EMBO/sd-character-level-ner huggingface dataset:
Long-range PCR of Iglo subclones from WT and two independent 53bp1-/- CH12 (TA and T1) clones. The Iglo subclones derived from the 53bp1−/− CH12 TA clone are listed as D01-D18, while the Iglo subclones derived from the 53bp1−/− CH12 T1 clone are listed as F03-F24. Gels show long-range amplicons (top) and AID genomic DNA PCR control (bottom).
d) Depletion of Prp5. Wild-type (lanes 1, 3 and 4) and snR81Δ pus1Δ (lanes 2 and 5) cells containing a FLAG-tagged PRP5 were lysed, and anti-FLAG IP was performed at a high concentration of salt. Cell extracts, before (lanes 1 and 2), and after [lanes 3 (mock), 4 and 5] anti-FLAG IP, were used for western analysis using anti-FLAG. The Prp5 band is indicated.
The indicated recombinant INVS proteins (lanes 1-10) were used for IVK. Akt phosphorylates WT (lane 6) and 1-898 (lane7) INVS, but failed to phosphorylate other subfragments of INVS (1-822, 1-746, and 1-670, in lane 8, 9, and 10, respectively), as detected using a phospho-Akt substrate antibody..
(a) Immunoblot analysis of LAMP-2A in CD4+ T cells (left) and liver, kidneys, thymus and lungs (right) of L2A-cKO mice (KO) and their control littermates (Ctrl).
D Cleaved caspase-3 and DNA fragmentation (TUNEL) median number of cells per mm2 were measured in treated xenografts. Data represent mean ± s.e.m. from at least 3 tumors per group. **** P<0.0001, one-way ANOVA.E Representative sections of the xenograft PDX analyzed in (D). Scale bars = 50 μm. Arrows indicate positive staining.
Seedlings of ChWT and AtWT were grown for 3 days in W then either kept under the same conditions or transferred to W+FR (R:FR, 0.02) for the indicated times. Plant material was harvested every 24 h. Transcript abundance of HFR1 and PIF7 was normalized to three reference genes (EF1α, SPC25, and YLS8). Expression values are the means ± SE of three independent biological replicates relative to the data of AtWT grown in continuous W at day 3. Asterisks mark significant differences (2-way ANOVA: ** p-value <0.01, *** p-value <0.001) between ChWT and AtWT when grown under W (black asterisks) or W+FR (red asterisks).
Schematic illustration for (A) the synthesis of PC polymer, and (B) the preparation of pcMNP.
B-D. The efficiency of DSB repair via SSA (B), de novo telomere addition (C) and BIR (D) in different alleles of SRS2. Average ± SD (n=3) is shown for each genotype in all experiments. Strains used: SSA: NK4691-4693; NK4805-4808; NK5104-5107; NK5066-5069; NK5062-5065; NK5058-5061; de novo t.a: NK1264; NK2375, NK2376; NK3332-3334; NK3308-3310; NK4217, NK4247; NK3353-3355; BIR: NK4070, NK4079; NK5321, NK5322; NK5536, NK5537; NK5450, NK5451; NK5452, NK5453; NK5454, NK5455.
E, PXR TR-FRET assay. TR-FRET ratio 520/495 nm are plotted against concentration of compound(s). Half-maximal inhibitory concentrations IC50 were obtained from interpolated standard curves (sigmoidal, 4PL, variable slope); error bars show standard deviation of n = 2 independent experiments each with four technical replicates.
E-F, Flow cytometric analysis of Granzyme B expression in CD8+ T cells isolated from MC38 tumours in A. Data presented as mean SEM and analysed by Kruskal-Wallis test with Dunn's multiple comparison (n=6 mice/group, 3 independent experiments).
Representative fused PET/MRI images of the transverse view of the thoracic region of lean (n = 5), diet induced obese (DIO) (n = 4) and leptin deficient (ob/ob) (n = 5) mice that received the PDE10A radioligand [18F]-AQ28A. Interscapular brown adipose tissue (BAT) in each image is highlighted by the crosshairs. The mean standardized uptake (SUV) value of [18F]-AQ28A in BAT throughout the dynamic scan was calculated with associated area under the curve (AUC). * P = 0.0128 (lean vs DIO) and ** P = 0.0031 (lean vs ob/ob) using unpaired 2-tailed Student's t test.
