EMBO/sd-character-level-ner huggingface dataset:
E-F: Type I IFNα production was then determined in cell culture supernatant from SARS-CoV-2 exposed TRIFKO or TRIG+MyD88KO (E) and RIG-IKO or RIG-I+MyD88KO (F) pDCs. Done with n=2
Assay of mitochondrial versus cytosolic aconitase activity in brain compared by genotype. Quantification of aconitase activity in two tissues (brain and liver) from animals of each genotype by band density. n=4 for WT, n=5 for KO (D-E) Activity of pyruvate dehydrogenase (D) and complex I (E) in GP by genotype and treatment status (veh = vehicle; pPanSH = 4'-phosphopantetheine). n=5 for both genotypes and treatment groups.
1H-15N HSQC spectra of full-length 15N-labelled pParkin: pUb (green contours) compared to that for the isolated 15N-labelled pUbl domain (grey contours). The spectrum of the full-length pParkin:pUb complex was collected using a 1H-15N CPMG, T2-filtered HSQC (Aguirre et al, 2017) to show only the more mobile regions of pParkin. In the spectrum of full-length pParkin many additional resonances arising from flexible loops in the protein are observed and are not labelled for clarity. Residues that experience small chemical shift changes are indicated by arrows.
l, CD31 MFI of total CD8 T cells (young KO, n=4; young WT, n=3; 60-wk-old KO, n=4; 60-wk-old WT, n=5).
D-I) Representative examples of fluorescence angiograms of IgG control (D), anti-VEGF-A (E), anti-ANG-2 (F) (all the 5 mg/kg) and three doses of anti-VEGF-A/ANG-2 (G,H,I), (at 3, 5, and 10 mg/kg).J,K) Bar graph of numbers of spontaneously occurring lesion number (J) and area by fluorescence angiography (K) after two weekly doses of antibody (antibodies at 5 mg/kg IP and anti-VEGF-A/ANG-2 at 10 [high], 5 [mid], and 3 [low] mg/kg IP) followed by analysis a week later in the early intervention model.L,M) Bar graph of numbers of spontaneously occurring lesion numbers (L) and area by fluorescence angiography (M) after two weekly doses of antibody (3 mg/kg IP) followed by analysis a week later in the late intervention model.
(D) RT-PCR analysis of the expression of miR-181a(-5p and -2-3p) versus MAP3K2 (left panel) or NOTCH2 (right panel) expression in γδ T cells isolated from thymic biopsies. Samples were cultured for 11 days with the indicated cytokines (n=6 independent biological samples).
E. Immunoblots of in vitro ubiquitinated ZMYND19, which was performed by mixing purified ZMYND19 with ubiquitin E1, UBE2H, ubiquitin and the 6-subunit hGID complex (ARCM8, RanBP9, WDR26, MAEA, RMND5a and TWA1) in the presence or absence of GID4 and a 10-fold excess of the PGLV GID4-specific peptide (n=2)
Model of Cvt and autophagy transport to the vacuole. There are many shared mechanistic features for the two pathways. 1, Cvt complex formation: prAPI is synthesized in the cytosol, oligomerizes into a dodecamer, and assembles into a Cvt complex; 2, double-membrane vesicle formation: the Cvt complex is enwrapped by a membrane source which, upon expansion and completion, forms the double-membraned Cvt vesicle (Cvt pathway) or autophagosome (autophagy); 3, vesicle targeting to the vacuole: the double-membrane vesicle is then targeted to the vacuole followed by fusion with the vacuolar membrane and release of the inner vesicle, termed the Cvt body (Cvt pathway) or the autophagic body (autophagy), into the vacuolar lumen. Subsequent breakdown of the Cvt or autophagic body releases prAPI into the lumen where it is proteolytically processed, in a proteinase A-dependent manner, to mature API. Major differences between the pathways include the following: 1, cargo selectivity: the Cvt pathway is a selective process and the Cvt vesicles appear to exclude bulk cytosolic components as cargo. In contrast, autophagy is nonselective and autophagosomes carry bulk cytosol, in addition to the Cvt complex, to the vacuole. prAPI is transported via both vesicle types. A recombinant, cytosolic marker protein, Pho8Δ60p, is transported to the vacuole via autophagy. Delivery of Pho8Δ60p to the vacuole can be monitored through cleavage of the COOH-terminal propeptide. 2, Vesicle size: Cvt vesicles are ∼150 nm in diameter, whereas autophagosomes are 300-900 nm in diameter. 3, Conditions for induction: the Cvt pathway is active in vegetative growth conditions while autophagy is induced under starvation conditions.
