EMBO/sd-character-level-ner huggingface dataset:
Mechanisms for the paracrine neuroprotective roles by Nurr1- and Foxa2-expressing glial cells.Figure 4A Real-time PCR analysis for pro-inflammatory cytokines and neurotrophic factors. BV2 microglia and primarily cultured astrocytes were transduced with C, N, F, and NF. Real-time PCR analyses were carried out 12 h after LPS (100 ng/ml, for pro-inflammatory cytokine expressions), IL-4 (10 ng/ml, other M2 markers), or without the treatment (neurotrophic factors). Significantly different from the control (C)*, N#, F‡ at P < 0.05, n = 3-6 PCRs; one-way ANOVA followed by Bonferroni post hoc test. B, C NO levels released (B) and arginase activity (C) were measured in the media and cells for BV-2 microglia cultures, respectively. Significantly different from the control (C)*, N#, F‡ at P < 0.05, n = 3 reactions, P-values: 0.027 (N-CM*), 0.033 (F-CM*), 0.018 (NF-CM*), and 0.033 (NF-CM‡) for the NO level, 0.011*, 0.025#, and 0.036‡ for the arginase activity; one-way ANOVA followed by Bonferroni post hoc test.
Precursor API is contained within subvacuolar vesicles in cvt17 mutants.Figure 5Precursor API is contained within subvacuolar vesicles in cvt17 mutants. (A) Isolated vacuoles (V) from cvt17 cells were lysed in PS0 buffer, loaded on top of an Optiprep step gradient, and centrifuged at 170,000 g for 60 min as described in Materials and Methods. Fractions VV, 0/1.06 interface; LD, 1.06 region; SV, 1.06/1.12 interface; HD, 1.12 region. (B) An aliquot of fractions VV and SV was treated with proteinase K either in the presence or absence of Triton X-100 as indicated. Because of the presence of protease inhibitors in the vesicle isolation procedure, an intermediate-sized API degradation product results from proteinase K treatment. The V fraction represents one-tenth of the load of the Optiprep gradient. Proteins were detected by Western blotting. The positions of prAPI and mALP are indicated.
Figure 2A: Cartoon representation of SARS-CoV-2 N-NTD. B: Topology diagram for SARS-CoV-2 N-NTD; η represents the 310 helix and β represents the β-sheet. C: The electrostatic surface potential of SARS-CoV-2 N-NTD. Red and blue colours indicate negative and positive potential, respectively. The RNA binding sites are highlighted in dotted circles and labelled. D: Surface representation of SARS-CoV-2 N-NTD coloured according to sequence conservation based the alignment of N protein sequences from seven human-infecting CoVs using the ConSurf server ; dark magenta indicates the most conserved, dark cyan indicates the most divergent.
BREX confers resistance to phage A The pglZ gene reproducibly appears within a six‐gene cluster in various genomes.Figure 1A The pglZ gene reproducibly appears within a six‐gene cluster in various genomes. Representative appearances are shown. B The BREX locus in B. cereus H3081.97. Coordinates below the genes denote the position along the NZ_ABDL01000007 contig in the draft genome of B. cereus H3081.97. Orange box within brxC represents the position of the ATPase P‐loop motif. C Operon organization of the B. cereus BREX system integrated in the B. subtilis genome. Expression throughout the operons was validated by RNA‐seq. Positions of promoters and terminators were inferred by 5′ and 3′ RACE, respectively. D-G Culture dynamics of phage‐infected wild‐type (black) versus BREX‐containing (red) strains of B. subtilis BEST7003. Bacterial strains were exposed to phage at time = 0 h, and optical density measurements were read in a 96‐well plate format. Each experiment was performed three times with three technical triplicates for each biological replicate. Error bars represent SEM. Shown are representative results for three of the ten phages tested; data for the remaining seven phages are found in Supplementary Fig S2.
