EMBO/sd-character-level-ner huggingface dataset:
(c, d) MDA-MB-231 cells were transfected with EGFP-fused empty EV, VPS39, or VPS41. Cells were immunostained with RAB7 (c, red) or anti-MT1-MMP (d) antibodies. Merged images with DAPI (blue) are shown on the right. Enlarged endosomes in the boxed region are highly magnified in the insets. Diameters of RAB7 positive vesicles are also shown. n, number of cells scored for each cell population. Bars, 10 μm, (inset 5 μm).
(H) Representative Iba1+ immunohistochemistry in the perivascular space of SPF, GF, ABX-treated, ASF, recolonized ASF, sDMDMm2, TLR2,3,4,7,9-deficient, SCFA-treated GF mice or FFAR2-deficient mice. Arrows indicate Iba1+ perivascular macrophages. Scale bar = 50 µm. (I-O) Quantification thereof. Each symbol represents one mouse. Three to four sections per mouse were examined. Means ± s.e.m. are indicated. No significant differences were determined by unpaired t-test or one-way ANOVA followed by Tukey's post-hoc comparison test. Data are representative of at least two independent experiments.
(B, C) The lysates of MCF10A-eGFP-LC3 cells transfected with indicated siRNAs for 48 h and left untreated (−) or treated with 500 ng/ml TRAIL for 2 h were analysed by immunoblotting. (C, lower panel) MCF10A-eGFP-LC3 cells were transfected with indicated siRNAs for 48 h and analysed for the indicated mRNAs by RT-PCR. Similar results were obtained in two independent experiments.
H) Expression of FoxM1 and PLK1 at protein level, n>=3 independent organoids per treatment.
B) Representative Western blots of the indicated proteins during the neuronal maturation in vitro (n= 3 independent experiments). C) Representative Western blots of the indicated proteins of WT and Mfn2 KO neurons at DIV7 (n= 3 independent experiments). D
B. Schematics depicting the rationale for designing a BRCT-Sgs1 chimera. The BRCT3/4-Sgs1 fusion protein is expected to engage at DNA lesions via the 9-1-1 clamp. For simplicity, the ssDNA-binding heterotrimer RPA and the obligatory Mec1 cofactor Ddc2 have been omitted from the diagram.
(A) Time lapse microscopy of A. castellanii infected with PflaA-GFP-producing L. pneumophila. A. castellanii amoebae were infected (MOI 5) with L. pneumophila JR32 (Ptac-mCherry-PflaA-gfp) and embedded in 0.5% agarose/PYG medium. Approximately 46 h post infection, GFP-positive (motile) bacteria emerged in the mCherry-positive intracellular cluster, which within 1.5 h covered the bacterial cluster and spread from the bursting amoeba. At 55 h p.i., primarily mCherry-positive/GFP-negative (non-motile) L. pneumophila remained clustered. Scale bar: 10 µm.
L Percentage of SA-β-gal-positive cells of p53+/+ and p53-/- HepG2 cells expressing SQLE siRNA or control siRNA (upper panel). Protein expression (middle panel) and representative images (lower panel) are shown . Sacle bar, 100 μm.
(e-g) Expression levels of atrogin-1 (e) and Mcip1 (f) and calcineurin phosphatase activity levels (g) in hearts of WT and α-MHC-miR-212/132 TG mice (n=5-9).
F. Left: Representative images of Boyden chamber invasion assay in 3D matrigel of MCF7 cells, treated with 20 ng/μl EVs derived from MDA-MB-231 cells, transfected the same constructs used in (e). Right: Quantification of Boyden chamber invasion 24 hours after EV treatment. Scale bars represent 200µm. Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, **** p ≤ 0.0001.
RARα protein and ATRA sensitivity in breast cancer cell linesTotal proteins were extracted from logarithmically growing cell lines and subjected to Western blot analysis.The panel illustrates representative Western blots for a number of cell lines. The blots were sequentially developed with RARα-specific and control tubulin antibodies. The positions of the RARα and tubulin bands (right) along with the position of a relevant molecular weight marker (left) are indicated. To normalize the Western blot signals in different gels, the same preparation of RARα-transfected COS-7cell extracts (COS-7) and MCF7 extracts was loaded in each gel. The blots are representative of at least two independent experiments providing similar results.
