EMBO/sd-character-level-ner huggingface dataset:
Quantification of secreted CCL6 into IMC-CM during the initial 24 h (0-24 h) and subsequent 48 h (24-72 h) of IMC culture by ELISA (n = 3, mean + SD).
Confocal IF images of RPE-1 WT, single KO (akap KO, pcnt KO and c5rap2 KO) and double KO (pc-ak-2KO, left panels; pc-c5-2KO, right panels) cells stained with the indicated antibodies. The yellow dashed line indicates the nucleus contour (N) and the arrows point the centrosome (CTR). GA marks the Golgi Apparatus. Scale bars: 5 μm.
(J) Basal OCR in Flp-In 293 HA-GFP or Flp-In 293 HA-IKKε cells treated with doxycycline (50 ng/ml) in combination with pyruvate deprivation for 16 hours, measured using Oroboros high resolution respirometry.
C. Schematics of the predicted binding sites of miR-200s on ZNF596 sequence. ZNF596-5'-UTR-mut contains a mutated sequence in the miR-200 binding site.
(B) Western blotting to detect the sfGFP levels at 6 hpf. Tubulin (Tub) was detected as a loading control.
(C) Cathepsin B (CtsB) activity in RPE lysates from 2-month-old miR-211-/- and control mice sacrificed 3h after light on at 10 AM (diurnal condition). CtsB was reduced in miR-211-/- compared to control mice. Bar graphs represent percentage of CtsB activity ± s.e.m. of independent experiments (n=3 mice) Mann and Whitney test (miR-211-/- vs WT), *p ≤ 0.05. Data information: (RPE) Retinal Pigment Epithelium
E) Similar to ssu72∆ mutants, stn1-S74D is defective in telomere recruitment. ChIP analysis of stn1-myc and stn1-S74D-myc using a non-tagged strain as a control. n = 3; *p ≤0.05 based on a two-tailed Student's t-test to control sample. Error bars represent standard error of the mean (SEM).
Rat hippocampal neurons at DIV3 were transduced with lentivirus coexpressing either hnRNPA3 targeting shRNA (shA3) or a control shRNA (shCtrl) and tag RFP. Three days after transduction (DIV3+3), neurons were transfected with (G4C2)80HIGH(+0) and analyzed at (DIV3+7). (B) Efficient knockdown of endogenous rat hnRNPA3 with its targeting shRNA.
Box plot showing the length of upregulated (UP), downregulated (DOWN), not affected genes (ALL), and pre-mRNAs affected by alternative splicing (AE, for Alternative exons) for ESCs (left panel); length of upregulated (UP), downregulated (DOWN), not affected genes (ALL), pre-mRNAs affected by alternative splicing (AE, for Alternative exons), and not affected genes that are only expressed in neurons (but not in ESCs) (ALL_notESC), for Neurons (right panel). n.s., p-value>0.05, **p<0.005; ****p<0.0001 as determined by Mann-Whitney t-test. Boxes delimit the first and third quartiles. The horizontal lines represent the data medians. Whiskers are drawn down to the 1st and 99th percentile. Percentage of genes that are downregulated in ESCs and neurons; plotted as a sliding window of 100 genes by length.
The model presents a non-canonical function for intracellular dopamine in the proliferation of the hematopoietic progenitor population. The progenitor cells during development employ the module of dopamine synthesis (TH and Ddc) and transporter (DAT) to build their levels of intracellular dopamine (iDopamine). In the earlier stages of lymph gland development, specifically at 48 to 72h AEL, this reservoir of iDopamine (as depicted by the red triangle) enables the progenitor pool to transit from S to G2 phase of the cell cycle. Later, as progenitor cells accumulate in G2, the Dop2R mediated dopamine signaling, confers mitotic competency to progenitor cells enabling them to transit from G2 to M phase. Specifically, Dop2R via DAT facilitates the build-up of iDopamine in G2 progenitor cells which poises them to enter mitosis such that in the presence of a mitogenic cue these cells divide. The activation of Dop2R and DAT function is reliant on extracellular dopamine (eDopamine) sensing whose levels in the system are maintained by progenitor based dopamine synthesis (via recycling) and non-autonomously by the PSC cells (which contribute later at 72h AEL). Thus the eDopamine levels support Dop2R signaling and DAT mediated uptake of dopamine by G2 progenitor cells necessary for their sustenance of mitotic competency. This contributes to the overall proliferative capacity of the hematopoietic organ and enables it to achieve its appropriate size. The importance of intracellular dopamine, either via synthesis or its uptake via DAT in governing progenitor cell cycle phasing either at S/G2 or G2/M transition, highlight threshold levels of iDopamine as a novel regulator of cell cycle control.
