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(A-D) Selected metabolite carriers of control (143B, solid lines, grey bars) and ρ0 cells (dashed lines, colored bars). A, isoforms of the nucleotide carrier (ANT1-3) and phosphate carrier (PiC); B, pyruvate carrier; C, dicarboxylate carriers; D, mitoferrins (MFRN1-2) and glycine transporter (GlyC). Plots and gene names are in corresponding colors. Data are presented as mean ± SD (n=4). *p<0.05, **p<0.01 (Student's t-test).
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G. Normalised RNA DIP-seq peak heights in the genes identified as associating with H-DNA. Data information: P values calculated with Mann-Whitney U test. In violin plots, bar = median; box = interquartile range (IQR); whiskers = upper and lower inner fences (1st / 3rd quartile + 1.5*IQR).
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C Representative immunofluorescence images showing expression of PB1-F2 (red). A549 cells were transfected with plasmids encoding indicated PB1-F2. At 18 h after transfection, cells were treated with MG132 for 6 h and subjected to immunofluorescence analysis. Magnification, ×100; scale bar, 100 μm.
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(h,i) Western blot analyses of TbMCU RNAi of BSF (h) and PCF (i) trypanosomes grown in the absence (0) or presence (2-8; 2-10) of tetracycline. Total lysates (30 μg) were subjected to 10% SDS-polyacrylamide gel electrophoresis before transfer to a nitrocellulose membrane and then stained with antibodies against TbMCU (top). One band of ~30 kDa was detected in T. brucei homogenates. Membranes were stripped and re-incubated with antibody against the voltage-dependent anion channel (TbVDAC) as a loading control (bottom).
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The minimum value of MSE in MT number (shown by black points) increases with the increase in binding cooperativity (in curves from left to right).
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(A) Cell lysates prepared from HeLa cells were solubilized with Triton X-100 and subjected to immunoprecipitation using preimmune sera (lane 1) or anti-Beclin antibodies (lanes 2 and 3). The immunoprecipitates were incubated with phosphatidylinositol, [γ-32P]ATP and 60 μM cold ATP in the presence of Mn2+ (lanes 1 and 2) or Mg2+ (lane 3) for 5 min at 30°C.
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A Schematic illustration of the NeutrobodyPlex. The displacement of serum-derived neutralizing IgGs binding to SARS-CoV-2 antigens upon addition of bipNb is measured. In presence of neutralizing IgGs, the fluorescent signal from anti-human-IgG-PE is inversely proportional to the applied bipNb concentration.
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G 1205Lu human melanoma cells or 1205Lu melanoma cells over-expressing mouse Bcl-XL were treated with various concentrations of ABT-737. To some aliquots the caspase-inhibitor zVAD-fmk (50 μM) was added. Relative numbers of apoptotic cells were determined as in EV 1B after 48 h. Data are means/SEM of at least three independent experiments. (1205Lu, n=4; 1205Lu 5 µM ABT-737, n=3; 1205Lu/Bcl-XL and 1205Lu + zVAD, n=3).
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(a) Nuclear localization of HLH-30 was quantified in day 1 adult animals expressing HLH-30::GFP. Animals were fed bacteria expressing control or tor dsRNA from hatching and raised at 20 °C (three biological replicates, ~50 animals each, mean±s.d., **P0.01, Student's t-test).
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(C) HeLa-GFP-Parkin cells were incubated with 1 µM valinomycin and 100 nM bafilomycin A1 for 0-3 h in the presence or absence of 10 µM epoxomicin. Cell lysates were subjected to immunoprecipitation using anti-NDP52 antibody or control IgG. Immunoprecipitates were analyzed by western blotting. Data are representative of five independent experiments. (D) Quantification of MTPAP co-immunoprecipitated with NDP52 in (C). Results are a summary of five independent experiments. Values are the means ± SEM. **p < 0.01 compared to cells treated with valinomycin and bafilomycin A1 for 3 h, determined with one-way ANOVA followed by the Tukey-Kramer post hoc test
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(c) RALB ubiquitylation at Lys 47 is crucial for formation of the RALB-SEC5 complex in response to poly(I:C) treatment. Flag-tagged SEC5 and the indicated HA-tagged RALB mutants were introduced into 293-hTLR3 cells. At 48 h after transfection cells were treated 100 μg ml−1 of poly(I:C) for 6 h. Flag-tagged SEC5 was immunoprecipitated with anti-Flag (M2), and analysed for co-precipitation by immunoblotting using anti-HA antibody.