(G) Epidermal sheets from tail skin, infected ex vivo with HSV-1 (MOI = 2) +/- FGF7 (10 ng/ml), were stained 48 hpi for Glyc-D (red) using DAPI as counterstain (blue). The infected area (red staining) was measured using Image J software. Data are expressed as A.U. = arbitrary unit. Background staining of hairs was subtracted manually.
A) Scheme depicting the topology of the CDP-DAG -and Kennedy (red) pathways producing PE and PC in wild-type (WT) yeast cells (left panel), and an example of a rewired condition in which PE synthesis is directed to the mitochondrial inner membrane (MIM) and PC synthesis to peroxisomes (pex) (right panel). Black arrows indicate PS (dashed) and PE (dotted) lipid transport that must occur to enable the sequential enzymatic reactions.
(D) Differential staining of promastigotes with both MTR (0.1 µM) and MTG (0.2 µM). Scale bar, 10 µm.
B Volcano plot describing the differential gene expression between si-SCR and si-SMaRT treated C2C12 samples. For each gene, log2 of fold-change versus -log10 of the unadjusted p-value is plotted. Points in red represent differentially expressed genes (FDR adjusted p-value < 0.05).
Representative traces of oxygen consumption rate (OCR) during substrate-uncoupler-inhibitor-titration (SUIT) protocol for mitochondrial respiratory capacity in permeabilized mouse soleus muscle fibers, PM (Pyruvate+Malate; LEAK respiration), ADP (OXPHOS capacity), Cyt c (cytochrome c, integrity of outer mt-membrane), G (glutamate;), S (succinate), U (Uncoupler, FCCP), Rot (rotenone), Ama (antimycin A; less than 2% residual oxygen consumption, ROX).
(D). Parasitemia (percentage %) of cultures of RBC infected by different P. falciparum lines (NF54, Dd2, SL, PfEMP1-KO). The parasites were kept in culture for six days in the presence (Neut.) or absence (Cont.) of neutrophils.
Fluorescence stainings for pMLC and the apical marker CD13 in the PV area on liver tissue sections from untreated mice or animals at indicated time points post PH. Arrows indicate BC. Scale bar, 5 µm Quantification of pMLC (d) intensity from images as representatively shown in (a,c) as well as Appendix Fig. S2A,B, at indicated time points post PH (solid line) or sham OP (dashed line). Data is normalized to untreated animals (timepoint 0). Mean ± s.e.m, n=2-5 (d) mice per timepoint.
F. Segregation of c.2241C> G, p.Y747X in PPP1R13L in the studied family: The affected girl VI10, is homozygous for the causative SV p.Y747X, as are the four fetuses that were aborted. The parents are obligate carriers as shown and, of the two healthy sisters, one carries the wild allele only, and the other is heterozygous for the causative SV.
The mRNA expression levels of LL-37 was measured by qPCR for WT- and LL-37-hDASCs. n=5. Error bars, S.E.M.
Lethally irradiated WT mice were reconstituted with BM from Lyzs-Cre (Cx BM Lyzs-Cre) or p38γ/δLyzs-KO mice (Cx BM p38γ/δLyzs-KO). Two months after the transplant, mice were fed the HFD for 10 weeks. (D) Plasma transaminase ALT activity.
D. Aurora A- and PLK1-mediated regulation of meiotic centrosome biogenesis during spermatogenesis. After spermatocytes enter meiotic prophase and complete the first round of centriole duplication, presumably stimulated by PLK4, the centrioles must mature in order to effectively act as MTOCs during the first meiotic division. PLK1 and AURKA regulate this maturation process by ensuring the recruitment of various maturation factors including TACC3, CEP164, and γ-tubulin (γ-TUB). PLK1 and AURKA are also required for the efficient degradation of β-catenin (β-CAT), a necessary step to ensure centrosome separation prior to bipolar spindle establishment at metaphase I. The mechanism by which the first and second rounds of centriole duplication are restricted to early meiotic prophase I and interkinesis, respectively, is not understood and warrants further investigation. However high levels of PLK1 are necessary to avoid a premature second round of centriole duplication, which insinuates that PLK1 counteracts the centriole duplication function of PLK4.
