EMBO/sd-character-level-ner huggingface dataset:
A Schematic representation of the proteomic experiments used to isolate novel proteins enriched at the Shigella-septin cage. (a) A SEPT6-STREP-FLAG construct was (b) transfected in HeLa cells for 24h. (c) Cells were infected with S. flexneri AfaI for 4 h, harvested, and (d) SEPT6-STREP-FLAG cage-associated proteins isolated through co-immunoprecipitation (Co-IP).
E) pH calibration curve for testing the effect of antimycin A on local pH at SU e.
(B) Venn diagram shows the number of differentially expressed genes in the opn4 dko anterior brain (dark blue circle), posterior brain (grey circle), and eye (light blue circle). The cutoff for differential expression was set at a significance level of α=0.05. Heat maps of all the differentially expressed genes are presented in Appendix Figure S1A-C. The number of differentially expressed genes that are shared between the data sets is indicated where the datasets overlap.
(A) NRCFbs at passage 1 were stimulated with recombinant Fstl1 (50ng/ml) or vehicle after cultured in serum-reduced conditions (FBS 0.5%) for 24 hours. The samples were harvested at the indicated time points after stimulation. The expression of ERK1/2 and tubulin were detected by immunoblotting. Error bars represent mean ± SEM. Statistical analysis was performed by one-way ANOVA and Tukey multi comparison test (n=3 for each time point). Three independent experiments were performed.
H Left, plasma triacylglycerol levels in 10-month-old WT and FADD-D mice following fasting for 20 h (n = 5 for each genotype). Right, plasma cholesterol levels in the same group of WT and FADD-D mice (n = 5 for each genotype). Data are expressed as means ± SEM. *P = 0.0124 (Student's t-test). NS, not statistically significant.
A. Schematic showing the %GA content along the mouse Rab13 3'UTR using a 30nt window size. Occurrences of the consensus GA-rich motif are indicated by a red rectangle. The exact sequence between nucleotides 153-216 is shown with GA motifs in red and deleted regions indicated by black bars. P-value by Fisher's exact test with Bonferroni correction.
(H) Fragments of EPG-7 containing amino acids 1-704 or 1143-1330 directly interact with UNC-51.
(B) Primary hippocampal neurons (DIV6+3) were transfected with either TDP-43 wild-type, TDP-43ΔNLS or an empty vector control together with GFP-RAB11 to visualize recycling endosomes and analyzed as in Figure 1. Quantitative analysis of recycling endosome movement (C) and vesicle number (D).
G. Clonogenic survival of 5-azadC-treated WT HAP1 cells and derivative cell lines expressing a truncated form of RNF4 lacking the RING domain (∆RNF4; Fig. EV1H) (mean±SEM; n=2 independent experiments).
Domain architecture of full‐length Swi6. The indicated mutations in red disrupt the dimerization property of the CSD (L315E) or the ability of the CD to bind H3K9me2 (W104A).
Cell viability analysis using CellTiter-Glo of A375 cells treated with the indicated drugs for 24 hrs following siCTRL, siRIPK1 or siCASP-8 knockdown for 48hrs (n = 3 biological replicates). Cell viability values are displayed as a percentage of the relative untreated control. DMSO (Unt), TNF (10 ng/ml) and SM (100 ng/ml). SM represents SM-164. Error bars represent SD and a one-way Anova was performed to compare the mean value of each treatment to the treated A375 siCTRL, **** P ≤ 0.0001.
(I) Cells treated with control shRNA and B56δ specific shRNAs were lysed and the levels of phosphorylated α-catenin was determined using pS641 α-catenin specific antibody.
(E) Representative immunostaining images of FX expression in NK1.1+, CD11c+, B220+ and CD4+ cells in tumour-bearing lungs (scale bar, 10 μm)
A-C, Pre-embedding immunogold labelling for EM visualizes otoferlin localization in random ultrathin sections through the basal part of IHCs in Otof+/+ (A) and OtofI515T/I515T (B) but not in Otof-/- (C) mice. IHCs are highlighted in beige. Scale bar 100nm.
U2OS cells were labeled with CldU for 10 min, followed by increasing IdU labelling times and subjected to DNA stretching. (A) Labelling scheme and representative DNA fibers. Scale bars: 5 μm.