Fig.Figure 4(A) EGRIN model of MTB predicts a module enriched with lipid metabolism genes from Path-seq data of in vivo infection. Overexpression data confirms the regulation of desA1 and desA2 by Rv0472c in both MTB and MSM. Graphic representation of linkages between module 276 genes, regulatory influences, functional associations, cell wall modifications, and homology to MSM. (B) Plot of read pile-ups from MSM with inducible overexpression of MSMEG_0916 shows ChIP-binding in the promoters of desA1 and desA2. Boxplots representing RPKM values from RNA-seq of MSM with inducible overexpression of MSMEG_0916. Significant log2 fold change (FC) between uninduced (-ATc) and induced (+ATc) samples for MSMEG_0916 (log2 FC = 4.99), desA1 (log2 FC = -1.32) and desA2 (log2 FC = -1.8) with multiple hypothesis adjusted P-values < 0.0001. Data is from three biological samples (induced) and nine biological samples (uninduced).
Increased arterial stiffness contributes towards the hypertension of CUL3WT/Δ403–459 mice.Figure 6Continuous blood pressure measurements were taken in mice under general anaesthesia with thermostatically controlled body temperature, right carotid artery pressure transducer catheterisation and ECG Lead II heart rate monitoring. CUL3WT/Δ403-459 mice have elevated systolic (SBP) (***P = 1 × 10−12) and diastolic (DBP) blood pressure (***P = 8.5 × 10−8), although they also present with 7% lower heart rates (*P = 0.0485) when compared to CUL3WT mice. Two-tailed unpaired Student's t-test; data are mean ± SEM. Pulse waveform analysis of blood pressure traces obtained in (A) reveals that CUL3WT/Δ403-459 mice have an increased pulse pressure (PP) [SBP - DBP] (***P = 2.1 × 10−10), augmentation pressure (AP) [SBP - anacrotic notch (AN) pressure] (***P = 3.5 × 10−6), dicrotic notch (DN) pressure (***P = 4.7 × 10−13) and mean arterial pressure (MAP) [1/3 × SBP + 2/3 × DBP] (***P = 1.3 × 10−9). This hypertensive phenotype is in part due to changes in vascular contractility in CUL3WT/Δ403-459 mice as evidenced by their higher augmentation index (AIx) [AP/PP] (**P = 0.0096), a marker of arterial stiffness, and is further supported by an increase in their diastolic pressure decay time constant (τbourgeois) [1/slope of diastolic pressure decay; measured 30 ms after DN and 20 ms before end DBP] (**P = 0.0083), a surrogate marker of increased vascular resistance. Two-tailed unpaired Student's t-test; data are mean ± SEM In vivo dose-responses to phenylephrine and angiotensin II. After baseline measurements were obtained from mice in (A), the right external jugular vein was cannulated for administration of bolus doses of vasopressors in increasing half-log steps. Dose-response curves were generated and data analysed using a logistical function to determine the estimated dose producing half-maximal response (ED50) and maximum response (Emax). The fitted Emax for phenylephrine was increased in CUL3WT/Δ403-459 versus CUL3WT (183.9 ± 2.5 versus 164.9 ± 1.4 mmHg) (***P = 1 × 10−6) indicating an increased vasoconstrictor response to adrenergic stimulation elevating systolic blood pressure substantially above the CUL3WT maximum. Similarly, the fitted Emax for angiotensin II stimulation was higher in CUL3WT/Δ403-459 versus CUL3WT (155.5 ± 1.8 versus 138.3 ± 2.2 mmHg) (***P = 1.7 × 10−6). However, there was no change between CUL3WT/Δ403-459 versus CUL3WT sensitivity (as measured by ED50) to phenylephrine (36.6 ± 5.1 versus 31.4 ± 2.8 μg/kg bw) (P = 0.3778) or angiotensin II (0.77 ± 0.16 versus 0.93 ± 0.13 μg/kg bw) (P = 0.4401). Two-tailed unpaired Student's t-test; data are mean ± SEM.
