EMBO/sd-character-level-ner huggingface dataset:
C. Multiple reaction monitoring (MRM) chromatograms for [13C3]-pyruvate in control (top) and [13C3]-lactate treated (bottom) HBVPs. The molecular mass for M1 and M3 of [13C3]-pyruvate were 89.9 and 45.0, respectively.
(A, Confocal images of Bmm-GFP (green) in 3rd instar larval fat bodies of different genotypes. DAPI (blue) stains nuclei. Scale bar represents 25 µm. (A) Knocking down CSN2 or overexpressing RDH/CG2064 in animals with DGAT1 overexpression (ppl>DGAT1) decreases the level and lipid droplet localization of Bmm-GFP. (B) The GFP intensity along the line across a lipid droplet in (A) was measured by ImageJ. The lipid droplet localization of Bmm-GFP, represented by two peaks, is clearly visible in fat cells from ppl>DGAT1 larvae, but it is lost in fat cells from ppl>DGAT1 larvae with CSN2 RNAi or overexpression of RDH/CG2064. More than 30 lipid droplets of each genotype were measured. One typical image curve is shown for each genotype.
Representative Western blots generated using extracts from the indicated cell types after the indicated perturbations. Bar graph showing quantification of the Western blots in (C). All values represent mean±SEM. Data points represent values from biological replicates. Statistical test employed was Student's t-test.
LV/tibia ratios in sham- and TAC-operated Wt and LXRα-Tgmice; n = 21 Wt sham, n = 24 LXRα-Tg sham, n = 24 Wt TAC, n = 26 LXRα-TgTAC. *P < 0.00001 versus respective sham, #P = 0.00004.
B. Immunostaining of NESTIN (green) and TUJ1 (red) of neural progenitors generated from shScr on day 8 and 10 of the neuroectodermal differentiation. Nuclei were counterstained with DAPI. Scale bar, 20 μM.
E) The dynein adaptor BicD2 associates with the nuclear membrane of HSPC (CD38-) and myeloid progenitors (CD33+) cells. Z stacks of representative cells are shown. Image contrast has been inverted. Stainings show DAPI and BicD2. Scale bar 5µm.
C) Percentual difference in non-synonymous mutation rate in E. coli for GK versus background i.e. versus the corresponding residue in non-gatekeeper positions.
(A) qPCR analysis of FSCN1, miR-143 and miR-145 expression in a 1205Lu xenograft nude mice model treated with the BRAFi Vemurafenib compared to control mice (n = 6). Paired Student t-test was used for statistical analysis. ***P≤0.001, ****P≤0.0001.
b, Western blot analysis of flag-tagged beclin1stop-transfected MCF7 clones. C, MCF.control cells (clone 38); B, MCF7.beclin1 cells (clone 1).
Alkaline Phosphatase (ALP) levels in the serum at endpoint (age = 5-6 months; n=29 wt, 19 ColAREG)
A Confocal immunofluorescence microscopy images of freshly purified pDCs co-stained with antibodies recognizing IDO1 (green) and markers of intracellular organelles and structures (indicated; red). Nuclei were stained with DAPI (blue). The merge imagine is shown for all stainings or without DAPI (no DAPI). Scale bar, 5 µm.
(C) Phase-contrast and immunofluorescence staining of smooth muscle markers (red) in HASMCs. Nuclei were counterstained with DAPI (blue). Scale bar: 12 m. Images are representative of three independent experiments.
(a) Domain organization of FKBP38, Omp25 and the chimeric proteins Omp25/FKBP38 and FKBP38/Omp25, as well as a summary of their localization and ability to undergo translocation during mitophagy as determined in (b).
Kaplan-Meier analysis of overall survival in breast cancer patients with recurrent lethal disease, classified according to p-JNK expression. p-JNK was determined by immunostaining of breast cancer samples in a tissue microarray; p-JNK low, n = 31; p-JNK high, n = 10. P value and hazard ratio (HR) were calculated by log-rank test.