Percentage of terminally differentiated cells (AEC I and ciliated cells) in day 23 BALO cultures with (+) and without (-) microinjected TR‑Mac
H 3D images with CXCR4 and Emcn immunostaining in Gja1i∆EC and control pancreas. The scale bars are 50 µm.
B Pulldown and Western blot validation of the interaction between N protein and G3BP1/G3BP2. Cells transfected with vector or construct encoding GFP or N protein from different human coronaviruses were compared in these experiments.
Length distributions of CAGE fragments initiating 2 nt upstream of motif-dependent 21U-RNAs. The total counts in each length bin are normalized to counts per million of mapped reads.
(E) Dermal infiltrating cells were quantified (n = 5 for each group). Data represent the mean ± SEM. **P < 0.01. 1-way ANOVA with Bonferroni's post hoc test was used.
(F) Correlation between average copy number alterations of genome (CNAs)/tumor and CEP55 mRNA expression in the METABRIC dataset, n=997 patients.
G Streptavidinpulldown of HSS-tagged MMS22L variants stably integrated and overexpressed in U2OS cells. Input and co-precipitated proteins were detected by immunoblotting.
Decreased SREBP-1/2 and SCAP levels in Golgi apparatus in Cideb-/- mice. IB of organelle fractions of the indicated proteins and quantification of IB data from 3 independent experiments. Data information: Data represent the Mean ± SEM; NS: not significant, *: p < 0.05, **: p < 0.01, ***: p < 0.001, by 2-tailed Student's t test.
D. Assessment of LCS-GR synchronized transport in GOLPH3 OE or KD HeLa cells. Micrographs show cells at the indicated trafficking time points. Scale bar, 20 µm.
A. Two pFastBac1 plasmids containing PTENα with a C-terminal His-tag with or without CUG816>CUC mutation was used for in vitro purification and mass spectrometry sequencing. The initiation codon of canonical PTEN (AUG1032) was mutated to AUA and the initiation codons of PTENα (CUG513) and PTENβ (AUU594) were mutated to CUC to avoid co-purification of PTEN, PTENα, and PTENβ with PTENε.
A. Summary of the DEGs in the NDIME-knockout cells compared with control cells at day 5 of neural differentiation.
D Activity of Rhom7 with/without its 7th TMD and/or C-terminal domain. rhomboid substrates that are uncleaved, cleaved by Rhom7, are marked by black, , and blue arrows, respectively. Controls, empty pBAD33 (empty) and wild-type S. sonnei (Ss).
(A) Upper panel, left: MCF-7/CD44+ cells were transfected with anti-miR-10b or a scrambled control, and qRT-PCR was performed. Upper panel, right: An aliquot of these cells was subjected to mammosphere-forming assays. The graph shows the mean ± SEM of the number of formed mammospheres per 4000 seeded cells in 3 independent experiments. Lower panel, left: Expression of miR-10b relative to RNU6B in MCF-7 cells stably transfected with a plasmid containing the miR-10b gene versus an empty vector. Results are the mean ± SEM values from 3 independent experiments. Lower panel, right: miR-10b-overexpressing MCF-7 cells analyzed by serial mammosphere assays. The mean ± SEM of the number of formed mammospheres per 4000 seeded cells in 3 independent experiments was plotted on each bar.
Direct sequencing of NOTCH3 cDNA from skeletal muscle of controls, proband, parents and two CADASIL patients. In the proband, residual mutant cDNA is amplified and the sequence shows only the mutant allele (A allele, arrow). Predominance of the wild-type allele (C allele, arrow) in the parents documents mRNA-mediated decay of the mutant allele (A allele), in contrast to what was observed for a canonical CADASIL mutation where there is balanced composition of mutant and wild-type alleles (arrows).
