EMBO/sd-character-level-ner huggingface dataset:
C-H Antibiotic-treated C57BL/6 male mice were transplanted with fecal microbiota from wildtype or Vil-Ogt KO mice and then induced with DSS for colitis (WT n = 5, KO n = 7) (H) RT-qPCR of inflammatory markers in the colon. (D: P = 0.0409; E: P = 0.0457; G: P = 0.032
Brightfield (BF), YFP and mCherry microscopy images for a co-existing dividing (high-flux) and a non-dividing (low-flux) TM6 cell expressing the flux sensor in 10g L-1 glucose minimal medium.
(C) Brains from w1118 and alix1 larvae were stained with anti-acetylated tubulin (green), anti-Cnn (white), anti-α-tubulin (red) and Hoechst (blue). Scale bars, 5 μm. The fluorescence intensities of acetylated MT, total MT and acetylated MT relative to total MT of 66 w1118 NBs and 65 alix1 NBs obtained from three independent experiments is shown graphically (±S.E), *p<0.05 and **p<0.01 (Student's t-test)
Expression levels (RT-qPCR) _of selected genes from panel A that are either strongly correlated with Alu RNA processing (left, r> 0.5) or only weakly/not correlated (right, r <0.5). Statistical significance (p value threshold 0.05) for anti-Alu greater than control (depicted as asterisk, n=3/group, unpaired directional t-test, error bars represent standard deviation from the mean). Pearson correlation co-efficient for each gene is depicted below the name of each gene.
(E). Relative expression of primary-let-7 family miRNAs as in (D) determined by qRT-PCR. Significance was assessed using 2‐tailed Student's t‐test, < 0.05*. Data information: All experiments were performed in triplicate. Error bars show SD.
(E-F) Effect of pairwise motif knockout (log2 scale) in core promoters CG7712 (E) and pain (F), respectively. The heatmaps display the mean expression fold changes compared to wild-type expressions for pairwise knockout of motifs compared to individual knockouts (diagonals). Additivity was calculated as the difference between the pairwise effect and the sum of two individual effects, Subadditive (in blue): > 0; superadditive (in yellow): < 0; Additivity values for effects > 3×SDnoise shown in the right lower corner of each pairwise effect.
BMPR1A overexpression rescues sphere formation ability reduced by HAND2-AS1 depletion in HCC samples. Representative sphere formation is shown on the left panel. Scale bar, 100 μm. Percentages of sphere-forming cells were calculated as means ± SD (right panel). n=4.
C Crystal structure of UBE2D2HTH (blue) aligned to UBE2SHTH (green, PDB: 1ZDN) (Ozkan et al, 2005; Sheng et al., 2012).
A Under basal conditions, Tau protein is involved in the maturation of newborn granule neurons in the DG. In the absence of Tau, newborn neuron dendritic arborization is transiently altered and PSD formation is impaired (decreased PSD density and area were found in the distal dendrites).B Acute stress decreased the survival of immature 1-week-old newborn granule neurons, an effect that is less pronounced in Tau-/- animals as compared to WT. Furthermore, acute stress also impairs dendritic branching and reduces PSD density and MFT area in 8-week-old fully mature newborn neurons of WT animals. In contrast, these effects are not observed in Tau-/- mice.C EE increases 8-week-old mature newborn neuron survival, dendritic branching, MFT area and PSD density in the proximal dendrites, and decreases PSD area in the distal dendrites of WT neurons. However, these effects are less pronounced or even inexistent in the absence of Tau. Actually, EE further reduces the density and area of the PSDs in Tau-/- distal dendrites.
(D) Western blotting of WT MEFs after the indicated FCCP treatments. The asterisk indicates non-specific bands of anti-Oma1 antibodies.
High ANCO1 levels are a good prognostic indicator in Basal Breast Cancer in patients. KM plot showing progression free survival in patients with stratified ANCO1 expression. n= 360 patients.
D Co-immunoprecipitation of EGFP-tagged E2F7/8 with CDH1-Flag after 48 hours of co-expression in 293T cells. Cells were treated with 10 µM MG132 for 5 hours prior to harvesting to limit immediate proteasomal degradation of E2F7/8 after binding to CDH1. Immunoblots are representative examples of three independent experiments. Asterisks indicate IgG bands; arrow indicates the CDH1-Flag band
C, D Western blot analysis of PPARγ protein levels in control and TRAF4 overexpressing cells in the absence or presence of MG132 or 3MA and quantification of protein levels normalized to β-actin expression.
