EMBO/sd-character-level-ner huggingface dataset:
(C) The effect of OPA1 overexpression on the number of AP‐containing mitochondria. Imaging of INS1 cells already expressing LC3:GFP and mtDsRed was performed 48-72 h after adenoviral transduction with either OPA1 overexpression or control (mitoPA‐GFP). The number of AP‐containing mitochondria in the OPA1 overexpression (OE, n=6) was normalized to the control (*P=0.001). Images show representative cells from each group. Red, mtDsRed; green, LC3:GFP. In the control cell, note the colocalization of APs with mitochondria. Scale bar, 10 μm.
A) Schematic of experimental design. Hair follicles (HFs) were pre-treated with (or without) palbociclib for 18h then further incubated either with/without paclitaxel for a further 24h. Subsequently, drug-containing media was washed out and HFs were cultured for an additional 24-48h period.
Confocal images of MDCK cells expressing mCherry-D4H. Colocalization with the cortical actin (phalloidin) indicates that mCherry-D4H is predominantly localized to the plasma membrane in DMSO treated cells. Within 24 hours of ML-SI1 treatment, the mCherry-D4H redistributes to intracellular punctae. Although minimal mCherry-D4H signal remained at the plasma membrane in ML-SI1-treated cells, the phalloidin signal (cortical actin) remained unchanged. Scale bar (10μm) shown in the panel on the top right applies to all panels. Bar graph showing quantification of mCherry-D4H punctae in DMSO or ML-SI1-treated cells. All values represent mean±SEM. Data points represent values from biological replicates. Statistical test employed was Student's t-test.
(B) Expression of mtDNA‐encoded subunit I of cytochrome oxidase (COX I) in INS1 cells infected with FIS1 RNAi and control RNAi lentiviruses and tested after 1 week.
PKA activities in testicular sperm from WT (+/+) and KO (-/-) mice. Graph shows average PKA activity in testicular sperm from KO mice (black bar) relative to that from WT mice (white bar), expressed as a percentage.
C. A549 cells were transfected with plasmids encoding FLAG-tagged ZIKVNS5 or FLAG alone for 24 hrs and then treated with epoxomicin (400 nM) for 24 hrs. Cells were harvested and process for immunoprecipitation (IP) using a mouse anti-FLAG or anti-myc antibody followed by SDS-PAGE and Immunoblotting. Representative panels are shown. The experiment was repeated three times.
D. qRT-PCR of exonA specific reaction normalized to sum of exon specific and wt specific (total) Stim1 (± SD) in tissues using cDNA derived from 3-4 mice.
Average peak current-voltage relation for the total K+ current recorded from Clrn2clarinet/+ (P15-16, n=7) and Clrn2clarinet/clarinet (P15-16, n=5) OHCs.
C. HA-tagged SHMT-M detection via immunofluorescence microscopy. DAPI was used to visualise the nucleus, and MitoTracker CMXros used to illuminate the mitochondrion. Anti-HA signal partially colocalises with the mitochondrion.
(A) NF40 tadpoles with the following genotypes foxm1-/- (mut), foxm1+/- (het) and foxm1+/+ (wt) were amputated and left to regenerate for 7 days. The images show representative tails at 3 and 7 dpa. The white arrowheads indicate the amputation site. (B) Quantification of the rate of regeneration. The ratio of the length of the regenerate to the length that has originally be amputated was compared for the whole tail at 3 and 7 dpa. The graph represents the mean+/-SD of 5 independent experiments from 3 different clutches with at least 5 tadpoles in each experiment.
(a) Cluster formation assays were conducted in presence or absence of 20µM mCherry-LC3B or mCherry, either pre-mixed with p62 or added 1" after the addition of GST-4xUb. Quantification of particle number (left) and size (right) are shown
(S) IF staining for eMyHC and Laminin on TA muscles 7 days after the second CTX injury of Ctrl or YY1iKO mice. Quantifications of the number of eMyHC+ fibers per area are shown on the right (n=3 mice, each). Scale bar = 100 μm.
Model of an epigenetically primed inducible locus before and after reactivation of TCR/CD28 signaling.