H) ERG was used to assess retinal function in response to large-field flash stimuli under both scotopic and photopic conditions. Representative photopic (light-adapted) and scotopic (dark-adapted) flash response series show increased amplitude and reduced latency after treatment with bispecific VEGF-A/ANG-2 compared with IgG control (both 3 mg/kg). ERG shows reduced depression of B-wave responses in JR5558mice treated with anti-VEGF-A/ANG-2 compared to IgG control.I) Maximum photopic ERG amplitude was increased using the rodent crossreactive bispecific VEGF-A/ANG-2 compared to single anti-VEGF-A or anti-ANG-2 treatments (all at 3 mg/kg). There was a significant increase in amplitude at stimuli >2 log (cd*s/m2) between the bispecific VEGF-A/ANG-2 and IgG control group under scoptopic and phototopic conditions. *Denotes significance after ANOVA and Dunnett's multiple t-test compared to IgG control compared for each stimuli separately, error bars show SEM with n = 8 animals per group. Under phototopic conditions anti-VEGF-A/ANG-2 reached significance at 2.58 and 2.30 cd*s/m2 with P = 0.0498 and *P = 0.0479, respectively. Under scotopic conditions all stimuli reached significance for anti-VEGF-A/ANG-2 with P-values of -2.3 cd*s/m2 (P = 0.0498); -1.93 cd*s/m2 (P = 0.0035); -1.33 -1.03 cd*s/m2 (P 0.0001); -0.73 cd*s/m2 (P = 0.0002); -0.43 cd*s/m2, (P = 0.0004); -0.13 cd*s/m2, (P = 0.0024) and 0.18 cd*s/m2 (P = 0.0031). In addition anti-ANG-2 treatment reached significance at -0.13 cd*s/m2 (P = 0.011) and 0.18 cd*s/m2 (P = 0.005), respectively.
A Schematic depicting ATP-generating pathways in eukaryotic cells: glycolysis, the Pentose Phosphate Pathway (PPP), fatty acid oxidation (FAO), the TCA cycle, and the mitochondrial respiratory electron transport chain (ETC). Blue stars mark pths targets. Green indicates individual metabolites with statistically significant upregulation in atosPBG compared to the control.
(d) Specific force (maximal tetanic force normalized to cross-sectional area, Po/CSA) from TA and VM muscles in C57Bl6/J mice, untreated mdx mice, and mdx mice treated with low and high doses of anti-IGF2R for 4 and 9 weeks. One-way ANOVA. *p<0.05; **p<0.01; ***p<0.001 (n=10 mice per group).
Growth curves of Vegfr3Luc;Tyr:CreERT2;BrafV600E; Ptenflox/flox melanomas treated with αPD-L1 or IgG (200ug/dose, 2 doses/week; left panel), or with vemurafenib (Vem, 50 mg/Kg, daily dose), BO-110 (BO, 0.8 mg/kg, 2 doses/week) or vehicle control (V, daily dose) as indicated. Data correspond to the average tumor size ± SD at the indicated time points. Red arrows mark the initiation of treatment (n= min 5 mice per condition). Statistics Two-Way-ANNOVA. p=0.0012 (αPD-L1), p=0.0007 (BO-110) and p=0.0353 (Vemurafenib).
(f) Starvation increases co-localization of GFP-EndoB1 (green) with Atg5 (red) in neurons. The T145A mutation of GFP-EndoB1 does not affect its co-localization with Atg5-positive entities. Arrows denote GFP-EndoB1- and Atg5- positive vesicles. The right panel shows quantified data as means ± s.e.m.; n=9. Uncropped images of blots are shown in Supplementary Fig. S8.
SH-4-54 significantly decreased plaque growth, as assessed by IC16 immunohistochemistry, while plaque load remained unchanged.
C-D. Flow cytometry analysis to assess levels of pS139 Histone H2AX (c). Histograms show the mono-parametric analysis of cell count against pS139 Histone H2AX intensity. Histograms are overlaid to appreciate changes in pS139 Histone H2AX intensity upon treatment (Red lines) relative to appropriate experimental baseline controls (Grey lines). Data are representative of two independent experiments.
(A) Confocal images of Proximity Ligation Assays performed on CD47 and CXCR4, CD47 and RAGE, CD47 and TLR4. Representative images from one experiment out of 3 performed are shown. MM cells were incubated overnight with 400 nM BoxA or PBS. Nuclei are in blue (DAPI), phalloidin is in green. Red dots represent physical contact of CD47 with CXCR4 or RAGE or TLR4. Scale bar, 20 μm. The intensity of red signal in PLA was quantified as described in Materials and Methods in individual cells (n as indicated). Insets are enlargements of the y axis. Mean and SD are indicated. Statistics: Kolmogorov-Smirnov test.