a and b, Schematic representation of the potential acetylation domain organization of BRD4 and its lysine mutants (AC1‒AC4).
C. Quantification of (B). The bar graph is quantification of bound Plx1. The intensities of Apc1-loop500 WT were arbitrarily set to 1.0. Error bars, SEM from three independent experiments.
C. BeadArray transcript analysis (Illumina) detected induction of multiple ISGs, including the cytokines CXCL10 and CCL5, but not other cytokine transcripts in Rnaseh2b-/- MEFs. Plotted, average fold enrichment versus p-value of significantly upregulated transcripts (p<0.05, after multiple testing correction) comparing two Rnaseh2b-/- MEF lines versus 4 Rnaseh2b+/+ MEF lines. 17 out of 29 transcripts are ISGs.
RAW264.7 cells were transiently transfected with control or miR-155 mimic for 24 h. Endogenous LC3 was stained with LC3 antibody followed by Alexa Fluor 488-conjugated goat anti-rabbit IgG (Green), and LC3 puncta (>1 µm) were detected by confocal microscopy (C) and quantified (D).
A VP1388 binds VP1390. Immunoprecipitation using α-FLAG antibodies from E. coli cells co-expressing the indicated C-terminal FLAG- and Myc-tagged proteins from arabinose-inducible plasmids.
F Increased levels of Nrf2 and its downstream target protein, HMOX-1, in the MOAP-1 deficient tumors. While p62 protein is upregulated in the tumors compared to the adjacent non-tumor tissues in both WT and MOAP-1 KO livers, no significant difference is observed in the p62 protein levels between the WT and MOAP-1 KO tumors. Lysates of the tumors and non-tumor parts of the livers from mice injected with DEN as described in (D) were prepared in RIPA lysis buffer containing 1% SDS and subjected to Western blotting. Actin as loading control. P, PBS injected control; N, non-tumor; T, tumor.
(A) HIV-1-infected primary CD4 T cells (strain CH058) were incubated with sera of HIV negative (HIV-; n=9) or ART-treated HIV-1-infected (HIV+; n=9) individuals (serum dilution 1:1000). The levels of IgG binding on infected (Gag+) cells were analyzed by flow cytometry. Results are expressed as the MFI on infected (Gag+) cells. Error bars indicate SEM. ****P<0,0001; Mann-Whitney test.
(B, C) Effect of GRASP55 depletion on SL biosynthesis monitored by [3H] - sphingosine pulse-chase assay in GRASP55 KO cells or cells treated with GRASP55 siRNA or following expression of GRASP55-GFP in GRASP55 depleted cells. GSL levels are expressed as fold changes respect to control. (C) The levels of GM and Gb were quantified and represented as GM/Gb ratio.
B: Number of tumor tissue DNA mutations passing INVAR filters for the 8 patients included.
B Degradation of V5-tagged HybA at times after blocking protein translation at T0 in the presence (+) or absence (-) of HybB. Rhomboid substrates that are uncleaved, cleaved by GlpG, black, red, arrows, respectively. Degradation products post rhomboid cleavage are marked by green arrows.
A Expression of KCNA5 (left) and KCNJ3 (right) in GFP+ pools of VM and AM CMs at day 31, as well as in ventricles and atria of human heart.
