EMBO/sd-character-level-ner huggingface dataset:
Precursor API is contained within subvacuolar vesicles in cvt17 mutants. (A) Isolated vacuoles (V) from cvt17 cells were lysed in PS0 buffer, loaded on top of an Optiprep step gradient, and centrifuged at 170,000 g for 60 min as described in Materials and Methods. Fractions VV, 0/1.06 interface; LD, 1.06 region; SV, 1.06/1.12 interface; HD, 1.12 region.
C Immunoblot analysis of p85PI3‐Kinase antibody immunoprecipitates reveals that GFP‐KSHV‐TK and its Y2F mutant but not Y120F associate with p85 of PI3‐Kinase.
Multiple tissue (eye, brain, adrenal gland, submandibular gland, oesophagus, lung, heart, liver, kidney, spleen, pancreas, stomach, duodenum, jejunum, ileum, caecum, colon, spinal cord, dorsal root ganglia, skeletal muscle, testis, epididymis, female gonad, skull) northern blot for CAVII. In the P56 mouse, CAVII is prominently expressed in the central nervous system including brain and spinal cord. Gapdh served as the loading control.
The following structural domains from 2019-nCoV S have been aligned to their counterparts from SARS-CoV S; NTD (top left), RBD (top right), SD1 and SD2, (bottom left) and S2 (bottom right).
(B-D) Co-immunoprecipitation (Co-IP) analysis of the interaction between (B) GFP-IRGM and Flag-RIG-I, (C) GFP-IRGM, and Flag-cGAS, (D) GFP-IRGM and Flag-TLR3 in HEK293T cell lysates. L.E, Long exposure of input blot. IgG (L), IgG Light chain; IgG (H), IgG heavy chain.
Schematic representation of the metabolic changes in RIRCD. We propose a mechanism that takes place in three phases. Phase 1 consists in FGF21 increase concomitant with the activation of the integrated stress response which has a protective effect leading to increased expression of proteins involved in amino-acid transport and offers a metabolic rescue by increasing lipid oxidation and TCA. The second phase consists of mTOR activation which leads to increased mitochondrial biogenesis and protein synthesis and in phase 3, the recovery, where we have a decrease in all stress markers.
The timing of the MG-132-sensitive step during SARS-CoV-2 infectious entry into Calu-3 and Caco-2 cells was assayed as detailed in D but using 60 µM MG-132 for Caco-2 cells and MOIs of 0.5 and 0.6, respectively. n = 2.
E: Control or ELDR overexpressed NOK lysates were subjected to Western blot analysis for Cyclin E1 using specific antibody. The membrane was reprobed with an antibody against Actin as internal control. Bottom panel shows quantitation. n = 3 biological replicates. Data are represented as the mean ± SD,
(I,J) ALG‐2::GFP is diffusely localized in the cytoplasm in wild‐type embryos. (I) Nomarski image of the embryo shown in (J).
(C) HeLa cells stably expressing GFP-mRFP-LC3 treated as in (A) were analyzed on a Cellomics ArrayScan system as previously described (mean ± SEM).
J, K qRT-PCR of IGF2 in isolated liver sinusoidal endothelial cells (LSEC)(J) or hepatocytes (HEP)(K) 1 day after PHx.
(F and G) WT (Atg5+/+) or autophagy-deficient cells lacking the key autophagy gene Atg5 (Atg5−/−) MEFs were treated with PI5P4K2C siRNA (5 days) or PI5P4K2C plasmid (48 hr) together with EGFP-httQ74 for 48 hr. The percentages of transfected cells with EGFP-httQ74 aggregates were assessed and shown in the graph; n = 500 cells (mean ± SEM). Representative confocal images are shown in (G). See also Figures S3 and S4.
A) Immunofluorescence staining for alpha-syntrophin and beta-sarcoglycan in the TA and triceps muscles of the Dup18-30 mice. A representative image is shown. Scale bars, 100 μm.
Shortened survival of BVE mice following reduction in Npc2 gene dosage. Genotypes of mice are as follows: +/+ = Braf+/LSL−V600E;CreER+/0;Npc2+/+, +/hypo = Braf+/LSL−V600E;CreER+/0,Npc2+/hypo, hypo/hypo = Braf+/LSL−V600E;CreER+/0;Npc2hypo/hypo. Median survival time (MST) for each genotype is indicated.