Drug synergy plots for ara-C and HU or dF-dC in primary patient-derived AML blasts. Each data point indicates an average delta score from a single patient sample subjected to a dose-response matrix experiment performed in triplicate, n = 16 for HU and n = 9 for dF-dC. Zero, >0, or <0 corresponds to additive, synergy, or antagonism, respectively, whilst >5 indicates strong synergy. Median, upper and lower quartiles, and range of delta scores are indicated by box-and-whisker plots.
(A) Dissected mouse aorta demonstrating lipid-rich plaques in brachiocephalic artery after 4 months of high fat diet compared to the normal diet in Apoe-/- mice. (b) (d) Cross-section of brachiocephalic artery from (a) (c) stained with Oil Red O. L: lumen. Scale bar: 4 mm. 3 mice per group.
I. EATR assay. Chondrocytes with indicated genotypes (ctrl=wild type) treated with FGF18 (50 ng/mL; 16 hours) where indicated. ER acidification was measured by FACS. Mean +/- standard error of the mean (sem) of N= 17 (veh), N=17 (FGF18), N=4 (FGFR3;4KO); N=4 (FGFR3;4KO FGF18) biological replicates. Analysis of variance one way (ANOVA) p<0.0001; Tukey's post hoc test ***p<0.0005; NS not significant.
Confocal microscopy images of whole-mount preparations of mid-basal cochlear sensory epithelia from Clrn2clarinet/+ (A) and Clrn2clarinet/clarinet (B) P6 mice immunostained for actin. Despite lack of clarin-2, the developing sensory epithelium of mutants is similar to that of heterozygous controls.
H Degradation of MAGE-A3/6 upon nutrient deprivation is dependent on a Cul4 E3 ubiquitin ligase complex. HeLa cells were transfected with vector control or the indicated dominant negative (D/N) Cullin constructs for 48 hrs before harvesting cells after 0 or 4 hrs EBSS treatment.
A-C. Immunofluorescence images of esg-GFP and Lysotracker staining with the midgut section from the R4 region in 14-day WT flies (A), 40-day WT flies (B), 40-day WT flies with ALA administration (C). esg-GFP (green; outlined by dotted lines), lysotracker (red). esg-GFP+ cells are outlined by red dotted lines in the images of lysotracker staining channel. D. Quantification of the dot number of Lysotracker in esg positive cells from experiments (A-C). n is indicated. The numbers of quantified guts from left to right are 9, 11, and 8. E. Quantification of the dot size of Lysotracker in esg positive cells from experiments (A-C). n is as indicated. F- Data information: DAPI stained nuclei are shown in blue. Scale bars represent 5 μm Error bars represent SDs. Student's t-tests, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
EdU-labeled viral DNA forms large foci in ThP1 cells infected by HIV-1. EdU images are shown in red, DAPI images in blue. (A) Left: nucleus of an infected cell at 48 h p.i. displays three large and bright EdU foci (colored arrows), as well as small and dim punctae (grey arrows). Center: Magnified views have colored borders matching the colors of the arrows. 3D images show that EdU foci are located within the nucleoplasm (Movie EV1, Appendix Fig. S2). Right: nucleus of an uninfected cell displays no EdU signal. (B) Graph shows EdU intensity profiles along lines shown in A, with colors matching the corresponding arrows.
K. Quantification of CFP+ MDA-MB-231 cells displaying different types of morphology in vivo, expressed as average number of events, observed from a total of 30 positions in n=5 mice/group (Control or RASSF1C). Mesenchymal, amoeboid and hybrid morphology were scored manually based on diameter and circularity (distance between the two furthest points). The higher distance between cell edges was defined as mesenchymal morphology, while the lower distance was considered amoeboid morphology. 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.
f, g, k, l, Electron micrographs of wild-type (WT) and Atg5-/- (KO) reticulocytes (f, g) and erythrocytes (k, l). An isolation membrane (asterisk), autophagosomes (arrows) and autolysosomes (arrowheads) are shown. Inset, engulfed mitochondria.
