EMBO/sd-character-level-ner huggingface dataset:
Oxidation kinetics experiment to investigate the influence of MIA40 on AK2 maturation. Experiment was performed as described in (D), except that 72 h before experiments cells were transfected with control siRNA or siRNA directed against MIA40. Endogenous AK2 oxidation depends on MIA40. Reported values are the mean of 3 independent experiments; error bars represent ±SD. Student's t-test was performed. * represents p<0.05, ** represents p<0.01 and *** represents p<0.001.
E. Graphical concept: cells treated with HU and XL413 for 24 hours would have stalled forks, which exist in a stable state due to inhibition of CDC7 and with an active ATR-dependent origin firing checkpoint. Upon washing and retreating of cells in the presence of HU the late origin checkpoint is maintained, in an ATR-dependent manner, and accumulation of DNA damage (pS139 H2AX) can be monitored independently from origin firing in the absence or presence of CDC7 (XL413) or MRE11 (Mirin) inhibitors. AZD6738 was used as a control to investigate molecular events occurring upon loss of checkpoint caused by both fork collapse and loss of the inhibition of origin firing. The increase in chromatin binding of CDC45 was used as a surrogate marker for origin activation, pS139 Histone H2AX was used to monitor fork stability, pS345 CHK1 was used to monitor the ATR-checkpoint signalling and pS40/41 MCM2 was used to monitor CDC7 kinase activity.
(c) Hierarchical clustering of up- and down-regulated DEGs in Arabidopsis in response to HS and HS+187 treatments. For every gene, FPKM values were normalized. Red bars denote an increase while green bars indicate a decrease in expression for a given gene. For the most relevant clusters, gene families significantly enriched are indicated based on gene ontology. The pink line in each cluster indicates an overall trend of differentially expressed genes in a particular cluster for different treatments. Data information: RNA-seq experiments were performed in three biological replicates. 5 d old seedlings +/-SA187 were transferred to new ½ MS plates before HS treatment. The RNA-seq was performed with LAT: 9 d old plants that were grown at 22°C were treated at 37°C for 3 h, then returned to 22°C for 2 d. At d 11, plants were heat stressed at 44°C for 30 min and incubated for recovery at 22°C for 4 d. HS: 11 d old plants that were grown at 22°C were treated at 44°C for 30 min and incubated for recovery at 22°C for 4 d to perform RNA-seq. (NHS): control plants were grown in parallel at 22oC for 15 d.
(D) Schematic representation for quantifying actin intensity profile along the cortex as in E
D. Immunoblot of RPE-1 cell extracts. Left: Representative blots. Asterisk indicates an unspecific band detected by the Fbxw5 antibody. Right: Quantification of MCAK/Uba2 signal ratio. Error bars show standard deviation of 6 independent experiments and asterisks the p-value of a two-tailed unpaired Student's t-test comparing each knockdown with the non-targeting control (**P < 0.01, ***P < 0.001).
(a) Scheme of the experimental design to monitor CMA activity in cultured cells using the KFERQ-PA-mCherry1 reporter.
C: HeLa cells were transfected with the indicated siRNAs (five control/non-targeting siRNAs and four PRMT1-specific siRNAs). PRMT1 depletion and endogenous p14ARF protein levels were analyzed by immunoblotting using α-PRMT1, α-p14ARF and α-β-TUBULIN (loading control) antibodies. The p14ARF signals were densitometrically quantified and normalized to the respective β-TUBULIN signal, as specified by the numbers below the blot, with the siControl_2 condition set to 1.
(F) Western Blot analysis of a cleavage experiment incubating modified H4 peptides (P1-P9) with soluble lysates from villi or crypts in the presence (+) or absence (-) of the commercial protease inhibitors cocktail. Lanes indicated as P correspond to the control peptide without lysate incubation. Notice the electrophoretic shift of peptides incubated with villus lysates (compared with control peptides) suggestive of post-translational modifications or binding to proteins absent from crypt lysates.
Aspect ratio (H) or roundness (I) of the mitochondria in (G); 18 fields examined from each treatment group.