Fluorescently tagged mimics of the microRNAs mmu-miR-20a-5p, mmu-miR-25-3p and mmu-miR-155-3p were nucleofected into activated B lymphocytes from C57/BL6 mice. Quantitative real-time PCR showing expression of nucleofected microRNA mimics in FACS-sorted FAM+ B cells with normalization to RNU1A1 and RNU5G
Schematic representation of the targeted mb‐1 locus harboring the CreERT2 construct and the "floxed" Syk locus. The construct is inserted between exons I and IV. The filled rectangles represent the exons of the mb‐1 allele. The open rectangle represents the CreERT2 construct followed by a poly‐adenylation (pA) site. The black circle represents the endogenous pA site of the mb‐1 allele. The "truncated" version of mb‐1 exon I shown here lacks the ATG start codon and is followed by the complete mb‐1 intron I with its splice donor and acceptor sites. Intron I was maintained to provide intron/exon splicing in the transcript and as a source of possible transcription regulatory sequences. The targeted Syk locus was targeted with 2 LoxP sites and has been described in Saijo et al ().
NIH-3T3 cells were treated with TGFβ or mock for 48h, and the oxygen consumption rate (OCR) before and after treatment with mitochondrial inhibitors was measured using the Seahorse bioanalyzer. Oligo, Oligomycin; Rot/Anti-A, Rotenone/Antimycin-A; PCV, packed cell volume.
Detection of forces between AFM tip functionalized with mAb against R-LPS and unlabeled WT cells. Height image and the corresponding adhesion image are shown on top and zooms of depicted areas (black squares, 0.4 x 0.4 μm2) below. The arithmetic roughness Ra and percentage of adhesion Padh are indicated below each area. Scale bar: 1 μm. Correlation between roughness and detection of R-LPS on unlabeled WT cells. The areas with the lower roughness (more regular surfaces) were assigned as areas 1. The boxplot represents the mean values (squares), the median (horizontal line), the 25% and 75% quartiles (box limits) and the standard deviations (whiskers). n = 9 bacteria. Error bars: s.d. Statistical differences were analyzed by t-test. **P < 0.01. *P < 0.05.
(A) Immunoprecipitation/Immunoblot of phosphorylated E3 ubiquitin ligases in LRRK2+/+ and LRRK2(G2019S)-expressing MEFs treated with vehicle (Control) or tunicamycin (1 μg/ml). Endogenous PERK, MARCH5, MULAN and Parkin were immunoprecipitated with antibody, and precipitates were immunoblotted with antibody indicated at the right. Data represent the ratio of phosphorylated to total protein levels. Error bars represent ±SD from independent experiments. Data information: For graph A the P values was determined by a Mann-Whitney U test. ns = not significant, *P < 0.05, **P < 0.01
(C) BN-PAGE analyses of OXPHOS mitochondrial complexes in fibroblasts from control and subject, overexpressing an HA-tagged version of wild-type SLC25A46. Each of the five OXPHOS complexes (I-V) was visualized with a subunit-specific antibody that recognizes the native complex as follows: COI (NDUFA9), COII (SDHA), COIII (UQCRC1), COIV (COX4), COV (ATP5A1). Overexposure of the blot shows a defect in assembled complex IV (asterisk) and some free unassembled COX4 subunit in the subject (arrowhead). Complex II was used as a loading control.
(E) UHMK1 expression in 100 GC patients was analyzed based on the following parameters: tumor stage, tumor status, and lymph node invasion status. Fisher's test was applied to calculate the exact P value. Data information: *P< 0.05, **P< 0.01, ***P< 0.001.
L-M. Representative images of eMHC (red) immunostaining of mdx-Control and mdx-CriptoMy-LOF diaphragm sections (L) and quantification of eMHC+ myofibers per area (mm2, M). Data are expressed as box plots displaying minimum, first quartile, median, third quartile and maximum (n=5 biological replicates; *P<0.05; Student's t-test). Data information: Nuclei were counterstained with DAPI (blue). Scale bar: 100 μm. Magnification of the boxes is 3.5 x.