(I) Immunofluorescence analysis of spine in PGIS model. Quantitative analysis of CaSR+, p-PLCγ+ and CaSR+ p-PLCγ+ cells number in spine of PGIS model. n=5, one‐way ANOVA, Bonferroni post hoc. Data information: AF: Annulus fibrosus; NB: New bone
B Radar plot showing that the EMT gene signature was not altered at the gene level in the ESRP1 knockdown model (LCC2 set). C Radar plot showing that the EMT gene signature was altered at the ASEs level (SE) in the ESRP1 knockdown model (LCC2 set).
(F and G) Immunostaining assay of GABA (green) in control and SOX1KO cells on day 35 of ventral neural differentiation (F), and quantiﬁcation of GABA+ cells (G), p=0.0001. Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). ***p<0.001 versus Ctrl group (unpaired two-tailed Student's t-test).
Tissue topology is affected by disruption of Canoe, but not Mud Representative image of a Canoe-shRNA follicle epithelium. Cell outlines are marked with Basigin::YFP. This egg chamber has no mitotic cells and AR of 1.58. Scale bars = 5 μm
E. The abundance of all detected polar metabolites was compared between iRBCs and uRBCs and presented as the log2 fold-change (iRBC/uRBC) with respect to the -log10P. Significance cut-off was set with −log10(0.05) + c/(x − x0). Each data point represents a single metabolite and the insets depict the extracted ion chromatograms for two metabolites that were either elevated (acetyl-CoA) or decreased (fructose-1,6-bisphosphate) in iRBC relative to uRBC.
Southern blot analysis of PCR-amplified fragments with a Myc-specific probe from two independent experiments (f). Frequency of IgH/c-Myc chromosomal translocations derived from two independent experiments (mean ± sd; Fisher's exact test) (g).
A 3D structure of a HA trimer (PDB 3UBE generated with PyMol). Each monomer consists of a HA1 (dark grey) and HA2 (light grey) subunit. The trimer can be divided into a membrane distal head which contains the RBS (yellow) and a proximal stalk region.
1603MED cells were treated with DMSO (vehicle, black), with LY364947 (red) or with SB431542 (orange). Immunoblot of phosphorylated Smad2 (P-Smad2), total Smad2 and β-actin upon inhibition of TGFβ/Activin signaling using LY364947 and SB431542 inhibitors for 24 hours. Bar graphs on the right panel represent the quantification of the relative level of P-Smad2 (P-S2) to β-actin. Bars represent the mean ± SD. Number of replicates is n≥3.
Illustration (A showing the translation activities of the Cnot6l 3"-UTR (WT and CPE mutated) in GV- (maintained by 2 μM milrinone) or MII- (released from milrinone) arrested oocytes. GFP signal indicated translational activation of Cnot6l 3"-UTR. An in vitro transcribed and polyadenylated mCherry mRNA was co-microinjected as a positive control. Scale b
Under conditions of magnesium starvation, MgtE is upregulated and open, poised to transport Mg2+ inside the cell. If other divalent cations, such as Mn2+ or Zn2+ are present in the environment at relatively high concentrations, MgtE can transport them or be inhibited by them, which causes toxicity. Under these conditions, the N-terminal cytosolic domain of YqgP binds Mn2+ or Zn2+, and activates YqgP for cleavage of MgtE between its transmembrane helices 1 and 2. YqgP also interacts with FtsH, and presents MgtE or its cleavage product(s) for processive proteolysis by FtsH. The cleavage of MgtE by YqgP is required for its full dislocation and degradation by FtsH. The presentation/adaptor function of YqgP is not dependent on its catalytic activity, but it requires its active site unoccupied. YqgP thus behaves also as a pseudoprotease which are common in the rhomboid superfamily. The connection of a rhomboid-like protease/pseudoprotease (YqgP) with a processive degradative membrane-bound protease/dislocase (FtsH) and its role in membrane protein quality control in B. subtilis that we identify here represent a striking analogy to the eukaryotic role of rhomboid-like pseudoproteases Derlins in ER-associated degradation.