B. Generalized Linear Model (GLM) plots showing observed Col/Ler crossovers per megabase (red) for SNP intervals grouped into hexiles or quintiles, by increasing values (left to right along the x-axis) of a given explanatory variable. Data were modeled with the glm2 function in R, using the binomial family with the logit link function. The formula used for the model was Crossovers ~ (SPO11-1 + nucleosomes + H3K4me3 + DNA methylation + SNPs/kb + width)^2. Predicted crossovers per megabase for each group of intervals were derived by sampling from the binomial distribution based on the probabilities of intervals within each group overlapping a crossover. The black box plots represent 100 samples, where the central band represents the median, the box represents the interquartile range (IQR), and the whiskers represent the minimum and maximum values that are no more than 1.5 times the IQR from the box. The final stepAIC-selected model was:
(a) THP-1 cells were transiently infected with BRLF1-expressing or empty control lentivirus. Twenty-four hours later, the control or BRLF1-expressing THP-1 cells were primed with 40 ng/ml TPA overnight and then were either uninfected or infected with HSV-1 (MOI=1) in serum-free medium for 12 h. The supernatants and whole cell lysates were collected and analyzed by western blotting to detect pro-caspase-1 (p45), cleaved caspase-1 (p20), pro-IL-1β, mature IL-1β, pro-IL-18 and mature IL-18 as indicated.
Graph reporting cell viability of control (shCTR) and antimiR-9 FaDu cells, overexpressing or not SP1, and treated with increasing concentration of Bleomycin (BLEO) for 72 hours and analyzed using the MTS cell viability assay. Data represent the mean (±SD) of three independent experiments each performed in sextuplicate. Two-way ANOVA with Sidak's multiple comparison test was used to verify the statistical significance. *p<0.05; **p<0.01; ***p<0.001.
(A) Stable RNAi screening of cancer-related genes was conducted to identify gene knockdowns that enhance reprogramming of MEFs into iPSCs. The graph shows the 10 shRNAs that were most strongly, positively selected in iPSCs compared to non-reprogrammed cells on day 14 of reprogramming (n=3 biological replicates).
H. Average speed of salivary gland sporozoites. Data points represent individual sporozoites, n indicates total number from 3 biological replicates. P-values are calculated using the Kruskal Wallis test followed by the Dunns multiple comparison test.
(A) Total cell lysates of peritoneal macrophages from Atx∆ΜΕ/∆ΜΕ mice and Atx+/+ littermates were subjected to immunoblotting analysis to confirm Atx deletion.
A (Left) Detection of XBP1 mRNA splicing in WT and PDI KO HepG2 cells treated with or without 5 μM Tg for 1 h. PDI KO was verified by protein immunoblotting. (Right) Quantification of XBP1 mRNA splicing levels. Data were shown as mean ± SEM of three independent experiments. *p < 0.05 (two-tailed Student's t-test).
The SnRK2 OST1 activates ABFs for expression of a luciferase reporter (LUC) in yeast. Luciferase activity is given on a Log10 scale as relative counts of light emission per second (rcps) normalized to the cell density. The OST1-mediated induction factor is indicated above the columns. In the absence of ABFs, the LUC activity was 3 x 103 rcps.
E Theoretical calculation of the fraction of A (or C) blocks in the shell vs the logarithm of the transcription rate (rescaled by the rate at which the transcripts are spontaneously incorporated in the paraspeckle). The numbers of segments of A blocks were 5.0 (cyan), 7.5 (orange), 10.0 (green), and 12.5228 (black). The parameters used for the calculations are shown in the Materials and Methods.
C Growth curve of GB16 cells infected with the indicated lentiviruses. Bars indicate mean ± s.d. (n = 3).
(A) Immunofluorescent staining of ABCA12 (green) and Insulin (red) in mouse islets showing extensive co-localisation in β-cells as well as expression in other islet populations (arrowheads, scale bar=25μm). (B) Co-expression of Abca12 (green) and Insulin (red) in MIN6 cells (scale bar = 10μm).