Whole-mount immunofluorescence of P6 mesenteries, showing valve defects in the mutant vessels. Quantification of lymphatic valve numbers (C), valve leaflet length (D) and vessel width (E) in Foxp2flox/flox;Prox1-CreERT2 and littermate control mice (n = vessels (C, E) or valves (D) [mice], as indicated).
Sucrose gradient UV profile of 60S/40S/IAPV-IRES reaction mixture after an overnight run. The peaks corresponding to 80S and 40S were used for RNA extraction and UREA-PAGE shown in the inset.
Western blot analysis of Galectin-3 and GPNMB in the spinal cord lysates from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. n=3. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ***, p<0.001, ****, p<0.0001.
(C) HeLa cells expressing HA-Parkin and Cas9 were transduced with sgRNA targeting PINK1 or a non-targeting sgRNA control, treated with AO (2 h) to stabilise PINK1 expression and immunoblotted for PINK1.
Relative human CD19+ B cell level in blood calculated by normalizing the levels at the day the animals were sacrificed to those before vector administration.
The above harvested limb (N) muscles were subjected to IF staining for Pax7 and Laminin. Scale bar = 100 µm (N) Quantification of the numbers of Pax7+ muscle progenitor cells per area are shown on the right (n=3 mice, each). Error bars represent s.d.'s of the mean. Student's t-test (two-sided): *P<0.05, **P<0.01, ***P<0.001.
B, C) Logarithm of the odds (LOD) scores of cancer associated gene KOs in NCI-N87 and NCI-H358 cells derived from screens with gRNAs (B) and RNPs (C). Bottom panels show distribution of positive (POLR2A) and negative (scrambled) controls for each experiment. LOD score of 3 is highlighted with a dashed line, indicating statistical significance.
Genetic constructs and 4-OHT treatments for neonatal LEC-specific Foxp2 deletion.
(E) WT and SKO cells were treated as in (B), LDs were visualized with LD540 and cells imaged live with widefield microscopy. Exemplary trajectories of peripheral LDs tracked for 40 s. (F) Analysis of cells treated and imaged as in (E). Bars: 1 - [Pearson's colocalization coefficient between subsequent frames/cell], ± SEM, n=187-221 cells, 2 experiments, **p<0.005 (Mann Whitney test).
PMN were treated with 1 µM PPP (blue) or 50 ng/ml IGF1 (green) for 30 min before assessing axonal transport using 30 nM AlexaFluor555-HcT. Example images of DIV6 PMN treated with 1 µM PPP or 50 ng/ml IGF1. PMN were stained with 30 nM AlexaFluor555-HcT. The scale bar is 50 µm.
(a) mRNA expression levels of autophagic marker genes in hearts of wild-type (WT) and α-MHC-miR-212/132 transgenic (TG) mice (n=9-10).
Representative images of colon tumors were shown. Scale bars, 10 mm. Tumor number, tumor size and tumor load in each mouse was measured.
(B) Upper panel, Distribution of distance to nucleus, normalized on cell size, quantified by image (as in a) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from two independent experiments for a total of 830 early endosomes in 13 shCTL/GFP cells (64 ± 6 endosomes per cell), 719 early endosomes in 10 shSTIM1/GFP cells (60 ± 6 endosomes per cell) and 820 early endosomes in 12 shSTIM1/GFP-STIM1 WT cells (68 ± 6 endosomes per cell) and analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,001; Bonferroni for shCTL/GFP and shSTIM1/GFP p≤ 0,001 *** (orange) and for shSTIM1/GFP and shSTIM1/GFP-STIM1 WT p≤ 0,001 *** (green). Lower panel, Distribution of distance to nucleus, normalized on cell size, quantified by image (as in a) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from two independent experiments for a total of 820 early endosomes in 12 shSTIM1/GFP-STIM1 WT cells (68 ± 6 endosomes per cell) and 400 early endosomes in 12 shSTIM1/GFP-STIM1 NN cells (33 ± 7 endosomes per cell) and analyzed a two-tailed heteroscedastic Student's t-test, p≤ 0,001 ***.