Roughness measurements on R-LPS labeled (green) WT and Δgmd cells. AFM images of whole bacteria and of the separated areas (coloured squares in first images, 0.4 x 0.4 μm2) are shown. The arithmetic roughness Ra is indicated below each area. Scale bars: 1 μm. Quantitative roughness measurement of R-LPS labeled WT and Δgmd cells. The areas with the lower roughness (more regular surfaces) of Δgmd cells were assigned as areas 1. mAb: monoclonal antibody. Ab: antibody. nWT = 13 bacteria. nΔgmd = 7 bacteria. Differences were statistically analyzed by t-test. **P < 0.01. ns: not significant.
Figure 6: Proposed ERCYS' working model Cartoon showing our working model, in cancer cells, basal ER stress promotes reflux of some PDI and PDI-L proteins including AGR2 to the cytosol. In the cytosol, AGR2 is able to bind and inhibit p53 function.
(E) Structure of human AK2 in complex with bis(adenosine)-5'-tetraphosphate (pdb:2c9y). Ak2 mutations identified in the remdesivir resistance screen are highlighted in magenta.
C Proportion of DAS events identified by AtRTD2-SUPPA in RNAi-ASCO1 compared to WT; Alternative 3' site (A3'), Alternative 5' site (A5'), Intron Retention (IR), Exon skipping (ES).
Hydrogen peroxide (H2O2) levels were measured in WT and MCK-KO , GA (F), and EDL (G) at rest and after a bout of exercise (n = 6 per group, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).
(h) Purified reformation tubules stained with antibodies against PI(4) P, PtdIns(4,5) P2 and PIP5K1A. Scale bar, 250 nm.
(A) Structures of two compounds identified as inhibitors of SERA6 autoprocessing and egress.
E GRIK1-activated KIN10 phosphorylates PIF4. In vitro phosphorylation assays were performed at 30 °C for 30 min using 1 μg of purified recombinant proteins (KIN10, GRIK1, or PIF4). 32P-labeled proteins were visualized by autoradiography. CBB, coomassie brilliant blue-stained gel.
V. cholerae ΔvrrA ΔmicV strains carrying the indicated reporter plasmids (x-axis) and either an empty vector control (pCtr), the pMicV, or the pVrrA plasmid, were cultivated in M9 and GFP fluorescence was measured. Fluorescence of the control strains was set to 1. The target genes were classified according to regulated only by VrrA
Baculoviral co-expression of human CSN1, CSN3 and CSN8 in Sf21VM insect cells, with CSN8 N-terminally Strep(II)- and CSN1 & CSN3 N-terminally His6-tagged, followed by affinity purification and SDS-PAGE displays banding pattern in line with the formation of a stable trimer CSN1/3/8.
Confocal microscopy images of live fibres from GFP-LC3:GAA−/− mice.Muscle was transfected with mCherry-LAMP1 only. The image (a single frame from the time-lapse series presented in Movie 5) shows lysosomes (red), LC3-positive autophagosomes (green) and a number of autolysosomes (yellow).Muscle was transfected with Flag-TFEB and mCherry-LAMP1. Massive formation of autolysosomes is indicated by yellow structures; the three lower panels provide a snapshot of the process of exocytosis. The structures at the plasma membrane are labelled with both LC3 and LAMP1, indicating that they represent amphisomes (a product of fusion between autophagic vesicles and late endosomes) or autolysosomes (a product of fusion between autophagic vesicles and lysosomes). Bar: 10 µm for all panels.
N. Line intensity profiles delineating expression of ADAM17 and phalloidin across individual ommatidia, n=10 fly retinas. Scale bars: 10μm.
(D) Immunoblot analysis of BAT from AdRiKO and control mice housed at 22°C or at 4°C for 8h for the indicated proteins (n=6/group, each lane represents a mix of 3 mice).
(N) 293T cells transfected with Flag-Atg1‐KR and various HA‐tagged Sqa contracts were subjected to immunoprecipitations with anti‐HA antibody. The immunoprecipitated proteins and the total cell lysates were analysed by immunoblotting with antibodies as indicated.