(H) Analysis of Pearson correlation coefficients (PCC) of CEP55 vs. MYC levels with R=0.9982, p=0.0016. Protein band intensities as shown in H were measured using ImageJ software.
F. Model for centriole duplication and centrosome separation patterns throughout the meiotic prophase and division stages. During the leptonema to zygonema transition the first round of centriole duplication occurs. As cells progress through meiotic prophase I, centrosomes mature and acquire distal appendages. During diakinesis centriole separation occurs, allowing the formation of a bipolar spindle during the first meiotic division. During interkinesis centrioles duplicate a second time and separate to form a bipolar spindle at meiosis II.
C The protein levels of IFNAR1 and TYK2 in RBM47-overexpressing or control 293T cells treated with or without DRB. The relative band density was quantified using the ImageJ software and normalized to GAPDH. The relative density of the control group was set to "1." Data information: Data are representative of n = 3 independent experiments. NS, non-significant; **P ≤ 0.01, and ***P ≤ 0.001 (Student's t-test).
(d) HeLa cells stably expressing EGFP-LC3 were treated for 4 h with 400 nM bafilomycin A1 in presence or absence of 10 μM calpastatin, 50 μM ALLM or 50 μM calpeptin. Calpain inhibitors were treated for 24 h before bafilomycin A1 addition. EGFP-LC3-II was detected with anti-EGFP antibody. Data from different calpain inhibitors are from different blots.
(F, G) HU induces a rapid Snf1 T210 phosphorylation. Exponential cells were treated by 200 mM HU for the indicated time. Protein extracts were prepared as described in the Methods and Materials. Three independent experiments were done. Quantitation of Snf1 T210 and Snf1 signals was performed by Image J. The relative ratio of Snf1 T210/Snf1 was shown in (H). Error bars represent standard deviations (SD) from three biological repeats.
G Cytokinetic defect and cell viability of Inn1‐Clb2m or Inn1‐Clb2mΔCdk cells in the absence or presence of Chs2V377I. In the bar graph, red dots represent values of duplicate biological replicates with bars representing the average. Significance is calculated using Student's t‐test. 10‐fold spot dilution assays are represented, together with the Western blotting analysis for Inn1 before and after its fusion to Clb2m. Tub1 served as a loading control.
B IL-2 production in the presence of wild type and K63-ubiquitination resistant FOXP3. Naïve CD4+ T cells isolated from Traf6fl/flCD4Cre+ or WT mice were activated overnight by anti-CD3/CD28 antibodies, then transduced by retroviruses carrying normal Foxp3, the K262R mutant, or an empty vector. Ires-GFP in the retroviral vector serves as an internal control. GFP+ cells were sorted out 48 hours post-transduction. The sorted cells were cultured for one additional day. Culture supernatants were collected for measuring the levels of IL-2 by ELISA.
Pie chart depicting the various speices of 5'-tsRNAs expressed in the three different states of stem cells tested.
(E and F) Quantitative data demonstrating the interaction between HMGB1-Beclin1 and Beclin1-HMGB1 using densitometry software to assay the relative protein band intensity in co-IP experiments as shown in A-D. **, P < 0.005 and ***, P < 0.0005; n = 3. UT, untreated. Data are means ± SEM.
Western blot analysis of total cell lysates of macrophages from SARS-CoV-2 naïve individuals (SC-naïve) (top) and COVID-19 infected individuals (bottom). Macrophages were stimulated with LPS or S-protein (1h). Control cells were left unstimulated. Antibodies against pro-IL-1β (31kDa) and β-actin (loading control) were used for detection. Representative example of three experiments performed with individual patients and SARS-CoV-2 naïve controls.
RPE cells transfected with control, FAM110A or CSPP1 siRNAs were collected and analyzed by immunoblotting with indicated antibodies.
(a) Control males were injected with either tesaglitazar (grey syringe) or vehicle twice per week for 4 weeks. Males were paired with control females to generate offspring.
