EMBO/sd-character-level-ner huggingface dataset:
(A-B) Old (red) versus new (green) histone H3 distribution patterns and percentage of signal strength with a single genomic locus labeled with fluorescent probes (cyan) for dad (A) and bam (B) in WT telophase female GSCs, marked by anti-H3S10p (gray). (C) Quantification of the probe association ratios with old versus new H3 for each candidate gene in WT female GSCs. Data gathered over 8 separate experiments. D
Quantification of mCherry-ATG8a puncta (I) (Graph represents data from three independent experiments with ≥ 30 cells per condition; mean ± SEM; ***p < 0.001, Student's t-test).
I Magnified still images extracted from Supplementary Movie S2. mCherry‐TBC1D5 co‐localizes with GFP‐ATG9 upon autophagy induction by mTOR inhibitor, KU0063794.
(D) Lysosomal-mitochondrial fractions were isolated from mouse fibroblasts untreated or loaded with cholesterol (50 μM). Top: Distribution of LAMP‐2A after Triton X‐114 extraction and sucrose density gradient centrifugation. Bottom: Ability of intact or disrupted lysosomal-mitochondrial fractions to proteolize [14C]GAPDH. Values are expressed as percentage of the degradation in fractions from untreated cells and are the mean±s.e. of triplicate samples.
(A) WT and SKO cells were treated with OA for 1 h and processed for ET. Representative single tomographic slices of ER-LD contacts. Orange arrowheads indicate narrow ER-LD contacts, blue arrowheads indicate widened ER profiles seen in SKOcells. (B) 3D-models of LDs and ER-LD contacts based on tomograms in (A). Yellow: ER, brown: LD, red: ER-LD contacts.
(b) Cells pulse-chased with EdU show a decrease in EdU intensity (x axis) over time (y axis), reflecting dilution of dye after cell divisions. (c,d) After a 96 h chase period, EdU levels were compared between cells with MBd numbers of >1, 1 and 0 (y axis) in HeLa (c) and SAOS-2 cells (d). In both cases, no significant differences were noted (c, P=0.2101; d, P=0.5609, one-way analysis of variance, with at least 800 cells analysed for each experiment, n=3), indicating similar cycling rates among different subpopulations of cells. (b-d) Each graph is a representative experiment. Cells analysed are shown by green points, the medians are depicted by vertical red lines, and horizontal red lines with ticks illustrate the interquartile range.
Maximum projections of representative regenerating trunks after FISH for smedwi-1 in starved conditions. The dashed line delimits the body of the planarian.
G. Schematic of TIRF microscopy-based MT stabilization assay reported in H and I. Various concentrations of unlabelled DCX variants were added to 9 μM unlabelled tubulin mixed with 1 μM HiLyte Fluor™ 488-labeled tubulin in the presence of surface-immobilised HiLyte Fluor™ 488-labeled GMPCPP MT seeds; e-field, evanescent field.
A. Schematic exon structure of Stim1 gene with conventional exons depicted in grey. Highlighted in red is the alternative exon 11 (named A), and additional mutually exclusive splicing of exon 13 (named L, green) or exon 13 (named B, blue). Alternative usage of 5'UTR regions are indicated with alt1 and alt2. Arrows indicate schematic location of primers, B. Schematic representation of primer annealing sites on the coding mRNA.
A minimal ecological scenario of alternating periods of feast and famine is used to study overall fitness of different strategies. Periods of famine and feast can vary between scenarios. Based on the observed relation between growth and death (Figs. 1 and 2), we assume that bacteria cannot independently choose growth and death rate, but are forced to trade-off growth against death according to the exponential relation γ(μ) = 0.21 d − 1exp (1.0 h μ).
(B) Mitochondrial calcium measured in liver mitochondria isolated from the indicated experimental mouse groups.
B Co-IP assays for the interactions of DJA6 with SUFE1 and SUFC. Total protein extracts of protoplasts co-transfected with designated constructs were subjected to immunoprecipitation, and then analyzed by immunoblotting with antibodies indicated on the right. Input (left lane) indicates that 100 μg total protein was loaded on the gel.
E0771-HER-2-PTPN2hi mammary tumour cells (2x105) were injected into the fourth inguinal mammary fat pads of female HER-2 TG mice. Five days after tumour injection mice were administered vehicle or DOX in drinking water followed by irradiation (4 Gy) on day 6 and the adoptive transfer of 6x106 FACS-purified central memory Ptpn2fl/fl versus Lck-Cre;Ptpn2fl/fl HER-2 CAR-T cells. Mice were then injected with IL-2 (50,000 IU/day) on days 0-4 post adoptive CAR-T cell transfer and (h) tumour growth was monitored.