F. Average time-course of mean TNF-SBP-mCherry fluorescence intensity in Golgi normalized to the initial fluorescence value. Shaded area represents the SEM. Control: n=11; U18: n=15.
PS decarboxylase activity in a psd1Δpsd2Δdpl1Δ mutant expressing Psd1, Psd1(ER) or Psd1(Mt) expressed as (A) percentage of the lipid-incorporated 13C15N-label recovered in PE,
C., D. Western blot analysis of in vitro ubiquitinated HBP1, which was performed by mixing purified HBP1 with ubiquitin E1, UBCH5a, and ubiquitin in the presence of the indicated hGID sub-complexes (n=3).
F: tga20 COCS were treated with POM1 (optionally pre-blocked with recPrP) and treated with bPIP (5µg/ml). At 14 dpi NeuN morphometry revealed POM1-induced ablation of cerebellar granule layer (CGL) and rescue by bPIP.
D Western blot analyses of proteins identified by the HSATIII-ChIRP experiment. Known nSB proteins (SAFB, SRSF1, SRSF7, SRSF9, and HNRNPM) were used as positive controls, and ELAVL1, PSPC1 and α-tubulin were used as negative controls. SRSF3, SRSF5, TRA2B and THRAP3 are newly identified nSB components.
NIH-3T3 cells were treated with TGFβ or mock for 48h and incubated with O-propargyl-puromycin (OPP) for the last 60 min. The translation rate was determined by flow cytometry for OPP incorporation into proteins. A representative plot is shown on the left, and the quantification is shown on the right. Values are relative to mock-treated cells.
(b) HeLa cells transiently transfected for 20 h with GFP-Atg16L1 and mRFP-GPi were cultured in starvation medium for a further 2 h. TIRF image with GFP-Atg16L1 (green) and mRFP-GPi (red) is shown. Arrows indicate co-localization between Atg16L1 and GPi. The percentage co-localization of GFP-Atg16L1 with mRFP-GPi is shown in the graph. n = 2 cells. Scale bar, 5 μm.
Western blotting showing accumulation of CMV CP and VISP1-Flag in systemically infected leaves at 14 dpi. Relative accumulation (RA) of CMV CP was calculated from band densities. Rubisco complex large subunit (RbcL) served as loading controls.
(H) Immunofluorescence analysis of STAT5 wild type and knockout MEFs with 4′,6-diamidino-2-phenylindole (DAPI) staining (blue) and anti-STAT5 antibody (red). Scale bars represent 25μm.
(B) Succinate yield (grams of succinate per grams of substrate) versus biomass yield (grams of dry weight biomass per grams of substrate) simulations under batch conditions, compared with experimental data. Both glucose and ethanol phases are shown.
Impact of Ctcflos KD on mitochondrial biogenesis. (S) Quantification of Mito Tracker staining as whole image fluorescence intensity subtracted by background and normalized to cell number comparing Ctcflos tr1 (ASO 1) KD and control. Mean and individual values, n=10 (technical replicates) the experiment was repeated a second time, for a total of two biological replicates, for the second replication see (Fig EV1P) (with 10 analyzed images), unpaired t test **p< 0.01.
Confocal images of PI-stained 6-day-old roots. GFP-tagged expression is shown in yellow. A-C) pBRAVO:GFP in WT (A), bravo-2 (B) and wox5-1 (C) knockout backgrounds. D-G) pWOX5:GFP in the WT (D), bravo-2 (E), wox5-1 (F) and bravo-2 wox5-1 (G) knockout backgrounds. Scale bar: 50 µm. Quantification of the GFP fluorescent signal of the roots in A-C (H) and D-G (I). Boxplot indicating the average pixel intensity of the GFP in the stem cell niche (n>25, 3 biological replicates, *p-value < 0.05 Student´s t- test for each genotype versus the WT in the same condition). Quantification was done by integrating the GFP signal in each root across defined areas that included the whole SCN (Appendix Figure S7). In the boxplot, box width represents the interquartile range (IQR=Q3-Q1), with the horizontal line denoting the median, while whiskers extend from Q1-1.5IQR to Q3+1.5IQR. White dots are the outliers and black dots are the experimental observations.
