EMBO/sd-character-level-ner huggingface dataset:
Figure 5 (A) Western blotting of fibrinogen in tumour-bearing and no tumour-bearing livers  (B) Scheme of the coagulation cascade related to FX and fibrinogen. Elimination of lung fibrinogen by activated FX (FXa) in B220+CD11c+NK1.1+HepELs  (C) IP-Western blot analysis shows protein-protein interactions between fibrinogen and Vtn/TSP  (D) Quantification of fibrinogen deposition areas after injection of CD45+ cells derived from the liver in tumour-bearing mice. Shown are averages (N = 7/ group) with SEM. 1-way ANOVA  (E) Quantifications of fibrinogen deposition areas in TCM-stimulating wild-type mouse lungs after injection of Vtn+ HepELs. Vtn+ cells were isolated from E0771-bearing wild-type or FX-/-mouse liver by using anti-Vtn beads (1 x 106 cells /mouse). Shown are averages (N=5/ group, 3 fields/ sample) with SEM. Welch"s t-test  (F) Separation of Vtn+/ CD45+ HepELs from tumour-bearing FX+/- and FX-/- mouse livers by a cell sorter (Moflo Astrios). Sorted Vtn+CD45+HepELs cells obtained from a littermate (3 animals each) were pooled, and 8 x 103 Vtn+CD45+HepELs cells were i.v. injected into a tumour-bearing mouse. Right graph shows fibrinogen depositions in the lung. Shown are averages (N = 3/ group, 9 fields/ sample) with SEM. 1-way ANOVA
Figure 1A Strains used in the study. Seven wine / European strains, and three other distant ones (all blue) were crossed to the S288C reference (yellow). B B Strategy for identifying suppression by standing variation. A temperature sensitive (TS) allele collection of ~1,100 partial loss-of-function mutants in the reference background (yellow) was crossed to the 10 wild yeast strains with potential suppressor alleles (blue), to produce large segregant populations selected to carry the TS allele. Each cross was performed in one or two biological and four technical replicates. The fitness of the resulting ~70,000 populations was measured at 26°C (permissive temperature) and 34°C (restrictive temperature). A subset of 38 candidate suppression events were used in bulk segregant analysis for linkage mapping of causal loci that display selection at restrictive temperature (black) but not permissive temperature (grey). D
Figure 3(A) Isolectin B4 stained vasculature in whole mount retinas of wild-type (WT) and global EVL-/- mice on postnatal days 3, 5 and 7 (P3, P5, P7) assessed by confocal microscopy. Scale bars 200 µm. (B) Analysis of the radial vascular outgrowth relative to retinal radius and normalized to wild-type littermates.
Fig.Figure 3Kinetics of ISG15, IRF7 expression at 0.75, 1.75, 3.75 and 8.75 days post-ΙFNα (600 IU/ml) treatment. Arrow indicates the time of HSV-1 infection at 18hr post-interferon treatment. n=9 biological replicates. Kinetics of PML mRNA expression at 0.75, 1.75, 3.75 and 8.75 days post-ΙFNα (600 IU/ml) treatment. Arrow indicates the time of HSV-1 infection at 18hr post-interferon treatment. n=9 biological replicates. Quantification of PML puncta at 1-, 3-, 6-, 8-, 10- and 15-days post-infection with HSV-1 in untreated and IFNα (600 IU/ml)-treated SCG neurons. n≥60 cells from 3 biological replicates. Representative images of P6 SCG neurons treated with IFNα (600 IU/ml) and stained for STAT1 at 18 hours and 8 days post-treatment. Scale bar, 100μm. Representative images of P6 SCG neurons treated with IFNα (600 IU/ml) and stained for Mx1 at 18 hours and 6 days post-treatment. Scale bar, 20μm.
