EMBO/sd-character-level-ner huggingface dataset:
Western blots showing co-immunoprecipitation of GAPDH from the total lysates and isolated mitochondria of PC12 cells with anti-GAPDH antibody. Anti-EGFP antibody detects the presence of polyglutamine repeats. Bottom panel shows co-immunoprecipitation of GAPDH in the total lysate of PC12 cells treated with formaldehyde to cross-link proteins. Ctr* = control. n = 3.
(b) The occupancy of dUTX on the promoter regions of BR-C and E93 genes detected by ChIP. SL2 cells overexpressing HA-dUTX were chromatin-immunoprecipitated with anti-HA and anti-GFP (IgG control) antibodies following ecdysone treatment. Results are shown as the fold enrichment of % input compared with IgG control. In the right hand panel abundance of H3K27me3 on the promoters of BR-C and E93 genes as detected by ChIP is shown. SL2 cells knockdown for dUTX (dUTX RNAi) were chromatin-immunoprecipitated with anti-H3K27me3 and rabbit IgG (control) antibodies following ecdysone treatment. Results are shown as the fold enrichment of % input compared with RNAi control. Data in all panels are expressed as means from three independent experiments, with error bars representing s.e.m. *P0.05 (Students t-test).
E, F VSV titer in the WT and lincRNA-EPS-/- iBMMs transfected with siRNA as described in (D) and infected with VSV (MOI 0.1) for 8 h was measured by plaque assay (E). The alteration rates of viral titers were calculated in lincRNA-EPS-/- iBMMs relative to WT group (F).
High-magnification representative photomicrograph of Golgi staining of the dendritic arbour of a CA1 pyramidal neuron in a Tardbpfx/fx mouse. Black arrows denote selected dendritic spines.
trypsin-like activity of the proteasome across nine tissues in individual mice. Each data point (n=9 females and n=10 males) indicates data from a single mouse performed in triplicate. Each central line and error bar indicate mean +/- SEM . * indicates p<0.05 by unpaired two-tailed students t-test comparing male and female samples.
D. Total lysates from mouse brain were immunoprecipitated with anti-TBC1D31 antibodies or with control IgG. The precipitates and an aliquot of lysates were immunoblotted with the indicated antibodies.
(F) RPE1 cells were either left untransduced (mock) or transduced with lentiviral vectors expressing the indicated Myc-ANKRD26 constructs. Subsequently, cells were treated either with DMSO or ZM447439 for 24h and subjected to immunoblotting; n = 3 independent experiments.
(A) Schematics of culture epithelial cells with supernatant from HEK293FT cells transfected with pcDNA3.1 empty vector or pcDNA3.1-hISLR-HA plasmids. Western blotting for HA in the supernatant from HEK293FT cells transfected with the indicated plasmids.
(C) Immunocytochemistry showing cofilin, p-cofilin, and dendritic marker MAP2 from Nedd4-2 WT or Nedd4-2 cKO cultured hippocampal neurons induced with or without cLTP at DIV 16. Representative dendrites and quantification from Nedd4-2 WT or Nedd4-2 cKO cultures are shown (n = 36-39 neurons). Scale bar: 5 µm. For quantification, data from cLTP induction were normalized to data from control (CTL) condition.
[d] NAD+ levels in wild type (WT), Xrcc1Nes-Cre, and Parp+/-/Xrcc1Nes-Cre forebrain tissue. Data are the scatterplots of individual measurements from at least three mice per genotype, with error bars representing the mean +/-SEM. Statistically significant differences are indicated (Kruskal-Wallis ANOVA with Dunn's post hoc test *p < 0.05).
1) The Bem1-Cdc24 complex is recruited to the plasma membrane via multivalent interactions with anionic lipids. The BC motifs in Bem1 provide the strongest affinity for anionic lipids at this step. 2) Upon their recruitment to anionic lipids, the Bem1 BC motifs may influence the local membrane environment, contributing to local Cdc42 activation by Cdc24 and Cdc42 nanoclustering.
a, COS7 cells stably expressing yellow fluorescent protein (YFP)-ATG5 were transfected with RFP-SEC61b; and teal fluorescent protein (TFP)-mito, and immunostained for TOMM20.