F Immunoassay of IRF3 in dimer or monomer form by native-gel and p-IRF3 (Ser396), p-TBK1 (Ser172), AKT2 and ACTIN by SDS-gel in WT and Akt2 KO PEMs with VSV stimulation for 6 hours. Data information: * Data are representative of two or three independent biological replicates
F Measures related to behaviour and neurological function, data generated by the SHIRPA (9 weeks old, F), n = 7f, 8m Uqcrh-/- and 8f, 9m WT animals. Prepulse inhibition of the acoustic startle as a parameter associated with sensorimotor gating (10 weeks, E right panel), n = 7 f/5 m Uqcrh-/- and 8 f/ 9 m WT mice. Sex is not differentiated. Data are shown as scatter dot plots with a line representing the median. *** p < 0.001, **** p < 0.0001, Wilcoxon rank-sum test.
Depletion of ASS1 decreased cell migration in SW-1116 cells. Scale bar represents 100 μM.
(E) Quantification of colocalization using the Pearson`s correlation coefficient (PCC) of the pC4-construct (GFP) and the cis-Golgi marker GM130 (0 min: ctrl n=63, #1 n=56, #2 n=64; 10 min: ctrl n=104, #1 n=126, #2 n=110). Shown are means ± SEM. Colocalization is significantly reduced by BET1 knockdown (siRNA #1 and #2) compared to control transfected cells. Significant differences of PCC (pC4:GM130) after 10 min induction with solubilizer were analyzed with a one-way-ANOVA followed by Dunnett`s post-hoc test. ***=p≤0.001. 0 min: ctrl 0.265±0.016, #1 0.268±0.017, #2 0.264±0.018; 10 min: ctrl 0.798±0.009, #1 0.726±0.011, #2 0.715±0.011.
In the absence of POT1 the telomeric C-strand is resected and RPA and recombination proteins associate with the overhang. RAD51-coated overhangs invade telomeric DNA of adjacent chromosome ends and the invading 3'end is extended by DNA polymerases. Accumulation of R-loops at telomeres facilitates strand invasion. In case of proper dissolution of the HR intermediates, telomeres are elongated and fragility is due to abnormal chromatin condensation after HDR. Defective dissolution of the HR intermediates leads to accumulation of branched DNA structures. Incomplete fill-in synthesis leads to accumulation of G-rich single stranded DNA.
D458 cell lines were treated with PBS (vehicle, black) or with ActivinB (green). Percentage of apoptotic cells measured by FACS analysis of cleaved caspase3 48h hours after treatment with ActivinB. Bars represent the mean ± SD. Number of replicates is n≥3.
C, Phosphorylation of TOC1 is eliminated or largely reduced in 5X and S175A. Total protein extracts (ZT13) from 10-day-old seedlings grown under 12h/12h light/dark cycles were subject to heat (30ºC 20min), pyrophosphatase (PP) and NaF/Na3VO4 (phosphatase inhibitors) treatments. TOC1-GFP at different phosphorylation states were separated by 8% SDS-PAGE (acrylamide:bisacrylamide 150:1) and subsequently detected by α-GFP.
Western Blot analysis of pCREB/CREB and p-c-Fos/c-Fos protein expression in lysates directly isolated from 143b xenografts at endpoint, after 14 days of vehicle or Erlotinib treatment
A Schematic representation of the zebrafish Grk2 protein showing the location of residues assayed for the effects of their mutation on rescuing activity.
Ronin fl/del and Ronin del/del (day 4) cells grown in 3D culture conditions for 48 h and stained for apical polarity markers - Podocalyxin and Par6, as well as Phalloidin, E-cad and tdTomato.
(e) Parameter exploration of phase synchronisation quantified using the Kuramoto Order Parameter (see Materials and Methods) where 1 indicates global in-phase activity and 0 indicates no co-ordination of phase between cells.
G: Quantification of preimplantation embryos derived from WT and Cnot6l-/- females that develop to the indicated stages after hCG administration and mated with adult WT males. The numbers of analyzed embryos are indicated (n)
(g) Phase shift showing absolute lag distance corresponding to in-phase peak in Venus::HES5 vs NGN2::mScarlet-I cross-correlation function of spatial intensity profiles from the same slice. 34 individual data points from 6 slices, 2 experiments; red line indicates average inter-nuclear distance in D-V; bars show mean±SD; 2-tailed Mann-Whitney test not significant, p=0.32.
