EMBO/sd-character-level-ner huggingface dataset:
Interaction of SNIPER1 H129Y-CLuc and SUMM2NB-NLuc (D), RPP4NB-NLuc (E) or CHS1NB-NLuc (F) as tested by split-luciferase complementary assay in N. benthamiana. Three biological repeats with four technical repeats each were carried out with similar results.
Left: Representative live-cell fluorescence imaging of GFP-AHPH in negative control and CAMSAP2 siRNA transfected hRPEs. Scale bar: 20 μm. Right: Quantification of GFP-AHPH fluorescence intensity.
A Representative photographs of fly eyes expressing (CGG)90-EGFP under a GMR-GAL4 driver, with various belle disruptions.
DNA methylation status of the Rasgrf1 differentially methylated region (DMR) in spermatogonia from chr7 piRNA clusterΔRMER4B/ΔRMER4B mice.
(A) CD144-enriched EVs were isolated from serum of IPAH patients (n = 37) and HCs (n = 34). The levels of miR-483-3p/-5p were measured by qPCR. Data information: Values are expressed as median ± interquartile range. Statistical test: Mann Whitney U test.
Fractionation and Western blot analysis of wild-type and Flag-tagged PDP2 (top), and wild-type and MTS-deleted (∆MTS) MRPL28 (bottom). Flag-PDP2 and ∆MTS MRPL28 were mislocalized. W, C, and M denote whole cell lysates, cytosol fraction and mitochondrial fraction, respectively. Tubulin and VDAC serve as fractionation quality controls.
B,C Effects of H2A mutations (B) and H2A.B mutations (C) on nucleosome resistance to MNase digestion. MNase digested nucleosomal DNA are analyzed by 10% Native-PAGE. All MNase digestion experiments are repeated twice.
EMSA of nuclear extracts of Jurkat cells transfected with indicated expression vectors and assessed with a probe covering the putative unmethyl- or methyl-CRE sequence in the TSDR
(F) Serum-free conditioned media (CM) was collected from vehicle-, doxorubicin-, paclitaxel-, palbociclib- or abemaciclib-treated BJ cells 8 dpt and expression levels of CXCL1 and CCL5 measured by ELISA (n=6 independent experiments). Data information: Data are means ±SD. One-way ANOVA *p<0.05, **p<0.01, ***p<0.001, N.S.= Not significant.
(I-K) Mouse brains: Neurexins and CA10 were immunoprecipitated from total mouse brain lysates and subject to heparinase treatment. (I) Samples were analyzed by immunoblotting using antibodies against neurexins, the 3G10 epitope (for the HS stub) and CA10. Stars indicate non-neurexin bands (see results). (J) Quantification of low molecular weight neurexin (LMW; white arrowhead) in relation to total neurexin amounts [upper band (line) + LMW]. Data shown as mean ±SEM (n=3 independent experiments); *, p< 0.05 by 2-way ANOVA and Holm-Sidak tests. (K) Quantification of the 3G10 signal normalized to the signal of the corresponding neurexin band. Data shown as mean ±SEM of 3 biological replicates. *, p< 0.05 by 2-way ANOVA and Holm-Sidak tests.
C. DNI of Δ31-160 variants is similarly inversely related to size of deletion and dependent on intact C-terminal H1-H2 portion. Immunoblot probed with mAb 3F4 showing PK-resistant (3F4) MoPrP co-transfected with indicated constructs into 22L-ScN2a cells (left panel). Δ31-160 was slightly more effective than Δ159. Right panel shows quantification of results as obtained from a triplicate experiment, using densitometry on ImageJ. Bars illustrate mean ± standard deviation. *, p<0.05.
(D, E) Dual and single colour kymographs of GFP-dynein (green) on dynamic Alexa568-microtubules (magenta) in the absence of EB proteins (E). Concentrations of the proteins present as in A.
