EMBO/sd-character-level-ner huggingface dataset:
Figure 5(a) Representative WB analysis of active 48 kDa and inactive 60 kDa calcineurin A and β-actin expression in the TA and VM muscles in untreated C57BL mice, untreated mdx mice and mdx treated with low and high doses of anti-IGF2R for 4 and 9 weeks. Densitometry analysis of data expressed as ratios of 48 kDa and 60 kDa calcineurin A/β-actin in arbitrary units. Two-way ANOVA. *p<0.05; **p<0.01; ****p<0.0001 (n=10 mice per group). (b) Representative WB analysis of CAMKII, p-CAMKII and GAPDH expression quantified and shown as CAMKII/GAPDH and p-CAMKII/CAMKII ratios in arbitrary units. Two-way ANOVA. *p<0.05; **p<0.01 (n=10 mice per group). (c) Representative WB analysis of PKCα, p-PKCα and β-actin expression levels quantified and expressed as the PKCα/β-actin and p-PKCα/PKCα ratios in arbitrary units (n=10 mice per group). All values are expressed as the mean±SEM.
Therapeutic response of orthotopic U87 glioblastoma to combination of TMZ with RGD4C/AAVP-Grp78-HSVtk plus GCV.Figure 4In vivo BLI of Luc expression for evaluation of tumor viability and tumor size of representative tumor-bearing mice from all experimental groups before initiation of therapy (day 9 post intracranial cell implantation) and at the end of treatments (day 27 post intracranial cell implantation). Individual tumor Luc intensities before (filled circles) and after therapy (open circles), on days 9 and 27 post cell implantation, respectively. Data shown are representative of two experiments, n=5. Average tumor Luc activity showing glioblastoma progression in each experimental group. Pre-treatment day 9 was set at 100%. Data shown are representative of two experiments, n=5. Survival benefit for tumor-bearing mice from all treatment groups. Data shown are representative of two experiments, n=5. Statistical significance was determined by Kaplan-Meier method (Kaplan-Meier survival fractions). Log-rank (Mantel-Cox) test was used.
Figure 7(Left panel) GBM cells have an excessive cholesterol accumulation caused by CYP46A1 down regulation, which leads to a reduced 24OHC production that in turn cause a suppression of LXR signaling and an induction of SREBP targets. (Right panel) Restoration of CYP46A1 activity by EFV impairs GBM tumorigenic properties by increasing 24OHC levels, which in turns decreases intracellular cholesterol levels. Mechanistically, EFV treatment leads to the up-regulation of LXR target genes including ABCA1, and down-regulation of SREBP1 activity and LDLR expression.
Synaptic vesicle component SV2 is reduced in GA aggregate containing neurons eGFP-GAn dipeptides were expressed in primary cortical or motor neurons for 48 hours, then immunostained for neurofilament (gray) and SV2 (red).Figure 6eGFP-GAn dipeptides were expressed in primary cortical or motor neurons for 48 hours, then immunostained for neurofilament (gray) and SV2 (red). A-B) Representative z-stack confocal images of neurites from eGFP, eGFP-GA50, and eGFP-GA100 expressing cortical (A) or motor (B) neurons. 60x magnification, scale bar indicates 5μm. C-D) Quantification of SV2 puncta along neurites in cortical neurons (C) or motor neurons (D) by ImageJ manual counting, normalized to eGFP-only expressing cells. (C) Cortical neurons demonstrated a significant GA-length dependent reduction, as well as a reduction in all cells containing GA-repeats greater than 50 (left panel). (D) Motor neurons demonstrated a significant GA-length dependent reduction, as well as a reduction in all cells containing GA-repeats greater than 100 (left panel). Evaluation of neurite length by NeuronJ software revealed no differences in total neurite length per cell in cortical neurons (C) or motor neurons (D) expressing any GA-repeat length compared with eGFP alone (right panels).
