EMBO/sd-character-level-ner huggingface dataset:
A Gene targeting strategy. Left: max genomic locus, targeting construct and max targeted locus. In vitro Flipase (Flip) deletion of the selectable markers lacZ and neo results in a max targeted locus with exons 4 and 5 (coding for bHLHLZip domain) flanked by two loxP sites (fl, flox allele). Arrows represent PCR primers used for genotyping MaxF9 and MaxF10. Right: genomic PCR analysis of tail DNA from F1 mice. PCR products of max wt (430 bp) and max flox (526 bp) alleles. M, 1kb ladder.
(B) Quantification of BrdU+ KI67+ cells located at the basal side of VZ areas in control and EML1-deficient conditions (3 batches, 3 organoids analyzed per batch). Data information: Data in graphs are represented as means ± SD. Significance based on Kruskal-Wallis-test P-values: ***<0.001, **<0.01, *<0.05.
A Comparison of the cryo-EM structure of H2A.Z.2.2-NCP with the structure of canonical nucleosome (PDB: 3LZ0) in disc view. Histone octamers containing H2A.Z.2.2 and canonical H2A are superimposed for comparison. The 125 bp DNA of Z.2.2-NCP in green color is shown in surface mode. The 145 bp DNA of canonical nucleosome is colored in grey. Histones H2A.B, H2B, H3 and DNA at SHL 6 through SHL 7 are highlighted to show the structural differences between two nucleosomes. The Z.2.2-NCP histones are colored in orange, warmpink, and cyan. Their counterparts in canonical nucleosome are colored in yellow, red, and blue. Histone H4 is colored in grey. B Close-up view of the structures of Z.2.2 C-terminal regions (top) and H2A C-terminal regions (bottom). Black and white arrows indicate last residue at the C-terminus of Z.2.2 (G106) and H2A (K118) that are observable in the structures.
B. Expression of endothelial Notch target genes in microvascular endothelial cells isolated from skeletal muscle of mice fasted for 24 hours (Fasted group) and then refed for 4 hours (Fasted+Refed group) normalized to mice fed for 24 hours (Fed group). n=5, data represent mean ± SEM, unpaired t-test.
(B) H&E stained sections from the distal small intestine from the rabbits infected with the indicated strains 18 hours after infection. Black arrows point to bacterial colonies closely attached to the epithelium.
A Expression of plasmid-based NL-3xF reporters in HEK293 cells with and without over-expression of EIF1 (two-way ANOVA with Sidak's multiple comparisons test; n=9-12/condition). Black asterisks refer to comparisons between Empty Vector-transfected and EIF1-transfected cells; green asterisks refer to comparisons between EIF1-transfected cells expressing AUG-NL-3xF and those expressing a different reporter. For all panels, *** P≤0.001, **** P≤0.0001 for the specified statistical test. Bars represent mean ± SEM (compiled from ≥3 replicates).
J Immuno-blots showing the levels of PIF1, PIF3, HY5 in given genotypes grown in the Dark or Light condition as noted: p5/+, mix of an heterozygous pap5-2 siblings progeny undistinguishable from wild type; p5-2, pap5-2 and pifq, quadruple pif1-1 pif3-3 pif4-2 pif5-3 mutant; Histone H3 (H3), RbcL and PAP8 were used as controls; n.a., not applicable.
F. Motilities of Ec-K74A-K87A strains with over-expression of wild-type rpoC gene (Ec-K74A-K87A-C) or carrying the control plasmid (Ec-K74A-K87A-V).
(A) Cartoon of the strategy for generation of pseudotyped lentiviruses. HEK-293T cells were transfected with a lentiviral construct containing the EGFP marker gene and two more plasmids encoding for the gag and pol genes of HIV-1 and for the S protein of SARS-CoV-2. Alternatively, the latter plasmid was replaced by another one encoding the G protein of VSV. The cell supernatants collected after 48 h of transfection were used to transduce HEK-293T cells stably transfected with human ACE2.
(A) Schematic diagram of Atg16L1 and various mutants. The magenta box indicates 239-242A and the cyan box indicates 194-195A.
Detection of Xbp1 mRNA splicing in primary hepatocytes isolated from WT and KI mice treated with 0.5 μg/ml Tm for 2 h (E).
