EMBO/sd-character-level-ner huggingface dataset:
D The expression of Ifnb1 in WT (n=3) and Akt2 KO (n=3) primary-MEFs with VSV treatment (MOI, 0.1) for 6 hours was measured by qRT-PCR (left panel). After VSV treatment for 3 hours, the culture suspension was discarded and wash 3 times with PBS, then primary-MEFs was cultured with fresh medium for another 15 hours for analysis of the VSV-infected (GFP) primary-MEFs by fluorescence microscope (middle panel, representative images) and by FACS assay (right panel). Bar, 100 μm. Data information: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 and ns, not significant (P > 0.05); using two-way ANOVA test Data are from three independent experiments or representative of three independent biological replicates Error bars mean ± SEM
(A) Autophagic activities were measured by an ALP assay ( Noda and Ohsumi, 1998). YTS3 cells (Δapg10PHO8::pho8Δ60) harboring each mutant APG10 on CEN plasmids were grown to 1 OD600/ml in SC medium lacking tryptophan and then transferred to SD(−N) medium. Lysates from the cells after incubation for 0 and 4 h were used for assay. Error bars indicate the SD of three independent experiments.
log2 fold change in gene expression in TB IL-2nil compared to TB IL-2 for the nearest gene to the DHSs ranked according to the fold change in DNase-Seq tag count for TB IL-2/TB IL-2nil. The DNase-Seq tag density plots are taken from Figure 2A for TB IL-2, TB IL-2nil and TN.
C. Frequency of mRNAs within each k-means cluster containing at least 2 of the RNA motif over-represented in k 5 mRNAs.
C) Percentage of 2-cell-like cells obtained upon transfection of control or Dux-targeting siRNAs in control conditions or in combination with sodium acetate treatment. Measurements were obtained from 2 independent cell cultures, performed across 3 independent biological replicates. Boxes indicate the range between the first and third quantile, the band depicts the median and the whiskers extend no further than 1.5-times the interquartile range. Individual dots indicate the measurements obtained in each technical replicate.
D and E. Mitotic timing and spindle angle histograms of control (GAPDH)-depleted U2OS cells and CENP-E-depleted cells.
H&E-staining (E left panel) and immunofluorescence of IgG deposits (E right panel) in the kidney sections were collected from WT and Akt2 KO bone marrow-reconstituted CD45.1 mice Bar, 50 μm. Data information: * Data are representative of three independent experiments
(B) Plasmids encoding FLAG-tagged full-length GSDMD, GSDMD C-terminus and Myc-tagged nucleocapsid were transfected into HEK293T cells individually. Exogenous proteins were purified using FLAG or Myc targeting antibodies coupled to magnetic beads 24 h post transfection. Purified proteins were then mixed and incubated for 2h, followed by immunoprecipitation with antibody against FLAG or isotype IgG. Input and precipitates were immunoblotted as indicated.
C-D. Volcano plots of genes that are differentially expressed in mock relative to 16hpi, showing the statistical significance (-log10 adjusted p-value) vs log2 fold change (mock/16hpi) for the stem cells (C) and enterocyte lineage (D).
F) Representative electron microscopy micrographs of mitochondria from ES (n=49 sections) and 2-cell-like cells (n=57 sections) generated across 2 independent technical and biological replicates. Scale bar, 1 μm. Representative images from 2 independent biological and technical replicates are shown. 162 and 99 mitochondria were analysed for 2-cell-like and ES cells, respectively.
A) H&E and immunohistochemistry reveal that β-catenin accumulates in tumors emerging in one-year-old female miR-424(322)/503-/- mice. The panel is a representative image of n=5 independent tumors. The scale bar indicates 100 micrometers (µM).
(f) Example cross-correlation function of Venus::HES5 with NGN2::mScarlet-I (blue), Venus::HES5 with brightfield signal (black), and NGN2::mScarlet-I with brightfield signal (red) from the same transverse slice of E10.5 spinal cord; markers indicate the presence of two types of co-ordination namely in-phase (red arrowhead) and out-of-phase (black arrowhead).
