EMBO/sd-character-level-ner huggingface dataset:
Figure 4Hinge 1 moves away from hinge 2 during transition from pre-SC (cotton) to post-SC (lime), thereby forming new interactions with the ribosome. In contrast, hinge 2 movement from pre- (moss) to post-SC (emerald) does not change the interaction with the ribosome. The HLH motif is displaced from h5 in the pre- (watermelon) to h15 in the post-SC (pink). Positioning of the FeSD (sage) interferes with the closure of NBD2 (blush) in the pre-SC (rose). Possible communication pathways from ribosome binding sites to the NBSs in the post‑SC. HLH is connected to the Q-loop of NBSI via β8. I304 of hinge 1 connects to α14 which is adjacent to the His-switch in NBSI. Analogously, hinge 2 binding to the SSU might be communicated via Y593 and R566 to α23 next to the His-switch of NBSII. Interaction pattern of the communication pathways between HLH and hinge 1 to NBSI as well as hinge 2 to NBSII is different in the pre-SC compared to the post-SC.
Figure 6 Figure 6. Model of the regulation of the balance between dynein plus end tracking and the initiation of processive minus end directed motility Three different hypothetical conformational states of dynein/dynactin characteristic for (i) EB and dynactin co-dependent plus end tracking, (ii) p150-dependent initiation and (iii) BicD2 and dynactin co-dependent processive motility are indicated by different coloured shaded areas. The dynactin component p150 interacts with the microtubule during initiation in a specific, GTP-sensitive manner, very different from its interaction with EBs during end tracking. Lis1 can stabilise the end tracking complex and in conjunction with BicD2 also promote the formation of the initiation complex, which is incompatible with EB-dependent plus end tracking. Lis1 may or may not dissociate from the processive dynein/dynactin/BicD2 complex. Blue lines indicate GTP sensitive interactions with the microtubule.
Excessive accumulation of TRM cells in an aged environment is dependent on TGF-βR signaling.Figure 4.signaling.A. OT-I T cells (CD90.1+) from young donors were adoptively transferred into young or aged C57BL/6 mice 1 day prior to infection with PR8-OVA virus. B. Representative flow cytometry plots in lungs at 50 d.p.i., showing the gating strategy for resident OT-I T cells (CD8+CD69+ i.v.CD45- Vβ5+CD90.1+) C, D. Donor OT-I cells were enumerated in young and aged hosts in the lung vasculature (Cir) or parenchyma (Res) (C), or in spleens (D) at 50 d.p.i. E. Relative transcripts (RT) of Il-15, Tnf, and Tgfb1 (left to right) from total lung samples obtained from aged and young animals at 60 d.p.i. was evaluated by qPCR. F, G. Wild type (WT, CD45.1+) or TGFbR2fl/fl dLck-Cre OT-I cells (KO, CD45.1+) were adoptively transferred from young donors into young or aged hosts (CD45.2+) one day prior to PR8-OVA infection. F. Resident OT-I cells were enumerated in the lung of young or aged mice at 50 d.p.i. F, G. Wild type (WT, CD45.1+) or TGFbR2fl/fl dLck-Cre OT-I cells (KO, CD45.1+) were adoptively transferred from young donors into young or aged hosts (CD45.2+) one day prior to PR8-OVA infection. G. OT-I cells in the spleen of young or aged mice at 50 d.p.i.
Figure 1Gel shift assay of biotin-labeled mascRNA and 5S rRNA with the cytosol (Cyto) and the postnuclear membrane lysate (Mem). Northern blotting of mascRNA (top panel) and western blotting of β-Tubulin and Mortalin (bottom two panels) in the cytosolic fractions and the postnuclear membrane fractions of HEK293 and HepG2 cells.