(k) Enzyme-linked immunosorbent assay of KC secretion by wild-type and RIP2-deficient MEFs infected for 0.5 h with M90T and incubated for 5.5 h in the presence of gentamicin.
(C) Northern blot analysis of pre-rRNAs from control and patient B-LCLs. (D) Log2 values of 18S-E/21S and 18S-EFL/21S for P1 and P2 were normalized to the values of the control and presented in a graphical format, as Log averages + standard deviation for two independent experiments.
(C) Same as (A) for the CPTAC dataset. The different proteomic datasets were colour-coded (green=Kinobeads, blue=CRC65 full proteomes and purple=CPTAC full proteomes).
(C) Denaturing immunoprecipitation (IP) of FLAG-Orm2, FLAG-Orm2-3A and FLAG-Orm2-3D. The control strain expresses untagged Orm2. Input and elutions (with FLAG peptides) were analyzed by SDS-PAGE and Western blot with the indicated antibodies.
Elp3cKOs HCs harbour a flatter stereociliary bundle that is centrally shifted. (F) Elp3cKO HCs possess a significantly larger bare zone (WT/KO IHC: n= 23/24 cells; OHC1: n=27/27; OHC2: n=27/29; OHC3: n=30/29; cumulative data collected from 3 animals per genotype; One-way ANOVA, Tukey's multiple comparisons test; ***p<0.001, *p<0.05 F=16.72, DF=7; mean±SD).
Walking speed of 10-day old adult male flies of the indicated genotypes was calculated Mean ± SD. Unpaired two-tailed t-test, biological replicates: Control, n = 63, WT, n = 45, T199A, n = 70, T233A, n = 87; 2TA, n = 43.
A Schema of experimental design. Organotypic cultures with established brain metastases from H2030-BrM cells were treated with DEBIO-0932 at 1 µM for 6h and subjected to laser capture microdissection (LCM) and proteomic profiling.
E,F HeLa cells were transfected with plasmids expressing the indicated R-Luc-let-7 reporters or the corresponding reporters carrying mutations in the let-7 binding sites and a plasmid expressing F-Luc as a transfection control. Renilla luciferase activities were normalized to those of the F-Luc and set to 100% in cells transfected with the reporter lacking the let-7 binding sites and analyzed as described in (A-D).
(L-O) Enlarged LGG-1 and SQST-1 aggregates are colocalized in epg-4 mutants (L and M). Simultaneously depleting epg-7 reduces the size of LGG-1 puncta and SQST-1 aggregates, which become largely separable (N and O). (L and N) DAPI images of the embryos shown in M and O, respectively.
I, Endogenous altFUS mitochondrial expression in HEK293 cells following fractionation (representative image from n=3), with Tubulin as a marker of the cytosolic fraction and VDAC as a marker of the mitochondrial fraction. We used siFUS transfected cells as a negative control and altFUS transfected cells as a positive control for altFUS expression (WCL = Whole Cell Lysate, Cyto = Cytosol fraction, Mito = mitochondrial fraction).
Densitometry (top) and qPCR analysis of native and variant CSF-1R expression in HEK293 cells relative to native-transfected at 24 and 48 h (**** p < 0.0001, *** p < 0.0005, , ** p < 0.005 one-way ANOVA with Sidak's post-test for multiple comparison, n = 3 biological replicates, error bars indicate SEM).
C2C12 cells were treated with 0, 0.5 and 2 mM SUC for 48 h. The enzymes activity of (C) SDH, (D) LDH
Parental AGS, ALPK1‑KO and TIFA‑KO cells were infected with H. pylori for the times shown. Total cell lysates were analyzed by immunoblotting using the indicated antibodies. CagA demonstrated a similar infection rate of the different cells. Asterisk denotes an unspecific band and the arrow indicates the band corresponding to phosphorylated p100.
(C) IGV plots representing SSB interacting with the tRFTyrGUA in samples that were treated with low levels of RNase digestion. SSB bound tRFTyrGUA reads mapped to multiple loci encoding tRNATyrGUA. (D) Similar to the IGV plots shown in (C), but depicting SSB interactions with tRFTyrGUA loci in samples without RNase digestion.