(C) Fluorescence intensity based analysis of pFTAA-positive area covered in the cortex of APP23p40+/+ (n=10) and APP23p40-/- (n=8) mice (left) and representative images for each genotype (right), scale bar = 1 mm. Mean ± s.e.m., statistical analysis: two-tailed unpaired t-test, **p=0.0051.
Representative immunofluorescence images of YAP distribution (right) and its nuclear quantification by Pearson's coefficient for correlation (left) of YAP and DAPI co-staining in H1299control and H1299RASSF1A plated on extracted ECM from H1299control or H1299RASSF1A cells with or without treatment with siP4HA2 or 4μM DPCA. (Correlation, Pearson's coefficient). (n=3, 300 cells per experiment) Scale bars 10µm. Data information: Unless otherwise indicated all statistical analyses were performed using Student's t-test 2-(tailed) of n=3 experiments and error bars represent the mean ± S.E.M.
U2OS-LacO cells transiently expressing Myc-LacI-Bub1 and EGFP-TOP2A (970-1531) were subjected to immunofluorescence staining with DAPI and antibodies for the Myc-tag and GFP. The relative enrichment of EGFP-TOP2A at the LacO repeats was quantified in 130 cells (J). Data information: Means and error bars representing S.D. are shown unpaired t-test).
A-D J-Lat 8.4 cells were mock-treated or treated with increasing concentrations of 5-AzadC or 5-AzaC. At 72 h post-treatment; and initiated (primers TAR) or elongated (primers tat) transcripts were quantified by RT-qPCR (D).
Two-month-old mice received tamoxifen and were fed on high-fat diet (HFD) for seven weeks before analysis.Body weight change during seven weeks of HFD, expressed as average fold change in comparison with the starting weight. n = 16, WT; n = 6, Vegfd−/−; n = 16, VCiΔR26; n = 5, Vegfd−/−; VCiΔR26.Body weight comparisons at seven weeks of HFD. Significant differences were determined using one-way ANOVA and Bonferroni post hoc analysis compared to WT. *P = 0.004; **P = 0.003. n = 16, WT; n = 6, Vegfd−/−; n = 16, VCiΔR26; n = 5, Vegfd−/−; VCiΔR26.
Measured log2(H/M) values at four time points as a function of their half-lives estimated here and elsewhere (Cohen et al, 2013). All log2(H/M) values shown here are averages of values obtained in 5 experiments (3 using lactacystin, 2 using epoxomicin). Proteins for which statistically significant differences at t=24 hours were observed (P<0.05, two-tailed Welch's t-test) are shown in red. Expected log2(H/M) values based on equation 4 are plotted as light blue lines. To minimize the masking of potential dependencies by the slight imperfections in the H/M normalization process (which introduces small offsets along the Y scale), average population log2(H/M) values of each time point (Fig. 6E) were subtracted from all measured Log2(H/M) values. Data for 1,416 proteins for which half-life estimates were available.
(G) Model for the dual function of the Dsc complex in EGAD-dependent proteasomal as well as ESCRT-dependent lysosomal membrane protein degradation.
H) Levels of ALDH1A3 differentiate between non-pro-invasive and pro-invasive tumors. High levels of ALDH1A3 in samples before treatment are associated to more invasive tumors after antiangiogenic treatment.
(D) Cells were transfected and immunostained for IFT20 (red) and γ-tubulin (green). Scale bar, 10 μm.
A-D. Example expression patterns for select genes identified by applying a general linear model (glm) including state, genotype, and interaction terms. Dots represent individual biological replicates (N = 3); lines highlight changes in mean values for replicates between each state (log2FC >1 and FDR < 0.05). A. State dependent expression is exemplified by Nanog which showed no difference between strains. B. Expression of Zfp277 exemplifies strain-dependence being consistently higher in B6. C & D. A significant genotype x state (GXS) interaction was identified for Nr5a2 (C, a marker for pluripotency) and Sox1 (D, a marker for neuronal differentiation).
E. The efficiency of PGC differentiation was detected by IF, 4 d after induction, using C-KIT and CVH antibodies. Scale bar: 60 µm (n = 3 independent experiments).