Figure 8 Figure 8. Geography of cyclic nucleotide signalling and functional relationship between cAMP and cGMP signalling to control pH-dependent egress In presence of cAMP produced by ACα and ACβ, active PKAc1 is released from its regulatory subunit PKAr anchored at the inner membrane complex by dual acylation. At low pH, PKAc1 activates an unidentified PDE leading to the degradation of cGMP and down regulation of PKG preventing parasite egress. Upon unidentified stimuli, PKAc1 activity is repressed and/or GCα activity stimulated to increase cGMP levels and activate PKG. PKG stimulates Ca2+ mobilization from intracellular store and PLC activity to produce IP3 and DAG leading to microneme secretion and gliding motility necessary for parasite egress and invasion.
| Advanced paternal age caused vocal communication deficits in offspring.Figure 1A. Experimental design for F1 offspring derived from either young or aged fathers (YFO: n=57, AFO: n=39). B. Body weight in YFO and AFO. Data information: Data are presented in the box plot or pie chart format. The central band in each box represents the median; boxes indicate the middle quartiles, and whiskers extend to the minimum and maximum values. *p<0.05, determined using Student's or Welch t-test. C. Total USV number in YFO and AFO. Data information: Data are presented in the box plot or pie chart format. The central band in each box represents the median; boxes indicate the middle quartiles, and whiskers extend to the minimum and maximum values. *p<0.05, determined using Student's or Welch t-test. D. Average duration (msec) of each syllable in YFO and AFO. Data information: Data are presented in the box plot or pie chart format. The central band in each box represents the median; boxes indicate the middle quartiles, and whiskers extend to the minimum and maximum values. *p<0.05, determined using Student's or Welch t-test. E. Maximum frequency (kHz) of each syllable in YFO and AFO. Data information: Data are presented in the box plot or pie chart format. The central band in each box represents the median; boxes indicate the middle quartiles, and whiskers extend to the minimum and maximum values. *p<0.05, determined using Student's or Welch t-test. F. Maximum amplitude (-dB) of each syllable in YFO and AFO. Data information: Data are presented in the box plot or pie chart format. The central band in each box represents the median; boxes indicate the middle quartiles, and whiskers extend to the minimum and maximum values. *p<0.05, determined using Student's or Welch t-test. G. Individual syllable categories. The black line indicates 20 msec. H. Ratio of each syllable type in YFO and AFO. Each color corresponds to the individual syllable categories shown in Fig. 1G. Red and blue colors indicate a statistically significant increase and decrease, respectively, while gray indicates statistically 'not significant' changes. I. Number of syllable types in YFO and AFO. Data information: Data are presented in the box plot or pie chart format. The central band in each box represents the median; boxes indicate the middle quartiles, and whiskers extend to the minimum and maximum values. *p<0.05, determined using Student's or Welch t-test. J. Normalized entropy in YFO and AFO. Data information: Data are presented in the box plot or pie chart format. The central band in each box represents the median; boxes indicate the middle quartiles, and whiskers extend to the minimum and maximum values. *p<0.05, determined using Student's or Welch t-test.
Figure 3A Identification of dsRNAs activated by TERT-WT or TERT-K626A using dsRIP-seq in U2OS cells. AluYb9 and tRNA-Thr-ACG as positive and negative controls, respectively. B Quantification of antisense/sense transcripts of ERVs activated by TERT-WT or TERT-K626A in U2OS and HeLa cells using strand-specific RT-qPCR. C Regression analysis of the correlation between TERT and TA-ERVs expression in 103 tumour samples across 11 cancer types. BRCA (breast invasive carcinoma), n = 17. cHL (classical Hodgkin lymphoma), n = 5. COADREAD (colon adenocarcinoma/rectum adenocarcinoma oesophageal carcinoma), n = 6. HGSC (high-grade serous ovarian cancer), n = 6. KIRC (kidney renal clear cell carcinoma), n = 12. LIHC (liver hepatocellular carcinoma), n = 9. LUAD (lung adenocarcinoma), n = 6. OSCC (oral squamous cell carcinoma), n = 8. PAAD (pancreatic adenocarcinoma), n = 10. PRAD (prostate adenocarcinoma), n = 6. THCA (thyroid carcinoma), n = 18. D MeDIP-qPCR analysis of TA-ERVs sites in HeLa cells ectopically expressing TERT-WT or TERT-K626A. Primer sets recognizing exon 8 of the human ZC3H13 gene and a gene desert on chromosome 12 were used for positive and negative controls, respectively. E ChIP-qPCR for TERT and Sp1 targets on TA-ERVs in U2OS cells with TERT ectopic expression and in HeLa cells. GAPDH promoter was used as a negative control, and VEGF promoter was used as a positive control.