Figure 4(A) Representative intravital image of calvarial bone marrow of Rosa26GO-ATeam/+; Tg(Acp5-tdTomato) male mice showing osteoclasts (left, tdTomato fluorescence) and FLIM image for ATP changes (middle and right, fluorescence lifetime of EGFP). The FRET efficiencies of each osteoclast were plotted from the mice upon exposure to low oxygen atmosphere (14% pO2) or ambient air (right, n = 11 from three mice for each SpO2). (B) Representative intravital image of calvarial bone marrow of Tg(Acp5-tdTomato) male mice showing osteoclasts (left, tdTomato fluorescence) and NAD(P) H autofluorescence lifetime images (middle and right). Average of autofluorescence lifetime of each osteoclast was plotted from the mice upon exposure to low oxygen concentration (14% pO2) or ambient air (right, n = 64 from three mice for each SpO2).
Figure 1A. Reconstitution of yeast V-ATPase from Hchim containing V1 (V1Hchim), lipid nanodisc reconstituted Vo (VoND), and recombinant subunit C. B. Coomassie-stained SDS-PAGE (from left to right) of Hchim, V1ΔH, VoND, and C. C. Representative ATPase activity assay (ATP regenerating system). At the indicated time, 200 nM ConA is added to the assay. D. Silver stained SDS-PAGE of V1HchimVoND. E. CryoEM maps of rotational states 1-3 of the in vitro assembled holoenzyme. F. Middle panel: Ribbon diagram of the state 1 V1HchimVoND holoenzyme. Subunit A, magenta; B, light green; C, tan; D, red; E, light blue; F, grey; G, orange; H, yellow; a, green; c8, pink; c′, orange; c″, yellow; d, cyan; e, blue; f, purple; Voa1, red. Left panel, top: Cross section of V1-ATPase at the level indicated. The three nucleotide binding sites are indicated by red arrowheads. Left panel, bottom: The central rotor of the V1 motor (subunits DF) rotates in steps of 120º. Right panels: Cross section of the c-ring at the level indicated. The c-ring of the Vo proton turbine rotates in ten steps, with each step stabilized by a transient salt bridge between a c-ring glutamic acid and the essential arginine of aCT (Arg735 in yeast). Each proteolipid subunit is organized in a four α helix bundle, with helices 2 and 4 forming the outer, and helices 1 and 3 forming the inner ring of the c-ring. Whereas the c and c′ subunits have the glutamic acid on α helix 4, c″ has the glutamate on helix 2, creating an unequal spacing of the c-ring glutamic acid residues, a unique feature of eukaryotic V-ATPase.
Figure 1A The schematic diagram showing the process to determine candidate target genes from chr17q12 amplicons in the METABRIC dataset. B Forest plots display the hazard ratios of genes at the 17q12 amplicon according to the DFS (top right) and OS (bottom right) of breast cancer patients in the METABRIC dataset. Genes located at the HER2 amplicon were nominated according to hazard-ratio levels (all P-values < 0.01). The HER2 co-amplification percentage of the indicated genes is represented as bar graphs (left). C The frequency of CDK12 amplification in HER2-amplified- and HER2-nonamplified breast cancer. The bar graphs indicate the frequency of HER2 and CDK12 co-amplified cases among the patients with HER2 gene amplification (left). Tables show the percentage of CDK12 amplification in the indicated cohorts (right). Amp, amplification; non-amp, non-amplification. D Scatter plot showing the correlation between CDK12 expression and its copy number alteration (CNA) in METABRIC (left). The r value was calculated as the Pearson's correlation coefficient. Box plots showing the mRNA levels of CDK12 in the indicated subtypes from METABRIC (right). P-values were calculated using one-way ANOVA, followed by post-hoc LSD test. E Survival analysis of breast cancer patients according to the expression of CDK12 in METABRIC (top) and KM plotter (bottom) using the Kaplan-Meier method with the log-rank test. F The results of NPI- and AOL-adjusted analysis showing the association between CDK12 expression and the risk of metastatic relapse (MR) in breast cancer datasets generated using bc-GenExMiner 4.0 (http://bcgenex.centregauducheau.fr).