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(F) Pre-existing MITOL on mitochondria moves to peroxisomes following CCCP treatment. Following doxycycline treatment for 3 hours to induce MITOL expression, cells were washed with fresh medium to stop the synthesis of new MITOL. After treatment with or without CCCP for more than 3 hours, cells were immunostained using anti-Flag, anti-Pex14 (peroxisomal membrane protein), and anti-Hsp60 antibodies. Higher magnification images of the boxed regions are shown in the bottom panel. Scale bars, 10 µm.
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A. Schematic of the methodology adopted for the identification of protein interacting partners of veal2 using a RAP-MS based approach.
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(E) Gross images of colons and quantification of colon length from control (n=6) and cKO (n=6) mice two days after 5-day DSS treatment.
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C-F GlaB inhibits MB‐SCs' self‐renewal and proliferation. (D, E) MB‐SCs isolated from Ptch1+/−miceMBs were treated for 48 h with GlaB (5 μM) or DMSO only. qRT-PCR analysis show Hh, proliferation and stemness target mRNA expression levels. For qRT-PCR, results were normalized to endogenous control (β2‐microglobulin and HPRT).
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D. Enlarged view of the central β sheet comprising residues Y130-K135 (β2), I141-S146 (β3), F165-K168 (β4) and A266-R271 (β8).
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F) Bar graph showing the number of neoaggregates per cell. Non-parametric unpaired t test FTLD-TDP-A vs FTLD-TDP-C, p=0.0003. Error bars represent mean ± SEM, n=3 independent experiments, 6 biological replicates for each condition.
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E. The CLS is required for KV10.1-induced tumorigenesis. CHO cells were transfected with the indicated constructs and implanted into the flank of nude mice. KV10.1ΔCLS transfected cells did not induce larger tumors than the control.
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(H) Graph shows the number of Satb2+cells in 4×104µm2 at P0 (WT n=5; hFOXM1-cKI n=5; two-tailed unpaired t-test, P= 0.0086). (I) Graph shows the number of Ctip2 +cells in 4×104µm2 at P0 (WT n=5; hFOXM1-cKI n=5; two-tailed unpaired t-test, P= 0.0025). (
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(M) Densitometry of AXL band intensities in (J) in S and R, normalized to AXL intensity in input. Data in (A) to (M) are representative of at least three experiments with graphs depicting means ± SE s; *P < 0.05, ***P < 0.01, and ****P < 0.0001 by Student"s t tests
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C A truncated construct that lacks the DOG1 antisense promoter region (pDOG1shDOG1::LUC) is not induced by ABA and is highly expressed throughout development. The graphs show mean emitted light intensity per plant.
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Centrosomes from WT, single and double KO cells, as indicated, were labelled for CDK5Rap2 Right panels show quantifications. A region of interest of 1,5 μm radius was drawn around the centrosome and fluorescence intensity was determined and normalized to WT mean.
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D. Wild-type, but not the PIP-mutant can correct the defective H2AX ubiquitination in HUWE1-knockout 293T cells.
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E. Subcellular localization of WT Yb and deletion mutants ∆Hel-C and ∆eTud. Myc-Yb is shown in green. Endogenous Armi is shown in red. DAPI shows nuclei (blue). Scale bar: 5 μm. Western blotting (right) showing WT Yb and deletion mutants ∆Hel-C and ∆eTud expressed in Yb-lacking OSCs.
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(G) qRT-PCR of fat-5 mRNA expression in wt nematodes grown on control and fat-5 RNAi expressing bacteria (unpaired t-test, n=3 biological replicates). Data information: bars represent mean±SEM; Across experiments, p value summary is *p<0.05, **p < 0.01, ***p<0.001, ****p<0.0001.
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Male C57BL/6J mice were injected with LV-shScrambled or shSUNCR1 lentivirus specifically into the gastrocnemius at 6 weeks of age. After two weeks of recovery, mice were fed with chow diet supplemented with 0 or 1% SUC for 6 weeks. SUNCR1 protein expression in gastrocnemius from mice transfected with shSUNCR1 lentivirus or LV-shScrambled (n=3).