F Pair‐wise analysis of differential splicing events in each iPKO replicate relative to the paired iPHet control. A3SS, alternative 3′ splice site; A5SS, alternative 5′ splice site; MXE, mutual exclusive exons; RI, retained introns; SE, skipped exons.
H, Expression levels of miR-203, Dnmt3a or Dnmt3b transcripts in iPSCs after induction of miR-203 (miiPSCs) and transduced with Dnmt3a and Dnmt3b cDNAs or empty vectors (as indicated in G). RNA expression was measured 24 hours after the transfection protocols and was normalized by a control miRNA (miR-142) or GAPDH mRNA, respectively. Data are represented as mean ± s.e.m. (n=3 independent experiments).
A Kaplan-Meier survival analysis of humanpatients (n = 3,935) with invasive breast cancers divided into two groups based on the gene expression level of Shp2 (see ).
Huh7.5 cells were transfected with the control vector or the Flag-tagged UVRAG expression plasmid for 24 hours followed by infection with HCV. (B) Real-time RT-PCR analysis of HCV RNA at 24 and 48 hours post-infection. *, p < 0.05.
E. Representative FACS readout of EdU/Propidium iodide cell cycle staining of PeTa cells 8 days after drug wash-out. F. Quantification of EdU/Propidium iodide staining depicted in Fig 7E. n = 3 biological replicates. Data are represented as means ±SD. *p<0.05, **p<0.01; ***p<0.001 (G1 phase: DMSO vs GSK-LSD1 p = 0.0104; S phase: DMSO vs GSK-LSD1 p = 0.0001; G2/M phase: DMSO vs GSK-LSD1 p = 0.0062; unpaired Student's t-test).
Primary hippocampal neurons (DIV6+4) were cotransfected with shTDP or appropriate controls and GFP to visualize neuron morphology. Dendritic morphology from at least 23 neurons per condition per experiment was quantified by Sholl analysis and statistically evaluated using two-way ANOVA with Bonferroni's (B, D) or Tukey's (F, H) post-test. Scale bar represents 100 µm. (G, H) Transfection of the indicated combinations of shCtrl, shTDP, ErbB4 or vector control (DIV6+5). shCtrl + Ctrl vs. shTDP + Ctrl: from 25 to 75 µm radius p < 0.001, at 87 and 112.5 µm p < 0.01 and at 100 µm p < 0.05. shTDP + Ctrl vs. shTDP + ErbB4: from 25 to 100 µm radius p < 0.001, at 112.5 µm p < 0.01. shCtrl + Ctrl vs. shTDP + ErbB4: no significant differences.
(A) Schematic representation of the fluorscence-2-hybrid approach for analysing interaction with endogenous proteins
Flow cytometric analysis of intracellular P53 levels shown in histograms (F) of LT-HSC in: (left panel) Molm-14-xenograft, n=6 red vs. non-engrafted control, n=4 black, or (right panel) IF injection of EV from Molm-14, U-937, HL-60 (red, n=5,5,3) or human CD34 cells (blue, n=6) normalized to vehicle-injected contralateral femurs.
(F) Immunoblotting and quantification of isolated brown adipose tissue (BAT) from male C57BL/6J mice injected with 5U insulin for 5 min (n=4-6).
' Staining for Dl-lacZ (purple) or Su(H)-lacZ (red) in esgts midguts expressing GFP alone (control), or expressing svb-RNAi. Samples were stained for GFP (green) and ß-Gal. Closeups show separate channels for GFP and ß-Gal. The graphs show quantification of the number of ICS (Dl-positive) and EBs (Su(H)-positive).
(B) Inhibition of SIRT1 enzymatic activity blocked CSAG2-induced decrease in p53 ac-K382. CSAG2 over-expressing HCT116 cells were treated with 1 μM doxorubicin/ 0.4 μM TSA with or without 1 μM EX-527 for 6 hr. Cell lysates were blotted for the indicated proteins.
B p97 translocates to ruptured lysosomes. Cells co-expressing LAMP1-RFP and GFP-p97 were treated as in (A) and stained with the pan-ubiquitin antibody FK2 (Ub). Percentage of cells showing recruitment of p97 in three independent experiments (mean ± SD).
(E) Top enriched GO pathways of DE genes in the SN of PD vs controls and the corresponding logP values, Wald test (DEseq2 analysis).