C. Quantification of doubling time for U2OS, U2OS-hTR, IMRB and IMRB-hTR cell lines (n=3). Statistical analyses were performed with Student's two-tailed unpaired t-test with Welch's correction for normality of distribution Data information: Data are shown as mean ± SD, with the red line marking the mean value.
H) Fluorescence microscopy demonstrates different survival capability of WT and Pvt1 inducible KO cells with or without Doxycycline (Dox) treatment.
The representative image of colon tissue harvested from mice of indicated groups is shown in (C).
A. qRT-PCR analysis of Fam134b isoforms in mock, TFEB S142A:S211A and TFE3 S246A:S312A over-expressing U2OS cells. Values were normalized to Hprt gene and expressed as fold change values relative to mock. Mean +/- standard error of the mean (sem) of N=3 biological replicates. Student's un-paired T-test *p<0.05; NS not significant.
Total nuclear AIF intensity from (D) was measured with ImageJ and plotted as a vertical scatter plot with the group mean intensity indicated with a black bar. AIF has translocated to the nucleus after WT cells were exposed to H2O2 but not in NEDP1 KO cells.
C Quantitative TMT proteomics of A375 cells grown in complete media (CM) or EBSS for 3 hrs. Number of proteins affected are shown. Autophagy related proteins are indicated in grey and MAGE-A proteins in blue.
B, RMD efficiency is decreased when the distance from a DSB to one repeat is increased. RMD assays were performed in U2OS (EGFP-SSA-3427-17) cells using the indicated sgRNAs/Cas9. The distance between the sgRNA/Cas9 cleavage sites and the repeat sequences is shown.
B) Boxplots showing all-atom analysis of the energetic effects of the introduction of GKs into a set of amyloid steric zipper structures. The upper whiskers indicate the largest value no further than 1.5 times the Inter-Quartile Range (IQR) from the upper hinge, the lower whiskers show the smallest value at least 1.5 * IQR from the lower hinge. Notches extend 1.58 * IQR / sqrt(n) from either side of the median and represent a 95% confidence interval for the median value. Grey shaded area indicates total energy associated with the introduction of GKs into zipper structures, the remainder of the plot shows the breakdown of this total energy in into constituent energy terms. Each boxplot shows the distribution of 72 observations.
(B) Stability of hydrogen bonds between BET1Asp68 and BET1Asp72 respectively was estimated using molecular dynamics simulation in three replicas. Parameter occupancy could be more than 100% if several stable hydrogen bonds could be established by residue. Bars represent average fraction of the simulated time the residue is involved in a hydrogen bond(s). Data represented are mean ± SD.
J Cholesterol concentrations of p53+/+ and p53-/- HCT116 cells were determined by FilipinⅢ staining.
(E) HCR for DIPgamma and DIPkappa transcripts in Drosophila stage 17 embryos. RNA expression of both genes is analyzed in control (elav>GFPRNAi) versus Dfd depleted (elav>DfdRNAi) animals, the ventral nerve cord is highlighted by a white dashed line, the Dfd expressing subesophageal ganglion (SOG) is indicated by a yellow circle.
MIR376A and MIR376B level changes in response to starvation stress. (A and B) TaqMan quantitative PCR (qPCR) analysis of endogenous MIR376A (A) and MIR376B (B) levels under control (CNT, no starvation) or starvation (STV, 1 to 8 hours) conditions. TaqMan qPCR data was normalized using U6 small nuclear 1 (RNU6-1) (U6) mRNA levels (mean ± S.D. of independent experiments, n = 5 for both A and B, ***p<0,01).
C Isolated primary ratneonatal cardiomyocytes were treated to hypoxia with serum free-medium for 6h and reoxygenated accompanying adding serum back for different time period in vitro and the protein level of CUEDC2 was tested at different time points during reoxygenation. Each experiment was repeated for three times.
Interaction between endogenous TEAD1 and HOXA4 by co-IP experiments in HEK 293T cells. The interaction between endogenous TEAD1 and YAP was used as a positive control.