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(F) Anti-GFP immunoblot analysis for the extracellular fraction of the seedlings exposed to Pst DC3000 AvrRpm1 for 48 h. (B, C, E and F) Arrowheads and arrows indicate an apparently full-length and processed form of PROPEP3-Venus, respectively. Asterisks indicate cross-reactive bands. The positions of the molecular weight markers are shown on the left of the immunoblots.
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Immunofluorescence images against the microglia marker F4/80 in the cerebellum of WT and Npc1nmf164 after 48 hours of a single dose of 5mg/kg PF. Graphs show mean ± SEM number (upper) and area (lower) of F4/80 positive cells (upper graph ****P< 0.0001; lower graph ***PWT Veh vs NPC Veh = 0.0008; *PWT Veh vs. NPC PF = 0.0286; ****PWT PF vs. NPC Veh < 0.0001; **PWT PF vs. NPC PF = 0.0022, n = 3 mice per group, > 20 cells analyzed per mouse, one - way ANOVA, Bonferroni post hoc). Scale bar, 10 μm.
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(A-B) Nociceptive withdrawal thresholds in control (AviliDTR without the Cre) and Sst-Cre::AviliDTRmice after systemic diphtheria toxin injection. No significant differences in thermal (A) or mechanical (B) withdrawal reflexes after ablation of SstCre positive neurons.
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(E) Schematic diagram of the mutant Pax5-Jak2 protein carrying the indicated amino acid changes that were introduced in the N-terminal part of the paired domain by CRISPR/Cas9-mediated mutagenesis in the Pax5Prd*-Jak2 allele
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The expression of the IL-6Rα (CD126) and signaling chains (gp130) was assessed by SYBR or Taqman qRT-PCR (B, C) respectively, on a panel of DLBCL cell lines. ABC- and GCB-DLBCL cell lines are color-coded in red and green; RC-K8 are depicted in grey, as their subtype is a matter of debate
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(G) Mcp3 is membrane-embedded. Mitochondria isolated from mcp3Δ cells expressing HA-Mcp3 were left untreated (I, input) or subjected to alkaline extraction. The supernatant (SN) and pellet (P) fractions were analysed by SDS-PAGE and immunodecoration with antibodies against the indicated proteins. Tom20 an integral MOM proteins; Aco1, soluble matrix protein. m, mature protein.
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C, D Flow cytometric analysis of the intracellular Ca2+ influx in purified splenic B cells derived from Tam‐treated mice. mb1‐CreERT2 or mb1‐CreERT2;Sykfl/fl were treated with (C) 10 μg/ml anti‐Kappa F(ab′)2 fragments or (D) 1 μM ionomycin.
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qRT-PCR analyses of mRNA expression of QKI-5 in A549 cells transfected with siRNAs of TFs, which have potential binding sites in QKI-5 promoter.
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A) Schematic display of the culture model using hippocampal neurons that were infected by a lentivirus co-expressing a synaptophysin-CFP fusion protein (SypCFP) together with either Nrg3 or Nrg3∆EGF at a low titer so that 10-20% of the hippocampal neurons were transduced with the lentivirus (depicted as a light blue colored neuron with a red nucleus). Presynaptic boutons formed by non-transduced (depicted as a light grey neuron with a white nucleus) and transduced neurons can be distinguished by the absence or presence of CFP labeling (grey and blue boutons, respectively)
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(D) Serum lactate levels of WTFlx and Ndufs3-smKO animals at different ages. Ndufs3 smKO male mice (filled black squares) showed increased levels compared to matched WTFlx males (empty black squares). Error bars represent SEM.
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(B) Representative western blot showing levels of IKKε and the SBP enzymes in IKBKE (IKKε)-silenced ZR-75-1, T47D, MDA-MB-468 and MCF7 breast cancer cell lines.
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fluorescence range over the lifetime of the cell before CIP exposure (F), and mean fluorescence during CIP exposure (G) of cells that died (n = 174) and cells that survived (n = 164). Gray and black lines indicate mean ± SD. The data shown are from 2 independent experiments. Significance by unpaired Mann-Whitney test: ns, not significant; **p = 0.001; ****p < 0.0001. Most survivors had a moderate growth defect before exposure to ciprofloxacin and lower expression of RecA-mCherrywt both before and after drug exposure.