The C9orf72 NRE non-AUG-dependent reporter constructs recapitulate localization patterns and pathological features identified in C9orf72 NRE models. The Dendra2 (green) c-terminal fusion was used to monitor cellular localization and fluorescence intensity for each DPR translated from the G4C2 strand in HEK293T cells transiently cotransfected with an NES-mIFP-mIFP-NES (NES-mIFP) fusion protein cytoplasmic marker.
c, Transmission electron microscopy (TEM) of crypts. Note autophagic vacuoles in various stages of evolution in Xbp1 Dgr;IEC hypomorphic Paneth cells.
E, F. Co-localization analysis of (E) NP:DAPI and (F) NP:Rab7 for each condition was performed on Z-stack confocal images images of WSN/33 (black) or HK/14 (red) infected A549s. Data represent the mean NP:DAPI co-localization ratios and the mean NP:Rab7 Mander's co-localization coefficient for individual cells from these 8 experiments.
E Growth charts / anthropometry of the patient before and after treatment with fucose
E) Distribution of response latencies for 3 Lamplight-driven responses to 405nm, as well as reversal caused by 525nm in sustained inhibition units. Two outliers with slow latency (>2.5s) in transient excitation group are likely responding to stimulus offset (N = 35 for Transient Excitation, N = 6 for Transient Inhibition, N = 7 for Sustained Inhibition and N = 5 for Sustained Excitation, all biological replicates).
B. Rif1-associated genes tend to be highly transcribed. Genes showing occupancy by Rif1 or Rif1-∆C594 that extends across 90% of their coding sequences were selected, and the transcription levels of these genes plotted compared to the transcription levels of all genes (shown at left). Number of genes analysed are 18 (Rif1, G1), 68 (Rif1, HU), 42 (Rif1-∆C594, G1), and 64 (Rif-1∆C594, HU). Boxes show the range of 25th to 75th percentiles, with horizontal lines within the boxes representing 50th percentiles. Whiskers represent 95% confidence intervals. Outliers are presented as open circles. *** indicates that p-value obtained by Students' t-test was below 0.001
E t-SNE plot of EPCAM+ epithelial cells from ER+ tumors (C). Top panel shows reclustering (resolution 0.05), bottom panel shows expression of MKI67.
(D and E) Representative immunoblot analyses of GFP-Atg8p expressing wild-type (WT) and Δach1 cells either combined with deletion of SCH9 (D) and aged until indicated time points. Blots were probed with anti-GFP and anti-GAPDH (loading control) antibodies to detect "free-GFP" indicative of autophagic flux (see Figures S6B and S6C for quantification).
(B) Lysates of MEFs were immunoprecipitated with anti-ULK1 or anti-FIP200 antibody or preimmune rabbit serum, and the resulting precipitates were subjected to immunoblot analysis with antibodies against ULK1 and FIP200.
D, E. The cleavage activity of Endouc was studied using materials presented at each lane. EndoucK242A: Endouc mutant; Extract: incubated in cell extracts; and Buf: reaction buffer. RNA probe without adding reaction buffer served as a negative control. The predicted cleavage sites (U) were mutated to generate mutant huORFchop transcript (unlabelled huORF-mt) and labelled by biotin (biotin-huORF-mt). Unlabelled competitor RNA was added in reactions at five times higher than that of the biotinylated probe.
(E) Inhibition of angiotensin II (Ang II)-induced TNF-α production by ACE2-Fc. Ang II was preincubated with indicated amounts of ACE2-Fc or IgG for 30 minutes. After that, the mixtures were added to RAW264.7 cells for 12 hr. The concentration of TNF-α in the culture medium was determined by ELISA. Error bars represent the standard deviation (SD), n=3. Statistical analysis was performed by unpaired two tail t-test. *P < 0.05. The dotted line represents the mean value of TNF-α in control group.
d) Reduction of punctate GFP-LC3 fluorescence in Bax/Bak−/− MEFs by silencing of Beclin 1 and APG5. Bax/Bak−/− MEFs that were transfected with GFP-LC3 together with the indicated siRNAs, were incubated without (NT) or with 20 μM etoposide for 24 h, and then examined by confocal fluorescent microscopy. The percentage of cells with punctate GFP-LC3 fluorescence was calculated relative to all GFP-LC3-positive cells. Data are shown as mean ± s.d. (n = 4).
