EMBO/sd-character-level-ner huggingface dataset:
Quantification of Vegfr3Luc emission in the , liver and lung of mice in experiment (I), respectively. N= 4 mice per condition. Statistical significance was determined by Two-Way-ANOVA.
B Luciferase reporter assays using direct FXR target inflammatory gene promoters (n = 3-6).
E. Detection of purified recombinant InlK protein with rabbit polyclonal anti-live Listeria antibody, rabbit polyclonal anti-killed Listeria antibody, rabbit polyclonal anti-InlK and a rabbit pre-immune serum. InlK was detected only with the rabbit polyclonal anti-live Listeria antibody indicating that it is expressed during the in vivo infectious process. BSA was used as control protein. Two different amounts of proteins were tested (500 ng and 200 ng) to access signal specificity.
A Extracellular flux analysis by measuring oxygen consumption rate (OCR) (left panel) and extracellular acidification rate (ECAR) (right panel) in LNCaP cells indicates that SDHA/SDHB silencing increased both activities compared to ENZA alone.
C. Ccdc108 interacts with IFT proteins. Interactions were further determined by coimmunoprecipitation of endogenous IFT proteins from HEK293T cells with GFP-Trap agarose beads.
(A) Representative images of E16.5 coronal brain sections immune stained for Tbr2 and BrdU. BrdU was injected intraperitoneally into pregnant mice at E16.5 for 2h of pulse labeling. Scale bar represents 20 μm. (B) Statistics of TBR2+ cells per 100μm2 surface of VZ/SVZ. The number of TBR2+ cells increased significantly in KO mice compared to WT mice. n=6 mice, independent replicates. (C) Statistics of BrdU+ cells per 100μm2 surface of VZ/SVZ. The number of BrdU+ cells increased significantly in KO mice compared to WT mice. n=6 mice, independent replicates. Date information: Representative images from at least three independent experiments. Error bars represent the means ± S.E.M.; Two-tailed unpaired t-test, P < 0.05(*). n.s., not significant.
A. Bacterial pull-down of purified GST-MVP with the L. monocytogenes strains WT+pPRT-empty, ΔinlK+pPRT-empty, ΔinlK+pPRT-inlK and WT+pPRT-inlJ. GST-MVP bound to InlK over-expressing bacteria (ΔinlK+pPRT-inlK) but not to other bacteria. GST-ScarA was used as control of the specificity of the MVP precipitation by InlK over-expressing bacteria.
Tofacitinib (n=6) or vehicle (n=7) was given orally to GRdim/dim mice. After 1.5 mg/kg LPS injection survival was monitored and p-values were analyzed with a Fisher's exact test.
C. RNA DIP-seq peak heights in wild type and primpol BOBSC cells normalised to a DT40 spike-in. n (wild type) = 32740; n (primpol) = 33721. D. Correlation of normalised RNA DIP-seq peak heights in the overlapping peaks between wild type and primpol. Blue line = 1:1 correlation; red line = linear regression through data. 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).
A PTAR1 protein expression in rat tissues. Proteins extracted from various rat tissues (15 μg each) were analyzed by immunoblotting with antibodies against PTAR1.
(G) RPE-1 hTERT p53-/- Cas9 parental (WT) and RAP80-/- cells were untreated (t=0 h) or irradiated with a 10 Gy dose. Samples were collected at the indicated time points, processed for immunofluorescence and stained with antibodies against BRCA1 and γH2AX. Shown is the percentage of cells with > 5 BRCA1 foci. A minimum of 100 cells per replicate were analyzed and the datapoints represent the mean ± S.D. (n=3 biological replicates). All scale bars are 5 μm.
A. Lysates of indicated tissues isolated from P30 rat were immunoblotted with the FBXO7 and γ-tubulin antibodies. The latter served as loading control.