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Schematic overview of highly confident (LD score at least 30) crosslinks between Elp1 (orange), Elp2 (yellow), Elp3 (pink), Elp4 (green), Elp5 (blue) and Elp6 (sand). The size of the used squares is adjusted to the length of the individual proteins and also indicated the location of the respective crosslinks. Inter cross-links are drawn as lines colored according to one of the linked subunits, intra crosslinks as arcs colored according the subunit, whereas "dimeric" cross-links (linking same residues of a protein) are depicted as red loops. Structural domains are indicated. Protein regions not present in the crystal structures and homology models are colored black. Figure was drawn using xiNET [76].
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E, F Measurements of glycogen (n=5 biological replicates) and TAGs (n=10 biological replicates) in fat bodies. Data information: All data are presented as the mean ± SEM (Student's t-test, **P<0.01, ***P<0.001, ns: not significant). All assays were performed on four-day-old fourth-instar locusts.
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B, Response of the strain to addition and removal of varying acetate concentrations (pH 7.0). FliMN-CheY concentration was estimated to be ~300 μM. Lines and shaded regions are the mean time spent in clockwise rotation ± SEM. The arrows indicate the estimated time points at which acetate entered or left the flow chamber. Black lines mark the linear part of the biphasic response to acetate removal. N is the number of cells.
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Schematic of PA14 (24 h) and undA mutant (24h) bacterial lawn choice assay in a tripartite plate and choice index. n ≥ 3 assays. Error bars indicate SEM.
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Line plot of log2 phosphopeptide intensity versus protein input amounts with each line representing an individual phosphopeptide. For every phosphopeptide a linear regression was performed and lines are colored according to the slope of the linear regression. Black line represents the linear regression of the median phosphopeptide intensities and the corresponding function is shown on top. Boxplot depicting the distribution of slope values resulting from linear regressions of individual phosphopeptides shown in B. Boxplot depicting the distribution of r squared values resulting from linear regressions of individual phosphopeptides shown in B.
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tiRNA and 5'-tiRNAAla production in IECs isolated from WT and Ang-/- colitis mice at indicated time point.
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E. Polarographic profiles of isolated mitochondria from wt (lower trace) and ATPIF1H49K|T/H (upper trace) animals. Histograms show a reduction in state 3 respiration consistent with the inhibition of ATP synthase in ATPIF1H49K|T/H mice. Bars are the mean ± s.e.m. of n= 3 mice/genotype, 3 traces/mouse; OL, oligomycin; Ant A, antimycin A.
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Overlap between DEGs in young HO-1-/- HSCs and DEGs changed by transplantation alone. 145 overlapping genes were excluded from further analysis.
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(D) Radial intensity profiles of Iba1 and 4G8 around the center of the nucleus of plaque-associated Iba1-positive microglia in male APP23p40+/+ (n=10) and APP23p40-/- (n=8) mice. Iba1 intensity declines until a radius of ~6 µm, marking the cell periphery. 4G8 intensity peaks inside the cell (~4 µm), but stays high outside the cell. This is very likely due to the close proximity to 4G8 positive plaques. Mean ± s.e.m., statistical analysis: two-tailed unpaired t-test with Bonferroni correction for the number of binned radii shows no significant difference between both 4G8 traces.
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E Damage-induced translocation of UBE2QL1 to lysosomes. The three best candidates (from D) were transiently expressed with N-terminal HA-tag in HeLa cells. Cells were treated with LLOMe or EtOH (untreated) for 3 h, fixed and stained for HA and LAMP1 as indicated and imaged by confocal laser scanning microscopy. Scale bar: 10 µm. F Automated quantification of (E). Shown are Pearson correlation coefficients (P.C.C) of HA and LAMP1 signals. Graph represents data from three independent experiments with ≥ 30 cells per condition (mean ± SD). ****P<0.0001 (One-way-ANOVA with Bonferroni's multiple comparison test).
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A. Identification of FASTKD2 interacting proteins by AP-MS and BioID. 26 high confidence interactors detected by both techniques are listed on the right.
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C, Co-immunoprecipitation to detect the interaction between endogenous HIF2α and USP33 in GSCs after inhibition of ERK1/2 activity. GSCs were cultured under 20% or 5% oxygen for 24 hours, then treated with the MEK inhibitor U0126 (10µM) for 30 minutes to inhibit ERK1/2 activity, and harvested for immunoprecipitation with anti-HIF2α antibodies. Co-immunoprecipitated products were immunoblotted with the indicated antibodies. Relative to 20% oxygen treatment, 5% oxygen treatment promoted the interaction between HIF2α and USP33 in GSCs. However, inhibition of ERK1/2 activity by U0126 treatment suppressed the interaction between HIF2α and USP33.