(A) Microarray-based transcriptome analysis of CD4+ T cell subsets from C57BL/6 mice. The heat map illustrates differentially expressed genes between CD4+CXCR5hiICOS+ Tfh cells, CD4+CXCR5-ICOS+ effector/memory T cells and CD4+CXCR5-ICOS- naïve T cells. Cells were purified from the spleen of mice seven days after immunization with NP-KLH with alum. Data are derived from three independent array analyses (10 mice/array) for each T cell subset.
D) Effect of DRP1 on BAX-induced LUV permeabilization. BAX was activated by cBID (blue lies), or mild heat (42°C, grey lines). Data are presented as mean ± SD of n=3 individual experiments. Significance was determined at the end-point of the kinetic measurement (180 min) by paired two-tailed Student´s t-test (* p < 0.05, *** p < 0.001).
I. MitoSox staining in myocytes expressing or not ATPIF1H49K. The right histogram shows the quantification of mitochondrial ROS. Bars are the mean ± s.e.m. of n= 3 experiments, 12 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 Student's t-test.
(C-G) Resembling the phenotype caused by Notch overexpression (D) or dSir2 mutation (E), HP1c knockdown (F) and mutant (G) flies also exhibit supernumerary anterior scutellar (aSC) bristles on the notum, as indicated by the enlarged views in the left bottom panes. Scale bars, 100 μm.
LFC change in YAP1 shRNA representation in 20 cancer cell lines and SCP-1 cells transduced with FUS-DDIT3 or EV. Error bars represent the mean ± SD of LFC scores for six independent shRNAs.
Western blot analysis of Flag-tagged proteins in cells with or without KLHDC3 or APPBP2 expression. The N-terminal Flag abolished protein targeting. GAPDH serves as a loading control.
A-G. Mammary ductal outgrowth in 3-7 weeks old wt or Sharpincpdm female mice. E. Representative carmine-alum stained images highlighting terminal end buds (TEBs) in 7 weeks old wt and Sharpincpdm mouse mammary glands and F. quantification of the number of TEBs per gland (n = 9 - 10 glands). Scale bar represents 500 μm.
(A) Quantitative western blot EPCAM, SCD, and USP3 in MCF10A cells 24 hours after treatment with H2O2 (200μM). HSC70 was used as a loading control. (B) Quantification of western results in (A) (n=9). A one-tailed Mann-Whitney test was used to test for statistical significance.
d, e, Reduced ATP levels in octyl alpha-KG-treated normal humanfibroblasts (**P = 0.0016, ****P  0.0001; by t-test, two-tailed, two-sample unequal variance) (d)
B) Size difference between the GS positive (closed circle) and negative (open circle) NF135 schizonts after treatment of AIP. Each dot represents the median of a biological replicate where ≥100 schizonts were measured. Three biological replicates were performed with the median from each plotted +/- s.d.. A two-way ANOVA was performed followed by a Dunnett's multiple comparison test with *** = 0.0002 and **** = 0.0001.
(A) Vertical section of macaqueretinal explant transfected with AAV2 hSyn:ReaChR-mCit after 10 days of incubation exhibiting mCitrine expresssion densely in neuronal processes in the GCL. (B) Vertical section of macaqueretinal explant transfected with AAV8 Y447 733F-CAG:ReaChR-GFP after 3 days of incubation. GFP expression was primarily observed in the cell bodies but also in processes of RGCs; green: endogenous GFP fluorescence; blue: DAPI; outer nuclear layer (ONL). scale bars = 10 µm.
(B) Visualization of selected top gene ontology (GO) enrichment terms for NRP and IDN clusters based on DEG analysis.
Realtime propidium iodide (PI) uptake assay from indicated THP-1 cells infected with type I or type II Tg, and untreated or treated with IFNγ and/or Dox as labelled. AU, arbitrary units.
E, Immunofluorescence microscopy of HEK293T cells transfected with SNAP-FZD5 and the indicated constructs. Cells were incubated with SNAP-surface-549 for 15 min and chased for another 10 minutes prior fixation. Representative images from one out of two independent experiments are shown. The white arrows show SNAP-FZD5 undergoing plasma membrane clearance. Scale bar = 20 μm.