F. Glucose tolerance test of male mice with indicated genotypes after 16 weeks in HFD. n=10.
E. Effect of an anti-RBD antibody on S1 subunit stimulated changes in the expression of cytokines in PBMCs. Left, a schematic showing the domain structure of S1 spike protein and anti-RBD antibody. Right, changes in cytokine gene expression in response to S1 spike protein in the presence or abscene of anti-RBD antibody. Gene expression was measured by qPCR. Cytokine release in the conditioned media was measured by Luminex. Full-length S1 and S1 subunits are purified from HEK293 cells. Data information, data are shown as the mean of three technical replicates; in (D), data are shown as the mean of 20 individual donors. Error bars denote SEM. ∗p < 0.05, ∗∗p < 0.01, Multiple t-test.
I Representative BrM-PDOC stained with proliferation markers (BrdU) and markers of the microenvironment (GFAP for astrocytes, Iba1 for microglia/ macrophages). Scale bar: 50 µm.
(A) Histogram representing CD86 expression in 5.2+ vs 5.1+ pDC isolated from indicated MCMV-infected MBMC; grey, 5.2+ and 5.1+ pDC from CTR MBMC; red, 5.2+ Ifnar1-/- pDC isolated from Ifnar1-TST MBMC; purple, 5.1+ WT pDC isolated from Ifnar1-TST MBMC. Dotted line shows isotype control staining. One histogram representative of 6 animals from 3 independent experiments is shown.
Diagram of mtDNA illustrating the binding site for two monomeric mitoTev-TALEs (8.5 and 11.5 RVDs) designed to target the m.8344 A>G in the tRNALys gene. The two mitoTev-TALEs differ in the number of RVDs. The A:T base pair at position T0 is shown in green and the G:C discriminatory base pair in red. The I-TevI endonuclease domain targets a 5'CNNNG3' sequence, in this case 5'CACTG3' shown in green which is spaced by 12 bp from the TALE-DNA binding site
(d) p85β (QR/AA) is more stable than wild-type p85β. HEK293T cells were infected with either a retrovirus expressing wild-type p85β or p85β (QR/AA). Cells were incubated with cycloheximide (CHX) for the indicated times, collected and analysed by immunoblotting as indicated. In the graph, the amount of p85β (wild-type or mutant) is represented relative to the amount at time 0.
G The indicated concentration of recombinantly expressed GST‐tagged Twi1p in which aspartic acid 526 was replaced by asparagine (GST‐Twi1p‐D526N) or GST alone was incubated with radiolabeled double‐stranded 27‐nt RNAs. Loaded RNA was analyzed by immunoprecipitatingGST‐Twi1p‐D526N with an anti‐Twi1p antibody and separating on a native gel, followed by autoradiography detection. The positions of double‐stranded 27‐nt RNAs (dsRNA) and each strand of RNA used to form the 27‐nt RNA duplex (ssRNA1 and ssRNA2) are indicated at the right.
A,B. The ACE-box elements in the promoter of tomato FER gene and oligonucleotides were used in electrophoretic mobility shift assays. Numbering is from predicted transcriptional start sites. The FER probe contained one ACE-box (FER-wt), whereas in the FER-mut probe the ACE-box core sequence was mutated. The wild type (WT) and mutated ACE-box sequences are underlined. The mutated bases were indicated in red.
D Schematic of the reporter constructed to assay protection of the fusion transcript, consistent with the color scheme in (B). Spliced sequences are indicated with chevrons (see Appendix Fig S3 for alignments). Bright pink indicates the AdML major-late intron used in place of the long intron between J and the first Cγ IGH exon. Only exons encoding secreted IgH were used.
[Ca2+]i changes in individual BMDMs were measured (A) using fura-2 during frustrated phagocytosis (n = 46-113) and (B) by dropping beads onto adherent cells loaded with Calbryte 520 (n = 64-159), in 1.8 mM extracellular Ca2+ (+Ca2+o) or Ca2+-free medium containing 100 μM EGTA (-Ca2+o) with or without prior loading with 25 μM EGTA/AM or 25 μM BAPTA/AM. The maximum fura-2 ratio changes (∆ 350/380) or fluorescence changes normalized to initial fluorescence (∆ F/F0) are plotted.
E. Serial dilutions of yeast cells were spotted on YPD plates and grown for 2 days either at 30 °C or 37 °C. Mutant yeasts are significantly retarded in growth and show increased temperature sensitivity.