Negative regulation of hepatocyte proliferation by HSC-expressed endosialin.Figure 3A Representative images of Ki-67 immunohistochemistry after 2, 4, and 6 weeks of CCl4 treatment of WT and ENKO mice (n = 5-8 mice per group and time point). Scale bars: 75 μm.B Quantitation of Ki67+ hepatocytes/HPF after 2, 4, and 6 weeks of CCl4 treatment. C Time course of EN expression after partial hepatectomy (2/3 PHx) determined by qRT-PCR of total liver lysates (n = 5/time point, sham: n = 3). D Representative images of Ki-67immunohistochemistry 2 days after 2/3 PHx of WT and ENKOmice (n = 5-9 mice per group and time point).E Quantitation of Ki-67+hepatocytes/HPF determined 1, 2, 4, and 8 days after 2/3 PHx.F Number of mitotic figures 2 days after 2/3 PHx of WT and ENKOmice (n = 5-9 mice per group and time point). G qRT-PCR analysis of total liver lysates 1 day after PHx for IGF2. H Western blot analysis of phosphorylated insulin-like growth factor receptor 1 (pIGFR1), phosphorylated insulin receptor substrate 1 (pIRS1) and β-actin 2 days after PHx. I Western blot analysis of phosphorylated and total extracellular signal-regulated kinase (ERK) and AKT 2 days after PHx. J, K qRT-PCR of IGF2 in isolated liver sinusoidal endothelial cells (LSEC)(J) or hepatocytes (HEP)(K) 1 day after PHx. L EdU-positive hepatocytes (in %) after 24-h stimulation with conditioned medium (CM) from either WT or ENKO HSC (3, 5, or 7 days of activation). HGF (40 ng/ml) and TGF-β (10 ng/ml) serve as positive or negative control, respectively. M EdU-positive WT and ENKO hepatocytes (in %) after stimulation with IGF2 (100 ng/ml). HGF (40 or 10 ng/ml) and TGF-β (10 ng/ml) serve as positive or negative control, respectively.
Figure 1Characterization of OAS1-3 expression in parental and OAS knockout PC3 cells, obtained using CRISPR-Cas9 technology. Left: Western blot (WB) analyses of the expression of OAS1, 2, and 3 in clones of OAS single-, double- or triple-knockout PC3 cells (KO, DKO, TKO), treated with IFNβ (500 IU/ml) for 24 h, to increase OAS expression. sgOAS1-3 - single guide RNA for OAS1-3. β-actin is shown as a loading control. Right: analysis of the expression of OAS1, 2, and 3 in PC3 DKO cells with increased expression of the remaining OAS, without IFNβ treatment. OAS1 expression in DKO2/3 cells was measured by qRT-PCR due to insufficient sensitivity of anti-OAS1 (see Fig EV1A), OAS2 and 3 expression was detected by WB. The gene expression data are presented as mean + SD of triplicates.**, p<0.001 in Student's t-test. Characterization of OAS1-3 expression in parental and OAS knockout HME cells, obtained using CRISPR-Cas9 technology. Left: WB analyses of the expression of OAS1, 2, and 3 in selected clones of HME cells in which OAS1-3 were knocked out, to produce OAS single-, double- or triple-knockout cells (KO, DKO, TKO), treated with 100 IU/ml IFNβ for 24 h to increase the levels of OAS expression. sgOAS1-3 - single guide RNA for OAS1-3. β-actin is shown as a loading control. Right: The expression of OAS1, 2, and 3 in HME DKO cells with increased expression of the remaining OAS, without IFNβ treatment. The expression of OAS2 or 3 was determined by WB analysis (asterisk, non-specific band). OAS1 expression in DKO2/3 cells was measured by qRT-PCR due to insufficient sensitivity of anti-OAS1. The gene expression data are presented as mean + SD of triplicates. **, p<0.001 in Student's t-test. OAS expression was assessed by WB with anti OAS1-3 in HME cells expressing ectopic OAS1-3 (OAS2hi, OAS3hi, OAS1hi) cells without IFNβ treatment or control HME cells (vec) treated with the indicated concentrations of IFNβ for 2 days (to compare the levels of induced and ectopically expressed OASs). β-actin and Ponceau stain are shown as loading controls (# - transfer artifact); ns, non-specific band.