D. Duration of mitotic arrest in MAD1-WT C14 or MAD1-3EK C12 cells arrested in nocodazole and then treated with indicated concentrations of AZ-3146. Note, the 1.25 µM AZ-3146 data is displayed in Figure 4D, but also included here to allow comparison with other drug doses. Graph shows cumulative mean (±SEM) of 3 experiments, 50 cells per condition per experiment.
(B) Graphs display the FLAG-Orm2 protein levels determined by densitometric quantification of Western blots in cell lysates of WT cells and the indicated mutants 0, 90 and 180 min after the addition of CHX. Each experiment was repeated at least three times. FLAG-Orm2 levels were normalized to Pgk1 loading controls, and each timepoint was related to t=0 min (set to 1). Data are presented as mean ±standard deviation.
A Constitutive expression of either MPCFERM or MPCOX can rescue the slow growth phenotype of the mpc1Δmpc2Δmpc3Δ triple deletion mutant. Growth tests were performed with cells transformed with MPC1, MPC2, or MPC3 expression plasmids or with empty vectors in indicated combinations. A serial dilution of yeast cells was spotted on agar plates with glucose‐containing synthetic minimal medium with (SD+AA) or without (SD−AA) amino acids.
Scatter plot and correlation coefficient (r) of ASK1 mRNA expression and liver fat content (C). Data were collected in lean subjects (n=14), obese subjects (n=23) and obese subjects with type 2 diabetes (n=19). Values are expressed as mean ± SEM (D).
G. Western blotting and quantitative analysis of MBP protein levels from homogenates of organotypic cerebellar slices at 6 dpl cultured in absence or in presence of 100 μΜ D-Asp Data information: The values represent the means ± S.E.M. Level of significance was determined by usin G, one-way ANOVA P=0.003 followed by Bonferroni post hoc test, *P<0.05 versus control, ˄P< 0.05 versus LPC (n=3
A) Plasma levels of selected candidate biomarkers analyzed in healthy subjects (n=131), pancreatitis patients (n=30) and PDAC patients (n=131). Data are expressed as a scatter-plot, mean ± SEM, *p<0.001 (Wilcoxon Rank Sum Test)
(E) MTPAP KD and control cells were incubated with valinomycin and bafilomycin A1 for 2 h. Cell lysates were subjected to immunoprecipitation using an anti-NDP52 antibody or control IgG. Immunoprecipitates were analyzed by western blotting. Data are representative of three independent experiments
Effect of TFL457 on the decrease of TrkB-FL surface levels induced by NMDA. Analysis was performed as before in cells incubated with CPPs (25 μM, 30 min) and NMDA-treated (1 h). Results obtained in excitotoxic cultures are expressed relative to cells treated with the same peptide but no NMDA.
D) Differential expression analysis of germline-specific and soma-specific genes, as classified in (Reinke et al, 2004). "All genes" is shown for comparison. (PolyA-selected RNA-seq libraries, n=3).
(C) Immunoblotting analysis of 22Rv1-P cells with different ESM1 overexpression in the nucleus and cytoplasm were performed with the antibodies indicated.
Three cohorts of mice (5 or 6 per group) were infected with 500 pfu of one of the three IAVs. Viral protein expression in mouse lung was determined by Western blotting 2 days after infection.
(F,G) Protein expression of mitochondrial ETC component genes was measured in AC16 cells after following treatments in comparison with control cells: (F) siRNA knockdown of FAM210A. (G) FAM210A overexpression.
Immunoblots from primary MDMs infected with Tg strains for indicated times. Cells were untreated or pre-treated with IFNγ before infection. Images are representative of n = 4 biologically independent experiments.
(C) HOIL-1[T203A/F204A/R210A] was assayed at 30°C in the absence or presence of the indicated ubiquitin dimers and tetramers. These mutations have been reported to impair the binding of ubiquitin to the NZF domain and their approximate location in HOIL-1 is indicated (schematic not to scale).