Figure 5Schematic model illustrating that Ku contributes to the low steady-state level of p53 under normal growth conditions by suppressing p53 mRNA translation and that this inhibitory mechanism is abrogated during DNA damage due to Ku acetylation, thereby allowing p53 upregulation.
Figure 6(A) Gene expression analysis of the indicated stress-induced genes in young and old cells isolated from YSC5106 WT, nat4∆ and H4R3K nat4∆ strains. Expression levels were normalized to ACT1, whose expression remains unchanged. Error bars, SEM of 3 independent experiments. P-values were calculated by unpaired two-tailed Student's t test: * p ≤ 0.05 compared to young wild-type; arrowhead p ≤ 0.05 compared to old wild-type. (B) RLS analysis for WT, nat4∆, pnc1∆ and double mutant strains in BY4741 genetic background. Values in parenthesis (here and hereafter) indicate mean lifespan. Statistical significance (here and hereafter) was determined by one-way ANOVA test: * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001; **** p ≤ 0.0001. ns = non-significant. (C) Mean RLS in BY4741 wild-type, msn2∆ msn4∆ double and msn2∆ msn4∆ nat4∆ triple mutant strains. (D) Mean RLS in BY4741 wild-type, nat4∆, fob1∆ sir2∆ double and fob1∆ sir2∆ nat4∆ triple mutant strains. (E) ChIP analysis performed in BY4741 wild-type, nat4Δ and Pste5-NAT4 strains grown under NCR and CR conditions. Chromatin was immunoprecipitated using antibodies against N-acH4 and Histone H4, and analyzed by qRT-PCR with the indicated primers. PNC1-P (Promoter), PNC1-S (Transcriptional Start), PNC1-E (End of gene). The enrichment from the antibody was normalized to Histone H4.
Figure 2A, ABR thresholds in OtofI515T/I515T (red, n=5) and Otof-/I515T (blue, n=7) mice were elevated compared to Otof+/+ mice (black, n=5) at an age of 3-4 weeks. The grey dotted line indicates the maximum loudspeaker output of 90dB; thresholds exceeding this value were set to 100dB for calculation of the mean ± SEM. At 12kHz, only the threshold increase for Otof-/I515T vs Otof+/+ is significant (Kruskal-Wallis test with Dunn's multiple comparisons test between all 3 groups).B, Grand averages of ABR waveforms ± SEM in response to 80dB click stimulation of the mice analyzed in A: The small wave preceding ABR wave I probably represents the summating potential (SP, hair cell receptor potential), which is intact in Otof mutants. ABR wave I is reduced in amplitude while subsequent peaks are better preserved in OtofI515T/I515T mice (Fig EV1).C, Mean ABR wave I amplitude ± SEM for different stimulus intensities (all differences between genotypes are significant; 2-way ANOVA with Tukey's multiple comparison test).D, At 8 weeks (circles) and 25 weeks (open squares), OtofI515T/I515T mice showed highly elevated ABR thresholds compared to Otof+/+ mice (n=7-8 each; p<0.001 at 12kHz, Mann-Whitney-U-test). Grey dotted line as in A.E, Grand averages of ABR waveforms ± SEM in response to 80dB Click stimulation in mice aged 8 weeks. OtofI515T/I515T (n=8) have drastically reduced ABR amplitudes compared to Otof+/+ mice (n=7). Otof-/- mice have no ABR (green, n=9).F, Mean ABR wave I amplitude ± SEM for different stimulus intensities for 8 week and 25 week old OtofI515T/I515T and Otof+/+ mice (p<0.001, 2-way ANOVA).