Averaged signals at promoter-distal (>10 kb) HIF-binding sites and at the promoters of hypoxia-regulated genes for comparison are shown for:I J), H3K4me3 ChIP-seqMedian RPKM (reads per kilobase per million reads, scaled to background signal) from normoxic (red) and hypoxic (blue) MCF-7 cells are plotted for ±10 kb flanking regions.
A Alignment of the amino acid sequences of IDOs restricted to the stretch of amino acids containing the YxxM motif (where x is any amino acid). Residues are highlighted based on increasing conservation level of symbols in the multiple alignment (light gray ≥ 44.4%; dark grey ≥ 66.6%; black ≥ 88.8%). IDOs, homologues of IDO1. Proto-IDOs, homologues of IDO2. Accession number for each specific gene is indicated.
Inverse correlation between Pom1/Tea4 and Tea4 observed experimentally following from the sub-linear relationship between Pom1 and Tea4 (see Fig. 1F, same data). Line shows linear regression (p-value<10-7).
H-I. Immunoblot validation of FOXO3a and STAT3 in response to ALKAL2 stimulation in the presence or absence of lorlatinib as indicated. The slower migrating FOXO3a band in SDS-PAGE in (H) likely reflects FOXO3a phosphorylation that is not seen in the presence of lorlatinib. Proteomic analysis was performed using 3 biological repeats. Immunoblots are representative of at least 3 independent experiments.
Mathematical modelling of death rate changes as bacteria adapt during entry to stationary phase, see Methods for details. The key assumption is that changes in maintenance rate β are due to changes of the proteome. To understand adaption, we thus need to understand how much bacteria can remodel their proteome when nutrients run out (A - left). We combine our key assumption with the following quantitative laws: 1. Death rate is set by maintenance rate; 2. Proteome sectors depend linearly on growth rate (Hui et al., 2015), 3. adapt at the same time-scale during nutrient shifts (Erickson et al., 2017). Combined, these relations allow us to compute how death rate depends on the proteome adaptation (A - right). We use the Flux Controlled Regulation (FCR) model (Erickson et al), to calculate the relative adaptation $\frac{\left( \phi_{X} - \phi_{X,0} \right)}{\phi_{X}^{'}}$ in various scenarios.
(C, D) Immunostaining of p62 and ubiquitin in the spinal cord sections from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. The number of p62 or Ub positive puncta was quantified. n=3. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ***, p<0.001, ****, p<0.0001. Scale bar = 10 µm.
A Illustration of the VpT6SS1 (vp1386-vp1420) activation cascade. Genes are represented by arrows indicating the direction of transcription. Genes belonging to the same operon are denoted by the same color. Locus numbers (vpxxxx) are denoted above. Positive regulators are denoted by a red frame. Dashed arrows denote transcriptional activation and are color coded according to the relevant induced operon. Numbers in black circles next to the positive regulators TfoY, VP1407, and VP1391 delineate the progression of the cascade.
Statistical evaluation of the number of myonuclei in myofibers of TA muscles from different genotypes (L) (n = 5 WT/5 linc-MYH KO/4 Ino80 KO/5 dKO/3 CreERT dKO animals in J/K, n = 6 WT/6 linc-MYH KO/5 Ino80 KO/6 dKO/3 CreERT dKO animals in L **p < 0.01, ****p <0.0001, > 31 MSCs /animal in K; ANOVA test with multiple comparisons against WT. Sidak-Holm correction was used. Data are mean ± S.E.M.).
In vivo analyses of tumor (B) in mice that were subcutaneously implanted with tumor tissues from two human liver cancer patients and divided into four groups.
(A) The two RecA domains are rotated relative to one another in FRH (cyan, large cell) compared to Mtr4 (green, RNA backbone in orange). The change in positioning of RecA-2 with respect to RecA-1 results in an overall displacement from the Mtr4 domain juxtaposition that ranges from 1.1 - 4.0 Å throughout RecA-2 with the largest differences at the external helices.