(c) Schematic representation of U2-pre-mRNA interaction. The U2 BSRR sequence and the pre-mRNA branch site sequence are shown. The arrows indicate several point mutations at the pre-mRNA branch site. Stem-loops I, IIa and IIb are also indicated.
CODIM super-resolution images (3 right side panels) of TNTs shown in the confocal expanded field images (left panels) of transfected cells showing expression of indicated GFP-tagged proteins (green). Cells were stained for F-actin with phalloidin (red). Scale bars in the expanded fields represent 5 µm and 1 µm in the insets.
F) GO term enrichment analysis for biological processes of the 25 most significantly up-regulated genes upon SARS-CoV-2 infected in small airway cells. P-values were determined using PANTHER Overrepresentation Test.
Spleen, mLN or PP cells from Vα14 TN iNKT mice and PP cells from an IL-4-/- mouse 1μg α-GalCer was added to the cultures to specifically activate iNKT cells. Blocking antibodies to IL-4 or isotype were added as indicated. IgG1+ and IgA+ class switched B cells were enumerated by flow cytometry after 4 days of coculture
G) Presence of autophagic proteins (BNIP3, LC3 and Parkin) on mitochondrial enriched fractions obtained from control and Mfn2KD C2C12 myotubes untreated or treated with CCCP (n=3 independent experiments). Data were normalized by TIM44 as a loading control and expressed as a fold change compared to young control mice and represent mean ± SEM. #p<0.05 Mfn2KO vs. control mice or Mfn2KD vs. control cells, *p<0.05 old vs. young mice or treated vs. untreated cells.
B UMAP visualization of all cells. Clusters are colored and labeled according to their inferred cell type identities.
E) Quantification of the mean 45Ca2+-store content at the beginning of the measurement (t0) (n = 5).
C. Scatchard analysis showing dissociation constant of 4D7 using I125-labelled and unlabelled 4D7 bound to full-length 30 amino acid peptide (n=3 biological replicates).
BALF was collected on day 21 and centrifuged to isolate cell pellets. Cells (primarily macrophages) were analyzed by qPCR for CD86 (F) and IRAK4 (G) (n=5).
(B) Immunoblot analysis of nuclear extracts isolated from Pax5+/+ (WT) pro-B cells and Pax5Jak2/+ lymph node tumor cells. The wild-type Pax5 and Pax5-Jak2 proteins were detected with an antibody raised again the N-terminal (N-term) paired domain of Pax5. The size of marker proteins is indicated in kilodaltons (kDa) to the left.
E, F RT-PCR (E) and qPCR (F) of KPM cells and parental tumors show Trp53f/f allele deletion (Δ) and Bap1 and Cdkn2a overexpression compared with PMC.
L Glucose uptake and lactate production were measured in Dgcr8−/−ESCs stably expressing Myc shRNAs and further infected with Mbd2 siRNAs.
(B) Western blot of mitochondrial OXPHOS respiratory complexes in C2C12 myotubes treated for 48H with C26CM and ferric citrate. (n=3)
g) Ubiquitylation at Lys 47 impairs RALB binding to EXO84. Flag-tagged RALB mutants were overexpressed in HEK293T cells and then immunoprecipitated with anti-Flag (M2) agarose followed by immunoblotting using anti-EXO84 antibody.
(E) HEK293T cells were transfected with the indicated constructs. The cells were lysed and subjected to immunoprecipitation with a Flag antibody. The lysate and immunoprecipitated products were subjected to western blotting. PY: PPEY motif; LY: LPTY motif. The ratio of mono-ubiquitinated to native Merlin in each lane of the lysate blot was quantified by Image J and is shown under the blot.
E) TE binning according to increasing 22G siRNA density in wild-type animals (grey, n=3). Mean normalized rpb-9 (mj261) mRNA reads (red, n=3) are overlaid with mean normalized wild-type mRNA reads (grey). (PolyA-selected RNA-seq libraries). The CEMUDR1 and Chapaev-2 transcripts are indicated with red (rpb-9 (mj261)) and grey (wild type) box plots. Central bands represent the median, boxes represent the 25th and 75th percentiles and whiskers represent the lowest and highest values, excluding outliers.