Figure 1YAP and/or TAZ antibodies and their target regions. Expression of YAP/TAZ and a smaller protein (asterisk) in different cell lines, protein expression was determined by immunoblotting (IB). The shRNA targeting TAZ, but not YAP, knocked down the expression of the smaller protein (asterisk). Antibodies targeting C-terminus YAP/TAZ, such as TAZ (CST) and YAP/TAZ, effectively pulled down the smaller protein (asterisk, dubbed as cTAZ hereafter) in RKO cells in an immunoprecipitation (IP) assay. cTAZ was not recognized by TAZ (SA), an antibody targeting N-terminus of TAZ. Exogenous TAZ/YAP was not processed proteolytically to cTAZ. RKO cells were transfected with the indicated plasmids expressing C-terminal HA-tagged TAZ or YAP. UCSC Genome Browser view of TAZ isoforms. Displayed tracks include a short (cTAZ?) and the full-length (TAZ) transcript of TAZ assembled using RNA-seq data of HCT-116 cells form SRA. The short TAZ isoform was similar to transcript ENST00000472417 annotated in Ensembl database. Below: the H3K9ac, H3K27ac, H3K4me1, H3K4me2 and H3K4me3 histone-modification signal peaks across TAZ gene in HCT-116 cells (data from ENCODE database). The red arrows indicate the primers (F: forward; R: reverse) used in (G). UTR and exons are shown in green blocks. RKO, but not HEK293A cells, expressed both full-length TAZ and cTAZ transcripts. RT PCR primers targeting different regions Alignment of TAZ and cTAZ protein sequences. cTAZ protein sequence was derived from the Sanger sequencing results of the short PCR product (RKO, F2:R1) Knock out of cTAZ in RKO cells using CRISPR/Cas9 technology. Monoclones (#3 and #14) were selected.
TIGAR expression modulates autophagy independently of p53.Figure 3TIGAR expression modulates autophagy independently of p53. (A) Quantitation of the percentage of GFP-LC3-positive cells displaying GFP puncta. U2OS cells stably expressing GFP-LC3 were transfected with scrambled or TIGAR siRNAs, and 48 h after transfection, cells were left untreated (t0) or treated with Bafilomycin A1 (100 nM) for 1 or 2 h (t1 and t2). The percentage of cells with GFP-LC3 puncta was calculated at the indicated time points. Data are shown as the mean and standard deviation from three independent experiments. (B) Quantitation of the percentage of GFP-LC3-positive cells displaying GFP puncta. U2OS cells stably expressing GFP-LC3 were cotransfected with scrambled or TIGAR siRNAs, and scrambled or p53 siRNA. After 48 h transfection, cells were left untreated or exposed for 5 h to nutrient starvation. The percentage of cells with GFP-LC3 puncta was calculated, and data are shown as the mean and standard deviation from three independent experiments. (C) Western blot showing the expression levels of endogenous p53 and TIGAR in U2OS cells cotransfected with scrambled or TIGAR siRNAs, and scrambled or p53 siRNA, and 48 h later exposed to nutrient starvation for 5 h. Actin expression was examined as a loading control. (D) Quantitation of the percentage of GFP-LC3-positive cells displaying GFP puncta. U2OS cells stably expressing GFP-LC3 were cotransfected with scrambled or TIGAR siRNAs, and scrambled or DRAM siRNA1/2. After 48 h transfection, cells were left untreated or exposed for 5 h to nutrient starvation. The percentage of cells with GFP-LC3 puncta was calculated, and data are shown as the mean and standard deviation from three independent experiments; * represents significant difference from starved control conditions (P<0.05); @ represents significant difference from untreated control conditions (P<0.05); # represents a lack of significant difference from control conditions (P>0.05).