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C-D. Jmjd2a(+/-); Jmjd2c(+/-) mice were inter-crossed. The number of (C) pups alive at weaning or (D) embryos recovered at E6.5 is presented. P values were calculated using exact binomial test with the most conservative estimate of expected (-/-;-/-) embryos (6.25 %, assuming no linkage between the Jmjd2a and Jmjd2cloci even though they are located on the same chromosome).
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] |
qRT-PC of mGPDH, myogenin and developmental myosin heavy chain (myh8, myl4 and myh3) in gastrocnemius (GA) muscle from C57BL/6J mice at indicated day after CTX intramuscular injection
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B The AtNPF6.3 sub-clade in rosids can be grouped into three haplotypes with residues corresponding to AtNPF6.3 T101, H356, T360 and F511, designated as Types A, B and C. All legumes have Types A and B, while a subset also have Type C, which is found only in legumes of the Hologalegena clade. All NPF6s from M. truncatula, and A. thaliana were used for tree construction and only the AtNPF6.3 sub-clade is presented. Rosid orders represented: Cucurbitales: Cucumis sativa; Rosales: Prunus persica, Trema orientalis, Parasponia andersonii; Fagales: Morella rubra; Malpighiales: Populus alba; Fabales: Trifolium pratense, Lotus japonicus, Phaseolus vulgaris, and Glycine max. Sequences were aligned using MUSCLE, the phylogenetic tree was constructed using PhyML. Branches with maximum likelihood support >0.80 are indicated by filled circles.
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Cells were pretreated with endosomal-pH interfering drugs at the indicated concentrations and subsequently infected with SARS-CoV-2 as described in Fig. 2A and 2B in the continuous presence of NH4Cl (A), chloroquine (B), bafilomycin A1 (C), or concanamycin B (D). The proportion of infected cells was quantified by flow cytometry as described in Fig. 1D, and data were normalized to control samples that were not treated with inhibitors. n = 2-6 biological replicates.
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D Volcano plot showing differentially expressed genes (adj. P.Val < 0.05) between ethanol- and R5020-treated mouse mammary organoids, n=3. Genes with log2(FC) > 2 are highlighted in red, genes with log2FC < -2 in blue. Names of genes with -log10 (adj.P.Val) > 10 and abs(log2(FC)) > 2 are indicated.
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A. U2OS cells were transfected with control (siLuc) or BRCA2 targeting siRNA (siBRCA2). After 48 hours cells were either mock treated or treated with 10 μM XL413 for 30 minutes and labelled consecutively with CldU (red) and IdU (green), followed by treatment with 4 mM HU for further 5 hours.
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E: Histological analysis of EGC proliferation by quantification of Ki67 (violet) and Sox10 positive EGCs at IM24h. Mice were treated as seen in (A).
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(C) Three-dimensional visualization of neural subtype developmental trajectories for individual samples from GW7, GW10, GW14, GW18, and GW23. Stage-dependent differentiation trends changed with development. The red arrow indicates the proliferative neural progenitor cell cluster (MKI67, PAX6, NES, and SOX2). Neural cell types are named and circled with dotted lines. Gray represents non-neural cell types (e.g., vascular and meningeal).
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Decreased Drp1S616 phosphorylation in PINK1-null MEF cells Lysates of PINK1-null (PINK1KO) and parkin-null (parkinKO) MEF cells (c) and their matched wildtype controls (WT) were immuno-detected with antibodies against either phospho (Ser616)-Drp1 (pS616), phospho (Ser637)-Drp1 (pS637) or Drp1. β-actin was detected as a loading control. Quantitation of pS616/Drp1 for each experiment is shown Student's test. *p<0.05, ***p<0.001, ns: no significance. Data was presented as mean ± SEM of three independent experiments.
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A-C - ChAT-eGFP mice were treated with (A) veh (n = 4) or β1-AR agonist (1 mg/kg dobutamine, Dob) (n = 3), (B) veh (n = 7) or β2-AR agonist (1 mg/kg formoterol, Form) (n = 7) or (C) veh (n = 4) or β3-AR agonist (1 mg/kg CL 316,243, CL) (n = 4 for MΦ; n = 3 for T cells and B cells) for 4 h and the percentages of total IWAT SVF cells and of total T cells, B cells and MΦ that were ChAT-eGFP+ were measured by flow cytometry.