C) Quantification of the rate of mitophagy in motor neurons expressed as the percentage of area with high ratio (543/458nm) signal normalized by the total mitochondria area. Data were collected from mice at 60 days (n= 3, 1 male and 2 females), 90 days (n= 4, 2 males and 2 females), and 120 days (n= 4, 2 males and 2 females). Number of neurons imaged: 60 days, n= 77 Non Tg and 87 SOD1-G93A; 90 days, n= 118 Non Tg and 173 SOD1-G93A; 120 days, n= 110 Non Tg and 130 SOD1-G93A. Comparisons within pairs showed that mitophagy is increased in SOD1-G93A spinal cords at 60 and 90 days compared to Non Tg. Results are expressed as mean ± SEM. For 60 days, **p= 0.0022; for 90 days, ***p= 0.0001; for 120 days, p= 0.094, all by unpaired Mann-Whitney test. Comparisons along time showed that mitophagy increases over time in both genotypes. For Non Tg, by unpaired Kruskal-Wallis's test with Dunn's correction, **p= 0.0046 and ***p= 0.0001. For SOD1-G93A, by unpaired Kruskal-Wallis's test with Dunn's correction, **p=0.0077 and *** p= 0.0001.
(D) Acetylated cohesinHalo488 was treated as in (C), the DNA-bound cohesin was further incubated with buffer, Wapl-Pds5, or Wapl-Pds5 plus Sororin, and then cohesinHalo488 particles were observed in the presence of ATP and 100 mM KCl. MSD versus time is shown. D indicates the diffusion coefficient (n = 45, mean ± s.e.m.).
(A) GFP-Chimeras were treated with the BCL-XL inhibitor A1331852 (n=8, 5 doses by oral gavage, 25 mg/kg body weight each dose). Control groups (n=8 each group) include untreated GFP-Chimeras and un-irradiated C57BL/6-Ly5.1 (wild-type) mice treated with the BCL-XL inhibitor A1331852 or left untreated. Mice were monitored for up to 200 days post-treatment (dpt). Data are presented as % survival.
A Immunofluorescence images of MMS22L foci formation at etoposide (ETP)-induced DSBs during S, M and G1 phases of the cell cycle in HeLa cells. Scale bar: 5 μm.B Quantification of a representative experiment from (A) shows number of MMS22L foci per nucleus during indicated cell cycle phases (n = 2; nnuclei ≥ 60).
(B) Adult muscles were transfected with YFP‐LC3 and with pDsRed2‐Mito. Lysosomes were inhibited by treating mice with 50 mg/kg of chloroquine for 7 days. Chloroquine treatment started at the day of denervation and lasted for 7 days, whereas for fasting experiments at the 6th day of chloroquine injection food was removed for 24 h. Muscles were exposed and observed in situ using confocal in vivo microscopy. At least five animals per condition have been studied. Scale bar, 20 μm.
(F) Nuclease activities of free MjMre11 (lane 3, 4), nucleotide unbound- (5, 6) and -bound MjMRcd complex (7, 8) towards a hairpin DNA. Each protein sample was incubated with a hairpin DNA (10 nM) in a 1:10 or 1:20 molar ratio (protein: DNA) for 30 min on 55°C. The error bars for the quantified values of uncleaved substrates on the right panel are calculated from the standard deviation from three repetitions of each experiment.
A) Barplot showing the percentage of significant genes in the muscle modules. Next to each module name we report the total number of genes that it comprises. B) Barplot showing the percentage of significant genes in the blood modules. Next to each module name we report the total number of genes that it comprises. C) Matrix with the values of the cross-correlation between blood and muscle module eigengenes. To enhance visibility, only correlations with absolute value above 0.5 are shown.
Cell death induction by EV20/MMAF (10 nM) analyzed by double annexin V and PI staining in BT474 and BTRH cells (50,000 events).
D Bioinformatic analysis shows that mRNAs whose TE is increased by Porthos have significantly shorter 5'UTRs than non-targets (p=1.69e-35). Box and whisker plot of log2(Mean 5'UTR length) of each genotype. Middle line of box represents median, upper and lower bounds of box represents 1st and 3rd quartiles of data. Whiskers represent 1.5*IQR (inner quartile range), points outside of 1.5*IQR are plotted explicitly. The corresponding table shows median/mean 5'UTR lengths in base pairs (bp) for all mRNAs expressed in S2 cells (non-targets) and for the subset whose TE is enhanced by Porthos (Porthos targets). Targets were defined using n=3 biological replicates of polysome-seq. 5'UTR length comparison is between n=8451 non-target genes and n=204 Porthos targets. Data information: Mean±SEM, ns=p>0.05, *p<0.05, ****p<0.0001. Welch's t-test
Immunoblot of M2 anti-FLAG immunopurifications from media collected from HEK293T cells overexpressing ERdj3WT and FTTTR variants as indicated. Media inputs (1:400) are shown as a control.