Figure 3(A) Consequence of miR-517a on EOC cell viability and 41 NSCLC cell lines (as in 2A). N, normal cell lines (IHH, HOSE, HBEC3, HBEC13, HBEC30, and HBEC34). miR-517a was found to significantly reduce cell viability (Z-score < -2) in 5 cell lines in the screen, and TCGA expression data revealed no significant change in expression of this miRNA in ovarian tumors. (B, C) In vivo delivery of neutral liposome incorporated miR-517a mimic reduced tumor burden by weight (B) and nodule number (C) in an orthotopic xenograft model using SKOV3 cells. Box-and-whisker plot from n=8. p-value from Student's T-Test. LD, low-dose (200 μg/kg); HD, high-dose (400 μg/kg). (D) Correlation of the consequence of ARCN1 depletion and miR-517a sensitivity in 12 NSCLC cell lines (plot as in 2D). (E) Immunoblots indicate miR-517a-induced depletion of ARCN1 and USP1 in the indicated cell lines. (F) Consequence of the indicated siRNAs and miR-517a on the viability of the indicated cell lines. (G) Immunoblots indicate that miR-517a suppresses expression of ARCN1 in multiple miR-517a sensitive cell lines.
Figure 6Size of individual cilia in stem cell and transit amplifying cell regions of WT and Prom1 KO mice (A) and their density in the respective regions (B). 3 animals were analyzed for each genotype. The number of quantified cilia is indicated (n). Clonogenicity analysis of CLESCs treated with either Hdac6 inhibitor (Tubacin) and appropriate controls (Nitubacin and DMSO, C) Colonies were stained with crystal violet Clonogenicity analysis of CLESCs treated with siArl13b and its siControl. Colonies were stained with crystal violet siRNA knockdown efficiency of Arl13b (E) in Ki67 FUCCI-CLESCs was evaluated real-time RT-PCR analysis. The results are in arbitrary values after normalization for GapDH siRNA knockdown efficiency of Hdac6 (F) in Ki67 FUCCI-CLESCs was evaluated real-time RT-PCR analysis. The results are in arbitrary values after normalization for GapDH Flow cytometry analysis and quantification of samples indicated in (E and F). Mutation strategy of Hdac6-binding site on Prom1. The lysine (K) 138 in the first cytoplasmic loop of Prom1 was mutated to glutamine residue (Q). TM, transmembrane domain. Representative IF double staining and 3D reconstruction of the Prom1 (green) and AcTub (red) at the apical domain of polarized MDCK cells expressing Prom1 and its K138Q mutant (top panels). Black-white inserts show Prom1 signals only. Same cells were analyzed by SEM (bottom panels). Note that Prom1 is asymmetrically distributed along the primary cilium (white arrows) as observed in vivo (see Fig 2C) and mutation K138Q significantly impacts on the primary cilium length. MV, microvilli. IF staining and 3D reconstruction of AcTub-labeled (red) primary cilium at the apical membrane of parental MDCK cells (MDCK) and those cells transfected with Prom1 or its K138Q mutant. The images were used to quantify the primary cilium length (Appendix Figs S6B and C). Arrows indicate primary cilia with more than 4 μm in length. Co-immunoisolation (IS) analyses were performed with paramagnetic beads using antibodies against either Arl13b (K) Recovered materials were analyzed by immunoblotting against the indicated proteins. Brackets and asterisks indicate the plasma membrane and endoplasmic reticulum-associated forms of Prom1, respectively, while arrows show Arl13b. Arrowhead, immunoglobulin. Co-immunoisolation (IS) analyses were performed with paramagnetic beads using antibodies against either Prom1 (AC133) or with anti-FITC antibody as control (L). Recovered materials were analyzed by immunoblotting against the indicated proteins. Brackets and asterisks indicate the plasma membrane and endoplasmic reticulum-associated forms of Prom1, respectively, while arrows show Arl13b. Arrowhead, immunoglobulin. The ratio Arl13b/Prom1 immunoreactivities was quantified (n = 3) (M).