Figure 1A Schematic representation of the workflow used for scRNAseq analysis of thymus and the generation of Dataset 1. Thymus were pooled from 6- to 8-week-old C57BL/6 female (n = 25) and male (n = 25) mice. Five single cell 3' gene expression libraries containing 18 000 thymoctes and 500 spike-in B cells were constructed and individually sequenced. B Schematic representation of intrathymic T cell development stages. T cell subsets straddling the bifurcation leading to αβ and γδ T cells were sorted and are colored in purple or brown, respectively. C Workflow used to sort the T cell subsets of interest. Thymocytes were first depleted from DP and SP T cells and then sorted by FACS. The sequential gating strategy used for sorting DN3a, DN3 γδ+, DN4γδ+, DN3b γδ- and DN4γδ- subsets is shown on the specified contour plots. CD71 expression was used to distinguish post-β-selected CD44-CD25+ DN3b γδ- cells from unselected CD44-CD25+ DN3a cells. DN4 γδ- cells constitute the progeny of DN3b γδ- cells and were characterized by their CD71+CD44+CD25- phenotype. The DN thymocytes gate corresponds to viable NK1.1- cells. Among TCRδ+ CD3+ DN thymocytes, CD24+CD44low cells correspond to DN3b γδ+ and DN4 γδ+ cells. DN3b γδ+ constitutes an intermediate stage bridging the DN3a and DN4 γδ+ stages whereas DN4 γδ+ cells constituted the end product of the intrathymic γδ developmental pathway characterized here. TCRδ+ CD3+ DN thymocytes also comprise a minor subset of CD24-CD44high cells (termed 'cluster B'; (Prinz et al., 2006)) that contain NK-like T cells.
Figure 2A. Western blot of nuclear and cytoplasmic protein extracts from splenic CD19+ cells isolated from C57Bl/6 mice and cultured with anti-IgM (α-IgM) for 4h, followed by the indicated treatment for 2h. Values above the blots indicate AhR protein quantification obtained by densitometry, normalized to Sam68 or Tubulin and compared to the DMSO-treated sample. Representative data of n = 3 independent experiments. B. qPCR analysis of Cyp1a1 expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for 24h as indicated. Cyp1a1 expression was normalized to Hprt1. Cyp1a1 expression among groups was normalized to Medium DMSO. n = 2 independent experiments; mean ± range. C. Flow cytometry analysis of Cyp1a1 expression, reported by eYFP, in splenic CD19+ cells isolated from Cyp1a1Cre R26R eYFP mice and cultured for 72h as indicated. Representative data of n = 3 independent experiments. D. qPCR analysis of Cyp1a1 expression in purified splenic B cell subsets isolated from C57Bl/6 mice and cultured as indicated for 24h. Cyp1a1 expression was normalized to Hprt1. n = 2 independent experiments; mean ± range.
Fig.Figure 6Schematic describing the measurement of spindle angle (θ) (Kikuchi et al., 2010). Z-stack images were obtained from 0.45 mm-thick sections of metaphase cells and the angle between the axis of metaphase spindle and that of the substrate surface, which is termed the spindle angle, was calculated. Results presented are scatter plots of the angle (θ) of the mitotic spindle (n=28 for all samples of vector, HA-WT, -3D, -3A, -R899X, -Q671X, and -R603X INVS stably transfected MDCK cells). Three independent experiments showed similar results. Statistical significance was determined by Mann-Whitney's non-parametric median test. Spindle angles were measured in MDCK cells transfected with the indicated INVS plasmids (+). The spindle axis was misaligned in cells expressing mutant forms of INVS as compared to cells expressing WT INVS or sham-transduced cells. Expression of 3A INVS and of clinically relevant truncated forms of INVS but not WT INVS, resulted in disorientation of the spindle axis during metaphase. Similar expression of all INVS constructs was verified by immunoblotting (Appendix figure S4A). WT INVS robustly inhibited the transactivation of INVS in a luciferase reporter assay, which could be reverted by C-terminal truncated INVS (R899X, Q671X, or Q603X), but not by a phospho-mimetic mutant or 3A INVS. Results presented are mean ± SE of the ratio of triplicates between sequentially measured firefly TCF/LEF signal and Renilla luciferase signal in HA-INVS transfected 293T cells. Dual-Luciferase reporter® Assay System (Promega) was used and experiments were performed in triplicates. Two independent experiments showed similar results. Statistical significance was determined by student's t test. The expression of HA-Dvl (upper panels) and the indicated forms of Flag-INVS (lower panels) are shown by immunoblots; α-tubulin was used as an internal control.