Longitudinal analysis of ear thickness in DKO* mice at different time points during psoriasis-like disease progression
(F) Tumours were harvested at the end of the experiment, four hours after the last dosage and subjected to immunohistochemistry analysis using cleaved Caspase 3 antibody (clCasp3) . Apoptotic sells were counted in 25 fields per each condition (left panel) and quantified as clCasp3 positive cells/field (right panel). Representative images are shown. Bar 100 μm
Electropherograms of the XRCC4 genomic region encompassing the nucleotide substitutions in available members of the family.
(B) Graph of the quantification of autophagic vesicles (AV) per photoreceptor found in EM sections of 1‐week‐old sav3 clones. Significant accumulation of AV is found in mutant cells. ***P0.001 in one‐tailed t‐test. N=45 pigmented cells versus 42 non‐pigmented cells.
D) Wild-type organoids, at early stages of development (1-2d) prior to crypt budding, form small spheroids that also exhibit either a columnar or a stretched epithelium where YAP is cytoplasmic or nuclear, respectively.
U2OS WT, PHF6 knockout and PHF6 knock out cells that were reconstituted with GFP-PHF6 were synchronized in G2 cells were lysed and analyzed using western blotting with the indicated antibodies
(d) A combined super-resolved image of NSP2-rich condensates (NSP2-SNAP in red) and Seg3 transcripts (cyan) in RV-infected cells 4 HPI. Scale bars = 2 μm (top), 500 nm (inset i, bottom).
B. Western blots of MDI protein in wild type (wt) and mdi1 flies, showing that mdi1 is a protein-null mutation. Tubulin was used as loading control.
B) Schematic diagrams of deletion mutants of chicken CENPC-CT. The fragments containing the canonical CENPC motif and the CM downstream region. CENPC643-864, CENPC643-740, CENPC643-740, and CENPC643-683 lack the CM upstream region. CENPC-CT and CENP-C619-689 contain the CM upstream region.
C, Unmixing result of Hb, HbO2 and lipid from liver, kidney, iBAT, and rpWAT. Each dot represents data from one animal, in total 8 animals (n = 8). Data represent the mean (+/- 95% confidence). The unpaired t test was used to verify the statistical significance. Lipid chow vs HFD liver: P = 0.3339; iBAT: P = 0.0068 Data information: In the figure, A.U. = arbitrary units.
D. RPE cells were transfected with non-targeting siRNA (siNT) or siRNA against Rev3l then 72h later cells were subjected to PLA by using 53BP1 and HP1α antibodies and processed as in (B). p-values were calculated by Mann-Whitney test ( ****: p<0.0001). Red lines indicate the mean values. Error bars: SEM. Three independent experiments were performed.
B. Diluting concentrations of 4D7 to bound full-length 30 amino acid peptide compared to scrambled, C-terminal and N-terminal 11 amino acid peptides as shown in A (n=3 biological replicates).
b. Multivariate modelling of the metabolome reveals distinct transitions over time (states I-IV) in response to iron chelation using deferiprone (DFP). OPLS-DA was computed and generated from combined LC-MS and GC-MS datasets from three independent biological experiments each with four technical replicates per time point in each experiment.
C, D RNAPII ChIP assays as in (A, B) but performed from LXR−/− BMMs. Error bars represent ± SEM for n = 5-9 (**P = 0.000000001, *P = 0.02 versus T0901317).
H. Representative images showing the preloaded FM4-64 fluorescence in presynaptic boutons of hippocampal neurons before and after 800 stimuli at 40 Hz. Scale bars, 5 μm.
Analysis of TFEB binding and modulation of the MYO1C promoter in human ECs. (A) Representative snapshot of TFEB binding on MYO1C in human ECs.
f, In vivo mitochondrial potential of +/−KRas tumours (n = 3); representative flow cytometry of two tumours, as control uncoupler CCCP was added to acquired −KRas.