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A. Schematic representation of the analysis workflow for the panels (C-F). Optimal and non-optimal transcripts are predicted based on the zebrafish optimality code (Fig 1F) and mRNA decay during the MZT in each species was analyzed.
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Flow cytometry analysis of tumours collected on Day 10 following treatment (n = 3 animals per group). ILP-TNF/Mel/SM significantly upregulated Granzyme B in CD3+CD8+CD161- cytoxtoxic T cells
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0
] |
(D) Chitin production is reduced upon Bch1 overexpression. Fluorescence images of chitin stained with calcofluor in Chs3-GFP WT, chs5 and GPD-BCH1 strains.
|
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Western blot analysis of caspase-1 cleavage in the supernatant of Prdx4 WT and KO BMDMs in response to Nigericin (10 µg/ml) stimulation for 1 h after priming with LPS (100 ng/ml), LPS-priming alone or without stimulation. Whole cell lysates were analyzed for pro-caspase-1 and Gapdh levels.
|
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(D) Chromatin recruitment of PPARγ at PPAR binding site contained in Cidecand Pcxpromoters (n=3-5, per group, per ZT, Two-way ANOVA, post hoc Holm-Sidak comparisons *p<0.05). H3K4me3 abundance at Cidecand Pcxpromoters (n=4-7, per group, per ZT, unpaired, two-tailed Student t-test *p<0.05).
|
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D HEK-293T cells expressing Flag-DENND2B were treated with 250 nM OA alone or with 50 µm PKD inhibitor CID755673 and cell lysates were incubated with GST-14-3-3. Total proteins and bound proteins were detected by Ponceau S staining and Western blot, respectively.
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] |
B. The rates of of LCVs positively stained for MavQ 2 h post-infection. At least 100 LCVs (n≥100) were scored for each sample.
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F Diagrams and co-IP results showing BTG4 binding to PABPN1L. Lysates from HeLa cells expressing HA-BTG4 and FLAG-PABPN1L (full length and C-terminal deleted) were immunoprecipitated with an anti-FLAG antibody. The immunoprecipitated proteins are detected by western blot with the indicated antibodies.
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Depletion of Prkrir, Pcbp4 and Tsc22d1 rescues TGF-β-induced reduction in the rate of cell division. (A) Lineage trees tracked by live imaging under control, Non treated control (NTC) and siRNA-mediated depletion of factors (X= cell death/cells could not be tracked till the end).
|
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(B) Quantification of the percentage of ciliated cells Data represent mean ± SD (n=3 experiments), 200 GFP-positive cells were scored per condition per experiment, *P < 0.05, Student's t-test.
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]. (C) Quantification of mean (±SEM) mEPSP amplitudes, in which 75 consecutive spontaneous events were averaged per cell, and then cell amplitudes were averaged per genotype. [UAS-RFP n = 15 cells, UAS-dNmnat n = 14 cells, UAS-Wnd n= 10 cells. 1-way ANOVA w/Tukey's multiple comparisons, DF=38, F=11.66, p = 0.0001. UAS-RFP vs UAS-dNmnat p=0.994 (NS), UAS-RFP vs UAS-Wnd p = 0.0003 (***)].
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B (Left) Detection of spliced XBP1 (S) and unspliced XBP1 (U) mRNA in shCtrl and shFAM20C HepG2 cells treated with or without 5 μM Tg for 1 h. (Right) Quantification of XBP1 mRNA splicing levels. Data information: data were shown as mean ± SEM of three independent experiments. *p < 0.05, **p < 0.01 (two-tailed Student's t-test).
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B Median fluorescence intensity of the distribution plots in A plotted against the indicated time after HPG addition. Linear regression line fitted from 5 minutes onwards.
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Kaplan Meier survival curve on the full lawn of P. aeruginosa for N2 (naive) worms and N2 worms pre exposed to 1-undecene odor. Survival assay was performed at 20°C.
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C. IP on Hela cells co-expressing VPS41WT-APEX2-V5, VPS41S285P-APEX2-V5 or VPS41R662*-APEX2-V5 and FLAG-RAB7 or GFP-Arl8b. The IP was performed on FLAG or GFP respectively. All VPS41 variants interact with Rab7 and Arl8b (n=3).