Figure 3A. Scheme of the experimental approach to quantitatively capture gene expression changes during mESC differentiation towards EpiSCs. B. Projection on PC1 and PC2 of gene expression profiles of mESCs differentiated towards EpiSCs. C. Hierarchical clustering of mRNA expression during differentiation of mESCs towards endoderm (yellow) or EpiSCs (green).
Figure 4A | hFwe-Lose predicts COVID-19 patients' death more accurately than other biomarkers. hFwe-Lose was compared with four known biomarkers (Ferritin, CRP, D-dimer and Neutrophils/Lymphocytes ratio, respectively) in predicting death of hospitalised patients. For each biomarker, only patients who had the information of the respective blood biomarker were used. 115 patients were used to compare Ferritin and hFwe-Lose. 120 patients were used to compare D-dimer and hFwe-Lose. 127 patients were used to compare Crp and hFwe-Lose. 153 patients were used to compare neutrophil-lymphocyte ratio and hFwe-Lose. With AUC as the criteria, hFwe-Lose significantly outperformed all four biomarkers in predicting death in both retrospective and prospective cohorts. AUC coefficients, as well as CI's are displayed on the plots. B | hFwe-Lose biomarker is superior to other markers in COVID-19 poor outcome prediction. All 283 patients were used to compare hFwe-Lose and age combined with comorbidities in predicting hospitalization (left) and death (middle). The AUC of age combined with comorbidities in predicting the hospitalization of the prospective cohort is 0.88 (CI - [0.81-0.96]). The AUC of hFwe-Lose in predicting the hospitalization of the prospective cohort is 0.90 (CI - [0.84-0.97]). hFwe-Lose outperformed age combined with comorbidities in predicting hospitalization. The AUC of age combined with comorbidities in predicting the death of the prospective cohort is 0.86 (CI - [0.72-1.0]). The AUC of hFwe-Lose in predicting the death of the prospective cohort is 0.98 (CI - [0.92-1.0]). hFwe-Lose significantly outperformed age combined with comorbidities in predicting death. The 105 patients who registered the information of all four known blood biomarkers (Ferritin, CRP, D-dimer and Neutrophil/Lymphocyte ratio) were used to compare hFwe-Lose, age combined with comorbidities, and the four biomarkers in predicting death (right). hFwe-Lose significantly outperformed age combined with comorbidities and the four biomarkers in predicting death in both retrospective and prospective cohorts derived from the 105 patients.
Figure 4Western blot analysis of CHX chase kinetics in HeLa cells showing accelerated endogenous RNF8 degradation in the soluble fraction (Cytosol and Nucleosol) of ∆ATX3 cell extract. Arrow represents the main RNF8 band and asterisks represents unspecific bands.   Graphs represent the quantifications of (A). RNF8 level at starting point (0h) was shown without equalisation (left). In order to nullify the difference in RNF8 level at starting point (0h), we equalised RNF8 level to 100% and then compared the degradation rate (right). (**P<0.01, ***P<0.001, ****P<0.0001; two-way ANOVA, n=2, mean +SEM).   Western blot analysis of CHX chase showing the kinetics of endogenous RNF8 degradation in the soluble fraction (Cytosol and Nucleosol) of ATX3 knockdown HeLa cells. The degradation was completely blocked after simultaneous inhibition of proteasome (MG132, 10µM). Western blot analysis of Flag-RNF8 denaturing-IP in HEK293 cells showing RNF8 hyper-ubiquitination in siRNA-mediated p97 or ATX3-depleted conditions. Western blot analysis of Flag-RNF8 denaturing-IP in HeLa cells showing RNF8 hyper-ubiquitination in ∆ATX3 condition. RNF8 hyper-ubiquitination was suppressed by reintroduction of GFP-ATX3-WT but not with GFP-ATX3-C14A or GFP-ATX3-UIM*.