Convergent alterations in the phosphoproteome status after resveratrol and/or spermidine treatment. (A-C) Human colon carcinoma HCT 116 cells were treated for 2 h with vehicle (Co, control), 100-µM resveratrol (Resv), and 100-µM spermidine (Spd), alone or in combination (Resv + Spd). (A) Representative phosphoprotein arrays are shown.
F: AUC distribution for the unseen test-set (samples from patients with gliomas, 40; controls, 53) for four predictive models (LR, GLMEN, RF, SVM) trained and optimized following the scheme described in B and the Materials and Methods section. For each models are shown the AUC for the 50 iterations. Horizontal line within the bars represent median of the underlying population. Boxplot whiskers show 1.5 interquantile range of highest and lowest quartile.
measurements of epidermal thickness of tamoxifen-treated mice. Combined results of two independent experiments are shown. Each symbol represents the mean of at least ten epidermal thickness measurements for each ear; the line represents the mean value.
The lifespan-extending and autophagy-inducing effects of spermidine in yeast are not mediated by Sir2. (A-E) EGFP-Atg8p was ectopically expressed in wild-type (WT) or Δsir2 S. cerevisiae undergoing chronological aging on small synthetic 2% glucose media with or without (Co, control) supplementation of 4-mM spermidine (Spd). (A) Representative images. EGFP-Atg8p localization (bottom) was visualized by fluorescence microscopy. Yeast cells undergoing autophagy (in which EGFP-Atg8p exhibits a prominent vacuolar localization) are indicated by arrows. Yeast morphology was monitored by differential interference contrast (DIC; top).
(D) Comparison of Arabidopsis FERONIA, ANXUR1 and GmLMM1. SP and TM indicate the predicted signal peptide and transmembrane domain, respectively. Two corresponding mutated sites in Gmlmm1-1 and Gmlmm1-2 are indicated by arrows.
Assay to monitor for loss of GAL1 from tetraploid RBY18 overexpressing the indicated genes. Cells were grown for 7 d at 37°C on PRE-SPO medium in the presence (gene OFF) or absence (gene ON) of doxycycline (DOX).
E-F. Overexpression of NADPH oxidase gp91phox [*p-value: 0.0435] (E.) and of the antioxidant enzymes SOD1 [*p-value: 0.0330], catalase (CAT) [*p-value: 0.0448] and GPx-1 [*p-value: 0.0443] (F.) in 21-months old lenses of VEGF-Ahyper mice with cataracts (+3), but not in 11-months old lenses with no cataracts. N=7/group (3 independent experiments).
HEK-293T cells transfected with various combinations (above lanes) of plasmids encoding Myc-ABRO1 and Flag-NLRP3 (WT) or Flag-NLRP3 (S194D) were treated with or without 100 nM SP600125 for 2 h. Immunoblot analysis of Myc- and Flag-tagged proteins in cell lysates immunoprecipitated with anti-Flag M2 beads.
(a) Scheme of the shRNA-mediated synthetic lethal screen. Huh7-IR and CR cells were infected with lentiviral vectors (MOI=0.5) expressing the shRNA library (human genome-wide pooled lentiviral shRNA library module 1, Vector: pRSI16cb, Cellecta) and cultured with 2μg/ml Puromycin for the selection of shRNA-expressing cells plus 7μM Sorafenib (Srf). After 4 weeks of culture, genomic DNA was extracted, and shRNA barcodes were amplified for next-generation sequencing to uncover the critical genes for Sorafenib resistance.
Figure 5. Differential lysine acetylation and protein expression in hda14 vs. wild-type leaves in isolated thylakoids (B, E) Volcano plots depict lysine acetylation site ratios (A-C, top row) for mutant vs. control, with p-values determined using the LIMMA package. Orange, protein with nuclear localization; Green, protein with plastidial localization; purple triangles, proteins of the Calvin-Benson (CB) cycle; blue diamonds (top row), proteins of the light reaction; localization information according to SUBA4 database. Blue circles (bottom row), proteins with lysine acetylation sites identified. Dashed lines indicate significance thresholds of either uncorrected p-values < 5% or Benjamini-Hochberg corrected FDR < 5%. A missing FDR line indicates that the 5% threshold was not reached by any of the data points.