Figure 1(A) Western blot detection of p-CHK2 Thr68, CHK2, p62 and LC3 in H1299 cells in normal medium (HBSS ''-'') or after 1 hr HBSS starvation (HBSS ''+'') pretreated with or without NAC (3mM). (B) Western blot detection of p62 and LC3 in H1299 cells transfected with the indicated shRNA in normal medium or after H2O2 (500μM) treatment. (C) Western blot detection of p62 and LC3 in H1299 cells cotransfected with the indicated shRNA and the indicated plasmid and cultured in normal medium or after H2O2 (500μM) treatment. CHK2 NTm, a shRNA nontargetable mutant CHK2 rescue plasmid. (D) Autophagic flux is shown by representative confocal microscopic images of 293 cells stably-expressing GFP-mCherry-LC3 transfected with the indicated shRNA following HBSS starvation and H2O2 (500μM) treatment for 3h. Scale bar, 10 μm. (E) Quantitation of autophagosomal (yellow) and autolysosomal (red) LC3 puncta following HBSS starvation and H2O2 (500μM) treatment for 1h (n=30). Data are presented as mean±s.e.m. from 3 independent experiments; **P < 0.01 (Student's t-test). (F) Representative electron microscopic image of autophagic vesicles or autophagosomes in H1299 cells transfected with the indicated shRNA in normal medium or after 3 hr HBSS starvation or treated with H2O2 (500μM). Scale bars, 500 nm. The red arrows indicate double-membraned autophagic structures. (G) Electron microscopic quantification of autophagy vacuole in H1299 cells transfected with the indicated shRNA in normal medium or after 3 hr HBSS starvation or treated with H2O2 (500μM). Data are presented as mean±s.e.m. from 3 independent experiments; *P < 0.05; **P < 0.01 (Student's t-test).
Figure 4A. Average 2D tSNE map of the 985 strains with at least one morphological or growth feature with a |s| > 3, plus the 240 independent WT replicates used as controls. Color-coded islands resulting from the dbscan algorithm (ε = 4.9, minPoints = 3) were defined by groups of strains clustering together with the same dbscan parameters in more than 90% of the generated tSNE maps. Dots in the scatter plot (left graph) represent strains color-coded based on their island affiliation (right graph). Light grey dots represent strains that were not consistently (less than 90% of the time) associated with one of the islands. B. Heatmap showing, for each island, the average score of each morphological and growth feature used for the construction of the map. C. Network representation of island 22 grouping filamentous mutants. The weights were directly derived from the average distances between corresponding mutant strains in the 2D tSNE maps. D. Internal structure of the mean and CV of width in island 16. The average gradients of phenotypes over the area of the island 16 are represented with arrows. E. Shown are the enriched "biological process" GO terms associated with false discovery rate below 0.05.
Figure 4Percentages of CD4+ and CD8+ T cells infiltrating the spinal cord of OTUB1fl/fl and GFAP-Cre OTUB1fl/fl mice were analyzed by flow cytometry at day 15 (n = 7 for OTUB1fl/fl group; n = 9 for GFAP-Cre OTUB1fl/fl group) and 22 (n = 4 for OTUB1fl/fl group; n = 5 for GFAP-Cre OTUB1fl/fl group) p.i. Representative dot plots are shown. Absolute number of infiltrating leukocytes in the spinal cord of OTUB1fl/fl and GFAP-Cre OTUB1fl/fl mice at day 15 (n = 7 for OTUB1fl/fl group; n = 9 for GFAP-Cre OTUB1fl/fl group) and 22 (n = 4 for OTUB1fl/fl group; n = 5 for GFAP-Cre OTUB1fl/fl group) p.i. was calculated based on flow cytometry results. Data show mean + SEM. Infiltrating CD4+ T cells were further analyzed by flow cytometry for their ability to produce GM-CSF, IFN-γ, and IL-17 at day 15 and 22 p.i., respectively. Representative dot plots are shown. Absolute number of infiltrating GM-CSF-, IFN-γ-, and IL-17-producing CD4+ T cells at day 15 (n = 7 for OTUB1fl/fl group; n = 9 for GFAP-Cre OTUB1fl/fl group) and 22 (n = 4 for OTUB1fl/fl group; n = 5 for GFAP-Cre OTUB1fl/fl group) p.i. was calculated based on flow cytometry results (mean + SEM). Relative expression of GM-CSF, IFN-γ, IL-17, TNF, IL-6, CXCL1, CXCL10, CXCL11, CCL2 and NOS2 mRNA in the spinal cord of OTUB1fl/fl and GFAP-Cre OTUB1fl/fl mice at day 15 and 22 p.i. was determined by quantitative real-time PCR. Data are presented as the relative increase over unimmunized control mice (n = 3 for all groups). Data show mean + SEM. Astrocytes were isolated from unimmunized and diseased OTUB1fl/fl and GFAP-Cre OTUB1fl/fl mice at day 15 p.i., respectively. Relative expression of CXCL10, CXCL11, CCL2, and NOS2 mRNA was determined by quantitative real-time PCR. Data are presented as relative increase of genes at day 15 p.i. over gene expression of astrocytes from unimmunized control mice (n = 3 for all groups). Data show mean + SEM. Primary astrocytes isolated from OTUB1fl/fl (n = 3) and GFAP-Cre OTUB1fl/fl (n = 3) mice were left untreated or stimulated with IFN-γ (10 ng/ml), IL-17 (50 ng/ml), and TNF (10 ng/ml), respectively, for 16 h. mRNA levels of CXCL10, CXCL11, CCL2, and NOS2 were detected by quantitative real-time PCR.