(A) Dual role of ChAPs in formation of the exomer complexes at the TGN. ChAPs differently stabilize Chs5 at the TGN and also have variable specificities for different cargoes.(B) Model of the dynamic assembly of the exomer cargo adaptor. (1) Chs5 and Arf1 initiate the complex formation. (2) Chs6 recruitment promotes assembly of the exomer intermediate. (3) Bch1 enhances stabilization of the exomer tetramer at the TGN membrane. (4) Arf1, exomer tetramer and the cargoes act together as the primer for the exomer coat mediated vesicle budding.
E) Immunofluorescence for KRT20 (green) in human colon organoids cultured in basic medium and either non-infected (left) or 48 h after SARS-CoV-2 infection (right), indicating a strong increase in KRT20 expression after viral infection. Scale bar: 50 µm. Quantification of fluorescence intensity below (n=8). Data are presented as mean +/- SD ,****: p≤0.0001, as determined by Student's t-test
E. Relative mRNA levels of flagellar genes in Ec-K74A-K87A strain comparing with that in Ec-WT (normalized to 1 for each gene). Diagram for the role of σ28 (fliA gene) in flagella regulon hierarchy Clarke & Sperandio, 2005Fitzgerald, 2014(; ) is shown in the left panel. Data are mean ± SEM from three replicates.
(B) Western blot analysis of the unbound soluble fraction An untreated input of each cell line is included for comparison.
(E) RAW264.7 cells were transfected with Myc-tagged Ago2 in the presence of miR-342-3p mimic or scramble for 24 hours. Immunoprecipitation was performed with Myc-antibody or IgG, and Socs6 mRNA was detected by qRT-PCR. Data are shown as the mean ± s.e.m. of n = 3 biological replicates.
(e) Immunoblot analysis of LC3-I and LC3-II in or wild-type, ASC-deficient (Pycard-/-; called 'Asc-/-' here) or caspase-1-deficient (Casp1-/-) BMDMs primed with LPS (20 ng/ml) and then left untransfected or transfected with poly(dA:dT) or left untreated or treated with nigericin for 4 h; numbers below lanes as in d. Actin serves as a loading control throughout. NS, not significant; *P 0.05 and **P 0.01 (unpaired t-test). Data are from three individual experiments
pat1 is more resistant to colonization by P. syringae pv. tomato DC3000. Bacteria were syringe‐infiltrated and samples taken 3 days post‐infiltration. Data are shown as log10‐transformed colony‐forming units/cm2 leaf tissue (cfu/cm2). Standard error of the mean is indicated by errors bars (n = 4). Statistical significance between the mean values was determined by ANOVA followed by Fisher′s LSD test.
(F) Representative images of Ki-67 immunofluorescent staining of chromosome spreads from control (Ctr) and DIA treated P/A synchronised B1dd/B2ko cells and quantification of Ki-67 staining intensity using cross-sections of chromosomes
(D) Visualization of selected top gene ontology (GO) enrichment terms of astrocyte clusters based on DEG analysis.
C. Quantification of the nociceptive responses in mice within 5 min after intraplantar injection of control saline or 500 ppm iodine, following the intraperitoneal injection of HC030031 (HC) (C) or vehicle.
A A schematic drawing of the hypothesis that astrocytes perform phagocytosis on behalf of phagocytosis-deficient microglia.
(B) A representative cell showing release of tethered EGFP. Scale bar represents 5 μm
G. Histograms of CMT orientation distributions in epidermal cells of the TZ and the EZ at time point 0 and 60 min after hormonal treatments as described above (C, E and F). n = 15-20 cells per root growth zone with 5-8 roots per condition in 4 independent replicates.
(A) Schematic overview of the experimental set up to isolate and identify acetylated histone peptides following UV irradiation. SILAC labeled cells are mock or UV (16 J/m2) treated one hour before harvesting. Heavy and light labelled cells are mixed in a 1:1 ratio followed by acid extraction to isolate histones. Histones are separated in 3 fractions each digested with either pepsin, trypsin or GluC. The limited digestion with trypsin is performed for 2, 10, 30 and 120 min. The different fractions of digested peptides are combined and followed by acetyl-lysine immunopurification. The acetylated-lysine enriched histone peptides are analyzed by LC-MS/MS
D, E. CDF plots of UPF3A/3B-independent (UPF3A/3B-indep., D) and -dependent (UPF3A/3B-dep., E) PTC+ isoforms and their respective PTC- isoforms. X-axis represents fold change upon UPF1 knockdown (siUPF1) versus negative control knockdown (siNC) in 3DKO#2 cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot.