a) Levels of dark, dronc, drice and rpr transcripts were measured from third instar larvae (L3), 6 h and 14 h RPF salivary glands from control (blue) and dUTX1 (red) by qPCR and expressed relative to the internal control gene rp49.f4(a) Levels of dark, dronc, drice and rpr transcripts were measured from third instar larvae (L3), 6 h and 14 h RPF salivary glands from control (blue) and dUTX1 (red) by qPCR and expressed relative to the internal control gene rp49. (b) The transcript levels of Atg genes relative to the internal control gene rp49 in the salivary glands of control (blue) and dUTX1 (red) were analysed by qPCR at L3, 6 h and 14 h RPF. Data in all panels are expressed as means from three independent experiments, with error bars representing s.e.m. *P0.05 (Student's t-test).
Figure 8UVR8 is localized in both the shoot and root, and is responsible for both shoot morphogenesis and root development. In the absence of UV-B light, MYB73/MYB77 positively regulate the expression of auxin-responsive genes and promote hypocotyl elongation and lateral root development and growth. However, in the presence of UV-B light, UV-B induces the monomerization and nuclear accumulation of UVR8, which then interacts with MYB73/MYB77 in the nuclei. This interaction inhibits the DNA-binding activity of MYB73/MYB77, thus repressing the expression of auxin-responsive genes and auxin responses.
Parkin promotes mitochondrial ubiquitination.Figure 3.(A) MEFs were transfected with GFP wild-type (WT), A240R, and T415N mutant parkin followed by CCCP treatment for 8 h. Cells were immunostained with antibodies for cytochrome c (red) and ubiquitin (blue). Arrows indicate mitochondrial aggregates. Bar, 10 µm. (B) The average percentages of ubiquitin-positive mitochondrial aggregates from three independent experiments from A are presented with standard deviation as error bar. (C and D) MEFs were transfected and treated with CCCP as described in A. Cells were subjected to the fractionation to isolate crude mitochondria. Cytoplasmic and mitochondrial fractions were subjected to immunoblotting analysis using antibodies for ubiquitin, parkin, cytochrome c, and cytosolic Hsp90.
Figure 3(A) Flow cytometry analysis of surface PRPH expression. NSC-34 cells were infected with EV-A71 S41 at MOI 10 for 1h before staining with Viability Dye and anti-PRPH antibodies. Data are expressed as Mean Fluorescence Intensity. (B) Antibody blocking assay. NSC-34 and SH-SY5Y cells were pre-treated with anti-PRPH or anti-IgG isotype antibodies, followed by EV-A71 S41 infection at MOI 10 and 0.01, respectively. Culture supernatants were harvested at 24h.p.i. and titrated by plaque assay. (C) Proximity ligation assay. NSC-34 and SH-SY5Y cells were infected with EV-A71 S41 at MOI 10 and 0.01, respectively. Cells were fixed at 48h.p.i. prior to PLA staining using anti-PRPH and anti-VP0 antibodies.