J. Optineurin and Tom20 immunofluorescence in Ifnb+/+ and Ifnb-/- MEFs transfected with Drp1 or phosphomimetic Drp1.
Absolute and relative antiviral response is calculated by the mathematical model for each cell line and patient-derived primary human hepatocytes prestimulated with 0, 1.2 or 608 pM Roferon by simulating the amount of occupied GAS and ISRE binding sites upon stimulation with 608 pM Roferon. For the absolute antiviral response, the baseline-subtracted area under curve (ΔAUC) from 24 to 28 hours is shown. For the relative antiviral response, the ΔAUC from 24 to 28 hours is divided by the corresponding ΔAUC in cells without pre-treatment.
B. Quantification of (A). The bar graph is quantification of bound Cdc20. The intensities of WT control in anaphase were arbitrarily set to 1.0. Error bars, SEM from three independent experiments.
a-b, Comparison of splenic CD8 Tn mitochondrial mass [Mitotracker (MT) green MF, a] and mitochondrial potential (MT Deep Red, b) of young and 45-wk-old Dj-1 KO and WT mice.
DC(Ctrl) and DC(NLRC3-OE) were stimulated with LPS (100 ng/ml) for specified time. DC lysates were probed for p-p38, p38, NLRC3 and GAPDH. Densitometry quantification of band intensity were presented in the right panel.
A Immunofluorescence staining of mPhb2 shRNA and control podocytes with a Tom20 antibody revealed a disturbed mitochondrial network in Phb2-deficient podocytes (scale bar: 10 μm).B Quantification of tubular and fragmented mitochondrial morphology mPhb2 shRNA versus control podocytes seen in (A) (mitochondrial network of n = 100 individual cells of mPhb2 shRNA podocytes and n = 108 individual cells of scrambled shRNA podocytes was assessed).C Morphometric image analysis revealed an increased ratio of mitochondrial count versus mitochondrial area in Phb2-deficient podocytes compared to control podocytes (n = 75 cell patches for scrambled shRNA, n = 58 cell patches for mPhb2 shRNA).D Morphometric image analysis showed a decrease in branch numbers in Phb2-deficient podocytes compared to control podocytes (n = 75 cell patches for scrambled shRNA, n = 58 cell patches for mPhb2 shRNA).E Morphometric image analysis detected a decrease in mitochondrial size in Phb2-deficient podocytes compared to control podocytes (n = 75 cell patches for scrambled shRNA, n = 58 cell patches for mPhb2 shRNA).
mig1Δ restores Rad53 phosphorylation of the snf1 mutants in the presence of HU. The experiments were done as in Fig 2.
(A) HEK293A cells transiently expressing the indicated mCherry constructs were treated in either full medium (F), starvation medium (S), or starvation medium with wortmannin (W) for 2 hr before immunoblot analysis.(B) Statistical analysis of (A) was performed by one-way ANOVA with Tukey's post hoc test. SEM for n = 3. ∗p < 0.05.
Cytokine concentration in Prdx4 WT and KO mice in response to LPS injection. (B) Cxcl1 levels in serum (left) or peritoneal lavage (right) at indicated time points after LPS or PBS injection. (C) TNF-α levels in serum (left) or peritoneal lavage (right) at indicated time points after LPS or PBS injection. (D) IL-1β levels in serum (left) or peritoneal lavage (right) at indicated time points after LPS or PBS injection. Each dot (B-D) represents an individual mouse. Horizontal lines indicate mean.