Number of lipid droplets (LD) found within membrane protrusions on transmission electron microscopy images of 1205Lu cells exposed, or not, to 3T3-F442A EV (3T3-EV) (n=28 for control and n=27 for 3T3-EV). Area of lipid droplets (LD) found within membrane protrusions on transmission electron microscopy images of 1205Lu cells exposed, or not, to 3T3-F442A EV (n=19 for control and n=25 for 3T3-EV).
Unsharpened cryo- EM density for the PKI region of the IAPV-IRES in class 1 with the SL-III and the tRNA/mRNA mimicking domain indicated.
Ultrastructures of epididymal sperm in KO mice. TEM images represent ultrastructures of separated sperm head (upper) and tail (lower) in the epididymis of KO mice. Images in the boxes are enlarged at right. BP, basal plates; Cp, capitulum; SC, segmented column. Scale bar = 500 nm.
B Treatment scheme of experimental timeline and histology of backskin sections of control (Ctr) and ABT-199 treated mice. Scale bar, 200 µm.
Superposition of the IAPV-IRES in complex with 80S (class 1) with tRNAs in different configurations indicated at the bottom. Alignments of the models were computed with the 40S body, excluding from the computation the ligands (IRES/tRNAs) and the 40S head. IAPV-IRES PKI components SL-III/ASL-like domain populates a space of the intersubunit space similar to a A/P-tRNA. IAPV-IRES PKIII (red) mimics the elbow region of a hybrid P/E-tRNA.
(E-F) M238P cells were transfected with two different sequences of siRNAs vs FSCN1 or with a control siRNA (72 h, 100 nM). (E) Images and quantification of cell area in cells stained for F-actin (red) and nuclei (blue). Data is represented as scatter plot with mean ± SD (n≥30 cells per condition). Mann-Whitney U test was used for statistical analysis. ****P≤0.0001. Scale bar 40 μm. (F) Images and quantification of focal adhesions (FA) number in cells stained for pPaxillin (green) and nuclei (blue). Focal adhesions number is represented as mean ± SD (n≥30 cells per condition). Each point represents the average number of focal adhesions per cell calculated for each field. Paired Student t-test was used for statistical analysis. ****P≤0.0001. Scale bar 40 μm.
C. Detailed DNA sequence depicting nucleotide positions within the Wt and ∆482 rab13 3'UTR.
ChIP analysis of NF45 and NF90 binding to the H42.9 loci in HeLa cells with the treatment of CX5461 or DMSO for 2 h. (n = 3)
(a) A histological section through mouse seminiferous tubules labelled for MKLP1 shows several MKLP1+ puncta in cells of the basal layer where stem cells reside. Scale bar, 20 μm. Inset: Enlargement of the cell marked by the arrow.
E Quantification of LC3 puncta in cells stably expressing HA‐Flag‐ATG9A, treated and presented as in (D). 100 cells were quantified in 3 independent experiments.
(E, F) THP-1 (E) or human CD14+ monocytes (F) were transfected with plasmids encoding FLAG-tagged nucleocapsid for 36 h, followed by pretreatment of 1 μg/ml LPS for 3 h and 10 μM nigericin stimulation for 30 min. Cells were lysed and immunoprecipitated with antibody against FLAG or isotype IgG. Input and precipitates were immunoblotted as indicated.
(A) Euc1 interacts with SUMO pathway proteins in a yeast two-hybrid (Y2H) assay. A Y2H reporter strain (PJ69-7a) was transformed with Gal4 DNA-binding domain (BD) and Gal4 activation domain (AD) fusion constructs in the indicated combinations. AD-SUMO-GG can be conjugated to SUMOylation substrates, while AD-SUMO-AA is conjugation-deficient. Cells were spotted on control media or selective media (- His) and grown for 3 and 6 days, respectively.
Quantification of sulfide levels in cerebrum and kidneys of Coq9+/+, Coq9R239X and Coq9Q95X mice (A).
(A) UMAP plot illustrating the color-coded aggregated transcript counts of published core signature genes for CAMs. The scale bar represents color coded sequencing depth-corrected log transformed transcript counts.