A Live-cell bioluminescence imaging (BLI) of HEK293 cells co-producing the indicated fusion proteins. mCitrine was excited at 500 nm, emitted fluorescence was detected at 535 nm. After substrate addition, short (460) and long (535) band-pass (BP) filters in a dual-view adapter were used to detect the emitted luminescence simultaneously at the respective wavelengths. BRET images were calculated by dividing the 535 BP by the 460 BP images using ImageJ. Scale bar = 20 μm.
Immunohistochemical detection of SPPL2c was performed on cryosections of Bouin-fixed wild type and SPPL2c-/- testis. The SPPL2c antiserum directed against a C-terminal epitope of the protease and diaminobenzidine as peroxidase substrate were employed. Nuclei were stained with hematoxylin. Scale bar, 100 µm (upper panel) or 50 µm (lower panel).
3-DZA inhibits localization of m6A RNAs HeLa cells were exposed to thermal stress in the presence of 3-DZA (100 µM) and stained as described above. Scale bar: 10 µm.
(D) Microglia isolated from wild type mouse pups were pre-incubated in starvation medium HBSS before addition of a pro-inflammatory stimulus (LPS followed by ATP). The autophagy blocker 3-MA was added for the final 1 h 45 min of the experiment, microglia were stained for LC3 and images taken by confocal microscopy. Representative images show a reduction of LC3-positive vesicles in 3-MA treated cells. Scale bar: 20 µm.
C. Triplicate images of tight junctions proximal to the apical faces of CPECs in Mpdz+/+ and Mpdz-/- mice. Scale bar, 100 nm
(A) T489 and S495, within Mig1C, are predicted to be the phosphorylation sites of SNF1 by global phosphorylation sites.
Immunoblot of anti-FLAG IP of 3x-FLAG tagged GFP, or FLAG-HA tagged H3.1 or H2B, from the non-nucleosomal fraction of 293T cells.
E Real-time RT-PCR of Alas2 mRNA in untreated or b-estradiol-treated WT and mutant clones. ***, P < 0.001 with respect to all values of WT1-3 (n = 4, mean +/- standard error (SE)) (left panel). Alas2 mRNA in intron 1 mutant clones was compared to that in intron 1/8 double-mutant clones. ***, P < 0.001 with respect to all values of intron 1 mutants 1 and 2 (right panel).
(C) The mRNA fractional abundances for aceB, aceA and the gluconeogenesis genes (summed abundance of maeA, maeB, pck, and ppsA genes) were estimated by RNA sequencing performed at various time points during the diauxic transition as indicated on the x-axis. The x-axis is truncated 2.3 hours into the shift and the "post shift" (pink) regime represents transcript levels when growth fully resumes on acetate, measured under steady state growth on acetate minimal medium. The series of RNA-seq through the growth transition was performed once.
(B) Distribution of APOE4 genotypes in the Phase IIa study, vs their baseline Aβ42/40 ratios. The dashed line at Aβ42/40 ratio of 0.09 represents a cutoff, which separates a normal ratio from an abnormally low ratio.
(A) Schematics of construction and screening platform to characterize a library of CRISPRa-mediated inducible promoters by targeted RNAseq and DNAseq.
b. Mitophagy time course. Representative photomicrographs showing time course of DFP treatment in mitophagy reporter cells (human ARPE-19 cells with stable expression of mito-QC). Mitochondrial networks are visible in yellow and mitolysosomes as red-only puncta signifying mitophagy. Nuclei are counterstained with Hoescht33342. Mitophagy appears maximal after 24 h of DFP treatment, with little difference between control and 7 h conditions. Inset shows details of mitolysosomes within the mitochondrial network of a highly mitophagic cell following DFP treatment. Arrows highlight mitolysosomes. Scale bar = 5 μm.
D Quantitative real time PCR for UCP1, using RNA from BAT from 10-week-old male WT and FADD-D mice on a SD. Data are expressed as mean ± SEM from three independent experiments (n = 6 total for each genotype). *P = 0.0018 (Student's t-test).
Frequency of Tau accumulation types observed in sensor cells treated with Tau aggregates (hepAGG), AD lysate, or Tau condensates. In cells having Tau accumulations we determined which accumulation types were present, regardless of the co-presence of other accumulation types and if multiple accumulations of the same type were present. n=number of cells with accumulations analyzed, resulted from the actual number of cells in the three replicates.