(f) Kymographs of Scc1GFP-TEVcohesin and Scc1GFPcohesin bound to doubly tethered λ-DNA and washed with 750 mM NaCl buffer. TEV protease flow in released Scc1GFP-TEVbut not Scc1GFP from DNA.
A BAK-6H on liposomes was activated (+cBID, bottom) or not (Control, top) with cBID for 60 mins prior to deuteration for 10 s, 60 s, 600 s, or 3600 s. Incorporation of deuterium was assessed by mass spectrometry and is expressed relative to a non-deuterated sample and a theoretical maximum. HDX-MS reveals that following activation with cBID, maximal deuteration of the BAK N-terminus (up to amino acid 58) occurred within 10 secs.
(B) The number of cell lines having data for the 9 types of modalities that were analyzed in the study.
D Schematic diagram of TFIID-dominated genes UTH1 and ATP2. The TATA/promoter region and ORF are represented by black and white boxes, respectively. Lines and numbers below the genes show that the relative positions of the ChIP PCR products used in all later panels.
(E) Dissection of the PARylation region of KLF4 into three zinc finger motif-containing domains, Zinc 1, Zinc 2 and Zinc 3. While no effect was observed on Zinc 1 and Zinc 3 domains, deletion of Zinc 2 domain led to significant attenuation of KLF4 PARylation.
(E) Representative adult midgut from control esgReDDM at day 14 after temperature shift in variable demand. ECs renewed are marked positively by persistent RFP labelling (red-only cells). (F and G) Few ECs had been renewed in 'Low' midguts after 14 (F) and 21 (G) days of tracing. Data information: Scale bars, 50µm.
(C) Larval NSCs of control (ctrl; yw), pr-set7716/Df, pr-set7716/Df with UAS-pr-set7 induced with insc-Gal4, and pr-set7716/Df with pr-set7-BAC at 24h ALH were stained for H4K20me1, Dpn, Mira and DAPI. Control: n=108; pr-set7716/Df: n=87; pr-set7716/Df with UAS-pr-set7 induced with insc-Gal4: n=167 and pr-set7716/Df with pr-set7-BAC: n=104. Data information: White arrows point to NSCs. Scale bars, 5 μm
(B) In a similar experiment, the apical polarized localization of de novo made SynA, used as a control of conventional secretion, is shown to be abolished in all three strains where RabE, AP-1σ or ClaH are repressed. Scale bars: 5 μm. mCherry-SynA PM/cytosolic intensity ratios are plotted with values being 0.52±0.02 for wild-type, 0.14±0.02 for thiAp-rabE, 0.24±0.02 for thiAp-ap1σ and 0.16±0.02 for thiAp-claH. The statistical evaluation was performed as in (A). There is a significant difference (****P<0.0001) of mCherry-SynA fluorescence in the apical PM membrane between the wild-type and the three strains lacking the post-Golgi proteins. Biological/technical replicates: 2/15 for each strain.
(D) RT-qPCR analysis of Nppa transcript level after Cand2 KD and PE treatment of NRCMs. Analysed by One-way ANOVA. n=11-12 biological replicates per conditions. Data information: Error bars indicate means ± SEM; * - P ≤ 0.05, ** - P ≤ 0.01, *** - P ≤ 0.001, **** - P ≤ 0.0001
(I) Cand2 mRNA levels 2 days after TAC and after Torin1 injection measured by RT-qPCR. n=4-6 biological replicates per mice group. Data information: Error bars indicate means ± SEM
K. Raw264.7 cells were co-transfected with eGFP(N-term)-Rab10 (epifluorescence, shown in green) and Myc-mkate2(N-term)-EHBP1L1 or Myc-mkate2 control plasmid (epifluorescence, shown in red). Representative photomicrographs are shown. Bounding boxes highlight vesicles in "High Mag" panels. Scale bars represent 10 μm, and 1 μm for "High Mag" images. L. % of eGFP(N-term)-Rab10 vesicles positive with pT73-Rab10 were calculated (from 25 cells analyzed for each condition from n=3 biologically independent experiments). Each dot represents the mean frequency observed in one cell. Error bars show ± SEM with significance was assessed by Mann-Whitney test. *** represents P<0.0005.