A, Coimmunoprecipitation (Co-IP) analysis was performed in A549 cells with antibodies against p53 or USP7.
C TFIISmut and the atntr1 mutant have opposite splicing phenotypes. Heat map with scale representing the absolute difference between each respective mutant and Col‐0 in alternative splice site usage. The colours represent the direction of the events as described on the axis. Each splicing event is labelled with the gene name and the type of alternative splicing event. The 3′SS/5′SS notation signifies upstream/downstream 5′/3′ splice site selection; ES marks exon skipping or exon inclusion; and IR represents intron retention or intron splicing.
(a) Ranking of genes by their selection frequency into the diagnostic signature out of 100 iterations (orange dot) during the 2-class classification. Y-axis = genes ranked by selection frequency. X-axis = importance measure of each gene across all 100 iterations. Green dots: Importance measure for each gene per iteration. A cut-off of 25% was selected to detect a 5-gene putative diagnostic signature (orange bar).
Quantitative RT-PCR results showing that UV-B represses the expression of auxin signaling genes. Six-day-old WT seedlings grown in continuous white light were transferred to UV-B light (2 W/m2) for the indicated period. Error bars are SD of three biological replicates.
(C) Graph showing the cumulative phase microscopy scores of dead (shrunk and detached) MCF-7 cells in tamoxifen-treated (filled) or nontreated (unfilled) cultures in the presence (▴) or absence (•) of the indicated caspase inhibitors (25 μM).
(G) Mfn2 KO cells stably expressing mCherry‐GFP‐LC3b and subjected or not to XBP‐1 silencing (Scr or KD) were treated with 1 μM Tg, 100 ng/ml Bref, or 0.5 μg/ml Tm for 24 h and examined by confocal microscopy. Scale bar: 10 μm.
(A) Representative images of C9orf72 iPSC-cortical neurons treated with DMSO (vehicle control) or 1 µM of DB1246, DB1247 or DB1273, for 4 days. RNA foci are shown in red and nuclei (DAPI) in blue. Scale bar represents 10 µm.
D Immunofluorescence of DNA-damage-associated nuclear protein PARP. Images show adjacent normal and tumor crypts of tissue P009T, marked by N and T, respectively, and tumor tissue of patients P008 and P009, as indicated. Scale bar 100µm. Significance was assessed by an unpaired t-test, after blinded analysis of 10 random images per tumor.
B) Log2 fold change (LFC) in TAUtg (x-axis) and APPtg mice (y-axis) after differential expression analysis, assessing the effects of age*genotype interaction. Color code for dots/numbers: grey = genes in hippocampus (n=15824); black = genes in APPtg-Blue (n=4236); green = genes significantly differentially expressed in APPtg mice (n=493); yellow = significantly differentially expressed genes in TAUtg mice (n=9); red = significantly differentially expressed genes in both (n=9).
Representative fundus images of each group of mice 35 days after induction of EAU. Arrowheads indicate area with retinal vasculitis and the asterisk indicates a region of vitreous haze, where the image appears blurred.
A Western blot gel images showing α-synuclein (α-SYN) levels in SN tissues from control (n= 9) and PD subjects (n = 18). The numbers on top of each gel panel show the ID of each sample.
(A) Sagittal planes of whole-mount immunostaining and quantification for TUBG on WT mouse embryos from E3.5 to E6.5. The insets are magnifications of selected centrosomes from the dotted areas denoting the inner cell mass (E3.5) or epiblast (E5.5 and E6.5). Bars represent mean ± s.d (two-tailed student's T-test or one-way ANOVA with Tukey's multiple comparisons tests). Scale bars: E3.5 and E5.5 = 15 μm; E6.5 = 30 μm and 3 μm (insets). E3.5: 88 ± 26% (n=73 cells from 5 embryos); E5.5: 92 ± 10% (n=270 from 3 embryos); E6.5: 79 ± 12% (n=12,082 from 3 embryos).