E. Model. Plk4 plays a decisive role in not only centriole duplication but also centriolar satellite integrity and primary cilium formation. The latter two roles, at least in part, are executed via PCM1 phosphorylation. Plk4 directly or indirectly phosphorylates PCM1 at S372 (I), which promotes its own dimerisation/oligomerisation (II) and interaction with other components of centriolar satellites (III). These processes ensure PCM1 acts as a structural platform for centriolar satellites. Processes II and III are not necessarily sequential steps. It is shown that centriolar satellites and PCM1 play a critical role in centriole duplication and assembly [25, 49]. Under conditions of serum starvation or developmental cues, centriolar satellites deliver various factors from the cytoplasm to the basal body, thereby helping formation of cilia [26, 30, 37, 50, 51].
(h) Pseudo-color look-up tables applied to mean nuclear Venus::HES5 and NGN2 staining intensity in motorneuron (MN) and interneuron (IN) domains. Venus::HES5 microcluster and single NGN2 high cell (red arrow) in IN domain; Alternating high-low expression of Venus::HES5 in MN, red arrows show high cells.
A) Diagram resulting from a vertex model simulation that includes cell proliferation. B) Diagram resulting from a vertex model simulation that includes cell proliferation and heterogeneous reduction of line tension among the tissuecells. C) Diagram resulting from a vertex model simulation with heterogeneous reduction of line tension and an impairment of the cell division when tension value is under the 30 percent of the initial value D) Similar simulation than in (C) with a threshold of 40 percent.
D. RT-qPCR of CCNA and cdk1 mRNA levels in H1299 cells upon transfection with si-GFP or si-YAP oligos and empty pCDNA3 or mutp53R280H expression vectors as indicated in the figure. Error bars represent mean + s.d., from three biological replicates. P-values are indicated in the figures; two-tailed Student's t-test was applied throughout.
B) i) Planar division orientation is initially random in the follicular epithelium, with a significant bias towards the egg chamber elongation axis evident at stage 6 (asterisk, p = 0.0031, Wilcoxon Signed Rank Test, Theoretical Mean of 45; p = 0.0218 when comparison to a randomly generated list of the same size). Number of cells analyzed: stage 2/3 n=16, stage 4 n=27 stage 5 n=30, stage 6 n=40. ii) Quantification of the angle of tissue expansion as calculated by vector addition of the minor and major axis of egg chambers. Number of egg chambers analyzed: stage 2/3 n=10, stage 4 n=15, stage 5 n=15, stage 6 n=10. iii) Quantification of cell elongation angles (as shown in E) with respect to the chamber elongation axis by stage from live egg chambers. Number of cells analyzed: stage 2/3 n=18, stage 4 n=49 stage 5 n=64, stage 6 n=97. Bars represent mean and standard deviation
Quantitative real-time PCR analysis of Yap/Tead target genes in the ligated left carotid artery of WT and Hoxa4 KO mice at 1 week after ligation (n=6). Mean expression level of six WT mice at the baseline was defined as 1.0.
(B) Mapping of the boundary of the FtsH generated proteolytic product of MgtE. Immunoblot comparing the SDS PAGE mobility of the N-terminal fragment of endogenous MgtE generated by FtsH in the presence of the pseudoprotease version of YqgP (catalytically dead YqgP.S288A, strains BTM78, BTM502, Table EV2) to the mobilities of in vitro translated reference fragments corresponding to MgtE 1-340, -355 and -370 shows that YqgP.S288A acts as an FtsH adaptor, and that FtsH processing of MgtE in the presence of YqgP.S288A stops at around amino acid 355, which is near or at the cytoplasmic end of TMH 3 of MgtE.
Time course of wound healing for control (A) and less flattened keratinocytes in the regenerated epidermis (E).
CD11b+ CD11c+ dendritic cells were enriched from WT or Rab39a KO spleens via magnetic negative selection. Cells were fed with 3 µm magnetic beads conjugated to pHrodo. After 4 hours, cells were harvested for flow cytometry to measure fluorescence of eaten beads due to phagosomal pH. For analysis, the background fluorescence of unstained beads was subtracted from the resulting gMFI and the fold change (dox/no dox) was calculated. Shown are three independent experiments with error bars indicating the SD. p values were calculated using two-tailed ratio-paired Student's t-test.