C BMMΦ were stimulated with LP for 6 days, fixed and stained for immunofluorescence by p53 (red) and DAPI (blue) for microscopy with Olympus ScanR; scale bar, 50µm.
C. Total cell numbers (mean +SEM) of MOG-specific Th17 cells isolated from the spleen, shown in (B, upper row).Cells (A-D) were isolated at day 9 after MOG/CFA/PTx immunization. Data consist of n=5 mice of each genotype. *p < 0.05, **p < 0.01, N.S. - not significant; two-tailed unpaired t-test. Experiments were performed twice with similar results.
Selected candidate lipids were tested for their inhibitory activity on R837-induced (5 μg/ml; 18 h) cytokine secretion in BMDCs. Concentrations of indicated lipids: PECPC (10 μM), PEIPC (10 μM), OxPAPC (40 μg/ml), DPPC (40 μg/ml), POVPC (40 μM), PGPC (40 μM), and KOdiAPC (40 μM). Representative data (mean ± SD of triplicate determinations) from one of three independent experiments are shown. ****P < 0.0001; ns, not significant; as determined by one-way ANOVA adjusted by Sidak's multiple comparisons test.
Release of IL-6 and/or TNF release (ELISA) fro (D) murine BMDMs (n=6 Data information represent data (mean+SEM) combined from 'n' (given in brackets for each panel) technical or biological replicate mic * p<0.05 according to Wilcoxon signed rank sum (C, D
D. Summary of microscopy analysis of ER-resident proteins co-localization with GFP-Snc1-PEM in cells overexpressing GFP-Snc1-PEM: WT (PEP4PRB1) vs pep4Δ prb1Δ (left), and ypt1-1PEP4PRB1 vs ypt1-1pep4Δ prb1Δ (right). Microscopy and quantification are shown in Fig 7A and 7C and S7 Fig. In YPT1 cells, whereas >60% of Hmg1 and Sec61 (green) co-localize with Snc1-PEM in strains defective in vacuolar proteolysis, Sec12, Sec13 and Kar2 are not changed significantly (blue and grey). Hmg1 and Sec61 (green) co-localize with Snc1-PEM in >70% of ypt1-1 and >80% of ypt1-1pep4Δ prb1Δ mutant cells, whereas Sec13 and Kar2 (blue and grey) do so in <15% of the cells. The level of Sec12 co-localization with Snc1-PEM is intermediate, ~38% in ypt1-1 and ypt1-1pep4Δ prb1Δ. Error bars represent STDEV. Results in panels A and B represent at least two independent experiments.
(A+B) CD31 staining for endothelial cells revealed increased tumor vascularization in mice bearing human EGFL7 (hE7)- or murine EGFL7 (mE7)-positive tumors (n = 3; one-way ANOVA)
(d) Cells were transfected with either control siRNA or with siRNA specific to MFN1/MFN2, IRGM or IRGM and MFN1/MFN2, and then labelled with MTR and analysed for mitochondrial morphologies. Data are means ± s.e.m. (c, n = 3; d, n = 4). Asterisk indicates P 0.05, double asterisks indicate P 0.01 and dagger indicates P > 0.05 (t-test).
(D). Identification of amino acid stretch 411- 441 on the Zinc 2 domain of KLF4 involved in mediating its PARylation modification in 293T cells.. PARylation for Flag tagged KLF4 deletion mutants were analyzed, respectively, by pulldown using PAR antibody followed by Western blotting using antibody against Flag.
Ub-KG(TAMRA) cleavage assay monitoring the effects of structure-guided wMelOTU mutations. These data were collected in parallel with those presented in Fig. 1G and the WT dataset is shown again for reference.
E. Sequence conservation of the 29 amino acid small protein, VcdP, in different Vibrio species.
Mice were infected with sub-lethal dose (25 pfu) of influenza virus and assessed as follows (E) Level of LDH in BAL, by LDH cytotoxicity assay Data information: Data are representative of three independent experiments with 3-5 mice per group and represented as mean ± S.E.M
Ultrastructural analysis of HSA-Cre EDL muscles revealed the presence of numerous autophagic vacuoles of different morphologies (autophagosomes and lysosomes, black arrows; multilamellar bodies, white arrow) containing amorphous material and possibly degraded mitochondria (M). Scale bars: 0.50 μm
(D) Western Blot analysis of hepatic CREBH and HRD1 protein levels in WT and HRD1 LKO mice. The mice were fasted 16 hours and refed for another 4 hours.