(B) Flow cytometry analysis of CD45+CD8+, CD11b+Gr1+ and CD4+CD25+FOXP3+ cell populations in the livers of the mice from the different treatment groups, as indicated (n=5 per group; (means ± SD, n=1, One-way ANOVA, Bonferroni test).
(B) tumor volume at the experimental endpoint, in tumors derived from xenografted shScramble or shCOUP-TFII-HCT116 cells and treated with sodium chloride or sodium L-lactate (60 l x g-1 body weight; 150 mM).
C Whole-body energy expenditure per kg lean mass of 26 week old male WT (n = 5) and NYKO (n = 5) mice after disease onset. Unpaired t-test was used for the comparison of two groups, ordinary one-way ANOVA for the comparison of three groups.
B Representative images of NFIB, ERO1L, VEGFA-positive lung metastases from TNBC PDX. Scale bar, 1 mm.
(H) Percentages of myeloid fraction (CD11b+Gr1+), c-Kit positivity, and B220 positivity in spleen samples (n = 3-5).
(B) Conservation of the first 70 nt of the ORF7a sequence among different SARS coronaviruses. The underlined sequences are related to the position of the SARS-CoV-2 miR-O7a. The conserved ribonucleotides of the CoV2-miR-O7a sequence are marked in red and in blue all the non-conserved ribonucleotides across the 70nt sequence. The bat and pangolin coronaviruses closely related to SARS-CoV-2 are marked in purple.
A. MS/MS analysis of peptides corresponding to amino acids 380-399 of STAT2. 293T cells expressing flag-tagged STAT2 were used.
(a) Wild-type FAK cells were suspended in 1.4% methylcellulose solution in growth media and plated on agarose for 3 days. Top and bottom right, cells were recovered and cytospins prepared that were stained for anti-pTyr-416-Src (red), LC3B (green) and with DAPI (blue) or for paxillin (red), LC3B (green) and with DAPI (blue). Higher-magnification images of the outlined areas are also shown. Solid arrows indicate localization of pTyr-416-Src in LC3B-positive puncta. Scale bars, 20 μm. Bottom left, immunoblotting was carried out on lysates from adherent cells and from cells recovered from methylcellulose using anti-pTyr-397 FAK, anti-FAK, anti-pTyr-416 and anti-Src antibodies.
(G) Blood metabolic panel based on n=3, 9.5 month old mice treated as indicated. Blood glucose was increased and blood triglycerides decreased in Gbeys/ys cells by 144DG11 (p<0.05).
(E) Close up on the interactions between GGG266-268 of IIId (cyan) and CCC1116-1118 of ES7 (gray).(F) Close up on the interactions between G295, A296 and U297 of IIIe (green), A136 and A288 of hIII1 (yellow) and U1114, U1115 of ES7 (gray).
(e) Colocalization of UVRAG-C-Vps in early endosomes. HeLa cells were co-transfected with EGFP-Vps16 and Flag-UVRAG, stained with antibodies to LAMP1, LAMP2, EEA1 and Rab5, followed by confocal microscopy. All images are representative of at least three independent experiments. Scale bars, 5 μm. The raw data for a and b are shown in Supplementary Information, Fig. S6
A. Representative H&amp;amp;E staining of lung tumors from EGFRL858R/Rhob-/-, EGFRL858R/Rhob+/- and EGFRL858R/Rhob+/+ mice treated or not during four days with erlotinib (12.5 mg/kg/day), with the AKT inhibitor G594 (25 mg/kg/day), or in combination with both drugs. Scale bar: 500 µm. B. Quantification of the tumor/lung ratio of mice treated or not with the individual drugs or with a combination of both.
A) Cell cycle analysis (FACS) of C33 cell line after treatment with etoposide. The DNA contents of the cells were evaluated by propidium iodide staining, (PE-A; Phycoerythrin). The inset shows the % of the cells in each cell cycle phase.
C) TMED2 mRNA expression in healthy controls (CT), colonic Crohn's disease (CC) and ulcerative colitis (UC).
I - Immunoblotting for UCP1 and GAPDH (loading control) in IWAT from ChATfl/fl (n = 7) and ChATfl/fl;LysM-Cre (n = 5) mice after 6 h CE. BAT served as a positive control (PC) for UCP1 expression. Film was subjected to a short and long exposure and size (kDa) is marked on the right hand side. #: non-specific bands.