(C, D) Dual and single colour kymographs showing that microtubule binding behaviour of p150 depends strongly on ionic strength: (D) At higher ionic strength (BRB80 supplemented with 60 mM KCl, see Methods), Alexa647-p150 (green) binds only weakly to the microtubule without a detectable plus end preference. Protein concentrations as in C. The Atto565-tubulin concentration was always 17.5 µM tubulin. The temperature was 30°C.
(B) Treatment with BoxA at increasing doses reduced the number of mice with detectable tumor lesions in a statistically significant dose-dependent manner (Spearman correlation: P=0.04). In this experiment, no BLI measurement was taken.
(D) Representative immunohistochemistry of KLF10 protein expression in the liver sections from NAFL and NASH mice. The bar chart showed the fold change of KLF10 positive cells per field (NASH vs. NAFL). n=5. Data information: * P <0.05, ** P <0.01-. Results are shown as mean ± SD. Student's t test
G, H Quantitative analysis of changes in H3K9cr (G, left panel of H) and H3K14la (right panel of H) levels by western blotting among different groups of the embryonic forebrain. Data are presented as mean ± SEM of three independent biological replicates, n = 3. Two-tailed unpaired Student's t-test was used to analyze statistical significance; NS: no significance, P < 0.05, P <0.001.
(e) Regular insulin (Ins) was injected into the tail vein of Atg7+/−-ob/ob mice that were treated with imatinib or PBS for 8 weeks. Seven minutes later, tissue lysates were prepared and subjected to immunoblotting.
(J) ATAC and H3K27ac peaks in the promoter and enhancer regions within the CD48 locus. ChIP-seq data for transcription factors obtained from the public database (GSE22178) were merged.
By tracking the patients' heterogeneous drug response caused by different genetics and environments, adaptive chronotherapeutics adjusts the dosing time: if the current dosing regimen leads to a weaker or stronger drug effect than the desired one, the dosing time is delayed or advanced by 1 h, respectively
Trajectories of the different tau biomarkers in preclinical AD using a local weighted regression method (Loess curve). Changes on biomarkers levels in CSF are represented as z-scores using Aβ PET in centiloid scale (CL) as a proxy of disease progression. Abnormal biomarker levels were determined as two standard deviations (SD) above the mean. Incipient Aβ pathology positivity was determined as Aβ PET higher than CL 12 (Mila-Aloma et al., 2020). All samples were run in singlicates.
P. FFA amounts in Skm extracts (wt, n= 8; LowOXPHOS, n= 8). Data information: Bars are the mean ± s.e.m. of the indicated (n) mice/genotype *p <0.05 when compared to wt by ANOVA and Student's t-test.
(C) Expression of RagC WT and 3A was induced by addition of tetracycline overnight. Cells were serum starved for 2 hr followed by insulin (100nM) stimulation for indicated time. Left: Lysates were analyzed by Western blot for the levels of the specified proteins and the phosphorylation state of S6K1. Right: Graph shows mean ± S.E.M. of quantitative analyses of the Western blots after normalization for total protein, n=3
(A) Relative expression of the BBSome subunits in the indicated organs and T cells measured by qPCR. CT values of the BBS genes were normalized to the geometric mean of the CT values of reference genes Gapdh, Tubb2a, and Eef1a1. The expression levels are normalized to those of brain (=1). Mean+SD. Three biological replicates (the result of each biological replicate is a median of three technical replicates).
Heat map represents cytokine secretion by in vitro expanded (C) murine splenic iNKT cells co-cultured either with thapsigargin- or tunicamycin- or DMSO-treated murine BMDMs. The heat map shows the average result of two pooled biological replicates.
K LAMTOR1 KD increased PI(3,5) P2 (0.5 µM)-induced TRPML1-GCaMP6m responses and the blocking effect of ML-SI1 treatment (20 µM). L Quantification of peak TRPML1-GCaMP6m responses as shown in K. N = 6-16 cells from 3 independent experiments. Data information: Data with error bars are represented as means ± SEM. Statistical significance was assessed by two-way ANOVA with Tukey's post hoc analysis *P < 0.05, **P < 0.01, ***P < 0.001, ###P < 0.001, n.s., not significant. traces represent the mean values of each group.
, Hydroxyproline content in lungs from control and F-CRTH2 KO mice treated with ISO. *P < 0.05 vs control, #P < 0.05 vs saline group (two-way ANOVA); saline groups, n = 4 each; ISO groups, n = 8 each.