A. The oncogenic activity of MYCN is potentiated by overexpression of ALKAL2. Kaplan-Meier survival curves for Rosa26_Alkal2;Th-MYCN, Alk-F1178S;Th-MYCN and Th-MYCN mice. Also shown are Rosa26_Alkal2N, Alk-F1178S and control (Ctrl) mice. Comparison of survival of Th-MYCN alone and Rosa26_Alkal2;Th-MYCN curves showed a significant difference (p=0.003; log-rank test).
A Treatment scheme of experimental timeline and Immunofluorescence staining of telogen backskin hair follicles (HF) for Integrin α6 (Itgα6, red), active Caspase 3 (aCas3, green) and DAPI (blue) in control (Ctr) and Bcl-2 inhibitor (ABT-199) treated mice. B: bulge, CH: club hair, DP: dermal papilla, HF: hair follicle, HG: secondary hair germ. Scale bar, 50 µm B Quantification of backskin HF with aCas3+ cells in bulge, hair germ and dermal papilla of Ctr and ABT-199 treated mice (n=4 mice biological replicates; mean ± standard deviation (SD); *** p<0.001, ns=not significant, two-way ANOVA test). nd=not detected.
D. Tissue specific kinases. Normalized proteomics data (Wang et al, 2015) from 31 tissues show that some kinases are only expressed in a few tissues. Many tissue specific kinases (darker color) belong to the highly active kinases (larger node size) in the yeast array.
C) and D) STAT3 knockdown in BCE cells. BCE cells were transfected with siNegative and siRNAs targeting STAT3. qRT-PCR were performed to examine STAT3 mRNA levels. STAT3 level in siNegative was set as 1. Data from three independent experiments were averaged and are presented in C. In D, cells transfected with siRNAs were treated with LIF (10 ng/ml) or vehicle for 15 minutes. Whole-cell lysates were subjected to Western blotting with the indicated antibodies. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test.
E. Visualization of the effect of MepS absence or its overexpression on cell width by phase contrast microscopy. Cultures were grown in LB at 30°C and aliquots of culture were taken at OD600≈0.1. The scale bar equals 5 μm.
(A) Protein lysates from MCF10A cells left untreated or treated with 500 ng/ml TRAIL or 5 μM rapamycin (Rapa, positive control) for 24 h were analysed by immunoblotting for phosphorylated p70S6K (P‐p70S6K), total p70S6K and GAPDH (loading control).
A) Top: schematic depicting hrpa-1 gene and a loss-of-function deletion allele (tm781), referred to as hrpa-1(∆). Bottom: to create a chimeric protein (HRPA-1HsLC), the third coding exon (blue) was replaced with a codon-optimized sequence encoding the majority of the human LC.
D Distribution of the different eye phenotypes following genetic manipulations The Drosophila were fed with or without CQ (30 flies per condition were randomly selected for analyses; *p < 0.05, ***p < 0.001, ꭓ2 test).
(b) Domain organization of Bcl-2, Bcl-xL, and the chimeric proteins Bcl-2/xL and Bcl-xL/2, as well as a summary of their localization and ability to translocate during mitophagy, as determined in c.
A) Viability of NCI-N87 and NCI-H358 cells upon transfection of 45 different gRNAs by solid phase transfection. Cas9 expressing NCI-N87 and NCI-H358 cell were seeded on pre-coated plates. 5 days post transfection, cell viability in each well were measured by CellTiter-Glo. Values were background subtracted, normalized to scrambled controls and plotted against each other. Blue dots represent scrambled controls, whereas the yellow dots represent POLR2A gRNAs. Green dots represent the genes that affect the viability in a cell line dependent manner. Results are representative of 3 independent experiments.