(A) qPCR analysis of circHIPK3 levels in scr and circHIPK3 KD stably expressing TREx cells. GAPDH was used as a housekeeper (n=3). (B) qPCR analysis of HIPK3 levels in scr and circHIPK3 KD stably expressing TREx cells. GAPDH was used as a housekeeper (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.
(A) Transcription profiles of ΔIndLon mutants grown in inducing (+) or depleting (-) conditions across the cell division and the MPN525 (DnaB) operons. The respective estimated protein copy numbers based on MS data are shown below.
mRNA expression levels extracted from RNA-seq data for , Odc1 (E) and Kap (F) in kidneys used for RNA-seq. Expression levels are normalized to WT ORX.
E Representative electrophoresis analysis of Proteinase K-treated recombinant PDIA1 variants. Mass spectrometric analysis of Proteinase K digested samples from total sample and from in gel trypsin digested protein samples (arrows indicate band 1 and band 2) indicated differences in the removal of the x-linker region. Bottom panel: Ratios of band 1 to band 2 were quantified in 4 independent experiments.
E Volcano plot for fold changes of immune genes enriched or depleted in RAD51-High tumours vs RAD51-Low tumours from TCGA. T-test; dashed line denoted threshold of significance, Bonferroni corrected for multiple testing.
B) BDNF stimulation leads to a decrease in the canonical (22 nucleotides) isomiRs of the miR16 family, miR-16-5p (p=0.005) and miR-15b-5p (p=0.02). In both cases, this is accompanied by an increase in the levels of shorter isomiRs; the 19-nucleotide isoform of miR-16-5p (p=0.04) and the 21-nucleotide isoform of miR-15b-5p (p=0.007). The relative isomiRs proportion was calculated as described in A (t-test type 2, n=3, error bars; s.d.).
M.tb CFU in control siRNA-treated (L) or RIG-I siRNA-treated (M) mouse BMMs pre-treated with IFN-ɣ plus EVs from uninfected (EVs_Control) or M.tb-infected (EVs_M.tb) BMMs. CFU was determined immediately after the 1 hr infection or 24 and 72 hr post-infection. Data shown are the mean ± SD of three independent infections and all data shown are representative of at least three independent experiments. * p < 0.05, ** p < 0.01 and *** p < 0.001 by two-tailed Student's t-test.
(I) Left panel: schematic drawing of the pGL3-TGFβR1 3' UTR luciferase reporter assay system. Middle and right panels: QKI-5-overexpressing and vector A549 and H1299 cells were transfected with pGL3-Luc reporter plasmids that were made by fusing the above-mentioned TGFβR1 3' UTR segments. Relative luciferase activities were determined as described in Materials and Methods and normalized to those in vector cells.
A The gene and protein structures of the Dof domain of CDF4. Cysteine residues conserved in the DOF domain are indicated in red, and the conserved DOF Zn-figure DNA-binding domain is found in CDF4.
B Mitochondrial transcript levels measured by qRT-PCR in RKO cells after 96 hours of 1 μM IMT1 treatment. Data are relative to DMSO-treated controls and are expressed as mean ± SD of n=4 independent experiments. Ordinary one-way ANOVA was used for comparisons to DMSO-treated controls (RNR1, RNR2, MT-COX2, MT-ATP6, MT-ND1: ***p<0,0001).
F Western blot analysis of KDM6A expression in podocytes cultured in normal, high glucose or high mannitol conditions for 24, 48 ad 72 hours. *P < 0.05 versus normal controls for the indicated time points (Wilcoxon two-sample test; n = 3).
D Effect of KLF10 knockdown on high glucose-mediated reduction of nephrin in primary podocytes. As noted, knockdown of KLF10 prevented downregulation of nephrin and upregulation of KDM6A in high glucose-treated podocytes. *P < 0.05 versus normal controls, #P < 0.05 versus control siRNA with HG incubation (Parametric ANOVA and a Bonferroni post hoc test; n = 3).