Subtelomeric DNA promotes recombination in the absence of Ccq1.Figure 7A Genomic copy number of his3+, ura4+ and TAS1 in indicated strains harboring the reporter genes tel1L::his3+ and tel2L::ura4+. Cultures from individual WT and freshly generated knockout clones (ccq1Δ, n = 16; clr4Δ, n = 5; ccq1Δ clr4Δ, n = 5) were pre-grown on selective media for several days and inoculated at day 0 to grow in liquid media with regular back-dilution (every 24 hours, approximately 7 generations). Samples were taken at indicated harvest times, and relative copy numbers of genomic regions were assessed by qPCR (normalization against intrachromosomal loci). Black and rainbow color lines indicate WT strains and individual ccq1+ deletion mutants (clones), respectively B qPCR analysis as in (A) but with strains harboring the minichromosome Ch16 m23::ura4+ (ccq1Δ, n = 14). Since Ch16 is unstable in ccq1Δ cell Note that Ch16 does not harbor TAS sequences
L-NAME Induces Autophagy and Reduces Mutant Huntingtin Aggregation/Neurodegeneration in Models of Huntington's Disease.Figure 7(A) Immunoblot analyses with anti-LC3 antibody show that rapamycin (8 hr) and L-NAME (24 hr) increased autophagosome synthesis in bafilomycin A1-treated mouse primary cortical neurons and HeLa cells. (B and C) Confocal microscopy images (B) and analysis of autophagic flux by automated Cellomics microscope (C) show that L-NAME increased autolysosomes in mRFP-GFP-LC3 HeLa cells. (D) L-NAME reduced EGFP-HDQ74 aggregates in EGFP-HDQ74-transfected Atg5+/+, but not in Atg5−/−, MEFs. (E) Drosophila expressing mutant huntingtin exon 1 (Q120) shows a significant decrease in neurodegeneration (p < 0.001, paired t test) upon L-NAME treatment compared to DMSO. (F) Expression of an endogenous negative regulator of NOS activity (NOS4) significantly attenuates neurodegeneration (p < 0.05, paired t test) in Drosophila expressing mutant huntingtin exon 1 (Q120). (G-I) Images from the retina of transgenic HD zebrafish show mutant huntingtin aggregates (arrows) (G). Treatment with rapamycin or L-NAME reduced the number of aggregates (H). L-NAME did not reduce aggregates in the presence of NH4Cl, which increased aggregate count (I). (J) NO inhibits autophagy by S-nitrosylating and inhibiting JNK1 phosphorylation, thereby reducing phospho-Bcl-2 and increasing Bcl-2-Beclin 1 interaction, which disrupts hVps34-Beclin 1 association. NO also S-nitrosylates and inhibits IKKβ phosphorylation, leading to reduced phospho-AMPK and TSC2 activity, which alleviates the inhibitory effect of TSC1/2 on Rheb (denoted by "×"), thereby allowing Rheb to activate mTORC1 and inhibit autophagy. Overexpression of NOS isoforms impairs autophagy by inhibiting the JNK1 pathway, whereas NOS inhibition by L-NAME induces autophagy by mechanism distinct from the NO pathways. Graphical data denote mean ± SEM, except in (E) and (F).