(B) Phage sensitive PY79 (WT) cells were infected with SPP1 at 2:1 (phages:bacteria) MOI, and placed in the outer ring of a transwell, as illustrated. Phage resistant BS12 (ΔyueB, PsigX-gfp) were placed in the inner ring. Fluorescence intensity from PsigX-gfp (AU) of the inner compartment was followed at 2.5 min intervals. Uninfected population served as a control, and its fluorescence was subtracted from the overall GFP signal of the infected culture. Shown is a representative experiment out of 3 biological repeats, and the average values and SD of 8 technical repeats.
(E) Real-Time RT-PCR analysis for IL-1β, VEGF, and MMP-13 mRNA levels in PC3 cells treated with 1μM NaHS for 24h Data information Data shown represent the means ± SD (n=3 biological replicates) Student's t-tes was used for the statistical analysis (*P<0.05; **P<0.01; ***P<0.001)
(A) Summary and representative immunoblots of total PKCα and p-PKCα in dPMNs that were pretreated without or with PKC inhibitor Go6976 for 1 h, and then treated without or with PMA (A) for 3 h. Panels A is summary analyses of immunoblots that were calculated based on the arbitrary unit (A)
F Measurements of mitochondrial respiration with complex II substrates (succinate and glycerol-3-phosphate) did not show significant differences between Phb2-deficient and control podocytes (n = 6).
A Membrane antibody array assay using CM from SOM230-treated or not CAFs (representative of n = 3). Controls are circled in blue dashed line and IL-6 in red square.
C) Merged and split channels confocal images (bar = 10 µm) of representative Tor1a+/+ and Tor1a+/- ChIs showing red dots and yellow puncta (indicated by white circles), quantified in (D): red dots: Tor1a+/+ n=13 cells, Tor1a+/- n=14 cells, t test ***P=0.0003; yellow dots: Tor1a+/+ n=13 cells, Tor1a+/- n=14 cells, t test **P=0.0048, N=5 mice/genotype). Measurement of the mCherry/yellow dots ratio indicated that the autophagic flux was not altered (Tor1a+/+ n=13 cells; Tor1a+/- n=14 cells, Mann Whitney test P=0.8842). Data in B,D) are represented as mean ± SEM
Western blotting showing that LAQ (5 or 25 mg/kg) treatment for 2 months up-regulates multiple myelin proteins (MBP, MOBP and MOG) in the corpus callosum in PLP-150Q mice, which were treated from 3 months of age. Ratios of MBP, MOBP or MOG to vinculin obtained from 3 independent experiments were presented on the right. One-way ANNOVA followed with Tukey's test. MBP: ***P=0.0009; MOG: ***P=0.0003; MOBP: **P=0.0067. Data are mean ±SEM
(A) Heat map of differentially expressed miRNAs during KSHV replication at 0, 16 and 24 hour identified through miR-Seq. miR-29b and miR-30c are highlighted in red, with T test analysis.
male C57BL/6J mice fed with chow diet supplemented with 0, 0.5%, 1% SUC for 8 weeks. lactate production were tested.
B Two different views showing the interaction of the two Homo sapiens (H.s.) eIF3j protomers with the 40S.
B Immunoblot analysis of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 mLIR+∆623-691 for 24 hours or not, and then treated as indicated.
(G) The representative immunofluorescent images and quantitative analysis show significantly increased STAT1 signal in the nuclear fraction of HEK293 cells with overexpression of hTau compared with the empty vector control (eGFP) (n=5). Scale bar, 10 μm. Data information: Data were presented as mean ± SD (Mann-Whitney test). , **, p<0.01 vs Ctrl.
Left: Representative YFPfluorescence microscopy and DIC images of cay1∆ strains expressing Cay1‐YFP. Scale bar, 10 μm. Right: Representative YFP and RFP fluorescence images of Cay1‐YFP‐ and Pot1‐RFP‐expressing cells. Arrows point to YFP and RFP foci within the same nucleus demonstrating lack of co‐localization. Scale bar, 5 μm.
C. Cells in (B) were subjected to QIBC analysis of γ-H2AX signal intensity (red bars, mean (A.U., arbitrary units); n>2000 cells per condition).