Figure 5Optic nerve parameters are unaltered in early EAE (9 days after injection). (A,B) Cryostat sections of the optic nerve from MOG/CFA-injected mice (own lab-made suspension; for comparison with commercial MOG/CFA suspensions, see Appendix Fig. S12) and CFA-injected control mice were stained with anti-Nav antibody (1:50 dilution) to label the node of Ranvier and with anti-CASPR1 antibody (1:500 dilution) to stain the paranodal region. Length of the node of Ranvier and length of the paranodal region were quantified in C) D) (E1, E2) Richardson-Blue stained semi-thin sections from the indicated optic nerve samples. (E2, E3, F2, F3) Transmission electron micrographs of the optic nerves from MOG/CFA- and CFA-injected animals. Abbreviations: ax, axon; my, myelin sheath. Axon number and myelin thickness were quantified in G) and H). Scale bars: 1μm (A,B,E,F)
Figure.Figure 3(A) Transcriptional and protein abundance changes between inducing (+) and depleting (-) conditions (48h and 72h of depletion for Lon and FtsH, respectively) in ΔIndLon and ΔIndFtsH mutant strains. Differentially expressed (DE) Lon/FtsH candidate substrates were identified as proteins with a significant increase in abundance upon protease depletion that could not be attributed to an increase in mRNA levels, i.e. log2(protein_FC/mRNA_FC) ≥ 1 (upper dashed line). Differentially detected (DD) candidates were identified as proteins not detected in the induced condition and detected in the depleted condition, and whose mRNA level did not increase more than 2-fold (vertical dashed line). (B) Overlap of substrate candidates between the two mutant strains. (C) Proportion of membrane and cytoplasmic proteins among candidate substrates. (D) Distribution of half-lives measured by a SILAC time course experiment (average from 2 to 4 biological replicates) for Lon/FtsH candidate substrates as compared to the other proteins. Lon candidate substrates showed significantly shorter half-lives (MWW two-sided test, ***p=6.53 × 10-4). Box shows the quartiles of the distribution, line shows the median, whiskers extend to 1.5 times the inter-quartile range past the low and high quartiles and define the limits for ouliers, shown as points. (E) Changes in the protein to mRNA fold changes ratio, log2(protein_FC/mRNA_FC), in the double mutant strain ΔIndLon_FtsH as compared to the predicted ratio, computed as the sum of the log2 ratios of both individual mutants. Proteins that showed a significant change in protein level in at least one of the individual mutants are shown (374 proteins). Proteins whose ratio deviated significantly from the predicted one (upper and lower dashed diagonal lines) reveal epistasis effects. (F) Functional classification of candidate substrates. Validated substrates are highlighted in bold. Asterisks indicate candidate substrates classified as pseudogenes or truncated gene variants.
| DND1 co-localizes with NANOS2 in P-bodies.Figure 3Figure 3 | DND1 co-localizes with NANOS2 in P-bodies. A−C, Sections of male gonads from E15.5embryos were immunostained with antibodies against DND1 (green) and DCP1a (red). D−F, Squash preparation of a male gonocyte from E16.5embryoimmunostained with antibodies against DND1 (red) and DCP1a (green). Arrowheads indicate co-localization of DND1 and DCP1a. G−I, Sections of male gonads from E15.5embryos were immunostained with antibodies against DND1 (red) and NANOS2 (green). Arrowheads indicate co-localization of DND1 and NANOS2. J−M, NIH3T3 cells transfected with HA-tagged Dnd1 and FLAG-tagged Nanos2 were then immunostained with antibodies against DND1 (J) (magenta), NANOS2 (K) (red), and DCP1a (L) (green). N−Y, Biomolecular fluorescence complementation assay. NIH3T3 cells transfected with VENUS-C-fused Dnd1 and VENUS-N-fused Nanos2 (N−U) or Nanos2 (C61A, C96A) (V-γ) were immunostained with antibodies against DND1 (N, S, V), NANOS2 (O, W, α) or DDX6 (R, Z). Then, the signals of VENUS fusion protein were visualized (P, T, X, β). Arrowheads in Z indicate P-bodies. DNA was labeled with DAPI (blue). Scale bars: 50 m in A for A−C; 10 m in D for D-F, G for G−I, J for J−M, N for N−γ. Insets in A-C and J-γ show an enlarged vision of each picture to better depict localization of each protein. See also Fig. EV2T-Y.