Autophagy is increased in AR113Q, CHOP −/− muscle.Figure 3A. Relative expression of MurRF1 and MAFbx mRNAs in proximal hind limbmuscle of 12 wk mice (n = 5-6/genotype). *p<0.05 by ANOVA, n. s. = not significant. B. LC3 and p62 expression in proximal hind limbmuscle of 12 wk mice was assessed by western blot. Right panels show quantification of signal relative to GAPDH. **p<0.01 by Student's t test. C. Relative expression of mRNAs encoding autophagy regulators in proximal hind limbmuscle. *p<0.05 by Student's t test. Androgen receptor protein expression in skeletal muscle of 12 wk mice. Hsp90 serves as a loading control. Right panel shows quantification of relative signal intensity (n = 3/genotype). D. Proximal hind limb muscles stained for the androgen receptor (in red) exhibit intranuclear inclusions. Nuclei are stained by DAPI (in blue). E. P-JNK and P-eIF2 alpha expression (top, middle) and XBP1 mRNA splicing (bottom) in proximal hind limbmuscle of 12 wk mice. Right panels show quantification of signal relative to loading control. **p<0.01 by Student's t test. n. s. = not significant.
Ccno‐deficient MCCs at embryonic stages show disturbed ciliogenesis and ultrastructural defects of deuterosome and centrioles A–B' SEM of tracheae from (A, A') wild‐type and (B, B') CcnoRA/RA embryos at E17.Figure 4A-B' SEM of tracheae from (A, A') wild‐type and (B, B') CcnoRA/RA embryos at E17. In comparison to wild‐type MCCs, Ccno‐deficient MCCs almost completely lack formation of multiple cilia and only single, or doublet (arrow) cilia are observed at E17. C-E The lack of multiple cilia at E17 stages is reflected by the almost complete absence of acetylated α‐tubulin staining as marker for axonemes in (D) Ccno‐deficient MCCs of E17 embryonic trachea as quantified in (E). FOV, field of view. F-I TEM of MCCs from E17 embryonic tracheae shows deuterosomes with forming procentrioles in (F, F', H) Ccno‐proficient and (G, G', I) Ccno‐deficient MCCs. Asterisks in (F, G) indicate microvilli that extend from the apical cell surface. (F', G') Deuterosomes in Ccno‐deficient MCCs are significantly enlarged (identical size bars in F' and G') and show irregular morphology, which is different to the annular shape of wild‐type deuterosomes as seen in (F', H). Procentrioles (arrowheads in F' and I) that are found at deuterosomes of (I) Ccno‐deficient MCCs were recurrently found being shorter and appeared less structured in comparison to (F', H) wild‐type cells. J The average length of procentrioles was quantified for wild‐type and Ccno‐deficient MCCs of E17 tracheae (49 procentrioles in n = 3 independent samples for wild‐types and 47 procentrioles in n = 3 independent samples for Ccno‐deficient MCCs).K The diameter of deuterosomes (41 deuterosomes in n = 3 independent samples for wild‐types; 38 deuterosomes in n = 5 independent samples for Ccno‐deficient MCCs) was measured in wild‐type and Ccno‐deficient MCCs of E17 tracheae.