A) Heatmap shows log2FC based alterations between the significantly different inflammation related proteins on Day 70 vs Day 0 in the CMA and placebo groups. Asterisks indicate statistical significance based on paired Student's t test. p < 0.05;
Alveolar macrophages from different donors were purified from BAL fluid by allowing them to attach to the culture dish for 2 hours. Subsequently, they were pre-treated overnight with either type I or type III IFNs (1 ng/mL IFN-λ1 and 10 U/mL IFN-α2, respectively) before infection with Sendai virus (SeV) and influenza A virus (IAV, strain PR8) for 6 hours as indicated. Total RNA was harvested and subjected to qPCR for quantification of the IFN response measured by IFNA2, IFNB1, and IFNL1. ISG response measured by ISG15 and RSAD2. Each colour corresponds to a donor; 9 different donors were analysed. The dashed line represents the detection limit. An ordinary one-way-ANOVA test was used for the statistical analysis: ns, not significant; *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
(B) Normalized CDFDA intensities quantified from intravital images depict plasma disappearance curves (A, B) Representative intravital images and analysis (mean ±SD) from 5 (sham), 4 (PCI T-LipoAS) and 3 (PCI Veh) animals. Sham and PCI animals treated with T-LipoAS showed a classical biphasic decay curve, while PCI vehicles showed a relatively linear decay and a higher area under the curve indicative of excretory liver failure.
Mammary organoids were isolated from 19-20 weeks old C57Bl/6 mice on normal (ND) Organoids isolated from ND mice were cultured in matrigel/collagen mix for 2 days followed by macrophage-conditioned or control medium stimulation for 24­h. Representative images of organoids in matrigel/collagen mix.
(C-E). Quantification of the relative fluorescence intensity of (C) ubiquitin, (D) p62 and (E) LC3 per microcolony (see Materials and Methods). Cells were processed as in (A) and a minimum of 30 microcolonies analysed for each bacterial infection per experiment. Results from representative experiments showing the relative mean fluorescence intensity ± SEM are shown. Similar results were obtained in at least 3 independent experiments. * p<0.05; ** p<0.01; *** p<0.001.
A: Sequence of the two peptides used for the pull-down assay. The peptides are composed of an amino-terminal biotin, a linker sequence and a random sequence (control peptide) or the FFAT sequence of ORP1 (FFAT peptide). The FFAT sequence of ORP1 is in bold and corresponds to residues 469-483 (Accession number Q9BXW6-1). Aromatic and acidic residues are in blue and red, respectively
Differential interaction heatmap for Piwi- and Control (EGFP)-KD shown in log2 fold change. Hi-C data is shown with RNA levels (RNA-seq signal density), H3K9me3 association (H3K9me3 ChIP-seq signal density), H3K27Ac association (H3K27Ac ChIP-seq signal density), H3K4me3 association (H3K4me3 ChIP-seq signal density), H1 association (H1 ChIP-seq signal density), and lamin association (Lamin DamID-seq signal density). The genomic region flanking the gypsy insertion (red dashed line) is shown for OSCs with EGFP- and Piwi-KD. FlyBase protein-coding genes are indicated, together with chromosome position.
(b) Diagram shows experimental set up with macrophages in the bottom of the well and XO added either in the dialysis cassette (DC, blue) or the well (black). XO activity panels show that the enzyme did not leak through the DC membrane. Secretion of IL6 and TNF was measured 24 h after addition of XO in each compartment. A representative result of two independent experiments is shown.
Lipid peroxidation was measured by C11-BODIPY 581/591 after cold stress for 5 h. Representative plots are shown in E). Quantification data F), whose raw value were normalized by the C11-BODIPY 581/591 without cold stress of non-treatment, are presented as mean ± SEM; n = , 3 (F), biological replicates. ***p < 0.001, **p < 0.01 by unpaired T-test.
b, Log2(heavy (H):light (L)) plot for autophagosome proteins from PANC-1 cells (experiment (Ex.) 3, Supplementary Table 3) and scheme for identification of candidate autophagosome proteins.
(C) 5-day-old seedlings of WT, rgi5x and rgi5x pRGI3::RGI3 #2 and #3 were treated with 10 nM flg22 or co-treated with 1 μM GLV2 for 7 days before measuring fresh weight. Shown is the mean of relative fresh weight compared to the MS medium control -/+ SD, n=32 biological replicates pooled from 4 experiments (Students T-test, **p<0.01).
(e) Immunofluorescence for endogenous Atg9 and Cx43 in control NRK cells and those knocked down for Eps15.