(D) MCF10A cells were transfected with indicated siRNAs for 48 h and analysed by immunoblotting for the indicated proteins immediately (upper panel) or after additional 24 h (middle panel) or 2 h (lower panel) incubation with (+) or without (−) 500 ng/ml TRAIL.
A. Quantification of oxygen consumption rate (OCR) showing the effect of lactate treatment on the respiration (induced) in various cells including HBVP, mBP, HASMC, BMEC and 3T3L1. The media was changed into glucose-, pyruvate- and glutamine-free media before OCR measurement and lactate (2mM) was added the media to measure induced OCR. (n=10 from independent experiments. Error bars indicate the standard error of the mean (SEM) from unpaired Student's t test.)
d, GST pull down (i) and immunopurification assays (ii) of CPAP's CC5 domain demonstrate its sufficiency in mediating CPAP-CDC protein interactions. The CC5 fragment is expressed as a GFP fusion protein in HeLa cells and immunopurified using anti-GFP antibodies. HeLa extracts were used as input controls. CAP350 does not co-purify with CPAP. Both Cap350 and ODF2 are not pulled down by CPAP's CC5 domain.
The level of phosphorylated Smad2 (P-Smad2) and total Smad2 (Smad2) was assessed by immunoblotting and β-actin was used as a loading control. Lower bar graphs show WB quantification of P-Smad2 (P-S2) normalized to β-actin. (B) 1603MED cells were treated with PBS (vehicle) or a blocking antibody targeting ActivinB (Ab α-ActB) or Follistatin. The p-values were determined by unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Bars represent the mean ± SD. Number of replicates is n≥3.
A. Immunodetection of BES1-CFP from heat-stressed plants, treated with ABA or Fluridone (Flu). 35S:BES1-CFP plants were treated for 24 hours with DMSO (control), 5 μM ABA or 10 μM Fluridone and heat-stressed as follows: lane 1: untreated control; lane 2: 45°C for 30 minutes; lane 3: 45°C for 60 minutes. The non-phosphorylated BES1 bands were quantified with ImageJ and the obtained values are shown in blue.
M238P cells were transfected separately with miR-143-3p, miR-145-5p or a negative control (miR-neg) mimics and RNA content was analyzed using whole genome microarrays (dataset 1, n = 2). (B) Overrepresentation of miRNA predicted targets in the set of downregulated transcripts following miR-143-3p and miR-145-5p mimics transfection using miRonTop webtool. Each arrow indicates the corresponding overexpressed miRNA.
B) Extracellular acidification rate of ES (blue), Zscan4+ (red) and 2-cell-like cells (green) across 3 independent biological replicates performed on the Seahorse extracellular flux analyser.
(h) Kymograph data obtained in the absence of coupling between cells; phase relationships are un-coordinated resulting in a KOP≈0.
Bar graph showing the relative expression of the indicated genes in the indicated cell types. Values were normalized to respective 'HN31+HRAS shRNA' average and represent mean±SEM. Data points represent values from biological replicates. Statistical test employed was Student's t-test.
Luminex analytes from WT CHIKV-infected joint cell lysates are categorized based on fold change states (up, down at 2 dpi relative to mock, and 6 dpi relative to 2 dpi. The numbers in the heatmap represent Log2 fold changes of analytes or genes. Analytes in complete or partial agreement with corresponding gene expression values derived from RNA-sequencing (RNA-seq) data appeared predominantly in the (A) up then down state (Mock to 2 dpi, then 2 dpi to 6 dpi, respectively),
(C, Sorted human CD14+ monocytes were electroporated with plasmids encoding nucleocapsid or control vector for 36 h and then stimulated with 10 μM nigericin for 30 min following pretreatment with 1 μg/ml LPS for 3 h. Cells were immunoblotted with antibodies against the indicated proteins (C). Data information: control vector used here was empty vector corresponded to the nucleocapsid-containing vector.