I. Quantification of number of invaded MCF7 cells in 3D matrigel, after incubation with EVs from MDA-MB-231 cells sorted for Greenhigh expression. MDA-MB-231 cells stably expressing a pQXCIP‑zsGreen or pQXCIP‑zsGreen-RASSF1C construct were sorted and EVs were harvested 24 h later, prior to seeding with MCF7 cells in Boyden chambers. Invasive potential of MCF7 cells was evaluated 24 h after incubation with EVs. 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 ≤ 0.001.
Autaptic munc18-1 null hippocampal neurons were rescued with a phosphomimetic Munc18-1 mutant, Y473D or wild-type Munc18-1 as control and assessed on morphology and synaptic transmission using whole-cell patch clamp electrophysiology(C) Left: typical examples of evoked release upon action potential stimulation.
(A) OI-RD image of a small molecule microarray (SMM). Each compound was printed in duplicate in adjacent vertical positions.
(f-h) MCF10A cells were transfected with scrambled siRNA (siNC) or siRNA against Furin, and immunostained with anti-E-cadherin (green) and anti-TGN46 (red) antibodies. Merged images with DAPI (blue) are shown on the right (f). Bar, 20 μm. Total cell lysate were immunoblotted with antibodies indicated on the right (g). Efficacy of Furin silencing was verified by qPCR (h).
(H) Immunoblots of protein lysates from ARPE-19 cells depleted of Calcineurin catalytic subunits PPP3CA and PPP3CB. Data are representative of three independent experiments.
C GCN5 activity measured by in vitro acetylation assay using Myc-GCN5 immunoprecipitated from HEK293T cells and purified histone H3 as the substrate. (mean ± SEM; n = 3 independent experiments; ***p < 0.001, Student's t-test).
E. Venn diagram showing the MOS-regulated decay genes, overlapped between the maturation-directed decay genes (downregulated transcripts from GV to MII oocytes from control individuals) and the upregulated genes in MOSAsn95Lys oocytes.
(g-i) Echocardiography analysis of cardiac dimensions and function in Sham-operated WT mice and miR-212/132 null and WT mice 3 weeks after TAC (n=4-11). (g) End-diastolic area, (h) end-systolic area and (i) fractional shortening. All values represent mean±s.e.m. *P0.05; **P0.01; ***P0.005; #P0.05 compared with WT TAC; ###P0.005 compared with WT TAC; PSR, picrosirius red (collagen stain). DAPI, 4′,6-diamidino-2-phenylindole; WGA, wheat germ agglutinin.
E. Representative time-lapse spinning disk confocal images of n = 3 of live COS7 cells stably expressing GFP-TMD (green) and in lower panels transiently expressing mScarlet-RILP (magenta) and SiR-lysosome-stained LE/Lys (orange). Zoom insets shows region of interest containing ER (GFP-TMD). First row represents ER (GFP-TMD) (green), the second row shows MDA-generated ER movement (magenta), third row shows a merge of the two preceding channels. Scale bar: 10µm, zoom insets 3µm. Images related to movie EV19 and movie EV20. Images were acquired for 90 frames at 1Hz. F. MDA quantification of panel (E) and figure EV3A normalized to 1 showing total average ER movement. Graph represents mean ±s.d. of analyses at multiple locations within the same cell (n=15 cells per condition from 3 independent experiments). All images acquired 90 frames at 1Hz. Significance two-tailed student t-test. **** P<0.0001 ns = not significant.
C-E Double staining of liver sections with A6 and HNF4 (C) or Sox9 and Alb (D) or CD133 and HNF4 (E) antibodies. Right panels show larger magnifications of stainings performed in PR-SET7ΔHepA liver sections.
Number of up- and down-regulated protein-coding genes (PCG) defined as differentially expressed in Epi-HOT, -HOTΗP and -HOTΗP cells compared to Epi-CTR by RNA-seq and DESeq analysis (fold change > 2 and adj. P-value < 0.05), including those associated with EMT (Gröger set, Dataset EV2) and already identified as HOTAIR/PRC2 targets (Gupta set, Dataset EV2); nd stands for non-determined.