Figure 1A, Run and tumble swimming modes in E. coli are regulated by CheY activation by phosphorylation or acetylation. The electron density map of the switch was produced by Thomas et al. (2006) and downloaded from http://dx.doi.org/10.1093/nar/gkv1126. B, Scheme demonstrating the internalization of Atto647-labeled CheY(I95V) to single cells by electroporation. C, Demonstration of single-molecule tracking in a single cell. Cell outline is shown as an ellipse. Left, Imaged FliM-YPet fluorescence. White dots indicate the estimated motor locations. White circles illustrate a 75 nm radius around these locations. Right, Contour map of the normalized sum of probabilities of the localization events of CheY(I95V)-Atto647 (from blue to red is low to high; black is zero probability). White circles show the motors' locations from the left panel. D, Survival probabilities of unmodified CheY(I95V)-Atto647 at the switch (ΔcheA background; strain EW668). 63 cells were recorded with a total of 1316 trajectories in which CheY was found to interact with FliM. Black line, a bi-exponential fit; dashed line, a fit of the fast decline process Survival probabilities of in which CheY was found to interact with FliM. Black line, a bi-exponential fit; dashed line, a fit of the fast decline process E, acetylated CheY(I95V)-Atto647 (presence of acetate, 50 mM, pH 7.0; strain EW668). 56 cells were recorded with a total of 1904 trajectories. Survival probabilities of in which CheY was found to interact with FliM. Black line, a bi-exponential fit; dashed line, a fit of the fast decline process F, phosphorylated CheY(I95V)-Atto647 (ΔcheZ background; strain EW669). 82 cells were recorded with a total of 2414 trajectories. Survival probabilities of in which CheY was found to interact with FliM. Black line, a bi-exponential fit; dashed line, a fit of the fast decline process G, phosphorylated and acetylated CheY(I95V)-Atto647 (presence of acetate, 50 mM, pH 7.0; ΔcheZ background, strain EW669). 40 cells were recorded with a total of 2660 trajectories. H, Experimental scheme of the FRET experiment. The attractant serine lowers the phosphorylation level of CheY. As a result, CheY dissociates from the switch and the energy transfer from YPet (conjugated to FliM) to mCherry (conjugated to CheY) is reduced. I, CheY interacts with FliM∆N and this interaction is sensitive to chemotactic stimuli. Each curve is the mean of two FRET measurements of cells in response to an attractant stimulus (0.1 mM serine; in the case of FliMwt, a single measurement was performed with serine; another measurement of FliMwt with 1mM aspartate produced similar results). FRET ratio is the ratio of mCherry to YPet fluorescence. CheY-mCherry and mCherry concentrations were ~170 µM in the case of FliM∆N and ~15 µM in the case of FliMwt Strains used: EW677 (FliMwt, red), EW659 (negative control of FliM∆N without CheY, purple), EW637 (FliM∆N, blue), and EW636 (FliM∆N ∆cheA, yellow).
Figure 7Under Fed condition, miRNPs remains bound to target messages and show reduced extracellular export. In cells Starved for amino acids and metabolites, HuR binding to co-targeted messages replaces miRNPs from target messages. HuR binds miRNAs and replaces miRNAs from miRNPs. In subsequent step, ubiquitination of HuR uncouples bound miRNAs on MVB and facilitate extracellular export of HuR-decoupled miRNAs.
Figure 4A No differences of Vdac1/VDAC1 expression between MEF cell lines (replicates/condition n = 3 and independent experiments n = 2). The graph shows fold change expression (mean ± SEM) in Tsc2-deficient relative to wild-type MEFs. B Flow cytometry results (independent experiments n = 3) showing a higher percentage of MitoSOX red-positive cells in Tsc2-deficient MEFs. C Flow cytometry results (independent experiments n = 3) showing higher intensity (X-axis, single channel intensity FL3 670 nm) of MitoTracker red-positive cells in Tsc2-deficient MEFs. D Higher basal cell respiration (as measured by oxygen consumption, Y-axis) in Tsc2-deficient MEFs. The asterisks indicate significant difference with two-sided t-test (P = 5x10-4; replicates/condition n = 5, and independent experiments n = 3). E Higher hydroxide peroxide levels in Tsc2-deficient MEFs across different numbers of seeded cells (X-axis). Significance corresponds to two-way ANOVA test (P = 1x10-4; replicates/condition n = 2, independent experiments n = 2). The bars indicate mean ± SD. F Left panel, western blot results showing overexpression of catalase (CAT) in Tsc2-deficient MEFs, and unaffected by exposure to everolimus (independent experiments n = 2). The CAT expression level is indicated by the ratio of the corresponding signal relative to loading control and basal setting (noted as 1(ref)). Right panel, Cat overexpression (log10-fold change) in Tsc2-deficient MEFs. The asterisks indicate significant difference with two-sided t-test (P = 1x10-2; replicates/condition n = 3, and independent experiments n = 2). The bars indicate mean ± SD. Dotted horizontal lines indicate 2-fold (top) and 0.5-fold (bottom). G Representative images of immunohistochemical detection of acrolein in LAM lung lesions.