A. Representative images of mice and body weight graph following the expression of mitochondrial ATPIF1H49K (days of doxycycline) (wt, n= 12; LowOXPHOS, n= 12).
(N) Expression levels of DEX responsive genes in normoxia and unique DEX responsive genes induced by hypoxia were measured in the liver of ADX mice after DEX stimulation during hypoxia (24h) via RT-qPCR. N=3-4 per group, one experiment. Data information: All bars represent mean ± SEM. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. ****P<0.0001, ***P<0.001, **P<0.01, *P≤0.05.
Performance in the Rotarod test of ASMko and wt mice treated or not with Ca074Me for 1 month expressed as mean ± SEM time of the four trials (C)
Boxplot showing Lamin DamID-seq signals of piRNA target or non-target TEs upon EGFP (control)- or Nxf2-KD. Boxplot whiskers, box, and central band show maximum, third quartile, median, first quartile, and minimum, respectively (n=10 for piRNA target TEs, n= 80 for non-piRNA target TEs). P-values were calculated using the Wilcoxon rank-sum test.
D. Parental HEK293T, S2/3 dKO1 and HOM1 cells were treated with Activin A for the indicated times. Data information: ns, not significant; *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001. The p-values are from two-way ANOVA with Dunnett's post-hoc test. In D quantifications are from a representative experiment and are the intensities of pSMAD1/5 normalized to Actin, expressed as fold change relative to untreated cells for each clone. In all panels, Western blots of whole cell lysates were probed with the antibodies indicated.
(C) Acetylated α-tubulin levels in cell lines (n=3). Data are presented as means + SEM; Student's unpaired t-test and ANOVA with Tukey or Dunnet's post hoc test: *p<0.05, **p<0.01, NS= no significance.
CRH-Cre male mice received stereotaxic delivery of AAV-EF1a-DIO-Kir2.1-P2A-dTomato or control AAV-Flex-mCherry vectors at 7-8 weeks of age and were maintained on chow diet for 7 weeks before switching to HFD. Weekly body weight gain after viral delivery (A, *p<0.0001, unpaired Student's t test), at 15 weeks after viral delivery.
I-L X-Gal and H&amp;amp;E staining of artificial muscle sections at 4 (I, K) and 8 weeks (J, L) after implantation, showing donor origin of muscle cells (nLacZ+ nuclei) and correlation between implant duration and myofibre maturation (I, J images are the results of the collage of several photos). Scale bar: (I, J) 200 μm, (K, L) 100 μm.
F Immunohistochemistry staining of αSMA in TGFβ-treated HFL1fibroblasts ± the IRE1α inhibitor 4μ8C. Scale bars = 20μm.
(G) Exophers may remain connected to the sending BWM cells via thin elastic tubes that allow further transfer of cellular material. Arrows: white - exopher, blue - muscle cell, red - cellular material transferred to exopher via elastic tube.
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.
Rose plots indicating the number of all detected and differently expressed tissues-enhanced proteins in mild (left) and severe patients (right) compared with healthy controls. Tissues labeled in orange represented tissues with the largest proportions (100% of all detected tissue-enhanced proteins) of altered tissues-enhanced proteins.
F. Sagittal paraffin sections of brains from P18 FBXO7+/+ and FBXO7-/- mice were subjected to immunohistochemistry using the GFAP antibody. Five independent litter pairs were analyzed (paired t-test, * p<0.05, mean +s.e.m.). Scale bar = 40 µm.
(a) Ingenuity analysis of genes differentially expressed between KRas;Atg5fl/+ and KRas;Atg5fl/fl pneumocytes determined by RNAseq (set selection using DESeq with adjP0.05, fold-change>2 cutoffs). Biological functions overrepresented in the differentially expressed gene sets are shown with the respective Bonferroni-Hochberg P-value indicating enrichment significance.