(B) Analysis of chromosome number in control and CEP55 knockdown MDA-MB-231 cells (sh#8) by Giemsa staining of metaphase spreads (left panel). Representative images showing chromosome spreads assessed by Zeiss AxioScope2 microscopy (right panel). n= number of metaphase spreads counted (mean ±95% confidence interval of two independent experiments).
Lipid-incorporation of [1-14C]acetate after a 1 h pulse in coS#2 and co acc1N/H relative to the cho2opi3 parent strain during culture on SD C+ medium. Data are shown as mean of 2 biological replicates.
(A-D) EVs were isolated from CCM of uninfected or HIV-1-infected Jurkat cells by differential ultracentrifugation and sEVs contained in the 100K pellet were further separated by velocity iodixanol gradient (D). (D) 12 fractions were recovered from iodixanol gradients of the 100K pellets obtained from CCM of non-infected and infected Jurkat cells and analysed by Western blot for the indicated proteins.
(B) Quantification of fluorescent DCF normalized to control (n=3 independent experiments/group; 30 spheroids quantified/experiment).
(G) Representative images showing the effects of a knockdown of the endogenous Spindly in HeLa cells. RNAi treatment was performed for 48 h with 50 nM siRNA. Before fixation, cells were synchronized in G2 phase with 9 μM RO3306 for 16 h and then released into mitosis. Subsequently, cells were immediately treated with 3.3 μM nocodazole for an additional hour. CREST serum was used to visualize kinetochores and DAPI to stain DNA. Scale bar: 10 µm. Three biological replicates were performed.
(H) MeDIP-qPCR was performed in WT and MCK-KO soleus muscle to assess differential methylation using primer sets from (G) (n = 4, means ± SEM, * p < 0.05, two-tailed student's t-test).
(C, D) Measurement of the intracellular ER-scission activity of FAM134B WT, G216R, S151A-G216R and SA-G216R. GFP-tagged FAM134B proteins were expressed in U2OS cells at same levels. The autolyosomal degradation of ER fragments labelled by GFP-FAM134B were blocked by Baf A1 or DMSO. GFP-positive puncta were quantified for each cell in (D). For all of the groups, at least 30 cells were included for quantification; Scale bars, 10 μm. ***P<0.001, one-way ANOVA, error bars indicate SEM.
(c-e) Control siRNA- or VDAC1 siRNA-silenced HeLa cells were transfected with the indicated combinations of EGFP-Parkin wild-type, VDAC1-Flag wild-type or appropriate empty vector controls. Cells were treated with CCCP for 2 h and 24 h and stained with anti-HtrA2/Omi (pseudo coloured; blue) and anti-Flag (red) to visualize mitochondrial morphology and re-transfected VDAC1, respectively. Wild-type Parkin was visualized by EGFP epifluorescence (green). Parkin-positive cells are surrounded by a line. Representative pictures of three independent experiments are shown. Scale bars, 10 μm.
Representative images of RNAscope for LINC00115 and IHC for ZEB1 and ZNF596 expression in two GBM specimens, Sample #1 (positive) and Sample #2 (negative). Scale bar, 50 μm. Images are representative of two independent experiments.
I-K The expression of FST and phosphorylation of CREB were detected by Western Blotting (I and K) and phospho-flow analysis (J) in MOLM-13 (I) and Ba/F3-FLT3/ITD (K) cells treated with Quizartinib and BRD7389 for one day, respectively. Data information: the experiments were performed in triplicates, and the data were presented as mean ± SEM. **P<0.01, ***P<0.001 (Student's t-test).
B Volcano plot of MISO results for all annotated skipped exons. ΔAS exons (in red) have Bayes factor > 10 and a ΔPSI absolute value > 0.10. Within the ΔAS exons, negative ΔPSI values indicate activation-excluded exons, whereas positive ΔPSIs reflect activation-included exons. Unchanged alternative exons (AS, not Δ, dark gray) have a Bayes factor < 10 and a ΔPS| absolute value < 0.10.
(E, F) Tuberculosis lung lesions of Mir342-/-B6 and Mir342-/-B6 mice supplemented with Socs6 siRNA (E), or Mir342+/+C3H and Mir342+/+C3H mice supplemented with SOCS6-overexpressing vector (F) at 21 dpi were detected by haematoxylin/eosin staining. Representative images from n = 3 biological replicates are shown.Scale bar = 100 μm.