Figure 4A, Effects of FliMN-CheY acetylation and phosphorylation on clockwise rotation of tethered cells containing FliM∆N FliN(A93D) motors. Acetate concentration was 10 mM each (pH 7.0). FliMN-CheY and FliMN-CheY~P were produced by using ∆cheA and ∆cheZ backgrounds (strains EW713 and EW714), respectively. Each data point is the average of all measurements at a given FliMN-CheY concentration, weighted by the sample number of each experiment. The concentrations shown are estimates based on the calibration curves for which a similar CheY expression system was used. Concentrations larger than 500 μM were calculated by the linear extrapolation of the calibration curve. B, Distribution of clockwise interval lengths at different average clockwise levels in ∆cheA cells containing FliM∆N FliN(A93D) motors and expressing FliMN-CheY (strain EW713), in the presence of acetate (10 mM, pH 7.0). C, Average clockwise interval length, calculated as the inverse of the rate constants from mono-phasic fits of the distributions in (B). D, Response of tethered ∆cheZ cells having FliM∆N FliN(A93D) motors to acetate addition and removal (red; strain EW714; FliMN-CheY concentration estimated at ~300 μM). Similar results were obtained with a ∆cheA strain (EW713). Tethered cells having FliM∆N FliNwt motors and containing FliMN-CheY (strain EW696) are shown Acetate concentration was 10 mM (pH 7.0). The data shown are the mean ± SEM. N is the number of cells. Black lines indicate the clockwise-decay rates of FliNwt motors' slow phase and of FliN(A93D) motors following acetate removal.
Figure 6(A) HeLa cells were transfected with the indicated siRNAs. Cell lysates were subjected to immunoblot analysis using anti-TDP-43, TFEB, LC3 and GAPDH antibodies. The relative densities of LC3-II to GAPDH are shown on the lower side. Data from three independent experiments represented as means ± S.E.M., ns, not significantly different; **, p<0.01, one-way ANOVA. (B) For EM analysis, HeLa cells were transfected with the indicated siRNAs. Double-membrane autophagosomes are indicated with yellow arrows, and autolysosomes are indicated with red arrow. Regions within the dotted boxes are magnified in the insets. Scale bar, 250 nm. (C) HeLa cells were transfected with the indicated siRNAs. After 48 h, the cells were incubated with Bafilomycin A1 (100 nM) for 24 h. Then lysates from the cells were subjected to immunoblot analysis using anti-TDP-43, LC3 and GAPDH antibodies. (D, E) HEK 293 cells were transfected with the indicated siRNAs. After 48 h, the cells were transfected with mCherry-EGFP-LC3. For Bafilomycin A1 treatment, the cells were then incubated with Bafilomycin A1 (100 nM) for 24 h. For starvation treatment, the cells were cultured for 22 h and then treated with Earle's Balanced Salt Solution for 2 h. Cells were fixed and visualized using confocal microscopy. Scale bar, 5 µm. The quantification data of yellow (autophagosomes) or red (autolysosomes) are shown in Figure 6E. Data from three independent experiments represented as means ± S.E.M., *, p<0.05; **, p<0.01, one-way ANOVA. (F) ATG5-WT and ATG5-KO MEFs were transfected with Nhtt-150Q-EGFP. After 6 h, the cells were transfected with the indicated siRNAs for 5 D, and then the cells were subjected to MTT assays. The relative cell viability from three independent experiments are presented as means ± S.E.M., ns, not significantly different; **, p<0.01, one-way ANOVA. (G) Similar transfection as in (C) was performed, and the transfected cells were incubated with Bafilomycin A1 or Earle's Balanced Salt Solution (starvation) as in (D). Lysates from the cells were subjected to immunoblot analysis using anti-TDP-43, p62 and GAPDH antibodies. The relative densities are shown on the right side. The data from three independent experiments are presented as means ± S.E.M., ns, not significantly different; *, p<0.05; **, p<0.01, one-way ANOVA.