Immunoblot showing increase in expression levels of differentiation markers Involucrin (IVL) and Transglutaminase-1 (TGase-1) as differentiation progressed indicating that keratinocyte differentiation protocol was successful. Protein levels on day 0 (D0), day 1 (D1), day 3 (D3) and day 6 (D6) of differentiation are shown. Immunoblot for JARID2 during D0, D1, D3 and D6 of differentiation (as in B) are shown.
(C) Quantification of Duolink-particle density of Figure 5A and B assessing PTX-treatment effect. n=3 independent experiments with 10 images averaged per condition and experiment; Three-way ANOVA followed by Tukey's post-hoc multiple comparison test; *p < 0.05; **p < 0.01).
(d) p-mTOR/mTOR ratios in WT and miR-212/132 TG H9c2 cells 24 h after normal and starvation (serum/glucose-deprived) conditions (n=6).
A Representative pictures of embryos at 18.5 days postcoitum (E18.5) and hematoxylin and eosin staining of whole-mount embryo sections from PR-SET7loxp/Alfp-Cre (PR-SET7ΔHepE) mice and control littermates (WT).
B, C. Average miR expression levels in unstimulated naive CD4 T cells non-infected vs HIV-1NL4-3 (B) or HIV-2ROD (C) infected after 24h (n=2, three pooled samples per library). Mean normalized read counts across libraries are shown. Library normalization was performed using the mean normalization method available in the Deseq package of Bioconductor (Anders Huber, 2010). Lines indicate changes of +/- 1 log2 fold between samples.
Quantification of (F) nuclear, (G) cytoplasmic, and (H) of nuclear/cytoplasmic poly(A)+ FISH signals. (I) Relative nuclear and cytosolic total RNA levels in sh1 and sh2 compared to shScr. Data are presented as mean ± SEM of n ≥ 3 independent biological experiments. *P < 0.05, ***P < 0.001, ****P < 0.0001 (shScr vs. sh1 or sh2); unpaired Student's t-test.
WT and Mfn2 KO MEFs were co-transfected with plasmids encoding: B) GFP and ERMITO-RLuc and ER-Mfn2 or control plasmid. After 24 h, the transfected cells were sorted and plated for another 24 h, after which RLuc was analyzed (n= 4 independent experiments). Data are presented as mean ± SEM.
(a) Transcriptional levels of hlh-30 and the mxl-3-dependent lipl genes measured in 5 h fasted wild-type (WT) or hlh-30(tm1978) young-adult worms depicted as mean ddCt+s.e.m. relative to wild-type ad libitum-fed worms show that hlh-30 is induced following fasting and HLH-30 induces lysosomal lipolysis. N = 4 independent experiments for lipl data, n = 2 independent experiments for hlh-30 mRNA. HLH-30 deficiency fully abrogates lipl-2, 3 and 5 (P0.0001), and impairs lipl-1 (P0.01) transcriptional activation following fasting.
(F) Characterization of SKMel28 sensitive- and resistant- cell lines (SKMel28S and SKMel28R). Determination of BRAFi half maximal inhibitory concentrations (IC50 values) (Log[Vem] (nM)). A representative experiment has been chosen among two experiments. Dotted line is used to determine the IC50 values.
Western blot analysis showing effects of TGF-α on phosphorylation of EGFR, YAP, AKT, and ERK1/2. ME180 cells were starved for 6 h after reaching cell confluence, then cells were treated with TGF-α (100 ng/ml) for 0, 5, 10, 30, 60 or 120 min.
(E) Tadpoles at NF50 were amputated, fixed at the indicated time and then processed for whole mount in situ hybridisation using a probe specific for foxm1. The two last panels show transverse section in the non-regenerating spinal cord (nr) and the regenerate at 3dpa. The red circle highlights the spinal cord and the asterisk the notochord.
Measurement of gene conversion efficiency in cells carrying an empty vector or expressing DPB11BRCT3/4 fused to wild-type or mutant versions of SGS1. Mutants include a helicase deficient allele of SGS1 (SGS1hd) or an allele lacking the critical amino acid residues responsible for binding to Top3 (SGS1TIM). Error bars represent SEM of at least 3 replicate experiments. P value was calculated with a two-tailed, unpaired t-test. * = p≤0.05; ** = p≤0.01; *** = p ≤0.001.