The electrostatic surface potential covering a range from -4 kT/e (red/acidic) to +4 kT/e (blue/basic) is mapped onto the Sir4 H‑BRCT structure to highlight the basic patch on the H‑BRCT surface. Sir4 H‑BRCT is shown in two orientations rotated by 180° and selected residues are labeled. Superpositions of Sir4 H‑BRCT-Esc1pS1450 (grey cartoon, peptide as sticks in atom colors), Sir4 H‑BRCT-Ty5pS1095 (blue cartoon, peptide as sticks in atom colors), and Sir4 H‑BRCT-Ubp10pT123 (green cartoon, peptide as sticks in atom colors) peptide complex structures reveal the highly similar conformation of peptide binders. Esc1pS1450, Ty5pS1095, and Ubp10pT123 peptides used for co-crystallization are indicated with residues modeled in the structures in bold and residues that contribute most binding to Sir4 H‑BRCT boxed.
B. Superposition of the yeast Aar2 (orange, PDB entry 3SBT; (Weber et al, 2011)) 3D structure and a homology model of human AAR2 derived from HHpred (marine), based on the yeast Aar2p structure (Santos et al, 2015). The inset on the right shows a close-up view of the C-terminal domain, where serines 253 (yeast) and 284 (human) are displayed as sticks. Residues 154-170 and 318-356 of yeast Aar2 as well as residues 1-18, 170-201 and 359-384 of human AAR2 are not shown for clarity.
(F) Representative images of Dp muscles isolated from Ctrl or YY1dKO mice 4 months after the TM injection.
G. The graph showing the ratio of intensities of JC-1 aggregates to those of monomers in (E).
(C) Spearman rank correlation between log2-fold changes of differentially expressed genes significant in either the somatic or process compartment color-coded for exclusive changes in the respective compartments. Representative genes are highlighted and labelled. The statistical significance of Spearman correlations was calculated in the standard way, using Spearman's rho statistic. Regression lines indicate fitted linear models, with the lightgrey shaded areas depicting the 95% confidence interval.
Cell size during starvation. Length and width of the cells are measured with phase-contrast microscopy and the volume is computed considering cell shape as a cylinder with two semi-spheres, as described in the graphical synopsis at the top (see also Table EV3 and Methods). Each measurement is an average of 200 cells. (A) Measured length and width of wild type cells starved in batch cultures and previously grown in the chemostat at different steady-state growth rates and of GlpK22 cells starved and previously grown in batch culture at μ = 0.9 h − 1 (see upper color legend). Note that, as shown in Schink et al. (2019), cell widths do not change from steady state growth to starvation, while lengths decrease. Both length and width increase exponentially with growth rate. (B) Starvation volume of the cells described in panel A, computed as explained in the graphical synopsis (see also Methods). In agreement with literature (Schaechter et al., 1958), it increases exponentially with growth rate (black line).
E RBPJF261R point mutant does not interact with L3MBTL3. IP of HA-tagged L3MBTL3 in the presence of FLAG-tagged RBPJ (WT and point mutants) in HEK293T cells followed by Western blotting using HA or FLAG antibody. RBPJV263R and RBPJA284R also show a reduced ability to interact with L3MBTL3. The experiment was independently replicated twice. WB: Western blot; IP: immuno-precipitation.
(C) HIF1α induces EMT by transcriptionally activating key mesenchymal transcriptional factors, including Snai1/2, Twist1/2, and Zeb1/2. Although to a less extent, inducing OGS directly with Pdk1/2 or small molecules also activate these factors.
C) Hoechst 33342 staining of healthy cell nuclei comprising the hair matrix (lined) and dermal papilla in untreated (vehicle) human HFs. 20 µm scale.