Radius of Tau:PEG condensates at different NaCl concentrations. N=3 experiments, 10 last data points per experiments shown, data shown as mean±SEM. Data information: Data have been compared by one-way ANOVA with Tukey test for multiple comparison. *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001
Scatter plot of LogFC of whole introns (grey) and HSATIII-target introns (blue) upon SRSF9 KD (X-axis) and HSATIII KD (Y-axis). 51,469 and 548 introns are plotted as whole introns and previously-reported HSATIII-target introns, respectively. Pearson's correlation (r) is indicated above.
A Schematic diagram showing the T-DNA insertion sites in rice osprr73T-DNA mutant (hereafter named as osprr73).
Rescue assays. Myc-Egg WT and its K1085R and STAA mutants were expressed in OSCs upon endogenous Egg depletion (siEgg). Western blotting (WB) was performed using anti-Egg and anti-Myc antibodies. RT-qPCR was used to quantify Stalker2 transposon expression level. The act5c gene was used for normalization. siEGFP: siRNA for EGFP was used as a negative control. Error bars represent SD from three independent experiments. *p < 0.05 (unpaired Student's t-test). n.s.: not significant.
(D) Glycolytic (red) and mitochondrial (blue) ATP production determined by Agilent's Seahorse machine and real-time ATP rate assay kit. HC and APBD patient fibroblasts were serum/glucose-starved for 48 h and then full medium was replenished for 24 h without (untreated), or with (chronic) 50 µM 144DG11. Acute, 50 µM 144DG11 was added on assay for 20 min after 24 h of serum/glucose replenishment. Readings were normalized to cell number as determined by Crystal Violet staining. Shown are mean and SEM values based on n=3-6 technical repeats. For all experiments (HC, p<0.01; APBD1, p<0.02; APBD2, p<0.09; APBD3, p<0.11; One Way ANOVA with Sidak's post-hoc correction for multiple comparisons) glycolytic ATP production was increased, as compared to untreated control, by acute, but not chronic, supplementation of 144DG11. Mitochondrial ATP production was increased only by acute supplementation of 144DG11 to APBD2 fibroblasts (p<0.06).
(E) qRT-PCR of cest-2.2 expression in the intestines of 5-day-old wt, gas-1(fc21), gas-1(fc21); cest-2.2 O/E and nuo-6(qm200) animals (one-way ANOVA with Tukey's multiple comparison test, n=3 biological replicates). Data information: points represent mean± SEM. Across experiments, p value summary is ns= not significant, *p<0.05, **p < 0.01; ***p < 0.001, ****p<0.0001.
Western blot showing HNF1β over-expression after lentiviral transduction of PANC1 cells. Expression of FOXA2 in wild type and over-expressing (O.E.) cells is shown. Vinculin: loading control.
(d) Interaction of recombinant of wild-type NP (NP K87) or a K87E mutant protein (NP K87E) with the indicated synthetic polyUC RNAs as measured by fluorescence anisotropy. Data information: Data are represented as the mean ± SEM of 3 biological replicates without 2 technical replicates each. Statistical analysis was performed using the Mann-Whitney test (*P < 0.05).
(C) Western blotting for pMst1/2, Mst1, pMob1 and Mob1 in colon epithelium from control and cKO mice two days after 5-day DSS treatment. β-actin was used as a loading control. The quantification of pMst1/2 versus Mst1 and pMob1 versus Mob1 were shown under the corresponding protein bands.
(F) GSEA of the highly significant enriched EGFR signaling pathway. IRF2BP1 knockdown correlates with an increase of genes involved in EGFR signalling.
E. Analysis of the DNA methylation level at the DT-75 locus by chop-PCR. McrBC is a methylation-sensitive restriction enzyme, and DNA hypermethylation results in a reduced level of the PCR product. Undigested DNA was amplified as a control.
A-G. Mammary ductal outgrowth in 3-7 weeks old wt or Sharpincpdm female mice. G. TEBs in paraffin sections from wt or Sharpincpdm mouse mammary glands stained with HE (upper panel) or immunolabelled with the indicated antibodies (lower panel). Scale bars represent 50 µm. Mean ± SEM.