(A,B) Expression of UVRAG under cell stress. HL60 and HCT116 cells were treated with doxorubicin (1 μg/ml), cisplatin (10 μm) and UV irradiation (5 min after 50 mJ/cm2) for the indicated time, and then apoptosis, autophagy and fluorescence intensity of UVRAG was assayed. Scale bar, 10 μm.
(a) Schematic of repressive interactions via Notch-Delta between neighbouring cells whereby the effects of HES5 protein in Cell 1 (marked as P1) on transcription in Cell 2 and vice-versa are represented using an inter-cellular Hill function J(P1, 2(t−τND)) where t denotes time and τND represents the intercellular time delay, the time interval required to synthesise the intermediate molecular species (detailed in Figure EV4a); HES5 auto-repression is represented using an intra-cellular Hill function G(P1, 2(t−τH)) where τH represents the inter-cellular time delay, the time interval required for protein to be produced and repress its own transcription.
E RT-qPCR analysis showing Fbxw7 mRNA levels in Day7 KO, KO+HA-MT5WT, and KO+HA-MT5Mut EBs. Data are represented as mean ± SD from three biological replicates. Student's t test, two-tailed. ns, not significant.
C: Co-IP results showing interaction of ZFP36L2 with CNOT6L and CNOT7. HeLa cells were co-transfected with plasmids expressing HA-ZFP36L2 and FLAG-CNOT6L/7 for 48 h before immunoprecipitation. Experiments were performed three times with reproducible results; a representative result is shown
A HA‐Flag‐TBC1D5 expression was induced in T‐REx HeLa cells for 20 h, lysates were subjected to GSTpull‐down, −AP2M1. Co‐precipitatedTBC1D5 was detected with anti−Flag antibody.
B. BrdU-sensitized U-2-OS cells stably expressing GFP-NLS-CDKL5 were pre-incubated with DMSO (mock), olaparib (5 μM), talazoparib (50 nM) or PDD00017273 (0.3 μM) for 1 h prior to micro-irradiation and live-imaging at the indicated times post-irradiation. One of three independent experiments is shown. Scale bar is 10 μm
Mice were treated as described in Fig.2A. LP cells were isolated from each mouse and were culture for 48h. Cytokine and chemokine production of LP cells were detected using multiplex cytokine assay. Color from blue to red indicates enrichment of gene expression.
Expression of CD69 on PBMCs from three healthy donors (A, B, C- n=3) was measured by flow cytometry following 24 h treatment with 3 µM of PH02 alone, or in combination with the indicated concentration of PEP005. Positive control samples were treated with PMA. Data information: Statistical significance, as determined by one-way ANOVA is indicated: *, P<0.05; **, P<0.005; ***, P<0.0005; ****, P<0.00005; ns, no significant difference. The exact P-values are indicated in the Appendix Table S1.
B) FP based activity assays on free PCNA-Ub (three concentrations of USP1 and PCNA-Ub) and activity of USP1 on increasing concentrations of Ub-Rho.
(B) Incidence of ankle pathological new bone formation in DBA/1 model. n=9 per cage of total 3 cages per group, Fisher's exact test. (C) Quantitative analysis of structural parameters of pathological new bone by μCT analysis. n=9 per group, one‐way ANOVA, Bonferroni post hoc.
(A) Heatmap depicting the expression of homeodomain encoding genes (columns) across n=537 single twitlow MNs for which spatial mapping information was available (rows). Rows and columns are arranged by hierarchical clustering. Normalized expression levels are color-coded. Arrows indicate selected clusters for follow up studies (see Fig 1D). Hox gene expression in individual cells as identified by scRNA-Seq is shown on the left by colored bars, clusters 1 to 60 expressing specific combinations of homeodomain genes are shown on the left.