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Changes in the concentration of plasma metabolites are associated with COVID-19 severity. The discharge group consist of all patients (mild and severe) that were recovered and discharged. L1, low-density lipoprotein subclass-1 (LDL1); VL, very low- density lipoprotein (VLDL); L5, LDL5; L6, LDL6; H2: high-density lipoprotein subclass-2 (HDL2); H3: HDL3; H4: HDL4.
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Epidermal cells transfected with control siRNA (siCtrl) or S100A9-targetting siRNA (siS100A9) were challenged for 72h with 200 ng P24 of HIV-1-R5 (left dot-plots) or HIV-1 primary isolate (right dot-plots). Cells were fixed, permeabilised and stained with langerin (Y-axis) and HIV Gag P24 (X-axis) fluorescently coupled antibodies. Samples were acquired on a Flow cytometer. The experiment shown is representative of four donors for HIV-1-R5 (n=4) and five donors for HIV-1 primary isolates (n=5). The same as above was done but on MoLC gated by size (FSC).
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D. As for C, but comparing genotypes in wild type or HEI10-OE backgrounds. Values for replicate individuals are plotted, in addition to the mean (red).
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Sexing of established ESCs (gDNA-qPCR, Zfy/Gapdh), performed as described in Figure 1B.
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Amounts of Aβ40 or Aβ42 in the TBS-soluble or Gu-HCl-extractable fraction from (A) 3-month-old or (B) 12-month-old hAPP/Mgat3+/+, hAPP/Mgat3+/−, or hAPP/Mgat3−/− brains (n = 5). P = 0.015 for TBS Aβ40, P = 0.034 for TBS Aβ42, P = 0.001 and 0.012 for Gn-HCl Aβ40, P = 0.024 for Gn-HCl Aβ42 in (A), P = 0.040 for Gn-HCl Aβ40, P = 0.047 for Gn-HCl Aβ42 in (B).
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AP staining of H8-Bptf or H8-Tbx3 exon-KO ES cells after LIF withdrawal. hnRNPLL-H8, hnRNPLL-KO ES cells; H8-Bptf KO, alternative Bptf exon was deleted in hnRNPLL-KO H8 cells; H8-Tbx3 KO, alternative Tbx3 exon was deleted in hnRNPLL-KO H8 cells; H8-Bptf/Tbx3 KO, alternative Bptf or Tbx3 exons were simultaneously deleted in hnRNPLL-KO H8 cells. Scale bar, 200 μm.
|
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(J) Quantitative Real-Time PCR analysis of eEF1A1 and eEF1A2 mRNA abundance in hearts from neonatal mice, adult wild-type mice (Adult) and adult wild-type mice 2 weeks after TAC surgery (Adult TAC, N=3 to 4 mice/group). *P<0.05, ***P<0.001. One-way ANOVA with Sidak´s multiple comparisons test.
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A: oxidative growth. W303-1Bcym1Δ strains harbouring the wild-type CYM1 allele (CYM1wt), the cym1R163Q mutant allele or the empty vector were serially diluted from 107 to 104 cells/ml. Five microliters of each dilution were spotted on SC agar plates without uracil, supplemented with 2% glucose, 2% glycerol or 2% ethanol. Plates were incubated at 37°C for 3-7 days.
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After NEBD, Cyclin B2 localizes to unattached kinetochores, mediated by Mad2 bound to Mad1 or by Mad2 bound to a yet unidentified kinetochore receptor (protein-X). Multiple SAC factors, including kinases, localize at the outer kinetochores. Mad2-mediated Cyclin B2-Cdk1 contributes to SAC signalling, in complement with Mad1-mediated Cyclin B1-Cdk1. As a scaffold recruiting multiple SAC factors to the vicinity, the outer kinetochore catalyses the assembly of MCC. As a consequence, MCC inhibits the activity of APC/C to preclude the anaphase as long as improperly attached kinetochores are present. The error-correction machinery promotes the establishment of correct bipolar microtubule kinetochore attachment. When all kinetochores achieve bipolar attachment, SAC signalling is silenced, and the cell enters anaphase. C: C-Mad2, O: O-Mad2, X: protein X, B1: Cyclin B1, B2: Cyclin B2
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E. Spatially restricted AC and DMZ cell clusters embedded in UMAP of whole embryo scRNA-seq data
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MQ can bind both high molecular weight (HMW) targets such as mutant p53 and low molecular weight (LMW) targets e.g. GSH and Cysteine. MQ conjugation to GSH (GS-MQ) is reversible, indicating that MQ can transfer between multiple HMW and LMW cellular targets. Thus, GS-MQ serves as an intracellular drug reservoir. MRP1 regulates GSH and oxidized GSH (GSSG) content and exports GS-MQ. Therefore, MRP1 inhibition potentiates the effect of APR-246/MQ through a dual mechanism: 1) inhibition of GS-MQ efflux and 2) disruption of the intracellular thiol balance sensitizing cells to oxidative stress. We postulate that a MQ reservoir is similarly formed by conjugation to other thiols (R-SH) targets, e.g. Cys. Furthermore, xCT and MRP1 collectively regulate LMW target availability and thus the intracellular reservoir of MQ, thereby governing sensitivity to APR-246.