(F) The SARS-CoV-2 titer in the pretreatment and full-time experiments was analyzed by real-time PCR.
C. WB of ApoliproteinA4 in jejunum of Pkd2flox/flox and Pkd2gutΔ/Δ male mice after one week of HFD. Quantification of bands normalized to loading control and relative to Pkd2flox/flox n=7.
D, PGE2 activates MEF2 via EP3 receptor. NRVMs were infected with the 3xMEF2-Luc reporter and serum-starved for 20 hours. The cells were stimulated with DMSO or 1 μM PGE2 for 24 hours in the presence or absence of different EP receptor antagonists: AH6809 (10 μM, EP1- and EP2-antagonist) or 798106 (200 nM, EP3-antagonist) or L161,982 (2 μM, EP4-antagonist) Data information: values are mean±s.e.m In (D), n=3, independent experiments, * represents significant interaction between the two treatments (P<0.05, Two-Way ANOVA, AH6809, P=0.1092; L798106, P=0.0002; L161,982, P=0.5579). The exact n and P values can be also found in the Source Data excel file for Figure 1
Interactions between 29 central enzymes (in rows) and 55 metabolites (in columns), grouped according to metabolic pathways (n=2, measurement replicates from same sample). The relaxation factor of every interaction is indicated in green. Previously reported catalytic and regulatory interactions are denoted with 'C' and 'R', respectively. Black rectangles indicate potential allosteric interactions (maximum chemical similarity between the interactor and substrates/products of the target is lower than 0.5). Histogram showing the relative occurrences of maximum chemical similarity scores in the protein-metabolite interaction map. Grey bars indicate the distribution of scores considering all possible enzyme-metabolite pairs, green bars indicate the distribution scores for interactions with ΔRF > 0.1805 (false positive rate < 5%).
(J) Representative kymographs of WT neurons co-expressing HA-BACE1-GFP and AP2-αΑ WT or AP2-αΑ Μut. Scale bar: 5µm top panels, x=2μm, y=5s bottom panels.
(A) Annealed Fo−Fc electron density map for the C‐terminal region (residues 119-122) of LC3(1-124). Left, LC3(1-124) bound to the HsAtg4B H280A mutant; right, LC3(1-124) bound to the HsAtg4B C74S mutant. Structure of the C‐terminal region of LC3 is also shown as a stick model, in which carbon, nitrogen and oxygen atoms are coloured green, blue and red, respectively.
A Representative confocal images of the Golgi apparatus in WT or PTAR1 KO HeLa cells. Cells were co-immunostained for GM130 (a cis-Golgi marker) and golgin-97 (a trans-Golgi marker). Images were deconvoluted using Huygens software. The lower panels show magnified images of the boxed region of the upper panels. Scale bars, 5 μm.
(G, H) mTORC1 activity in the spinal cord (hindlimb level) was assessed by immunofluorescence using an antibody against the phospho-ribosomal protein S6 (phosho-S6 Ser 235/236). Data information All scale bars 50 µm.
Skm (C) BCAA levels in wt and LowOXPHOS mice (wt, n= 4; LowOXPHOS, n= 4). Bars are the mean ± s.e.m. of n= 3 experiments, 6 replicas/condition. Data information: Bars are the mean ± s.e.m. of the indicated (n) mice/genotype *p <0.05 when compared to wt by ANOVA or Student's t-test.
(f) Mouse fibroblasts were cotransfected with the human RXR receptor, a relevant reporter luciferase plasmid and the non-retinoid-regulated Renilla reporter to control for transfection. Values show relative luciferase units detected in cells subjected to the indicated concentrations of ATRA or the three retinoid derivatives for 12 h. Cells transfected as in e were treated with 10 μM of ATRA alone or in the presence of the indicated concentrations of the three retinoid derivatives or the antagonist BMS614 for 12 h. Values are shown as RLU. Values in c-f are mean ± s.e.m.; n = 4-6.