Figure 1A Circular genome plot for Actinomyces sp. oral taxon 171 str. F0337 with genes encoding AITD-like peptides. In this GView image, red and blue tracks show genes on forward and reverse strands, respectively. AMSIN genes and their immediate upstream and downstream genes are shown. ABC, ATP binding cassette. HP, hypothetical protein. The BioProject database accession number for the genomes is PRJNA43131. The AMSIN gene cluster was verified by PCR amplification (inset) and DNA sequencing. Arrows in green mark binding positions of the two specific primers. B A neighbor-joining tree of bacterial defensins with the fungal defensin micasin as outgroup (Zhu et al, 2012). The evolutionary distances were computed by the p-distance method. Numbers on the nodes represent bootstrap values (from 500 replicates) and only >50% are shown. The scale bar represents the number of amino acid differences per site. Branches in green and red indicate peptides from actinobacteria and myxobacteria, respectively. Two clusters comprising members with structural variations are boxed in different colors (orange, dimer; cyan, vicinal disulfide). C Comparison of precursor organization of AITDs with different origins. NCSS, nonclassical signal sequence; SP, signal peptide; PP, propeptide; MP, mature peptide. D Sequence comparison between unicellular AMSIN and multicellular AITDs. Only the top BLASTP hits obtained by AMSIN as query searching against the GenBank database were chosen for alignment. The completely conserved cysteines are shaded in yellow and the nonconserved underlined once. Identical noncysteine residues are shaded in different colors based on their side-chain nature (red, acidic; purple, aromatic; blue, basic; cyan, polar and uncharged; green, hydrophobic). Residues in the N-terminus and the C-loop of AMSIN-1, which form a continuous hydrophobic surface in its dimer, are underlined twice in red. E LRT statistics for M1/M2 (df=2) and M7/M8 (df=2) and the corresponding tail probability p. F Weblogo of bacterial defensins showing the evolutionary conservation (the sign in yellow and green respectively denoting completely and highly conserved positions). Positions under positive selection are denoted by red arrows and their structural location is indicated.
Figure 6A Negative stain micrograph of a sheet formed by purified UMOD filaments in 100 mM NaCl (top). Analysis of this material by correlation averaging reveals a periodic pattern (bottom) with a two-fold symmetry axis perpendicular to the plane of the sheet (white symbol). Scale bars: 250 Å (top) and 125 Å (bottom). B UMOD sheet model, generated by antiparallel juxtaposition of multiple copies of the UMODfl composite map, according to the 2D information shown in panel A. Due to lack of information in the direction perpendicular to the plane of the sheets, the exact position of adjacent filaments relative to this plane is unknown; for simplicity, the depicted model has been generated by assuming that the cores of the filaments making up the sheet lie on the same plane. Individual filaments are alternately colored light and dark grey, with N-terminal protein regions highlighted in pink and magenta, respectively. The zig-zag view of two adjacent filaments in the sheet resembles the projection of a double helix (see inset of Fig 1A) and the regular presentation of UMOD branches generates a molecular Velcro surface for the capture of UPEC. C Comparison of the UMOD sheet model with the bottom part of panel A suggests that the diffuse density protruding into the space between adjacent filaments (cyan arrow) corresponds to the glycans attached to N396 and N513 (light and dark blue arrows, respectively). D Detail of a porcine ZP filament model, generated by superposition of homology models of adjacent ZP3 and ZP4 subunits (green and purple, respectively) onto the structure of UMODfl (semi-transparent grey), and projection of the residues of the interdomain linker of another ZP3 subunit onto the UMOD ZP-N/ZP-C linker (red). A cluster of experimentally verified glycosylation sites is shown, with side chain atoms depicted as spheres and boxes highlighting the proximity of ZP3 N271 and ZP4 N220, whose N-glycans mediate sperm binding in pig (Yonezawa, 2014). Note how these residues are also close to the conserved N- (dashed underline) and O- (site 1, single underline; site 2, double underline) glycosylation sites in the ZP3 interdomain linker. The invariant ZP3 Trp that follows site 1 is shown in stick representation at the interface with ZP4. E Detail of the ZP3/ZP1 interface of an avian egg coat filament model, assembled and represented as described for panel D. The box highlights the location of O-glycosylation site 1, important for in vitro binding of chicken ZP3 to sperm (Han et al, 2010).