(A) WT and SKO cells stably expressing HPos-Cherry were incubated with OA for 4 h and LDs were labelled with LipidTox Green. The HPos-Cherry signal was bleached and signal recovery to LDs monitored using airyscan imaging. Representative images of 10 acquisitions/genotype, 2 experiments. Circle denotes bleached region, arrowheads indicate HPos signal accumulating around the LD. (B) Analysis of HPos-Cherry recovery to LDs after photobleaching, performed by confocal microscopy after 2-4 h OA loading. Data is normalized to both pre-bleach and post-bleach intensities, ± SEM, n=22-25 bleached LDs/genotype, 2 experiments.
Diagram of the break-induced replication (BIR) assay used in this study. Red line represents galactose-inducible HO endonuclease cut site.
a, Cytokine production from macrophages stimulated with LPS (100 ng ml-1) for 24 h. Statistical significance was determined by the Student's t-test. *P  0.01.
(b) Wortmannin treatment releases UVRAG from the ER. HeLa cells were treated with 100 nM wortmannin for 1h, and processed for confocal microscopy using anti-UVRAG and anti-PDI antibodies (top panel). UT, untreated. Insets highlight the relative localization of UVRAG at the ER. Confocal co-localization is indicated (bottom left panel). Data are mean±s.d.; n = 75 cells for each group from three independent experiments; ***P0.001. Endogenous UVRAG and PDI expression before and after wortmannin treatment were confirmed by immunoblotting (bottom right panel).
(B) Non-reducing SDS-PAGE and immunoblot of recombinant BAK and BAK-Ub following treatment with 25 mM TCEP
Mitochondrial extracts from control 143B cells (left), COX1∆ cybrids (right), and COX2∆ cybrids (middle) were immunoprecipitated using antibodies against: (C) CIII subunit CORE2. Samples were subsequently analyzed by SDS-PAGE and immunoblotting with the indicated antibodies. In, input. IP, immuno-precipitate. FT, flow-through. Ig, unrelated immunoglobulin used as a negative control.
(B) SAXS data indicates that FRH-Δ114 is monomeric and flexible. The crystal structure of the large cell structure predicts the solution scattering curve (left, χ2 = 0.92) and fits well to the calculated molecular envelope (right).
(B) Quantification of the percentage of cells presenting LC3 puncta (i.e., stimulated cells) upon incubation with the different conditions. ** p<0.01 (paired Student's t-test, n = 100 cells/condition). These data are representative of two independent experiments.
C. Illustration of the role for RAB13 mRNA localisation, local translation and compartmentalisation of RAB13 function in defining the orientation of EC filopodia dynamics, motile EC polarity and blood vessel pathfinding.
Immunoblot analysis of Sgs1 N-terminus (amino acids 1-647) from cells treated with increasing doses of the DNA alkylating drug MMS in the absence of RAD9 and/or MEC1. This truncated Sgs1 protein was expressed from its native promoter in this and all subsequent experiments.
XPT of siRNA treated DC3.2R cells after 48 hours of knockdown. Treated cells were fed with the indicated amounts of Ova-latex The cells were then exposed to RF33.70-Luc Reporter CD8 T cells overnight. RLU indicates relative luminescence units produced by reporter T cell stimulation. Error bars show SD of >3 replicate wells. * p < 0.05 vs control I-Ab using two-way ANOVA. Representative plot of 3 independent experiments.
(d) Persistence of Venus::HES5 in 20μm regions expressed as continuous time intervals when signal in the band is high or low compared to its mean (see Methods); individual datapoints (gray) indicate quantification of high and low persistence time obtained from over 300 thin bands collected from multiple tissues with 2 z-stacks per tissue and 2 repeats (left and right of ventricle) per z-stack; dots indicate paired medians of 5 independent experiments; statistical test is paired t test of median per experiment with two tail significance and p=0.7171.
(A) Representative Western Blot analysis of the endogenous p150Glued co-immunoprecipitated with EB1 in shCTL or shSTIM1 ECs (left) and its quantification by normalized densitometry (right). Negative control (CTL) was performed incubating cell lysate with protein A- or G-Sepharose and empty mouse IgG. Results are the average ± SD of three independent assays. shCTL value of each biological replicate was normalized on itself and so shSTIM1 experimental value. Results were analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,001; Bonferroni for shCTL and shSTIM1 p≤ 0,05 *.