Atg5–/– or wild-type (WT) lobes were grafted into athymic (nu/nu) mice (nu/nuAtg5–/– or nu/nuWT, respectively).figf4Atg5-/- or wild-type (WT) lobes were grafted into athymic (nu/nu) mice (nu/nuAtg5-/- or nu/nuWT, respectively). Data are representative of three experiments with n ≥ 4. a, Expression of activation markers on lymph node CD4 T cells in nu/nuAtg5-/- or nu/nuWT chimaeras. b, The changes in body weight over time are shown. c, The appearance of nu/nuAtg5-/- or nu/nuWT chimaeras. The colon (arrow) and uterus (arrowhead) are highlighted; note the absence of fat pads (asterisk) in nu/nuAtg5-/- chimaeras. d, Haematoxylin and eosin staining of organs from nu/nuAtg5-/- or nu/nuWT chimaeras. Arrows indicate infiltrates.
Lactobacillus acidophilus NCK2187 and its SlpA bind to murine SIGNR3 to induce regulatory signals A B6 mice were orally gavaged with 109 CFU NCK56 or NCK2187, and the colonic gene expression of C‐type lectin receptors were measured by RT–PCR.Figure 5A B6 mice were orally gavaged with 109CFU NCK56 or NCK2187, and the colonic gene expression of C‐type lectin receptors were measured by RT-PCR. Each box represents an individual mouse; n = 4. Data represent three individual experiments. B Binding of SlpA to various hFc fusion proteins was analyzed by flow cytometry. Gray tinted line = SlpA‐coated beads only; orange = SlpA‐coated beads + secondary antibody; green = SlpA‐coated beads + control fusion protein; blue = SlpA‐coated beads + SIGNR1‐hFc; red = SlpA‐coated beads + SIGNR3‐hFc. Binding assay results were confirmed five independent times. C Binding of SlpA to SIGNR3, but not SIGNR1 expressed by CHO‐S cells. Gray tinted line = untransfected CHO‐S cells; blue = untransfected CHO‐S cells + labeled SlpA; green = SIGNR1‐transfected CHO‐S cells + labeled SlpA; red = SIGNR3‐transfected CHO‐S cells + labeled SlpA. Binding assays in CHO‐S cells were performed three individual times. D Binding of SlpA to recombinant human DC‐SIGN/CD209‐Fc chimera was analyzed by flow cytometry. Gray tinted line = SlpA‐coated beads only; orange = SlpA‐coated beads + secondary antibody; green = SlpA‐coated beads + control fusion protein; red = SlpA‐coated beads + DC‐SIGN‐Fc. Binding assays were performed and confirmed three times. E Binding of SlpA to DC‐SIGN expressed by CHO‐S cells. Gray tinted line = untransfected CHO‐S cells; blue = untransfected CHO‐S cells + labeled SlpA; red = DC‐SIGN‐transfected CHO‐S cells + labeled SlpA. Binding assays in CHO‐S cells were performed three individual times. F, G IL‐1β production by colonic DCs of naïve WT B6 GF or B6 Signr3−/− (KO) mice treated with NCK56 (blue) or NCK2187 (green) four times, or left untreated (black), as determined by flow cytometry. n = 5 mice/group. Data represent four individual experiments and are shown as mean ± SEM. *P 0.05. Black asterisks compare NCK2187 to untreated (PBS) mice, and red asterisks to NCK56‐treated mice. H Frequency of colonic FoxP3+ Tregs in KO mice treated with NCK56 or NCK2187 was measured by flow cytometry. n = 5 mice/group. Data represent four individual experiments and are shown as mean ± SEM.
Fig.Figure 2(A-C) mRNA expression of Bmal1 (black), Rev-erbα (grey) and Per2 (red) in HIOs (A), kcHIEs (B) and bHIEs (C). (D) Average expression of Bmal1 (black), Rev-erbα (grey) and Per2 (red) in HIO, kcHIE, and bHIE. (E) Amplitude of Bmal1 (black), Rev-erbα (grey) and Per2 (red). AU stands for arbitrary units.
Figure 1Family F1 has three affected individuals with homozygous mutations, family F2 has two affected individuals with heterozygous mutations, and family F3 has two affected individuals with heterozygous mutations. Thus, all seven patients (P1 to P7) carry at least one mutated allele and have thyroid dysgenesis (TD) and macroplatelets. The patients are represented with filled symbols and unaffected family members with open symbols. NA, not available thyroid ultrasonography, *mild thyroid asymmetry (possibly normal) with normal thyroid function, N, not mutated, m, mutate