(A) Flag‐tagged DAPK (100 ng) was incubated with GST (900 ng) or GST-beclin‐1 (750 ng) in the presence of Ca2+, calmodulin and [γ‐33P]ATP for 30 min or 60 min. Phosphorylated proteins were visualized by X‐ray film exposure, and GST/GST-beclin‐1 levels were visualized by Ponceau S staining. The autophosphorylation of DAPK indicates that its catalytic activity was intact in all samples.
(A) Normal proline but decreased whole-brain glycine levels in the brains of PtenΔC/ΔC mice (P21), as determined by ELISA analysis of the S1 fraction, obtained after the removal of unbroken cells and large debris (see Materials and Methods for details). (proline, n = 10 mice for WT and 8 for ΔC, glycine, n = 9 mice for WT and 8 for ΔC, *P < 0.05, ns, not significant, Student's t-test). The error bars represent SEM.
(B) Association of PAUSS with the number of proautistic genotypes of the 8SNP risk model in the discovery sample.
(A) Chromosomal instability readouts, of later passage lines, assessed by average chromosomes loss per metaphase, average number of structural rearrangements per metaphase and percentage of metaphases with marker chromosomes (n=20 for each dataset and error bars denote SD).
(D) Import of Mcp3 is dependent on Tom40. Mitochondria isolated from wild-type and tom4025 cells were incubated with radiolabelled Mcp3 for the indicated time periods. Next, mitochondria were reisolated and analysed by SDS-PAGE and autoradiography as described in (B). As a control Ugo1 was imported into the same mitochondria. Organelles were reisolated and analysed by BN-PAGE and autoradiography. The band corresponding to the Ugo1 dimer at around 150 kDa was quantified. The mean with standard deviation is shown (n=3; SD).
D. ssDNA formation in siRNA-treated MCF-7 cells after HU treatment. BrdU (20 μg/ml) was added during the last 24 h of siRNA treatment and was removed by a brief wash prior to HU treatment (4 mM, 2 h), pre-extraction, and fixation. BrdU in ssDNA patches and PCNA were detected without a DNA denaturation step. Scale bar, 10 μm. Diagrams show the frequency of PCNA-positive BrdU foci.
PKM2 S-nitrosation in pulmonary endothelial cells from WT and YF mice; n=5-6 independent cell batches (Unpaired Student's t test). Dithiothreitol (DTT) treatment was included to demonstrate specificity of the SNO signal. The blots show non adjacent bands cropped from the same membranes.
B Western blot showing ATM and KAP1 phosphorylation and total protein levels in WT and SirT7-/- primary fibroblasts after IR (8Gy). ATM inhibitor (ATMi) KU-55933 was added 30 min prior to irradiation where indicated. One representative blot from 4 independent experiments is shown.
Rab25 deletion mutants do not alter cellular glycogen and ATP levels. Ovarian cancer cell lysates were collected 24 h post transfection. (a) p < 0.05 versus empty vector transfected cells.
(A) DVL3 co-immunoprecipitates KMT2D in MDA-MB-468 cells (upper panel) and MCF7 cells (lower panel). IgG heavy chain (Hc) was blotted for as a control for equal antibody capture for immunoprecipitation and whole cell extracts (WCE) as a positive control.
(A) Fluorescent western blot analysis of Atxn1, Msk1, and Rsk3 in seven different brain regions of wild-type mice at 9 weeks old (n = 3). Each protein levels were represented relative to the protein levels in brainstem. Mean ± SD, **P<0.01, ***P<0.001 ****P<0.0001, one-way ANOVA. Data information: BS: brainstem, CBM: cerebellum, MB: midbrain, ST: striatum, HC: hippocampus, CTX: cortex, OB: olfactory bulbs.
Structure of SR34 RNA isoforms. Large black boxes indicate exons, narrow black boxes indicate UTRs, black lines indicate introns. Colored boxes indicate protein domains affected by an AS event. RS domain: Arg/Ser-rich domain. Red arrows indicate probes used for gel electrophoresis. Protein domains were retrieved from Uniprot database (https://www.uniprot.org).