H, Number of pups delivered by Rb1d/d dams was normalized by pre-implantation P4 treatment on days 2 and 3 (Group 2)(mean ± SEM, Student's t test). The same data of Rb1f/f and Rb1d/d dams without P4 treatment in Fig 1E were used. The numbers of pups in 20 Rb1f/f and 37 Rb1d/d dams without P4 treatment and 7 Rb1d/d dams with P4 treatment were evaluated.
C. The in vitro synthesized [35S]Met-labeled Bax E69C protein with or without the additional mutations (G108E and/or S184V) were activated by the in vitro synthesized [35S]Met-labeled tBid L105C protein and targeted to the Bax-/-/Bak-/- mitochondria that were pretreated with NEM. The resulting mitochondria were isolated and oxidized by CuPhe for 0 or 30 min. The resulting "0 min" samples (1 equivalent each) and "30 min" samples (1 equivalent each) were analyzed by non-reducing SDS-PAGE and phosphor-imaging. The remaining "30 min" samples (4 equivalent each) were immunoprecipitated (IP) by either Bax- or tBid-specific antibody, and then analyzed by non-reducing SDS-PAGE and phosphor-imaging. The identities of the four major products, indicated on the right side of the image, were based on their Mr and recognition by the respective antibody. n = 2.
Similar experiment comparing the impact of RNAi inactivation of lrr-1, tim-1 and tipn-1 upon CMG-MCM-7 ubiquitylation and the association of CUL-2LRR-1 with the worm replisome. Asterisks indicate non-specific bands in the immunoblots.
(A, B, C) Confocal image of a Tm1eg9 homozygous egg-chamber expressing EmGFP-Tm1-I (green) and Khc-mKate2 (magenta). oskar mRNA labelled with osk1-5 FIT probes(Hovelmann et al., 2014) is in yellow.(B', C') oskar mRNPs co-localizing with both EmGFP-Tm1-I and Khc-mKate2. Colors indicate the maximal co-localization distance (C'). Panels B-C' represent the boxed regions in panel A.
(H) Representative western blots showing HTT (ab-MAB5492) and HTT pS13 (ab-CHDI-90001039-1) from the detergent soluble fraction and HTT aggregates (ab-MAB5492) from the detergent insoluble fraction in TBK1 orthologue (ikke-1 or unc-51) RNAi-treated C. elegans lines expressing HTT N513 Q15 and HTT N513 Q128. (I) Quantification of the fold change in the ratio of pS13 HTT to total HTT compared to non-targeting RNAi from the experiments like in H (n=4).
a, b) Agreement plot. Red = differentially expressed (DE) in febrile infants, blue = DE in afebrile infants, purple =DE in febrile and afebrile infants.
F. Heatmap analysis of FOXM1 downstream targets between SATB2 silencing H2S GSCs (shSATB2) and control H2S GSCs (shNT) from microarray analysis. Differentially expressed genes had a 1.5-fold or greater expression difference.
(a) Cells were transfected with control siRNA or with siRNA specific to IRGM (top) and DRP1 (bottom) for 48 h and protein samples from these cells were then analysed by immunoblotting with anti-IRGM and anti-DRP1 antibodies. Actin was used as a loading control.
Glucose uptake of L6 cells with insulin stimulation (10 nM or 100 nM, 20 min) after iron treatment (250 µM, 1 h or 24 h).
D Immunoblotting of protein markers of tight junction (ZO-1), adherens junction (β-CATENIN, α-E-CATENIN and PLAKOGLOBIN), and desmosome (PLAKOGLOBIN and DESMOPLAKIN) in colon E Densitometric analysis of Plakoglobin protein levels in (D) (WT n = 6, KO n = 5, P = 0.021)
I, J Micrographs of IF for GFP and E-cadherin (I) and GFP and SMA (J) counterstained with DAPI of MM134 glands 1 month after intraductal injection of NSG:EGFP+ mice, n=4. Scale bars, 50 μm.