Transgenic plants expressing 5′SS wt and 5′SS strong constructs were used to perform ChIP experiments using total PolII antibodies. Line charts present ChIP profile of total PolII on minigene. Reporter gene structure is shown with black boxes representing constitutive exons; grey boxes, alternative region; white boxes, promoter and terminator regions; black lines, introns. Red lines show amplified regions. Above gene structure, a 0.5 kb scale is shown. Arrows on gene structure show localisation of primers used for splicing analysis. Error bars represent ± SD of three independent transgenic lines, **P 0.01 and *P 0.05 of t‐test. Bottom panel shows a schematic representation of 5′SS strong‐NTR1‐dependent and 5′SS wt‐NTR1‐independent consensus as described in . Source data are available online for this figure
Tlr7wt/wt female mice (n=6) and Tlr7-Y1025D mutant Tlr7ki/wt female mice (n=6) and Tlr7ki/ki female mice (n=5) were treated with indicated dose of IMQ for 4 days. E Representative p-p65 staining of the dorsal skin. Scale bars: 100 μm.
E Poly(A) tail assay results showing poly(A)-tail length of indicated transcripts in WT and Pabpn1l-deleted oocytes and embryos. The poly(A) tails of Actin are used as an internal control. Each sample was prepared from 100 oocytes or embryos. Plots show the averaged relative signal intensity (y-axis) and length of the PCR products based on mobility (x-axis).
E. HCT116 cells stably expressing control (empty vector) or OMA1-Flag, and HCT116 cells infected with control or shOMA1 (OMA1 knockdown) lentiviral particles and further cultured for 5 days, were then treated with DMSO or 20 μm CCCP for 4 hours. Cell lysates were analyzed by Western blotting with antibodies against NDUFA4, COX4L1, NDUFB5, DNUFB6, MT-CO2, OMA1 or Tubulin. The black arrowhead indicated the full-length COX4L1 or NDUFB6, and the red arrowhead pointed to the cleaved band. The asterisk indicates a nonspecific band.
(C) Immunostaining of mouse cathelicidin (CRAMP) in skin sections from WT and Raptor cKO mice injected with LL37 or control vehicle (n = 6 for each group). Bottom right panels, magnified images of dotted line areas. Epi, epidermis; Der, dermis; Scale bar: 50 μm.
(b-c) Sporadic labeling of Atoh1+ cells after 4-OHT induction. Following irradiation, entire colonic organoids exhibit full lineage labeling of Atoh1+ cells, characteristic of multipotent stem cells (N=3 per condition). Data information: Scale bars =100μm Data are represented as mean ± SD analyzed using Student's t-test (c)
C, FRET assay of the indicated protein combinations using CFP-YFP pair in N. benthamiana leaves under HS (39ºC for 40 min). EV, empty vector (negative control). Upper and lower box boundaries represent the first and third quantiles, respectively; horizontal lines mark the median of at least eight replicate measurements, and whiskers mark the highest and lowest values. The experiment was repeated three times with similar results. P values denote statistically significant differences for comparisons to plants expressing EV (two-tailed t-test).
B. Representative E-cadherin (E-cad) and DAPI immunofluorescence images of AECs treated apically with TGFβ1 or vehicle control after 72 h in the co-culture system (scale bars 25 µm).
F Scaled signature expression and single gene expression moments per cell, under control (grey) and preferred treatment (color) conditions, as indicated. 10% of cells populating the end of latent time are displayed in bold. It is of note that latent time is linear and thus cannot capture multiple populations located at developmental end points. Densities at the side lines display expression in all cells.
b, Normal compartmentalization of Atg5-/- grafts in cytokeratin-8-positive (red; K8) cortical and cytokeratin-5-positive (green; K5) medullary regions; n = 8.
(d-f) Representative images of isolectinB4-stained P17 retinas from OIR-challenged Pald1+/+ and Pald1-/- mice (detailed view in the insets) (d). Scale bar: 1 mm (inset 250 µm). Quantification of neovascular tuft area (e) and avascular area (f). Each dot represents the mean of both retinas per mouse. Mean±SEM, unpaired t-test, n=3 litters, 4 Pald1+/+ and 3 Pald1-/- pups. Data information: *p < 0.05, **p < 0.01.