(F) HEK 293 cells were transfected with the indicated siRNAs. After 48 h, the cells were re-transfected with EGFP tagged TFEB-WT or TFEB-R245-247A, along with LAMP1- RFP for 24 h. Then the cells were incubated with Torin-1 (250 nM) for 1 h, Earle's Balanced Salt Solution (starvation) for 2 h or incubated with both. Cells were fixed and visualized using confocal microscopy. Regions within the dotted boxes are magnified in the insets. Scale bar, 5 μm.
(B,C) HEK293T cells were co‐transfected with the indicated constructs. Cell lysates were subjected to IP using anti‐FLAG antibodies. The resulting precipitates were examined by immunoblot analysis with anti‐FLAG and anti‐HA antibodies.
Cultured hippocampal neurons were infected at 14 DIV with lentivirus for expression of both shRNA against PSD-95 (sh95) and sh-resistant PSD-95-EGFP. Thus endogenous PSD-95 was replaced with either wild-type (WT), E17R, or T19K PSD-95. Cultures were treated with or without BIC (50 μM) at 17 DIV for 24-48 h or left untreated before fixation and staining for surface GluA1. (A) Representative confocal microscopic images of PSD-95-EGFP fluorescence (green) and surface GluA1 immunostaining (red) at low (top panels; scale bar: 20 µm) and high enlargement (bottom panels; scale bar: 5 µm).
F) Western blot analysis of brain lysates from female APP/PS1 and APP/PS1 PD-1-/- mice for the expression of APP and APP C-terminal fragments using antibodies 6E10 (transgene expression) and CT15 (transgene and endogenous expression). Tubulin was used as a loading control.
(B-C) Representative confocal image (low magnification) of brain slices from R6/2 mice ip injected with g7-NPs-NBD-Chol and sacrificed after 24 hrs (B) or 2 weeks (C) and relative co-localization of NBD-Chol and g7-NPs. Scale bar: 10 m (D) g7-NPs quantification in brain slices at the same time points in (B-C). DAPI was used to counterstain nuclei. Data in (D) are expressed as number of g7-NPs (evaluated based their size) for 100 m2 sem. Statistics: **P<0,01 (48 hrs vs 7 days; 7 days vs 14 days), ***P<0,001 (24 hrs vs 7 days; 7 days vs 14 days) determined by one-way ANOVA followed by Newmann-Keuls multiple comparison test.
Average relative intensities of a line‐scan FRAP experiment on Swi6‐EGFP in heterochromatin (blue line), euchromatin (green line), and clr4∆ (red line). The curves have a gliding average of 40.
Comparison of regions annotated "LTR" in RepeatMasker with the regions annotated TssA, TssAFlnk, Enh, EnhG, TssBiv, or EnhBiv in the 15 core marks model of the Epigenomic Roadmap consortium (referred to as PEs for Promoters and Enhancers). For each tissue, the Jaccard index comparing PEs to LTRs is divided by the average Jaccard index (1000 iterations) obtained when comparing PEs to randomly selected genomic locations (of the same sizes as the LTRs). Only the 10 tissues with the highest and the lowest score are shown. Full list in Appendix Figure S1A.
Schematic depicting the pleiotropic role of AosR. Oxidative environment induces disulfide bond formation in AosR and transcription of mec-cysO-cysM through an auxiliary promoter resulting in enhanced L-cysteine biosynthesis. This further induces genome-wide transcriptome changes. The latter set of changes in indirectly regulated genes can be mitigated by the addition of L-cysteine in the media.
C. DCCmut/mut mouse with splenomegaly and systemic lymphadenopathy. Left panel: black and white arrows indicate respectively the inguinal and mesenteric lymph nodes. Right panel: enlarged spleen in a lymphoma-bearing mutant mouse (left) as compared to control organ (right).