(B) Walktrap community (Igraph) analysis of the cells revealed 7 distinct cell clusters within the t-SNE graph (colored according to the Walktrap clusters), highlighted in blue, yellow, green, red, light-blue, magenta and orange. Differential expression analysis revealed genes specifically expressed in each cell cluster. Examples of two to three specifically expressed genes from each cell cluster are presented
(D-E) qRT-PCR measurement of Ifnb1 transcripts in mouse peritoneal macrophages that were left unstimulated or stimulated with 2'3' cGAMP (0.1 μg/mL) (D) or ISD (1 μg/ml) (E) for 4 h in the presence of DMSO or indicated compounds (10 μM). The data are presented as the relative fold induction of Ifnb1/Gapdh transcripts. A 90% reduction of IFNB1 transcripts in mouse peritoneal macrophages in comparison to the DMSO group was selected as the cutoff value for follow-up study, which has been indicated by the red dashed line. The arrow indicates the group that meets the cutoff value. The data shown are mean ± SEM from n=3 biological replicates.
Representative images of adult nerfin-1 (I-J', green ) and pros clones (K-L', green), scale bar = 5μm. In nerfin-1 clones, the size of the NBs (Ase+, blue) was significantly reduced upon 6 days of histidine dietary withdrawal, quantified in (H) (n=33,20). In pros clones, the size of the NBs (Ase+ blue), and cellular growth measured as the ratio of nucleolus (Fib, white)/nuclear (Ase, blue) volume was not significantly altered upon 6 days of histidine dietary withdrawal, quantified in (H) (n=9,8)
(B) Venn-Diagram of differentially expressed proteins between somatic and process compartment.
G. Representative images showing mTFP (cyan) and Venus (yellow) fluorescence in control (upper panel) or MCT12 (lower panel) siRNA treated HBVPs in a 2 well chamber assay system with BMECs. VECAD (purple) immunostaining was used for endothelial staining. H. Quantification of the mTFP/Venus fluorescence ratio of Laconic in control (blue) or MCT12 (orange) siRNA treated HBVPs. (n=8 from independent experiments. Error bars indicate the standard error of the mean (SEM) from unpaired Student's t test.
HEK293, RPE, or U2OS/MycBioID-FAM111A cell lines were induced with doxycycline to express wild-type or mutant FAM111A for 24 h (HEK293), 48 h (RPE), or 72h (U2OS). The colonies were fixed then stained with crystal violet.
(e) MEFs stably expressing EGFP-Bcl-2(H235R) and FLAG-Parkin were incubated in the absence or presence of CCCP (30 μM) for 4 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to cytochrome c and to FLAG (rabbit polyclonal). The fluorescence of EGFP-Bcl-2(H235R) was also monitored directly. Higher-magnification views of the boxed areas are shown in the right panels of each set.
K Representative images of mCherry-Atg8a (red) and DAPI (blue) in Drosophila larval fat body in which dGcn5 is overexpressed (OE) or silenced (KD) using the pan-fat body driver (cg-GAL4). Drosophila (cg-GAL4/+) was used as the control (Graph represents data from three independent experiments with ≥ 30 cells per condition; mean ± SEM; *p < 0.05, ***p < 0.001, Student's t-test; Scale bars, 10 µm).
Pom1-tdTomato (red) and Tea4-GFP (green) profiles were quantified along the cortex of the same Schizosaccharomyces pombe cells. Curves are averages from 385 individual profiles.
E) Workflow for determining follicle shape shapes. Segmentation of an egg chamber with an aspect ratio of 1.5 reveals that follicle cell elongation is usually perpendicular to the elongation axis of the egg chamber. Cell outlines were marked with Basigin::YFP. Scale bars = 5 μm
CD11b+ CD11c+ dendritic cells were enriched from WT or Rab39a KO spleens via magnetic negative selection. Cells were fed with 3 µm magnetic beads conjugated to Alexa fluor dye. After 4 hours, cells were harvested and resuspended in 1 mg/ml Trypan blue to quench fluorescence of uneaten beads. Cells were run for flow cytometry to measure phagocytosis. The ratio of KO cells with beads / WT cells with beads was then obtained. Graphs show three independent experiments and p values were calculated using two-tailed ratio-paired Student's t-test. Error bars show SD between experiments.
Flow cytometric analysis of surface H2-Kb and I-Ab levels of siRNA treated DC3.2R cells. Shown are results after 48 hours of knockdown. Representative plot of 3 independent experiments