B, C Quantification of activity level and cumulative freezing duration at 12w during seconds 90-210 of day 2 in WT, Syne4-/- mice, Syne4-/- mice injected with AAV.Syne4, and Syne4-/- mice injected with AAV.GFP, n=14 for WT, n=16 for Syne4-/-, n=9 for Syne4-/- + AAV.Syne4, n=5 for Syne4-/- + AAV.GFP. (C) Activity level. (B) Cumulative freezing duration.
Diagram detailing experimental method for isolation of mutant clones. After transfection with eGFP Cas9 plasmid carrying dual gRNA, GFP+ HAP1 cells were individually sorted into 96-well plates. A total of 10 plates were prepared for each biological replicate (n=3).
(B) In vitro degradation of UbLRad23-GFP-95 by purified S. cerevisiae proteasome. The graph plots the amount of substrate over time, estimated by fluorescence intensity monitored by plate-reader (green) or electronic autoradiography of SDS-PAGE gel bands (red), normalized to the initial substrate amount as described in Methods. (C) Michaelis-Menten analysis of UbLRad23-GFP-95 degradation by different concentrations of purified S. cerevisiae proteasome (green, 10 nM; red, 40 nM). (D) UbLRad23 inhibits UbLRad23-GFP-95 degradation. The initial degradation rates of UbLRad23-GFP-95 at different concentrations of purified UbLRad23 domain are plotted and fitted to the equation describing competitive inhibition. (E) The UbLDsk2 domain is a competitive inhibitor of UbLRad23-GFP-95 degradation. Lineweaver-Burk plot of UbLRad23GFP95 degradation with different concentrations of purified UbLDsk2 domain. (C-E) Proteasomal degradation of UbLRad23-GFP-95 monitored by fluorescence intensity in a Tecan plate reader as described in Methods.
B Bar graph showing the most significant gene pathways enriched with up-regulated genes of the 'stringent set' in the fdWT vs fdsc-αDEC comparison.
I) Bar plot for dwell times of ∆helix-7 Ago2 as a function of N. For all bar plots (E, G and I) error bars are the SD of three independent experiments carried out on different days.
Western blot analysis of cholesterol homeostasis related proteins (LDLR, ABCA1, P-SREBP1 and N-SREBP1), c-PARP, PCNA and SOX2 in GBM cells treated with EFV (0 - 20 μM) for 72 h.
E. Western blot analysis of GSNOR in HEK293 cells treated for 8 h with 100 μM H2O2 in the presence or absence of trigonelline (Trig). Densitometry of GSNOR immunoreactive bands is normalized to GADPH, selected as loading control, and expressed as arbitrary units. Values shown represent the means ± SD of n = 3 independent experiments. *, p<0.05; **, p<0.01.
B) Kaplan-Meier curves of CBS gene expression versus overall survival in patients with IDHwt, IDHm with or without 1p/19q co-deletion. Statistical significance for the survival analysis is shown as: pv: p-value, ns= non significant.
(B) OM45 was tagged with GFP in the genome of atg32Δpex3Δ and atg32Δpex3Δatg36Δ cells, which were transformed with an empty plasmid (−) or a plasmid encoding OM45-Pex3 (+). The cells were grown for up to 3 days in glycerol medium and samples were taken at 24 h intervals and processed for anti‐GFP western blotting. GFP* indicates the relative protease‐resistant degradation product and reflects vacuolar breakdown.
Quantitative data showing the ratio of SA-β-gal positive hOSEs at their 9th passage with or without ectopic expression of LATS2.
Tetrad analysis of rpb1‐S751F, rad52Δ and mre11Δ crosses. Δ indicates double mutants that fail to grow.
H-I. Representative pictures of triple immunostaining with VEcad (red), KLF4 (green) and pSMAD3 (white) on Control and CriptoMy-LOF TA sections at day 5 after injury (H) and quantification of VEcad/KLF4/pSMAD3 triple positive cells per area (mm2; I). Data information: Nuclei were counterstained with DAPI (blue).