D and E. Body weights were lost earlier both in male (D) and female (E) of SOD1G85R/ Sig1R−/−mice. Data are shown as mean ± SD. *: p < 0.05 in SOD1G85R/Sig1R+/+ vs. SOD1G85R/Sig1R−/−, †: p < 0.05 in SOD1G85R/Sig1R+/− vs. SOD1G85R/Sig1R−/−. n = 8 (SOD1G85R/Sig1R+/+), 13 (SOD1G85R/Sig1R+/−), 8 (SOD1G85R/Sig1R−/−) in male (D), and n = 6 (SOD1G85R/Sig1R+/+), 16 (SOD1G85R/Sig1R+/−), 9 (SOD1G85R/Sig1R−/−) in female (E). The used animals were the same in the panels B and C. The animals used in the panels D and E were the same in the panels B and C. *: p < 0.05 in SOD1G85R/Sig1R+/+ vs. SOD1G85R/Sig1R−/−, †: p < 0.05 in SOD1G85R/Sig1R+/− vs. SOD1G85R/Sig1R−/−. Two-way ANOVA with subsequent post hoc Tukey's test.
C. Prognostic parameters in ACC patients. Results are presented as hazard ratios (HR) including 95% confidence interval (CI). The significance level was set at α=5% for all comparisons. The results for SF-1, FATE1 and combined SF-1/FATE1 expression levels are shown both in univariate and mutivariate (adjusted for age, sex and ENSAT tumour stage) analysis.
(k) Western blot analysis of GFP and alpha-tubulin (control) in cells transfected with MS2-GFP or LINE-1-MS2 and MS2-GFP and treated with control or Bafilomycin (2 h, 400 nM). All error bars represent s.e. of the mean. All experiments were replicated a minimum of three times.
(J) EGFP-DFCP1-expressing PPM1D+/+MEFs were treated with etoposide (10 µM) for the indicated times, followed by immunostaining with an anti-Ulk1 antibody. Representative images of EGFP-DFCP1 (green; left), anti-Ulk1 (red; center), and a merged image (right) are shown. The nuclei were stained with Hoechst 33342 in the merged image. A magnified image of the area within the dashed square is also shown. Arrowheads indicate DFCP1 puncta localized close to Ulk1 puncta.
Pyridostatin (PDS) was administered intravenously (i.v.; 7.5 mg/kg/day), NU-7441 was administered intraperitoneally (i.p.; 10 mg/kg/day), over the indicated periods of time, and paclitaxel (PACLI) was administered intravenously (i.v.; 20 mg/kg/day) on indicated single days. Vertical dashed line indicates end of treatment. Tumour volume was measured at the timepoints shown on the graph and expressed relative to tumour volume at the beginning of treatment. Each experimental group included n = 6 mice. Error bars represent SEM. P values were calculated at day 36 or 38 using an unpaired two-tailed t-test ****, P ≤ 0.0001.
F Correlation of protein fold changes in KO in respect to WT hepatocytes under basal condition and upon HBSS (2 h). Only genes previously found in CLUH RIP experiments in HeLa cells (Gao et al., 2014) are plotted. Inset shows magnification of upper part of the graph.
(C) HeLa cells were transfected with pEGFP-LC3 for 20 hr and incubated for 4 hr at 37°C or 18°C.
(F) Viability of spheroids was quantified by measuring intracellular ATP concentrations. Note that no significant (n.s.; Student's t-test) decrease in cell viability was observed for any concentration tested (n=10).
d. Colocalization patterns of Sst subtypes with CA1 and CA3 subtypes. Sst subtypes that colocalize with the CA1 subtypes have high transcriptional similarity. Colocalization was defined as the percent of neighbors that are of that subtype (Materials and Methods)
6-week-old male CD36 wild-type (WT) or knockout mice (CD36KO) were administered with AAV-GFP (Ctrl) or AAV-KLF10 (KLF10OE) through tail vein injection, and then kept on WD/CCl4 for 12 weeks. n=5 per group. (B) Representative immunofluorescence staining of KLF10 and CD36 (left), and the quantitative results (right). Data information: * P <0.05, ** P <0.01, *** P <0.001. Results are shown as mean ± SD. 1-way ANOVA
(A) Log2 fold changes of the levels of hsa-miR-let-7a, CoV2-miR-O7a.1 and COV2-miR-O7a.2 in DICER1 knockdown SARS-CoV-2-infected A549-ACE2 cells compared to control cells analyzed by stem-loop RT-qPCR. Results from three independent replicates are shown.