H) Immunofluorescence analysis of CaSR+ (Green) and OCN+ (Red) cells in human spinal tissue.
(D Immunoblotting analysis for EGFR signaling in BT549 cells with GFP or MIG-6 knockdown.
(C-E). Wild type (WT), CDKL5­-disrupted (CDKL5Δ/Δ) or siRNA-transfected cells were subjected to indirect immunofluorescence analysis with the indicated antibodies at laser tracks. Quantification of ELOA-pSer311 signal at the laser tracks is shown. Data represent mean ± SD of total pELOA Ser311 intensities in different biological replicates as indicated (n). For simplicity, only intensities greater than zero are shown. Statistical significance was assessed by one-way-ANOVA-test or unpaired t test with Welch's correction. Asterisks **** indicate P-values of <0.0001. Scale bar is 10 μm
CD8+ HER-2 CAR-T cells generated from Ptpn2fl/fl versus Lck-Cre;Ptpn2fl/fl versus Lck-Cre;Ptpn2fl/fl;Lck+/- splenocytes were stained for intracellular p(Y418)-SFK and p(Y418)-SFK MFIs were determined by flow cytometry.
A. HeLa cells were starved for 8 h with HBSS and subsequently exposed to SA (30 min, 300 µM), and immunostained for Sec24C or TRAPPC2 and eIF3. Scale bar 10 µm.
The most significantly changed canonical pathways between fetal organoid at day 3 and 30 of culture.
Western blotting assays showed stable expression of ASS1WT and ASS1 K234R via an viral infections into Caco-2 or Caco-2 LOC113230 FL cells, respectively .
HCoVs.a to h. Inhibitory activity of EK1C4 in cell-cell fusion mediated by the S proteins of SARS-CoV (a)
Locomotion was assessed by counting body bends per minute. Wild type animals were compared to aak-2(ok524) mutant animals. 2-sample, 2-tailed unpaired t-test *p < 0.0001, wild type n = 35, aak-2 n = 39 animals across at least 3 days. Data show mean ± standard deviation.
Western blot analysis of Galectin-3 and GPNMB in the brain 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.
D. discoideum producing the LCV/PtdIns(4)P probe P4C-mCherry was infected (MOI 5, 48 h) with L. pneumophila wild-type strains (JR32, Corby), or phospholipase triple mutants (∆plcABC, ∆plaACD) harboring the Ptac-mCerulean-PflaA-gfp reporter construct, and fixed and treated with an anti‐ubiquitin antibody, LCV escape and cytosolic localization of the bacteria was assessed by confocal microscopy through quantification of amoeba containing intact, P4C-mCherry-positive LCVs or ubiquitin-decorated, cytosolic bacteria. (A) Representative images of amoebae harboring L. pneumophila confined within LCVs or released from the LCV to the cytosol are shown (scale bars: 5 μm).
(g) Pulldown of UVRAG-C2 domain GST-fusion proteins by liposomes bearing the indicated phosphoinositides. GST-Hrs-FYVE and GST-FAPP1-PH are also shown.
B: Heat map of shRNA reads in D6C and D6F populations compared with ESCs. shRNAs specifically depleted in D6C and D6F are labeled as Groups XI and XII, respectively.
Bacterial inoculation promotes plant growth and alleviates LP stress. Arabidopsis seeds were germinated on 1/2-strength MS media for 3 days and then transplanted to either HP or LP media for another 5 days. The seedlings were then transferred to vermiculite and inoculated with Pto DC3000 or B. subtilis. (B), The seedlings were harvested, and the shoot fresh weight was measured 4 weeks after inoculation. The data shown indicate the means ± SDs (n = 30, n refers to the number of seedlings per group), Central bands: median, boxes: interquartile range, whiskers: max./min; n.s., not significant; *, p < 0.05, **, p < 0.01 (Student's t test). Data information: All experiments were repeated three times with similar results.
(D) Mean number of Rb−/− myotubes after 3-MA treatment, bezafibrate, or DMSO/vehicle as indicated. Counts are mean ± SD of six fields (n = 4).