Thiol tracker staining by flow cytometry 48h after seeding of the indicated untreated cells (n = 2) Data information: TP53 status is indicated for each cell line. Data are represented as mean ± SEM. See also Figure EV5 and Appendix Figure S5.
Both wild-type (IWT) and R1285Q mutant (IR1285Q) FANCI efficiently associate with FANCD2. Fluorescence changes occurring when RED-tris-NTA-labelled FANCI (IWT or IR1285Q; both at 60 nM) is incubated at increasing concentrations of FANCD2 (ranging from 2.48 nM to 5.08 µM). Titrations were conducted twice (two technical replicates) and all data points for each protein-combination were used in fitting of a one-site binding model. Apparent Kd values (mean ± SEM) derived from fitting of a one-site binding model to the 24 data points of the two technical replicates are shown.
Peak SARS-CoV-2 replication precedes innate immune activation. (A-I) (A,C) Representative images of NF-κB p65 (A) (red) and IRF3 (C) (red) nuclear localisation in mock or SARS-CoV-2 infected (MOI 0.4 TCID50VERO/cell) Calu-3 cells at 24 hpi. SARS-CoV-2 N protein (green. (E and G) Representative images of IL-6 mRNA (E) detected by FISH (red) and N protein (green) , or IFIT1 mRNA (G) (green) with N protein (red), both with nuclei (DAPI, blue) in mock or SARS-CoV-2 infected (MOI 0.4 TCID50VERO/cell) Calu-3 cells at 24 hpi. (B, D, F, H, I) Single cell analysis time course quantifying the Integrated Nuclear Intensity of NF-κB p65 (B), IRF3 (D) , or overall integrated intensity for IL-6 (F) or IFIT1 (H) mRNA over time in N protein positive cells and N protein negative cells (I). n=2. Kruskal-Wallis test with Dunn's multiple comparison. * (p<0.05), **** (p<0.0001). Scale bar represents 50µM.
Automated microinjection of mouse neurons. Automated microinjection was performed on organotypic slices of mouse E16.5 dorsal telencephalon using Dx-A555 Phase contrast image of automated microinjection into mouse neurons. Scale bar is 100 µm.
(E) Correlation statistics for the localization of endogenous MITOL and PMP70 in the presence of NMS-873. Dots indicate individual Pearson correlation coefficient data points. In the box-plots, the center lines show the medians, box limits indicate the 25th and 75th percentiles as determined by the R software package, and whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles. Means and the number of samples are shown on the box and the X-axis, respectively. Statistical significance was calculated using a one-tailed Welch's t-test.
(G) The reads obtained by DNAse-seq (Song and Crawford, 2010) in T47D-MTVL cells around PRBs in the absence and in the presence of hormone were quantified and expressed as signal/bp (to account for peak length variation) for up and down-regulated genes. Up-genes: CORO2B, KCNH1, KLF15 and ATP10A; down-genes: KRT23, BCAS1, IGFBP5 and PGR. (*) P-value <0.05, ** P-value <0.01.
(D) Tangential eye sections through MARCM clone mutants for ftfd that express either no transgene or an RNAi construct against yki (UAS-ykiIR) with Tub-Gal4 and aged 14 days at 29°C. Because the transgene UAS-ykiIR is on chromosomal arm 2 L, the same as ft, clones generated with this system carry two copies of UAS-ykiIR and therefore downregulate yki very effectively. No other cell outside the clones expresses the construct and is therefore wt for yki. Mask panel is presented on the right of each section. A quantification of photoreceptor numbers (far right) displays a very significant increase in the number of wt ommatidia (N=210 and 219 from four eyes). ***P0.001 in two‐tailed t‐test. If all classes of ommatidia are considered, χ2‐test=232.30; P0.001 for 3 degrees of freedom.
Branching analysis of LPS-activated microglia by Monocle 2 leads to 9 distinct clusters in a two-dimensional state space inferred by generalized regression modelling (see Materials and Methods) showing the major difference of "subset LPS" (in yellow) compared to the other clusters corresponding to "main LPS" (in red). Monocle estimated a pseudotime for each cell along the inferred cell trajectory within the state space showing a delayed activation pattern of "subset LPS" compared to the other fractions.