D. CpD Lysine (41,850 missense) heatmap for missense score correlations for all possible non-synonymous SNVs. Spearman's rank r between 0.16 and 0.81. Data information: color intensity represents two-tailed Spearman's rank-order correlation coefficients between 0 and 1.
(H) Quantification of the percentage of MEF cells with nuclear TFE3 upon DMSO (Control) or Torin-1 (250 nM) treatments for 1 h (mean ± SD of three independent experiments, one-way ANOVA analysis versus DMSO treated wild-type cells, ***p < 0.001; n>400 cells per condition).
(K) Immunoblotting of the lysates and anti-Flag immunoprecipitates of HEK293T cells transfected with Flag-STING and HA-TBK1 in the presence of DMSO or indicated concentrations of Palbociclib. The data shown are representative of n=3 biological replicates.
(A) Effect of NAF‐1 knockdown on starvation‐induced autophagy. H1299 cells infected with CTRL or NAF‐1 shRNA were starved for 4 h in EBSS with DMSO (vehicle) or Baf A1 (100 nM). Cell lysates were analysed by immunoblot.
A Subcellular localization of TFEB in WT or GCN5 KO HEK293 cells treated with or without Torin1 (Scale bars, 10 µm).
eatmap showing changes in gene expression levels along pseudotime for the enterocytes and goblet lineages. Dendrograms on the left of the heatmap indicate the results of hierarchical clustering of the genes. Colored bars above the heatmap indicate the types of cells ordered along the pseudotime, colored according to A.
(C) Lysosomes with high (CMA+) and low (CMA−) ability for CMA isolated from livers of fed or 48 h starved rats were processed as in (A). Top left: Levels of two CMA components (LAMP‐2A and hsc70) and of an unrelated lysosomalmembrane protein (LAMP‐1) in each of the four groups of lysosomes. Bottom left: Percentage of total lysosomal LAMP‐2A present in each fraction, determined by densitometric quantification of the immunoblots.
a) Clinical course of the disease. Normalized weight at day n was calculated as follows: % of initial weight of the animal at day n.
(j) The migration of CD4+ cells from chicken small intestine (SI) and colon induced by ligand C10ORF99. Data information: All data shown are representative of at least three independent technical replicates. Error bars indicate SD (n=3). UD, undetermined, ***P-value < 0.001; **P-value < 0.01; NS: no significance (t-test).
E, Expression of PIL1, AT5G02580 and CDF5 in 3-d-old SD-grown seedlings at ZT18. Data from 3 independent experiments were averaged. Error bars indicate SEM. Different letters denote statistically significant differences based on Wilcoxon test (p<0.05).
LD biogenesis is initiated in the ER. Nascent LDs harboring seipin at their ER contact recruit proteins and lipids from the ER to promote LDgrowth. LDs remain associated with the ER during maturation, allowing continuous cargo exchange between these compartments. In seipin deficient cells, ER-LD contacts are morphologically abnormal, either missing, rudimentary or aberrantly extensive. Most newly formed LDs lack functional contacts with the ER. HPos, a model ER-to-LD targeting peptide can initially reach LDs but its access to LDs is later perturbed. ACSL3, a lipid biosynthetic enzyme normally targeted to the LD surface remains in the ER or at ER-LD junctions. Oleic acid flux into neutral lipids is initially intact but subsequently impaired. In contrast, ADRP, a cytoplasmic coat protein, reaches LDs independently of seipin. Defective ER-LD contacts result in discontinued cargo exchange and arrested LD maturation, where the majority of LDs fail to grow beyond the diameter of ~200 nm.