C, Distribution of clockwise interval lengths at different FliMN-CheY~Ac concentrations in the strain FliMN-CheY was acetylated by acetate (10 mM, pH 7.0). The black lines illustrate the slopes of the short- and long-clockwise interval distributions. The color bar indicates the estimated FliMN-CheY~Ac concentration.
B, C Pharmacologic inhibition of ISCU (N = 8/group) did not influence miR-210 expression in the lungs either after Norm + SU5416, NS P = 0.8634 (B) or Hyp + SU5416, NS P = 0.9786 (C).
B. CryoEM density map of the human CENP-A nucleosome, color-coded for histones, in complex with CENP-CCR (magenta). CENP-CCR binds CENP-A nucleosome through hydrophobic region (big box) and arginine anchor (small box). Interacting residues in each of the regions are shown in (C).
(B) Macroscopic evaluation of the pregnant uterus and fetus. Compare to the fetal death and reabsorptions in ZIKV-infected mice, rISG20-Fc treatment rescued this phenotype by decreasing pregnancy loss (resorption).
WISH analysis of prox1, hhex and foxa3 expression in WT, hs:dnYap and hs:Yap transgenic embryos heat shocked at 24 hpf and fixed at 36 hpf. Arrow and bracket highlight the hepatic bud. Scale bar: 200μm
E qPCR analysis of IFNB mRNA levels in HT-DNA-treated WT and the indicated rescued cells (U937) (top). Immunoblotting analysis of indicated proteins (bottom). n = 3 biological replicates. Data information: Error bars, mean with s.d , *P < 0.05, **P < 0.01, ****P < 0.0001, two-tailed t-test. NS, non-significant. WT, wild-type. IB, immunoblotting. HT-DNA, Herring testes DNA.
(C) PCA plot of the average metabolic flux profile computed using the iMAT algorithm (Shlomi et al. 2008; Methods) representative of each of the experimental groups, the labels are the same as (A).
Experimental setup used to screen for chromatin regulators involved in the IR-induced G2 checkpoint response and recovery. Unless stated otherwise, 5 Gy of IR was used.
I) Violin plots of the nuclear circularity index of HeLa cells transfected with Control (grey) or H2A.Z.1 (blue) siRNA either alone or in combination with siRNA-resistant GFP:H2A.Z.1WT (WT) or GFP:H2A.Z.1KR (KR) plasmids. The nuclear circularity was analysed using the NIS Elements AR analysis software (NIKON). At least 140 nuclei from three biological replicates were analysed for each condition. Mean and SD are shown. Data sets were statistically analysed using the Wilcoxon rank test in R. ***=p<0.001.
A. Arginine methylase inhibitor decreases SIRT7 methylation. HEK293T cells expressing Flag-tagged SIRT7 were treated with increasing doses of AdOx as indicated for 24 hrs. After immunoprecipitated with Flag-beads, SIRT7 was analyzed by western blot and detected by an antibody against mono-methylarginine (α-me1). Relative methylation ratio (Ratio) was calculated by normalizing arginine methylation level against the Flag-SIRT7 protein. WCL, whole cell lysate
Gli1 protein levels were measured by Western blot in WT and Mecp2 null neurons, following SAG treatment (200 and 400 nM). Representative bands of Gli1, Mecp2 and α-tubulin are depicted above the histogram, which shows the mean ± S.E of the percentage of Gli1 expression levels, compared to the untreated WT samples (*p<0.05, ***p<0.001, by two-way ANOVA, followed by Bonferroni post hoc test). Two-way ANOVA indicated a significant interaction (F (2, 20) = 3.788; p<0.05), a significant genotype effect (F (1, 20) = 4.362; p<0.05) and a significant treatment (F (2, 20) = 13.5; p<0.001).