D Quantitation of sarcomere organization. Left panel: Immunostaining of cTNT, MLC2a (myosin light chain) and a-actinin at day 60 post cardiac differentiation. Right panel: The bar graphs at the right panel represent the sarcomere regularity from 3 independent experiments. Error bars represent standard deviation for the comparison between control and BTHS patient TAZ10. Significance was analyzed using Student's T-TEST **P = 0.002 and ***P = 0.0006. Scale bars: 50 µm.
D. Schematics of the predicted binding sites of miR-200s on LINC00115 and LINC00115 mutants.
(A) FAK+/+ cells were treated with dasatinib, then lysates were immunoblotted with anti‐FAK, anti‐FAK Y397, anti‐FAK Y925, anti‐PY416 Src, anti‐Src and anti‐actin. FAK was immunoprecipitated and then immunoblotting performed using anti‐Src, anti‐FAK or anti‐Ret.
The smaller image for Bcl-2 in survival/death in normal cells indicates that the binding to Beclin1 is weak under stressed conditions.
Confocal single plane images of third instar larval wing discs stained with anti-Ct (red) and (B) E(spl) m6-BFM-gapGFP (green), (C) E(spl) m7-HLH[VK00037]-GFP (green)
a) Schematic diagram depicting the experimental setup. b) Isolation of single myeloid cells from the retina under healthy conditions (d0) and three (d3) or 7 days (7d) after laser pulse for unbiased sampling and single-cell RNA-seq (scRNA-seq). Increased cellular heterogeneity in lesioned mice compared to healthy controls (d0), shown by May-Grünwald-Giemsa stained cytospins. Scale bars represents 10 µm. c
(A) Proportion of mtDNA cluster following 48 or 96 hours of growth in medium with (+) or without (-) 25 mM glucose (HG), 5 mM glucose (LG), ß-hydroxybutyrate (BHB) or 1 mM pyruvate. At least 50 cells per cell line were counted per condition, n = 2 experiments. Data are expressed as mean ± SEM. Representative images appear below the charts. Scale bar 15 µm
F, Expression levels of DNA replication factors were not altered by the lack of BRPF3. Each point represents the expression levels of a gene in control and BRPF3 depleted cells (GSE65065). Replication factors were classified as described previously (Alabert et al, 2014). Total genes (grey), DNA replication factors (colors) and BRPF3 (black) expression levels are shown. Continuous black lines mark 1.5 fold change in expression levels.
C HeLa cells were treated with control or siRNA targeting GABARAP, GABARAPL1 and GABARAPL2. 72 h after transfection cells were immunostained with anti−LC3B, anti−ALFY and anti−p62 antibodies. Scale bars, 10 μm.
RNA sequencing on ileum samples of C57BL/6J mice treated with water or 25 mM ZnSO4 water for 7 days and then injected i.p. with 200 µg Dex (Rapidexon) solved in 200 µL PBS, or with PBS only. 2h after injection the ileum was isolated (N=3 per group). (C) Scheme of numbers of genes upregulated in ZnSO4, Dex or ZnSO4+Dex treated mice (LFC>0.8, p<0.05). Significant expression of genes in the RNA sequencing was assessed with a Wald test with negative binomial distribution in DESEQ2.
Time dependent Ago2 phosphorylation and its miRNA binding in LPS treated macrophage cells. RAW 264.7 cells were transfected with FH-Ago2 expression plasmid and treated with LPS (1ng/ml) for different time points. Primary cells (PEC) were isolated from BALB/c mice and endogenous Ago2 was immunoprecipitated with anti-Ago2 (eIF2C2) antibody and phospho tyrosine level of Ago2 was measured using 4G10 antibody. Relative intensities of phospho-Ago2 against total amount of immunoprecipitated Ago2 were quantified and mentioned below the lanes (mean+/- s.e.m., n=3) (F, upper panel). Similar experiments were done with FH-Ago1 and Ago3 and levels of Phosphotyrosine in immunoprecipitated FH-Ago1 and FH-Ago3 were measured in RAW 264.7 cells (F, lower panel).
Protein clusters obtained after quantitative proteomics of WT (green) and atg2-2 (magenta) samples treated as described (E) Protein cluster of proteins which accumulate upon NAA treatment and are removed in WT but not in atg2 after swapping to 6-BA (F) Protein cluster for proteins that accumulate to higher levels in atg2 than WT upon treatment with 6-BA.
(C) Schematic depicting EI24 truncation mutants. FL, full length; △, deletion of the indicated regions.