B) ROS levels (DHE intensity) and mean number (N) of yH2A.X foci in proliferating and senescent (3 days after 20Gy X-ray) MRC5 fibroblasts treated with or without 100nM Rapamycin and/or 2.5mM of the antioxidant NAC. Data are mean±S.E.M of n=3 independent experiments; Asterisks denote statistical significant P<0.05 One-way ANOVA.
E) Overall survival in patients with stage I (n=269) lung adenocarcinoma with high (top 50%) and low (bottom 50%) NK cell gene expression signature expression.
DC(WT) and DC(NLRC3-KO) mice were immunized with MOG(35-55) peptide in CFA adjuvant and pertussis toxin to induce EAE. Representative flow cytometry data showing intracellular production of IFN-γ and IL-17A by CD4+ T cells in the spinal cord and brain from DC(WT) and DC(NLRC3-KO) mice 26 d after EAE induction after restimulation with MOG(35-55) peptide.
Quantifications of YAP activity (nucleo-cytoplasmic ratio) and p-Jun Ser63 nuclear intensity in Ctrl, Cytochalasin D (CytoD), CytoD + AP condition.
(C-E) Flow cytometry analysis of the % of PI-positive shCtlr, shGp96 or shNMHCIIA HeLa cells. Cells were treated with (D) 1.5 or 3 nM LLO for 15 min; or (E) 0.1 nM LLO for 10 min followed by LLO washed out and recovery for indicated times. Levels of PI incorporation by untreated cells were subtracted from all LLO-treated samples. Values are the mean ± SEM (n≥4) and p-values were calculated using one-way-ANOVA with Tukey post hoc analyses *p<0.5, **p<0.01, ***p<0.001.
Under normal growth conditions, MadR exists in equilibrium between the free and DNA-bound forms, and a basal level of desA1 and desA2 expression is maintained. DesA1 and DesA2 acts with other enzymes of the fatty acid synthase-II (FAS-II) complex to produce mycolic acids for new cell wall. Infection of macrophages and early stress cues shifts the equilibrium towards the free form of MadR and the repression of desA1 and desA2 is released. The desaturase protein levels increase, introducing double bonds that allow cyclopropanation and other modifications to alter the cell wall. These changes enable the bacteria to withstand intracellular stresses and establish infection. As infection continues and stress is sustained, MadR binds tightly to the promoter of desA1 and desA2, leading to stringent repression of the desaturases. MadR-mediated repression of desA1 and desA2 leads to irregular fatty acids of medium length and the pausing of mycolic acid biosynthesis to enter into dormancy. The DNA-bound form of MadR is shown in complex with a yet unknown co-factor that leads to repression of the desaturases.
(G) Live-cell microscopy workflow and automated image analysis via NECtrack to quantify TNF-induced necroptosis kinetics in L929 cells. Distributions of death times and death rates are computed from raw counts of live and dead cells based on nuclear propidium iodide (PI) staining.
(b) Up-regulated genes, with boxplots across all samples, include IFI6, ACE2, SHFL, HERC6, IFI27, and IFIT1, based on data from (c), which is the total set of DEGs. The full set is shown in an intersecting heat map, with a core set of up-regulated genes (orange) distinct form the set of down-regulated genes (purple), compared to genes that are not significantly differently expressed (grey) in any comparison (DESeq2, q-value <0.01, |logFC| >0.58).
I Schema showing HSP90 scores in matched pairs of primary tumor and brain metastasis. Red: increase of HSP90 score from primary to brain metastasis; green: decrease of HSP90 score; gray: no changes in HSP90 score.
A Co-immunoprecipitations of V5-tagged tau and GFP-Parkin. The V5 tag was used to pull down tau and the membrane was probed for V5 (using an antibody raised in a different species) and GFP. IP = immunoprecipitation, Flow = flow-through lysate following removal of beads. Data information: Scale bars = 10 μm. Data are given as mean and SEM, ** = p < 0.01, **** = p < 0.0001.
K Quantified epoxomicin-sensitive proteasome activity (difference in slope of turnover of fluorescent chymotrypsin substrate between epoxomicin-treated and untreated samples; see Appendix Figure S2) from lysates of animals treated as in (J). *P<0.001, using ANOVA with Dunnett's posthoc comparison to the empty RNAi vector control, with N=3 trials. Error bars indicate SEM.