(F) Distance measurement between GlyR SSDs and GABAAR SSDs (blue bar; mean ± SD, n = 395 synapses from three independent experiments) and between double labelled GlyR SSDs (yellow, mean ± SD, n = 218 synapses from two independent experiments).
D) Sorted human CD14+ monocytes were electroporated with plasmids encoding nucleocapsid or control vector for 36 h and then stimulated with 10 μM nigericin for 30 min following pretreatment with 1 μg/ml LPS for 3 h. Otherwise, cells were stained with PI and the percentage of PI positive cells was calculated (D). Student's t-test was used and data were shown as means±SD of three technical replicates. **, P<0.01; NS, non-significant. Results were repeated for three times with similar results. Data information: control vector used here was empty vector corresponded to the nucleocapsid-containing vector. Student's t-test was used and data were shown as means±SD of three technical replicates. **, P<0.01; ***, P<0.001; NS, non-significant. Similar results were observed for at least three times.
(A) μCT images of pathological new bone formation in DBA/1 model. n=9 per group.
EmGFP intensity in LATS2 knockdown, or forced expression of a constitutively active form of YAP (YAP-S127A). Scale bars indicate 100 μm.
(F) Subdural EEG recordings from untreated 3-10-month-old mice were analyzed to compare their number of spikes at baseline. n = 8 NTG, 6 hAPP-J9, 6 hTau-A152T(L1), and 8 hAPP-J9/hTau-A152T(L1). *P < 0.05, **P < 0.01 by logistic regression analysis for three-way interaction of the three transgenes with Holm adjustment (A-E) or by two-tailed Welch's t test with Holm adjustment (F).
(b) Cardiomyocyte cell size of neonatal miR-212/132 null and WT mice (n=5-6 isolations).
(C) Levels of morphology proteins from gba+/+, gba+/−, and gba−/− isolated mitochondria were analyzed via immunoblotting with the indicated antibodies.
Quantification of fibroblast density (number of PDGFRαH2BEGFP+ cells, right; n=3 biological replicates per time point) and dermis volume (left) with age (n=7 E12.5; n=8 P0, P6; n=9 E16.5, E17.5, P4; n=10 P10, P50; n=11 E10.5; n=12 E18.5, P2, P21; n=20 P12 biological replicates).
A, Cyclin E overexpression results in increased RMD when the DSB is close to one repeat. The U2OS (EGFP-SSA-3427-3) cell line carrying Tet-on-cyclin E plasmid was used, and RMD frequency was determined with or without induction of cyclin E expression by doxycycline (DOX, 0.5 µg/mL), which was added 24 hours before transfection of the indicated sgRNAs/Cas9. Cyclin E expression levels were validated by Western blot, using KU70 as the loading control.
C RT-qPCR analysis of Fbxw7 mRNA levels in WT and Mettl5 KO cells during the indicated time points course of EB induction. Data are represented as mean ± SD from three biological replicates. Student's t test, two-tailed. ns, not significant.
B-E. Study of gene and protein hypothalamic expression of the chemokine CCL2 (B, C) in icv LPS injected mice. Real-time PCR analysis for CCL2 (B) at different times after injection (from 1h to 24h), normalized to values in control icv saline injected mice (n=6 per group).
BxPC3 cells were transfected with CDH1Luc or p16Luc reporter together with TGIF1 or TGIF1.2TA in the presence or absence of KrasG12D and luciferase activity was measured 48 hr following transfection as described in (E) (n=6).
D Macroscopic appearance of livers in P240 PR-SET7ΔHepA mice and control littermates (WT).
B-E. Study of gene and protein hypothalamic expression of the chemokine CCL2 (B, C) in icv LPS injected mice. at different times after injection (from 1h to 24h), normalized to values in control icv saline injected mice (n=6 per group). Measurement of CCL2 (C) ) concentration by EIA after icv LPS injection (black bars) or icv saline injection (grey bars) in mice at 1h, 6h and 18h after injection.