Figure 3A) CD8 T cells in WT mice were depleted by administration of anti-CD8 mAb 1 day prior to infection with 10^5 FFU LCMV. Anti-N mAb KL53 or PBS control was passively transferred IP on days 1 and 3pi. Viral titres in the spleen, lung, liver and kidney of all mice were determined by FFA day 8pi. B) Spleens from WT and KO mice +/- mAb KL53 day 8pi with 0.5 x 10^5 FFU LCMV were analysed for the presence of LCMV N-specific CTLs by staining with the class I N396-404 tetramer. C) Spleens from naïve WT and KO mice day 10pi with 0.5 x 10^5 FFU LCMV were stained with N tetramer. D) Macrophages were depleted in WT mice by administration of clodronate liposomes 1 day prior to infection with 0.5 x 10^5 FFU LCMV. KL53 was administered on days 1 and 3pi, and N396-specific CTLs in the spleen were measured day 8pi by tetramer staining.
c-Jun activity up-regulation by RAF inhibitors causes resistance to apoptosis.Figure 3c-Jun and p-c-Jun(Ser63) changes as measured by RPPA in six melanoma cell lines in response to different doses of RAF and MEK inhibitors for 10 h (or 5 h in the case of WM115cell line) and 48 h. B, C Synergistic apoptosis induction in four cell lines (WM115, WM1552C, LOXIMVI, and COLO858) treated for 72 h with combinations of vemurafenib and JNK-IN-8. (B) Dose-response profiles for apoptosis induction with vemurafenib and JNK-IN-8 combination. C Synergistic apoptosis induction in four cell lines (WM115, WM1552C, LOXIMVI, and COLO858) treated for 72 h with combinations of vemurafenib and JNK-IN-8. (C) Excess over the predicted Bliss independence (EOBI) calculated for different combined doses of vemurafenib and JNK-IN-8. D c-Jun expression in WM115 cells transfected with JUN siRNA relative to no RNA and non-targeting controls quantified in triplicate 48 h after transfection. E, F Apoptosis in WM115 cells with or without 48 h JUN knockdown after 96-h treatment with increasing doses of vemurafenib E, F Apoptosis in WM115 cells with or without 48 h JUN knockdown after 96-h treatment with increasing doses of selumetinib (F)
ARMC8α but not ARMC8β recruits GID4 to the core complex in an assembly that does not prevent binding of the WDR26/RanBP9 module.Figure 4A. Schematic representation of ARMC8α (Q8IUR7-1), ARMC8β (Q8IUR7-6) and GID4 (Q8IVV7-1) proteins. The binding site of GID4 and the C-terminus of ARMC8α is indicated. B. Western blot analysis showing the levels of ARMC8α and ARMC8β in HeLa Kyoto cells treated for 72 hr with control siRNA or siRNA pools against ARMC8 (n=3). C. Transiently expressed FLAG-GID4 and HSS-tagged ARMC8 isoforms (α or β) in HEK293T cells. The presence of GID4 in isoform-specific ARMC8 immunoprecipitates was visualized by immunoblotting (left panels). The right panel shows a western blot of transiently expressed and immunoprecipitated HSS-WDR26 from HEK-293T cells and the presence of endogenous ARMC8 isoforms (α or β) was probed by immunoblotting (n=2). D. Baculoviral co-expression in Sf9 cells of the 5-subunit hGID complex (5mer; Strep-RanBP9, His-WDR26, FLAG-MAEA, His-RMND5a and His-TWA1) along with His-GID4 in the presence of ARMC8α or ARMC8β. Strep- or His-pulldowns revealed the presence of GID4 in ARMC8α, but not in ARMC8β, complexes (n=3). E. Immunoblot analysis of in vitro ubiquitinated GID4-hGID complexes containing either ARMC8α or ARMC8β (6mer; ARMC8, RanBP9, WDR26, MAEA, RMND5a and TWA1) . Where indicated, the reaction was carried out in the presence of 20-fold molar excess of the PGLV GID4-binding peptide (n=3). F. Western blot analysis of in vitro ubiquitinated HBP1 by the hGID 5-subunit complex in the presence of the different ARMC8 isoforms (α or β) (n=2). G. Schematic representation illustrating that in contrast to ARMC8α, incorporation of ARMC8β prevents hGID activity towards GID4 substrates. H. XL-MS analysis of the 6-subunit hGID complex (RanBP9, WDR26, RMND5a, MAEA, TWA1 and ARMC8β). Cross-links within the different complex subunits are indicated by green lines, and cross-links within the same subunit by purple lines. The predicted domain boundaries within the different subunits are colored as follows: LisH domain in light orange, CTLH domain in dark orange, RING domains in blue, TWA1's CRA domain in light blue and RanBP9's CRA domain in light grey, WD40 in dark cyan, ARMC8β in dark red, and the SPRY domain in light magenta. I. Comparison of the cryo-EM maps of the 5-subunit hGID complex (RanBP9, WDR26, RMND5a, MAEA and TWA1) and the 6-subunit hGID complex (RanBP9, WDR26, RMND5a, MAEA, TWA1 and ARMCβ). J. A difference map (red) shows the extra density in the 6-subunit hGID complex corresponding to ARMC8β.