I, J The average number of CFU-F colonies formed (I) and the average cell number per colony (J) were shown (n=4 independent experiments). The statistical significance of differences was assessed using one-way ANOVAs with Tukey's multiple comparison tests. All data represented Mean ± SD. *p<0.05, **p<0.01, ***p<0.001.
E, F. Binding of the Fabsc- and IgGsc-molecules to PSMA-expressing LNCaP (E) or 22Rv1low (F) cells was assessed by flow cytometry, as described in the methods section. The EC50 values were calculated using GraphPad Prism software and are presented below the figure.
A scatter plot similar to (C) but where genes are colored according to their mode of regulation derived from anota2seq analysis. A relaxed threshold (p<0.05) was used to identify a set of transcripts regulated via translation, which did not pass thresholds used for identification of changes in mRNA abundance or translational offsetting (FDR<0.1). Confidence ellipses (level 0.7) are overlaid for each mode of regulation. A bar graph indicates the number of mRNAs regulated via each mode.
(C) The average quantified filamentous growth is shown for BY4741 and Σ1278b yeast spotted onto media supplemented with either a vehicle control (DMSO 0.1% (v/v) or the indicated compounds at a concentration of 20 µM across four biological replicates. Error bars represent the standard deviation of the mean between the averages of the replicates, and asterisks indicate p-value < 0.05 for a two-sided student's T-test comparing normalized values to the DMSO control (n = 4 biological replicates).
A) Mouse intestinal organoids immunostained for YAP (green). Note the mostly cytoplasmic localisation of YAP at 48h in the organoid. Irradiation with 4Gy of X-rays drives strong nuclear localisation of YAP in many cells, which is reversible by treatment with the Src family kinase inhibitor Dasatinib. The Dasatinib treated organoids exhibit increased cell death after irradiation, as indicated by pyknotic nuclei (white arrow). n > 10 organoids in each experiment. This experiment employs the same control batch of 2-3d organoids also shown in Figure 6A.
E. Histograms show the percentage of the different replication patterns observed in each experimental condition (average and SD of two assays). Circle dots in each column represent the values of individual replicates. Statistical analysis: two-way ANOVA followed by Bonferroni post-test. p-values of individual comparisons are indicated.
B-D Effects of feeding a HFD as a function of time on levels of acetylated and SUMO2‐modified proteins (D) in mouse liver (pooled from 3 mice).
(F) Percent area coverage of Iba1-proximal Siglec-F relative to total Iba1 across all analyzed thalamic, cortical, and hippocampal regions of 6 month WT (non-Tg) and 5XFAD mice. Box indicates quartiles and whiskers indicate the last datum within 1.5 inter-quartile range; n = 15-40 images (3-5 animals); *: p < 5e-2, **: p < 1e-2, ***: p < 1e-3, ****: p < 1e-4; ns: not significant, using unpaired Student's t-test, two-sided.
H, I The percentage of SQST‐1::GFP‐positive puncta that overlap with (H) or are close to (I) NUC‐1::mCHERRY‐positive structures in each strain. At least 10 embryos were scored per strain. Data are shown as mean ± SD. **P 0.0001; N.S.: not statistically different.
HeLa cells stably expressing CHMP4B-eGFP were transfected with siRNAs against (D) ALI 48 h post-transfection cells were used for live-cell imaging experiments. LLOMe was added using perfusion system D. siRNA mediated depletion of ALIX shows no significant change on dynamics of CHMP4B recruitment Data information: The quantification graphs represent average CHMP4B foci per cell quantified from three independent live-cell imaging experiments per condition. Error bars correspond to 95% confidence intervals. Data from >56 cells per condition were analyzed in each experiment. Right panels show knockdown efficiency of siRNA oligos as detected by Western blot (*, nonspecific immunoreactivity)
Scatter plot and correlation coefficient (r) of ASK1 mRNA expression , plasma alanine aminotransferase (ALAT) (B) Data were collected in lean subjects (n=14), obese subjects (n=23) and obese subjects with type 2 diabetes (n=19). Values are expressed as mean ± SEM (D).