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D) Representative images of NMJs in the soleus muscle at 130 days. Muscles were immunostained for neurofilament H (NF-H, in red) and stained with α-bungarotoxin (α-BTX, in green). Scale bar, 20 µm.
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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.
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(D) Plot showing the time course of T. thermophila cell growth in the presence of CA4 (20µM) or parabulin (50µM; error bars corresponding to the standard deviation of triplicate biological measurements). Control experiments are done with DMSO alone.
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(G) Representative picrosirius red staining of cross sections of left ventricles. Scale bar: 50μm.
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H Luciferase activity in 293T cells transfected with scramble or USP19-specific siRNA and ISRE luciferase reporter after SeV infection for indicated time points with or without Beclin-1.
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Oct4-eGFP reporter MEFs or WT MEFs were infected with combinations of shRNAs. (D) Representative FACS profiles of mouse-specific pluripotency cell surface marker SSEA1+ iPSCs on day 14 of reprogramming and (E) quantification of the percentage of SSEA1+ iPSCs in MEF cultures that were infected with the indicated shRNAs targeting Vim and/or Tnfaip2 [n=5 biological replicates; data were normally distributed (P>0.05 as per Shapiro-Wilk test) but showed unequal variance; data were analyzed by Brown-Forsythe and Welch ANOVA and Dunnett's multiple comparisons test].
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Venn diagram showing 1055 genes uniquely downregulated in the "main LPS" cluster (red) and 29 genes exclusively decreased in the "subset LPS" (yellow) compared to their corresponding controls (blue) (FDR<0.05). A total of 87 genes were shared between the two LPS populations.
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Densities (cells/mm2) of GFAP+Ki67+ cells in V-SVZ whole-mounts 24h after TMZ treatment. Arrowheads point to dividing NSCs under regenerative condition. n=6, *p= 0.0173. Scale bar: 10 μm.
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Deubiquitinating activity of UBP13 against K48- and K63-linked ubiquitination. Diubiquitins linked through K48 or K63 (K48 Di-Ub or K63 Di-Ub) were incubated alone or with GST-UBP13 or GST-UBP13C207S for 18 h. Deubiquitination of the diubiquitins was analyzed by western blot with the α-ubiquitin (α-Ub, P4D1) antibody. The presence of GST-UBP13/UBP13C207S recombinant proteins was confirmed by the α-GST antibody.
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C Experimental workflow for validation experiment using a different promoter (EF1α), reporter gene (luciferase) and quantification method (qPCR).
|
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(B) At 48h post-transfection of wtSPINK6 plasmid in 293T cells, cell lysate and concentrated supernatant (50×) were applied to the detection of SPINK6 protein and β-actin by WB.
|
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(C) Immunoblotting of cell lysates prepared as (B) with antibodies to respiratory chain subunits NDUFB8 and COXII, and GAPDH as loading control. Means ± SEM of n=3 experiments
|
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Representative images showing colony formation in hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells with or without pRB knockdown or LATS2 knockout. hOSEs at the 7th passage were incubated in the growth medium in a soft agar culture system for 9 days before imaging.
|
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Primary astrocytes from OTUB1fl/fl and GFAP-Cre OTUB1fl/fl mice were transfected with SOCS1-MYC plasmids. Twenty-four hours after transfection, cells were treated with cycloheximide (CHX, 100 μg/ml) for indicated times. SOCS1 protein levels were analyzed by WB (upper panel). The lower panel shows the relative protein levels of SOCS1 normalized to Tubulin (n = 3 for both groups).
|
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