Ageing reduces POMC neuronal autophagy and lipolysis.Figure 5(A) Immunoblots for Atg7 in MBH from young (3 mo), middle‐aged (12 mo) and aged (22 mo) fed and 6‐h‐fasted (Stv) mice (n=4), and (B) LC3‐II in MBH explants from 3 mo and 22 mo fed mice in presence or absence of lysosomal inhibitors (Inh) (n=11-13). Mean±s.e.m values for (B) steady‐state LC3‐II and (C) LC3‐II flux are shown (n=11-13). (D) Immunoblots for p62 and NBR1 flux in MBH from 3 mo and 22 mo fed mice in presence or absence of Inh (n=11-13). (E) Immunofluorescence microscopy for POMC (green) and p62 (red) (n=4), (F) immunoblots for POMC and ACTH (n=4), and (G) immunofluorescence for α‐MSH in MBH from 3 mo and 22 mo mice on RD (n=4). (H) Body wt and (I) eWAT wt of 3‐mo‐ and 22‐mo‐old mice on RD (n=9-13). (J) Serum fatty acids and (K) glycerol from fed or 6‐h‐fasted (Stv) 3 mo and 22 mo mice (n=7-9), and (L,M) after intraperitoneal Iso in 6‐h‐fasted 3 mo and 22 mo mice (n=5-6). (N) Immunoblots for adipose triglyceride lipase (ATGL) in eWAT from 3 mo and 22 mo mice. Values are mean±s.e.m. P values are as compared with controls. *P0.05, **P0.01, ***P0.001. Nuclei are blue (DAPI). Scale inset: 10 μm. Yellow arrows indicate merged signal. ACTH, adrenocorticotrophic hormone; Con, control; eWAT, epididymal fat; Iso, isoproterenol; MBH, mediobasal hypothalamic; mo, months; MSH, melanocyte‐stimulating hormone; POMC, proopiomelanocortin; RD, regular chow; wt, weight.
Phosphorylated tyrosine 65/85 interact with Crk family membersA schematic representation of the Crk SH2 consensus binding motifs in KSHV‐TK.Figure 7A A schematic representation of the Crk SH2 consensus binding motifs in KSHV‐TK. B Immunoblot analysis of GFP antibody immunoprecipitates reveals that GFP‐KSHV‐TK but not Y2F or GFP associates with CrkI, II and L. C Immunofluorescence microscopy analysis reveals CrkII associates with GFP‐KSHV‐TK but not the Y2F mutant. Scale bars, 20 μm. D Immunoblot analysis of RFP antibody immunoprecipitates reveals that RFP‐KSHV‐TK specifically associates with the SH2 domain of CrkII and CrkL. E Immunofluorescence microscopy analysis of phosphotyrosine epitopes in cells expressing GFP‐CrkII SH2, GFP‐CrkL SH2, RFP‐KSHV‐TK or a combination of CrkII/LSH2 and RFP‐KSHV‐TK. Arrowheads represent contracted KSHV‐TK‐expressing cells. The SH2 domains of CrkII or L block KSHV‐TK‐induced cell rounding. Scale bars, 20 μm.