(E) Failure of SKM1 or SKM2 expressed under control of the BAM3 promoter to complement CLE45 insensitivity of the bam3 mutant (7-day-old seedlings; 3 independent transgenic lines per construct are shown).
The intact architecture of the recA locus is required for pulsatile expression, which decreases in the absence of positive regulation and is abrogated in the absence of negative regulation. The presence of DNA damage is the main factor triggering RecA pulses. Schematic of M. tuberculosis reporters of DNA damage (magenta) and rRNA expression (green) during CIP treatment. In this study we classified three subpopulations of bacilli under optimal growth conditions, with no, moderate, or high DNA damage response (magenta gradient scale). The rRNA reporter helped us to visualize the metabolic state of the bacilli and was crucial for early detection of survivors. Following the first drug exposure, 62% of DNA-healthy cells survived, whereas 64% of cells with moderate and 82% of cells with high DNA damage died, suggesting that pre-existing DNA damage in cells treated with ciprofloxacin is detrimental. During the recovery phase, all survivors resumed metabolic activity first, and then underwent multiple divisions until they formed a new microcolony. At the time of second drug exposure most survivors died, indicating that survival of the first drug exposure was not due to drug resistance. However, 0.3% of cells that survived both the first and second drug exposure exhibited drug resistance. In sum, the random state of DNA damage experienced by M. tuberculosis before exposure to a drug targeting DNA replication has consequences for the onset of drug tolerance and the ultimate efficacy of treatment.
(E-F) mRNA levels of inflammatory genes in liver and lung of the of WT (n=7), R6/2 (n=4), R6/2-emp (n=4) and R6/2-Chol (n=5) mice.
C Enlarged image of GAS-associated FBXO2 Graphs show the signal intensities of EmGFP-FBXO2 and mCherry-LC3 measured along the arrows in the merged image. Green and red arrows indicate the signal peaks observed in EmGFP-FBXO2 and mCherry-LC3, respectively. White arrow indicates bacteria that are targeted by FBXO2 but not by LC3.
U87 cells were treated with increasing concentrations of LXR623 for 24h in the presence or absence of cholesterol. Thereafter, whole cell protein lysates were collected and analyzed by capillary electrophoresis for the expression of phosphorylated AMPK (threonine 172) and total AMPK.
Graph reporting the normalized Luciferase activity of miR-9 promoter, expressed as fold over the untreated condition, in FaDu cells treated with Cetuximab (CTX) for up to four hours. Data represent the mean (±SD) of three independent experiments performed in duplicate and one-way ANOVA test was used to verify the statistical significance.
E Immunofluorescent images of the distal femur in 8-week-old Lepr-Cre; tdTomato mice. Notch3 (green), tdTomato (red), CD31 (gray), DAPI (blue). Sinusoid (a), arteriole (b), artery (c) and avascular bone marrow (BM, d) regions were shown. Arrowheads indicated Notch3+ tdTomato+ adventitial cells closely associated with ECs. Arrows indicated Notch3- tdTomato+ reticular cells in the bone marrow that were not associated with ECs. Scale bars were 10 µm. F Localization quantification of Lepr-Cre+Notch3+ cells relative to bone marrow ECs (n=5 biological replicates from three independent experiments). Cells within 5 µm diameter of ECs were considered adjacent. G
(A) Pairs of loci were labeled with YFP-ParBpMT1/parSpMT1 and mCherry-ParBP1/parSP1 at genomic positions 400 kb and 600 kb (inter-domain) or at 600 kb and 800 kb (intra-domain). Box plots show the distribution of inter-focus distances for cells of different sizes. Asterisks indicate statistical significance (***, Student's t-test p-value <0.001; ns, not significant). For the region of the chromosome containing the labeled loci (indicated by dashed grey lines), the corresponding region of the Hi-C map generated at each time point indicated is shown, with the same region from wild-type cells shown at the bottom. For complete Hi-C maps, see Fig EV4; for representative microscopy images, see Fig S3.
(J) Quantification of the distance of APP puncta present in EEA1-positive early endosomes to its centroid over the endosome radius. The closer the ratio is to 1 the closer APP is to the endosomal membrane (i.e., distance equals radius) (n=3, NsiControl=6, NsiCD2AP =6; **P=0.0051, t-test, mean ± SEM).