J IFA of DHHC2 expression in the dhhc2::6HA and dhhc2::6HA;∆isp1/3 zygotes. Scale bar = 5 μm.
E Quantified endogenous poly-ubiquitinated protein levels relative to actin control for each indicated lane for the blot in (B). ****P<0.0001, ANOVA with Dunnett's posthoc comparison to wild type. N=3 trials. Error bars indicate SEM.
H. Representative FACS readout of Annexin V/DAPI staining of PeTa cells after 6 days of 100 nM GSK-LSD1 DMSO treatment. I. Quantification of Annexin V/DAPI staining depicted in Fig 3H. n = 3 biological replicates. Data are represented as means ±SD. ****p<0.0001 (Early, Late, Total; unpaired Student's t-test).
(A) Schematic of protein degradation using AID and SMASh systems. The SMASh tag consists of the self-cleaving viral HCV NS3 protease fused in cis to a constitutive destabilising peptide. The tag detaches itself from the target protein in the off condition. Upon inhibition by the protease inhibitor, asunaprevir (Asv), the tag remains on the target protein and exposes it to the cellular degradation machinery, while the old protein is depleted depending on its specific half-life. The AID-tag relies on the expression of the plant F-box protein TIR1 that combines with mammalian Skp1 and Cul1 to form a functional SCF E3 ligase that is activated to ubiquitylate the AID degron tag upon stimulation by the hormone Auxin (IAA). In the case of the double tag combination newly synthesised proteins are depleted by the two independent degradation systems. Old proteins are destabilised by the mAID-tag (mini-AID).
(B) Coomassie-stained SDS-PAGE gel showing a salt-stability test of the (IFT88/52N)-(IFT-B2) interaction. Pre-assembled IFT-B2 complex was bound to IFT88/52N-GST immobilized on GSH-beads. The beads were then divided into five aliquots which were washed with buffers containing increasing concentrations of NaCl. After these washes the bound material was eluted and analyzed. IFT172ΔC is the only salt-labile component in this complex and is already washed off at a NaCl-concentration of 150-200 mM, whereas all the other IFT-B2 proteins remain associated even after washing with 1 M NaCl.
[b] Video monitoring and recording of generalised running/bouncing seizures in mice of the indicated genotypes from P15-P19. The point of death of Xrcc1Nes-Cre mice by fatal seizure is indicated (cross). Note no seizures from mice of other genotypes were detected. WT (n = 9 mice), Xrcc1Nes-cre (n = 3 mice), Parp1+/- /Xrcc1Nes-Cre (n = 3 mice), and Parp1-/-/Xrcc1Nes-Cre (n = 3).
(K) Female C57BL/6J mice were put in normoxia or hypoxia for 6h and injected i.p. with 5 mg RU486 or vehicle (DMSO). Liver was isolated and stress GRE gene expression was measured via RT-qPCR. N=5 per group, one experiment. Data information: All bars represent mean ± SEM. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. ****P<0.0001, ***P<0.001, **P<0.01, *P≤0.05.
(A) Schematic representation of the KB-AT-23 expression cassettes used to test the secretion signal peptides SSP1, SSP2, SSP3, SSP4 and SSP5. hAAT: human alpha-1 antitrypsin promoter; His: N-terminal 6X-Histidine tag; HA: C-terminal tag derived from the human influenza hemagglutinin; BGHpA: bovine growth hormone polyadenylation signal.
(E) Flow cytometric analysis of TFRC expression in intestinal epithelial cells (IECs) from wild-type (WT) and Otud1─/─ mice treated with AOM/DSS. MFI, mean fluorescence intensity. (n = 4 biological replicates, mean ± s.e.m., **P = 0.0062, two-tailed unpaired Student's t-test).
(C) Co-precipitation of TJP1 pre-mRNA in anti-hnRNPL RIPs, using nuclear lysates from control and NTRAS-silenced HUVECs (n = 6 independent biological replicates). Data information: data are represented as mean ± S.E.M. n.s.: non-significant, *p < 0.05, **p < 0.01. two-tailed paired t-test