(B) The FDR q-values of the top GO:Molecular function (top panel) and GO:Biological process (bottom panel) (https://toppgene.cchmc.org/enrichment.jsp) for the indicated up- and down-regulated genes is shown.
B Quantification of the rapamycin-induced interaction between NL-FKBP12 and PA-mCit-FRB. Plasmids encoding the fusion proteins were co-transfected in HEK293 cells and 24 h later treated with the indicated concentrations of rapamycin. After an additional incubation for 4 h BRET was quantified upon substrate addition. After cell lysis in buffer with indicated rapamycin concentrations, LuC ratios were determined. EC50 values were obtained with non-linear curve fitting.
Bronchial epithelial (BEAS-2B) cells were infected or not with influenza A/Scotland/20/74 (H3N2) virus (IAV) at MOI=1 for 4 h and treated or not with succinate (Suc; 4 mg/mL / 24.7 mM) for 20 h. (d, e) Panels show the basal replotted ECAR and OCR (d), and glycolytic capacity (ECAR max) and maximal respiration (OCR max) (e) in cells infected with IAV and treated (green symbols) or not (pink symbols) with succinate. Data were normalized with respect to mock-infected, untreated cells (orange symbols), and were also normalized for DNA content. Data information: Data are the mean ± SEM of d, independent experiments. Statistical analysis was performed using the Kruskal-Wallis test with Dunn's post-test d, e) (*P < 0.05)
Flow cytometry of intracellular Foxp3 staining in CD4+ naïve T cells transduced with control retrovirus (MigRI) or retrovirus encoding C/EBPβ and cultured for 2 d under conditions as indicated. Representative experiments are shown in the upper panel and pooled data from 4 (A are shown in the bottom. Dot plots are gated for CD4+GFP+ and numbers indicate percent Foxp3+ cells in the gate. Error bars represent mean ± s.e.m
(H) Venn diagram of TA/PGG/EGCG-inhibited genes and RhpS-activated genes at 4-fold cut-off.
E. Bar graph representing the proportion of chromosome mis-segregation observed in both cell lines after auxin addition. Only movies in which the dCas9 mScarlet-I dots were clearly visible during the whole division were taken into consideration for the analysis (N = 6 - 10 cells).
U2OS cells stably expressing H2B-EGFP were transfected with indicated siRNAs and after 48 h they were filmed in 5 min intervals. Time frame closest to the nuclear envelope breakdown (NEB) was set as 0 min. Representative examples are shown (n=3). Black bottom line indicates the time frames from NEB to the metaphase-to-anaphase transition. Scale bars indicate 10 μm.
(A) Wild-type MEF cells were infected with Salmonella for 25 minutes. Phospho-ATG16L1, total ATG16L1, and LPS were stained and analysed by immunofluorescence. Representative immunofluorescent images are shown (scale bars, 10 μm and 1 μm). Data information: Unless otherwise indicated experiments were performed twice. Data are represented as mean and p values were determined by Student's T-Test.
E. Hemolymph sporozoites were isolated and observed on glass slides by live cell imaging. Arrow indicates direction of a motile sporozoite. The graph shows the fraction of motile hemolymph sporozoites. Black dots: individual experiments with 10-20 mosquitoes. Bars: mean. Significance for (E) determined by One-way analysis of variance with Tukeys Multiple Comparison test.
Box plot showing lengths of S3-LCEs in each GO cluster. **p < 0.01, ***p < 0.001, ****p < 0.0001 compared to "organelle organization" by Steel-Dwass test. The box plot shows the interquartile range (boxes), the median (central band) and the minimum and maximum except for the outliers at the ends of whiskers (n = 8,115 for "Other RBP-dependent exons", n = 3,078 for "All SRSF3-dependent exons", n = 595 for "ORGANELLE ORGANIZATION", n = 57 for "DNA-BINDING TRANSCRIPTION FACTOR BINDING", n = 27 for "LYSINE-ACETYLATED HISTONE BINDING", n = 513 for "POSITIVE REGULATION OF TRANSCRIPTION", and n = 75 for "HISTONE MODIFICATION").
Representative images of TRF1 immunofluorescence and quantification of the percentage of TRF1-positive cells in skin and intestine sections of wild-type and Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet for 7 weeks.
