, followed by recovery in drug-free medium. Kinetics of SG dissolution are reported. Images were taken over a time period of 4 hrs every 10 min. Dashed lines = 95% confidence intervals. Number of cells counted: 159 (siRNA control); 166 (siRNA Hsp90 α+β).
(B) Schematic representation of DPPA2, DPPA4 full-length and DPPA4 truncated proteins. The conserved domains are shown: SAP (light green), C-terminal (dark green).
E. Representative FACS plots showing analysis of in vivo BrdU incorporation assays. Mice were received 2mg of BrdU (i.p.) at d13 (left) or d28 (right) after 5-FU treatment. 20hrs later, BrdU incorporation in BM LSK cells was assessed using anti-BrdU antibodies. Bar chart at right indicates percent of BrdU+ LSK cells at d13 and d28 after 5-FU treatment (n=6 per genotype and time point). Data information: Data presented as mean ± SEM. The statistical significance was assessed using repeated-measures two-way ANOVAs with two-tailed Student's unpaired t-test analysis (D and E). *p<0.05, **p<0.01 and ***p<0.001.
e, Fluorescence microscopy showing ARF1-eGFP (green) and Golgi membranes (blue, GM130) after infection with Shigella M90T and the indicated mutants (red; mCherry-expressing bacteria). Scale bar, 10µm.
(D) Loss of interaction between Frizzled 4 (FZD4) and ß-Arrestin 2 (ARRB2) in GRK2-/- fibroblasts. Proximity ligation assay (PLA) between expressed FZD4-GFP and ARRB2-Flag showed significantly reduced proximity events between the two proteins in GRK2-/- cells. White dashed lines outline the transfected cells. Central band, median. Box, 1st-3rd quartile. Whiskers, 10%-90% percentile. Mann-Whitney U test; number of biological experiments and the total numbers of analyzed cells are indicated. Scale bar, 10 µm.
(G) Mitochondrial ATP content in mouse quadriceps (n=5-9). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001.
Staining for mouse IgG (red) as a surrogate parameter for vascular leakage and CD31 (green) is shown in GL261 glioblastoma sections following different anti-angiogenic treatments (C) with quantification in (D; n=3).
G Cytoplasmic and nuclear proteins were extracted from Caco-2 cells transfected with control siRNA, CASP4 siRNA or CASP5 siRNA and the indicated proteins were detected by immunoblots.
A Schematic showing the formation of control, MECP2-KO, and mosaic MECP2-KO/control neurospheres (WT83/Q83X cell lines were used).
Summary of lethal dose 50 (LD50) of bendamustine, CY, Cpd A (HDAC inhibition only), and Cpd B (nitrogen mustard only) against 11 human cancer cell lines.
(E) IGV track view of acetyl-histone H3 (K9) occupancy on the kif26ab gene region in MZsinhcaf mutant and wild type zebrafish embryos. The increased ChIP-seq peaks are highlighted with red dashed rectangle.
After starvation, LNCaP cells were transfected with control (CTRL) siRNA or AR siRNA. Cells were then treated with R1881 for the indicated times. Controls were treated with vehicle for 48 h.B-E Same as in (A), but mRNA expression levels of the indicated UPR genes were determined by qPCR at indicated time points after R1881 stimulation. Expression in cells transfected with CTRL siRNA was set to 100. Bars represent SE. P-values are shown indicating significant difference between AR siRNA- and control siRNA-transfected cells using unpaired Student's t-test.
C Cartoon of constructs containing ChHFR1, AtHFR1, ChHFR1* and AtHFR1* derivatives under the 35S promoter used for transient expression of transgenes in N. benthamiana leaves.
Associations between CSF T-tau, Ng and NFL (panels A-C). Black squares: CN (n=109), red circles: MCI (n=187), blue triangles: AD (n=93). Associations are shown for Spearman correlations. Aβ42 and T-tau were measured using the the INNOBIA AlzBio3 kit (Fujirebio, Ghent, Belgium), Ng was measured using an in-house immunoassay for Ng (Portelius et al, 2015) and NFL was measured using the NF-light® ELISA kit (Uman Diagnostics, Umeå, Sweden).
(B) Fat mass or volume of white adipose tissue (WAT). Adult mutant females showed higher WAT volumes. Unpaired t-test, n=8 mice.
(C) STXBP4 promotes the association of α-catenin with AMOT and LATS1. HEK293T cells were transfected with the indicated SFB-tagged constructs and subjected to the pulldown assay.