(C) p-H3 staining analysis of KLF4+/+, KLF4-/- MEFs, KLF4-/- MEF with transfection of wild-type or KLF4-Zinc 2-YYR/AAA mutation. n=4, p values were labeled in figure, one-way ANOVA assay.
A Birthdating of adult-born neurons prior to recombination was conducted in 24-week old mice. For marker expression analysis, BrdU was injected i.p. every 24 hours for three days (B and C); for morphology analysis, CAG-RFP was stereotactically injected into the DG (D-G). Tamoxifen was applied i.p. every 12 hours for five days. Mice were sacrificed 3dpT and 13dpT.
(C) Immunofluorescence analysis of the old APPPS1 tissue cultured alone or in co-culture with young WT brain slices (14 DIV) and immunostained with CD68 (red), Ki67 (green) and M3.2 (blue) Scale bar: 50 µm.(D) Quantitative analysis of Ki67 and CD68 double positive microglial cells in the old APPPS1 tissue cultured alone or in co-culture with young brain slices (14 DIV) reveals increased microglial proliferation upon co-culturing of old and young brain slices. The values are expressed as percentages of CD68 and Ki67 double positive microglial cells from the total number of CD68 positive cells and represent mean ± SEM from 3 independent experiments, each experiment including 2 independent slice culture dishes (**P < 0.01).
(C) Boxplots depicting block 1 effects for tested core promoters. Effects of different block 7s were merged in each column (within the same block 1): the median SD is 0.66 for developmental promoters compared to 1.23 for constitutive promoters (lower right corner); Wilcoxon rank-sum test ***p = 3.1×10-4, significant. The middle hinge represents the median. The Interquartile range the difference between the 75th and 25th percentiles. Individual points represent values over 1.5 times the interquartile range. 3-4 biological replicate measurements. (D) Boxplots depicting block 7 effects for tested core promoters. Effects of different block 1s were merged in each column (within the same block 7): the median SD is 0.54 for developmental promoters compared to 0.64 for constitutive promoters (lower right corner); Wilcoxon rank-sum test p = 0.3, not significant. Block 7 with column "w/o B7" represents the results obtained from promoters without block 7 sequence. Developmental and constitutive promoters are highlighted in green and red, respectively. The middle hinge represents the median. The Interquartile range the difference between the 75th and 25th percentiles. Individual points represent values over 1.5 times the interquartile range. 3-4 biological replicate measurements.
B. The ability of the Myc share in predicting the transcriptional outcome can be represented in terms of a Receiver operating characteristic (ROC) curve, which represents the Sensitivity (true positive rate) and Specificity (true negative rate) of a predictor (i.e. Myc share) in discriminating between two classes (i.e. up- and down-regulated genes), using different thresholds. The largest the area under the curve (AUC), the largest is the predictive power, in a scale from 0.5 (random classification: grey line) to 1 (perfect predictor). For each system, the dot corresponds to the variation of Myc at which promoters begin increasing their share of Myc binding.
(F) Normalized expression (based on FPKM from RNA-seq) of genes identified by RNA-seq to be uniquely changed in FusΔNLS/ΔNLS mice (Trove2, Uhmk1, Ssh3, Vtn, Snrpb, Ephb3). Error bars represent SEM in 4-5 biological replicates.
TEM analysis of HeLa cells treated with DMSO or MG132. Note the layered structures (red arrowheads) in the mitochondrial matrix (ii, iii), budding from mitochondria (iv), attached to mitochondria (v-vi), away from mitochondria (vii) or inside the MAPAs (viii, ix) in MG132-treated cells. Scale bar=500 nm. M, mitochondrion. N, nucleus.
(A) Western blot of soluble HTT (ab-MAB5492), HTT pS13 (ab-CHDI-90001039-1) and HTT aggregates (ab-MAB5492), upon coexpression of the HTTex1 72Q eGFP or HTTex1 72Q eGFP S13A/S16A variant with TBK1 KD, TBK1 or TBK1 Δ690-713 for 48 hour in HEK293 cells. (B) The graph indicates the calculated fold changes in HTT, HTT pS13 ratio to total HTT and HTT aggregates all compared to the levels in TBK1 KD from the experiments like in A (bottom panel normalized to Tubulin, n=3).