At 4 DIV, cultured cortical neurons were transfected with indicated plasmids. Three days later, neurons were treated with 10 μg/ml poly(I:C) for 24 h. Neuronal morphology was monitored by GFP signals at 8 DIV. Mean values SEM of representatives of three independent experiments are shown. The numbers of analyzed neurons in the representative experiments are indicated in each column. Data were analyzed by two-way ANOVA with Bonferroni's multiple comparison test. Scale bar, 20 μm. *** P < 0.0001, ns: non-significant.
(A), Age-related click and pure tone-burst (8, 16, 24, 32 kHz) ABR thresholds (dB SPL, mean SE) in DIA1(R1204X)-TG (5 weeks, n = 6; 10 weeks, n = 16; 25 weeks, n = 42) and control mice (5 weeks, n = 6; 10 weeks, n = 16; 25 weeks, n = 33). Note the progressive hearing loss of DIA1(R1204X)-TG mice starting at high frequency sounds from 10 weeks. **P= 0.0039 (24 kHz) and **P< 0.0001 (32 kHz) at 10 weeks and **P< 0.0001 (click), **P< 0.0001 (8 kHz), **P= 0.0001 (16 kHz), **P< 0.0001 (24 kHz), and **P< 0.0001 (32 kHz) at 25 weeks by Bonferroni's post hoc test following two-way ANOVA.
Total intracellular glutathione (GSH+GSSG) as shown by GR re-cycling assay in untreated HCT116 (R248W, WT and -/-) cells 48h after seeding (n = 3, 5 or 2 respectively). Indicated values are fold change to mutant TP53 cells. Part of this data is shown in Fig. EV4. Data information: TP53 status is indicated for each cell line. Data are represented as mean ± SEM. See also Figure EV5 and Appendix Figure S5.
(A) Depletion of the kinesin 1 heavy chain UNC‐116 suppresses necrosis induced by both mec‐4(d) and deg‐3(d) toxic alleles.
(C) fEPSP recording from Nedd4-2 WT (left; n = 7 slices from 6 mice for TAT and n = 6 slices from 6 mice for TAT-pS3) and Nedd4-2 cKO (right; n = 9 slices from 9 mice for both TAT and TAT-pS3) hippocampal slices of mice at age 6-8 weeks. The slices were pretreated with TAT or TAT-pS3 peptide (20 μM) for 1 hr before the induction of L-LTP at Schaffer collateral synapses. Representative fEPSP traces were recorded before and 180 min after LTP induction (Scale bars: 0.5 mV, 5 ms). Summary bar graphs showed the fEPSP slopes measured 160-180 min after L-LTP induction at Schaffer collateral synapses.
The Na+ in shoots and roots of TS-670 and three independent SlHAK20Hap1-YFP transgenic lines during salt stress. The 21-day-old TS-670, Hap1OE-1, Hap1OE-2 and Hap1OE-3 plants grown in 0.25× Hoagland which were then treated with 50 mM NaCl for additional 0 and 7 days.
(B) High magnification view of boxed regions in (A) pseudo-colored to show actin depletion in anaphase. Scale bar -1 µm.
C Average H3K27me3 (left) and H3K27ac (right) levels in FL erythroblasts around the TSS of extended list of Scl activated and repressed genes show that Scl repressed genes have on average more H3K27me3 and less H3K27ac as compared to Scl activated genes.
E Double-immunolabeling of Sororin (green) and REC8-myc (pseudocoloured in purple) on a spread mid zygotene spermatocyte. The sex univalents (X,Y) are indicated. Scale bar: 10 µm.
F) Telomerase activator Ccq1 is hyperphosphorylated in ssu72∆ cells. rap1∆ cells were used as positive control for Ccq1 phosphorylation status. Western blots were performed using Ccq1-flag tagged strains.
(F) TIRF images of Ramos cells transduced with endophilin A2-GFP and mCherry-ClathrinLC on antigen-loaded PMS. Scale bar = 5 μm. White arrowheads highlight endophilin A2 colocalization with antigen clusters.