Different forms coloured thus - cAMP-bound full-length (dark/light blue), cGMP-bound full-length (red), apo Bd1971∆EAL (yellow/orange) and half-occupied cAMP Bd1971∆EAL-mid (dark/light green). Residues from the opposing monomer labeled by a '. (A) Comparative conformational shifts when aligned on C-helix dimer. One monomer from the half-occupied form is empty (mid A) and adopts a similar pose to the apo form; the other monomer has bound cAMP (mid B) and adopts a pose halfway between the apo and bound forms. (B and C) The occupied cNMP monomer of Bd1971∆EAL-mid structure (green) possesses other features conformationally intermediate between the apo (yellow) and bound (blue) states, namely the position of M59 and the juxtaposition of the D63:R110 pair. (D) Comparison of nucleotide conformations between the three differing bound states of the Bd1971 cNMP sensor. The cAMP ligand in the Bd1971∆EAL-mid structure (green), is present in the syn form, with nucleotide base pointing toward the cyclic ribose phosphate. This conformation is like that observed for cGMP (red), but opposite to that of cAMP in the full-length (blue, occupied at both sites) complex. The interaction of R111' with the syn cAMP in Bd1971∆EAL-mid kinks R108 such that it cannot make a contact with the backbone carbonyl of I55, leaving M59 in upward conformation.
Human, mouse and total tau protein levels in cortical TBS-extracts of rTg4510, rTg4510-Mapt0/0, and control mice: The amount of human tau (Tau13 antibody) was comparable in rTg4510 and rTg4510-Mapt0/0, moTau (Tau/5) was comparable in WT and rTg4510, and total tau levels (hu+moTau, DAKO antibody) were (expected) highest in rTg4510 mice. Mean±SEM, n=3 mice/group, non-significant.
A-H. (A) Experimental design for the mouse model in Fig. 7A-H. p53+/+ and p53-/- C57BL/6N male mice (p53+/+ mice n=8;p53-/- mice n=6) were fed with HFD diet for 10 weeks and were administered PBS or terbinafine (80mg/kg) every day for 8 weeks. (B) Mice body weight of p53 +/+ (left) and p53-/- (right) mice. (C) Representative liver photos of mice (left), changes in liver weight (right), H＆E staining (D) and Oil-Red staining (E) of liver tissues are shown respectively. Total liver cholesterol concentrations (F) and triglyceride levels (G) of each group were examined. (H) SQLE mRNA expression of mice liver tissues by qRT-PCR.
A. PHSL1-CDC20 ama1∆ cdc28-as2 cells were treated with 1Na-PP1 at t = 3 h in SPM to inhibit Cdc28-as2. At t = 5 h (left) or t = 9 h (right), Cdc28-as2 was activated by washing cells with conditioned SPM (cSPM) lacking 1Na-PP1 (washout). Top, time-lapse series from the imaging of Mpc70-GFP and RFP-tubulin. The weak, nuclear signal from Ndt80-GFP serves to confirm entry into meiosis. Middle, quantification of spindle formation and Mpc70 loading to SPBs. Bottom, quantification of control experiments. Cells were washed with cSPM plus 1Na-PP1 at t = 5 h (left) or t = 9 h (right) in SPM.
Schematic illustration of the assay on micropatterned substrate. Tubulin was first added alone to measure the nucleation capacity of each micropattern, and then washed out. Later on, actin was added followed by actin and tubulin. Finally, actin was rinsed out and gelsolin was added to fully disassemble actin filaments. Representative images showing microtubules (top line) and the merged images of actin and microtubules (bottom line) during the four steps of the assay; in the presence of tubulin only, in the absence of tubulin and presence of actin, in the presence of tubulin and actin, and finally in the presence of tubulin and gelsolin but in the absence of actin filaments (from left to right). Scale bar: 10 μm.
During reprogramming with mES medium, Bmi1, Ctcf, Ezh2, Kdm2b, and Wdr5 were overexpressed simultaneously with the four Yamanaka factors (OKMS+5F) or Oct4 (O+5F). All factors were delivered simultaneously via a retrovirus system on day 0 and 1. Reprogramming with only Yamanaka factors (OKMS) or Oct4 (O) served as control. The expression of pluripotency markers was determined with qPCR on day 6 during reprogramming (E).
(f) Time-lapse images during extracellular trypsin treatment of HeLa cells show retention of most MBds (MKLP1-GFP, red). Two MBds (yellow arrows) are lost on treatment, indicating digestion and/or dissociation. Time (h:min) post trypsin. Scale bar, 5 μm.