(C) Western blot analysis of ATXN1(82Q) after overexpression of either wild-type or inactive RSK3 in Daoy cells expressing ATXN1(82Q) (n = 3). Data information: RSK3 antibody used in is only suitable for detecting overexpressed RSK3 but not for endogenous RSK3. Mean ± SD, *P<0.05, **P<0.01, ***P<0.001 ****P<0.0001, one-way ANOVA.
Representative blots showing expression of key proteins associated with cell cycle arrest in hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells analyzed using Western blotting at the 7th passage. β-Actin was used as a protein loading control.
F. FACS plot of diseased intrathymic grafts (CD45.2-gated), demonstrating that Myc/Bcl2+DN2 cells could produce multi-lineage leukemia within a T-cell supporting environment; Myc/Bcl2+GMPs remained myeloid restricted under these conditions. Numbers indicate cell frequencies within the gates (mean±SEM) representing six independent experiments.
D, H1299 cells treated were subjected to transmission electron microscopy. Representative images are shown.
A Schematic of the RCA assay. The Φ29 polymerase produces long telomeric single strand concatemers of the circular DNA in a self-primed reaction.
(M) Plot of the fold change in expression of TJP1 (AT and endothelial layers) and CDH5, CD31, and CD146 (endothelial layers only) in infected LoCs at 1 and 3 dpi (n=3 biological replicates in each case) vs, uninfected controls (n=3 biological replicates). (N) Plot of the fold change in gene expression of endothelial cell specific coagulation markers - Tissue Factor (F3), Tissue Factor Pathway Inhibitor (TFPI), Thrombomodulin (THBD), Plasminogen Activator Inhibitor (SERPINE1) and von Willebrand Factor (VWF) in infected LoCs at 1 and 3 dpi (n=3 biological replicates in each case) vs. uninfected controls (n=3 biological replicates). Data information: In all plots, bars represent the mean value and error bars represent the standard deviation. Scale bar = 20 μm. P-values are calculated using a one-way Kruskal-Wallis ANOVA test, * represents p≤0.05, ** represents p≤0.01, ** represents p≤0.001.
(L-M) Representative confocal images of Irgm1+/+ and Irgm1-/- mouse BMDMs processed for IF analysis with (L) dsRNA (green) and Tom20 (red) antibodies. (M) The graph depicts the percentage of Irgm1+/+ and Irgm1-/- mouse BMDMs with dsRNA aggregates.
B Relative abundance of mRNA for the cyp-34A4 gene. Values are based on qRT-PCR analysis, with the relative levels for each gene normalized to the value observed in the wild-type control. ***P<0.001, ANOVA with Dunnett's posthoc comparison to wild type. N=3 trials. Error bars indicate SEM.
G) U2OS (EGFP-BIR-5085) cells and two PIF1 knocked-out (KO) clones derived from the same cells by CRISPR were assayed for the percentage of EGFP positive cells by FACS 4 days after I-SceI lentiviral infection. ata 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 < 0.01, ****P < 0.0001 and n.s. (not significant) P>0.05.
Nuclease assays with MR, MRN, pCtIP or pCtIP T847A, as indicated, on 5'-end labeled dsDNA. Reactions were incubated for 2 h.   Quantitation of experiments such as shown in (H). Averages shown; n = 4; error bars, SEM.
M (left) Immunoblotting of ASNS in MeWo cells mock- or si-ASNS-transfected for 24 hr and then incubated with LDHAi for 48 hr. (right) Proliferation of MeWo cells mock- or si-ASNS-transfected for 24 hr and then incubated with LDHAi for the indicated times. Data information: Statistical analysis was performed by ordinary one-way Anova for the comparison of more than two groups. Unpaired t-test was used for the comparison of two groups, and two-way Anova was used for the proliferation. Data are shown as the mean ± SD, n = 3. ns: not significant, *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001
B Completion of DNA replication is delayed in the irc5-Δ1 mutant after MMS treatment. Intact chromosomes were isolated from wild type (W303-1a) and irc5-Δ1 (IL012) cells and processed for PFGE. M, 0.03% MMS
Relative levels of CIP2A-BP were determined by polysome profiling and qRT-PCR in MCF-10A and TNBC cells either mock treated or treated with TGF-β. Relative levels of LINC00665 were determined by qRT-PCR in MCF-10A and TNBC cells either mock treated or treated with TGF-β.