H. Coomassie-stained SDS-PAGE gel of purified proteins. I. The amount of co-purifying iron in purified proteins in (H) was measured by inductively coupled plasma mass spectrometry (ICP-MS). Data are shown as means ± SD of three biological replicates. P=0.032 (Welch Two Sample t-test).
(A) UASp-GFP-mCherry-DrAtg8a/+;nosGAL4/+ flies conditioned on yeast paste had diffuse GFP-mCherry-DrAtg8a staining in midstage egg chambers. (B) Nondegenerating midstage egg chambers from starved flies contained autophagosomes (yellow) and autolysosomes (red). (C and D) Egg chambers early in the degeneration process showed follicle cells that take up portions of the nurse cell cytoplasm (C) followed by condensation and fragmentation of the nurse cell nuclei and further uptake of the nurse cell cytoplasm into follicle cells (D). (E) Late stage degenerating egg chambers lose all GFP staining and fluoresce red.
Immunoblots from cells treated with indicated drugs for 24 hours (left) with densitometric quantification normalized with β-actin (right).
(C) Volcano plot of differential gene expression between p53-/-;MDMXSG/SG and p53-/-;MDMXwt/wt MEF lines.
E. miR-10b mimic regulates 5'UTR Luciferase reporters of some splicing factors genes bearing wild type (WT), but not mutated (Mut) miR-10b binding sites. Statistical significance of the differences was determined by Student's t test, with p-values < 0.05 indicated by asterisks, p < 0.01 by two asterisks, and p< 0.001 by three asterisks. Numbers of replicates and exact P-values are included in Appendix Table S4.
A. Experimental scheme for B-G. Whole-cell patch-clamp recordings were made from neurons in CA1 of organotypic hippocampal slices treated with inactive control, GSK3α or GSK3β inhibitor, or AR-18 (all at 10 µM). EPSCs were elicited with CA3 Schaffer collateral stimulation, and low-frequency stimulation (LFS) was used to induce LTD. For inactive control, GSK3α and GSK3β inhibitor compounds, the experiment was performed blind with respect to treatment group.
(B) Proteasome activity was measured in treated and control untreated WT neurons using pZsProSensor-1 vector (green). Cells were co-stained with anti SMI-32 (blu). Proteasome activity was quantified by measuring the green fluorescence (inversely correlated with proteasome activity) in 10 different cells (taken from 4-5 coverslips for each group) and expressed as fold to WT.
Single IHC exhibits different modes of Ca2+-control of release. The overlaid ΔF image of Rhod-FF (red) and iGluSnFR (green) shows synaptic Ca2+-influx and glutamate release at three neighboring modiolar synapses (individual synapses are color coded based on their clusters). E' The relation between Ca2+-influx and glutamate release of given synapses in the voltage range of -57 to -17 mV plotted with 1 mV increments. A power function was fitted until the 25% of normalized iGluSnFR AUC(ΔF/F0). Synapses showed different Ca2+-dependencies (m = 2.0, 1.3, 7.4; green, purple, orange). '' Dynamic ranges of corresponding Ca2+-influx (gray) and glutamate release (color-coded) with V1/2 depicted. Note that the synapses from cluster 1 (purple), employing Ca2+-nanodomain-like control of release (m = 1.3), exhibit wider dynamic range than the other synapses. Mean glutamate release (iGluSnFR-AUC) as a function of depolarization voltage in the three identified clusters (mean ± SEM, Cluster 1: n = 27 synapses, Cluster 2: n = 22 synapses, Cluster 3: n = 6 synapses). The Ca2+-cooperativity (m) (G) show differences for the three clusters. Cluster 1 is composed of linear synapses with wider dynamic range and lower threshold compared to the other clusters. Pillar synapses are depicted as white-filled circles, and modiolar ones are depicted as gray-filled circles. Box plots indicate first quartile (25th percentile), median and third quartile (75th percentile) with whiskers reaching from 10-90%. The clusters were compared
MCF10A cells were plated on slides pre-coated with laminin. Cells were treated for 60 minutes with either EtOH, DMSO, 25uM 4HNE, 5uM RSL3, 4HNE and 10uM KRIBB1 or RSL3 and KRIBB11. Cells were stained for total HSF1 and counterstained with DAPI. Images were taken at 20x magnification. Scale bar is 50 microns. Shown is one replicate of three independent experiments (n=3).