Impact of MB on cytotoxicity of OT-1 CTLs against EG7 or EG7-L1. Splenocytes from OT-1 mice in culture were stimulated with 10 nM of OVA257-264 (SIINFEKL) for 3 days to generate mature CTLs. CTLs were incubated with CFSE labeled EG7-L1 cells in the presence of MB at indicated concentrations. Cytotoxicity was determined by flow cytometry analysis. Data are representative of three independent experiments. (effector to target ratio = 5:1, unpaired t-test). EG7-L1: EG7 overexpressing PD-L1.   Statistical results of (B).   ELISA measured of LDH release to assess the cytotoxicity of OT-I CTLs on EG7-L1 in the presence of MB. Anti-PD1 antibody (aPD-1) served as positive control.   Data information: Data are representative of three independent experiments. Unpaired t-test; Error bars denote s.e.m. **P < 0.01; ***P < 0.001; ****P < 0.0001.
a-c, RFA1::FLAG DDC2::MYC cells were arrested in G2 and released in YP galactose to induce HO endonuclease. After 30 min, the culture was split in two: +VPA and -VPA. a, Samples were processed for western blot using anti-Rad53, Srs2 and Ddc2 antibodies.
A. Immunostaining of Tom20 and Drp1 in N2As depleted of Ifnb (δIfnb) by CRISPR/Cas9 and matching nontargeting control (NTC).
G Sensitivity of scc2-4 to DNA damaging agents at permissive temperature (25°C) or semi-permissive temperature (30°C). Logarithmically growing cultures of wild type (Y39), and scc2-4 (Y4366) strains were 10-fold serially diluted and plated onto solid YPD containing indicated concentrations of DNA damaging agents
Amounts of Aβ40 or Aβ42 in the TBS-soluble or Gu-HCl-extractable fraction from 3- to 4-month-old Mgat3+/+ or Mgat3−/− brains (n = 7-8). An outlier value was rejected by the Smirnov-Grubbs' test (P < 0.05). P = 0.045 for Gn-HCl Aβ40.
(e) Dual Periodic acid-Schiff / Alcian blue staining to identify Paneth cell secretory vesicles (light blue / pink - marked with black arrows) and goblet cells (dark blue / purple - marked with red arrows). Note Paneth cell secretory vesicles are restricted to crypt base in both control and Huwe1 deficient small intestines (inset - black arrows). Scale bars = 100µm.
B. Closer view of phalloidin binding pocket as marked with red box in A. The density of phalloidin from EM map is shown around the ligand.
Vessel parameters in the P6 developing retina. G. Radial outgrowth (distance between optic nerve and vascular front).
C) Representative image of NK cell infiltration (red) into A549 tumor spheroids at the time of addition of NK cells and at 20 hours after the addition of NK cells, scale bar: 400 μm.
Representative images of endogenous BRD7 (green) and γH2AX foci (red) in paraformaldehyde-fixed MDA-MB-468 cells after treatment with CPT (1 μM) for different intervals. Visualized by immunofluorescence using anti-BRD7 and Alexa Fluor 555 anti-γH2AX antibodies. DNA staining with DAPI; Scale bars, 2 μm.
(B) Ectopically-expressing Sc-CCM1 rescues the respiration defect of Sc+Sb-chr7. Spot assays for the wild-type S. cerevisiae (Sc) and the chromosome 7 replacement stain (Sc+Sb-chr7) carrying an empty plasmid (+ vector) or the plasmid with the S. cerevisiae CCM1 gene (+ Sc-CCM1).
C) Quantification graph of NSC diameter for genotypes in (A). n=246 NSCs for control; n=494 NSCs for msps RNAi; n=457 NSCs for UAS-klp64D + msps RNAi. ****p<0.0001.
(B) Top: In vitro kinase (IVK) assay of B-Raf complexes purified from either WT or BrafAVKA knock-in brains from both founder strains revealed a reduced MEK phosphorylation potential regardless of their purification from NLB or RIPA lysates. Botttom: Quantification of IVK differentials: #215 samples indicated in black, #273 samples in grey.
HCC4006 cells were (B) transduced with control (AdCont) or RHOB-overexpressing adenoviruses (AdRHOB). RHOB overexpression was monitored by western blotting. (***: p<0.0001 vs. control cells). Data are representative of at least three independent experiments.
F Increased levels of bright Rfa1-YFP foci in cells lacking Irc5. At indicated time points culture samples of wild type (W3775-12C) and irc5-Δ1 (TB041) cells were collected, washed and processed for microscopic analysis. Error bars represent mean value ± standard deviations of mean (n=5). Unpaired t-test was used to calculate the P-value. Representative microscopic photos of cells are shown. Scale bars: 5 μm