C. Fit of the Sec62 domain crystal structure into the respective cryo-EM density of the ss-bound heptameric The map is low-pass filtered to 15 Å.
B, C, Analysis of GFP transfer after transplantation of Nrl::GFP donor photoreceptors into wildtype C57BL/6J (B) and Nrl-/- (C) recipient retinas after 14 (wt, n=9; Nrl-/-, n=7) and 21 (wt, n=6; Nrl-/-, n=4) and 90 (wt, n=5; Nrl-/-, n=4) days. Tissue is stained for GFP and nuclei (Hoechst). In this and all following figures, donor cells (D) are located above, and acceptor cells with GFP (A) are located below the outer limiting membrane (white dashed line), which delimits the apical border of the outer nuclear layer (ONL). In wildtype recipients, donor cells are typically located above the outer segment region (between the grey dashed lines). In Nrl-/- recipients, donor cells are located in the inner segment (IS) region. Plotted is the ratio of the numbers of GFP+ photoreceptors in the ONL (acceptor photoreceptors) and GFP+ donor photoreceptors in the subretinal space (SRS) over time.
(C, D) RNA immunoprecipitation assay. Quantification of GFP RNA levels upon immunoprecipitation of Myc-tagged Fmr1 or Flag-tagged Ythdf. Bars show average ± SD of technical triplicates (C) or Flag-tagged Fmr1 in the presence of overexpressed HA-tagged Ythdf. Bars show median ± S.E.M of biological triplicates. P-values were determined with an unpaired, two-tailed Student's t-test. (n.s. = not significant; p<0.01 = **) (D). Rpl15 levels were used as a normalization control and the enrichment of mCherry is shown as a negative control for background binding.
(F) ATG5-WT and ATG5-KO MEFs were transfected with Nhtt-150Q-EGFP. After 6 h, the cells were transfected with the indicated siRNAs for 5 D, and then the cells were subjected to MTT assays. The relative cell viability from three independent experiments are presented as means ± S.E.M., ns, not significantly different; **, p<0.01, one-way ANOVA.
(b) Representative electron micrograph of a viroplasm (V) formed in NSP5-EGFP cells infected with rotaviruses 8 hours post infection. Inset - double-layered particles emerging from the surface of a viroplasm. Scale bar = 300 nm.
Co-immunoprecipitation assays using HIF1α-, and CEP41-specific antibodies were performed in HEK 293T cells expressing GFP-CEP41 under normoxia or hypoxia. An IP using IgG-specific antibodies was performed as a negative control. NOR, normoxia; HYP, hypoxia.
A. Timeline followed to analyze proliferation of CMs and heart improvement in mice subjected to MI followed by administration of FIJs treatment.
A U2OS cells treated with RBM14 siRNA and stained with antibodies against centrin-2 (green) as well as HsSAS-6 (magenta). DNA is shown in blue. Insets show approximately twofold magnified views of fluorescent foci around the centrosome. Scale bar, 5 μm. Histograms represent the frequency of mitotic cells with the indicated phenotype. Values are mean percentages ± SEM from three independent experiments (n = 60 for each condition).
Construction of AAV-U6-gRNA-CMV-RFP vector expressing PRKG2 gRNA under the U6 promoter and RFP protein under the CMV promoter, respectively. AAV-gRNA-PRKG2 was injected into the corpus callosum (CC, indicated between two dotted lines) in PLP-150Q/Cas9 mouse at 2 months of age and the injected tissues were isolated 4 weeks after injection (lower panel). Ctx: cortex, Str: striatum, LV: lateral ventricle. Scale bar: 100 μm
(A) Genome-wide distribution of BRD4 in untreated (UT) and LPS treated macrophages. The numbers on the top represent total peak numbers.
A) U2OS cells were treated as in 2B after which mRNA was isolated and analyzed by qPCR. Error bars represent SD, n=3. Statistical significance was tested using a paired two-tailed t-test (NS for P>0.05, * for P≤0.05).
C) HT29 cells were infected with the indicated Shigella strains in the presence or absence of RIPK1 inhibitor, RIPK3 inhibitor, or caspase inhibitor (z-VAD), and then incubated for 8 h. Cell lysates and aliquots of cellular supernatants were subjected to cytotoxicity assay