H, I. siRNA-treated U2OS cells were transfected with empty vectors (EV) or plasmids containing Plk4 or siRNA-resistant Plk4-myc WT* or KD* and immunostained with the indicated antibodies. Cell peripheries are marked with solid lines, in which cells with yellow lines are successfully transfected (positive in myc signals), while those with white lines represent non-transfected cells. Quantification of PCM1 distribution is shown in I. Data represent the mean + SD (>200 cells, n=3). Statistical analysis was performed using two-tailed unpaired student's t-tests. ****p<0.0001, **p<0.01, n.s. (not significant). Scale bar, 5 μm (H).
(I) Venn diagram showing the overlap between the genes that failed to be activated in SCNT 2-cell embryos and derepressed in D-SCNT. Heatmap, GO terms showing the expression pattern of 257 overlapping genes.
(E and F) Immunoblots showing ATG4C and BECN1 protein levels following control miRNA (MIR-CONT) or MIR376A overexpression. ACTB was used as a loading control. ATG4C/ACTB or BECN1/ACTB densitometric ratios were marked.
E. Quantification of excretion numbers of Drosophila of indicated genotypes. Excretions are quantified in 30 fields for each group of 12 Drosophila. Tests were repeated as three independent experiments. Data information: Error bars represent SDs. The statistical tests used in other panels were student's t-tests. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
Average ATAC-Seq signal at the 411 IL-2 pDHSs which contain a STAT binding motif.
BRAFi-resistant M238R cells overexpressing FSCN1 were obtained after transduction with a FSCN1 lentiviral construct. M238R transduced with a Ctrl lentivirus were used as control. (H) Crystal violet viability assay of M238R cells stably overexpressing FSCN1 during 6 days with the indicated doses of the BRAFi Vemurafenib. Data is represented as mean ± SD from a triplicate representative of at least 3 independent experiments. Paired Student t-test was used for statistical analysis. ****P≤0.0001.
C, D Weight of m. tibialis anterior (TA) and m. digitorum longus (EDL) of male linc-MYH KO and ctrl mice at 10 weeks (n = 9 KO/10 WT for TA, n = 10 KO/11 WT for EDL; Student's t test, two-tailed, **p < 0.01, ***p<0.001). Data are mean ± S.E.M.
Neurons expressing M18Y473D are not impaired at SV docking. Autaptic munc18-1 null hippocampal neurons expressing M18Y473D or M18WT as controls were analysed with electron microscopy on chemically fixed samples (D) The active zone (AZ) length is similar (M18WT: 561 ± 24 nm; M18Y473D: 646 ± 59 nm, multilevel analysis, p = 0.161).(B-E) M18WT : N=6 autaptic neurons, n=137 synapses; M18Y473D: N=8 autaptic neurons, n=116 synapses.
Identification of the ENU-induced hearing loss pedigree MPC169, subsequently named clarinet. ABR phenotyping of pedigree Muta-Ped-C3PDE-169 at 3-months of age identified 8 mice with elevated hearing thresholds (red triangles) compared to their normal hearing colony mates (n=61, black triangles). Indeed, all eight affected mice were found to not respond to the highest intensity stimulus (90 dB SPL) at the three frequencies tested, or the click stimulus, and so their thresholds are shown as 95 dB SPL.
B, The Fa-CI plot of drug combinations (candidate drug plus BI2536) in KRAS-mutant (BEAS-2B-KRAS) and wild-type (BEAS-2B) cells. The data are mean values of two independent experiments (n=2) where all drugs are used at their IC50 determined in BEAS-2B-KRAS cells. Note that combination treatment with AZD4547 and BI2536 exhibit the leading therapeutic efficacy and safety profile, manifested by the greatest synergy (CI=0.25) in BEAS-2B-KRAS while the two drugs are antagonistic in BEAS-2B cells (CI>1).
(D) HASMCs were cultured in the growth medium (M231 + SMGS) at day 0 then switched from growth conditions to differentiation medium (M231 + SMDS) for 8 days. Quantitative real-time PCR analysis of mature let-7 family in HASMCs. SNORD47 was used to normalize the variability in template loading. Histogram of qRT-PCR results are three independent experiments.
I. GST pull-down assays of yTBP (61-240) with Kap114p or Kap114p (Δ347-371) in the presence or absence of RanQ69L. GST-fused yTBP (61-240) was incubated with recombinant Kap114p and His-tagged RanQ69L at a molar ratio of 1:4:8 Kap114p:yTBP:RanQ69L. Unbound (S) and bound (B) samples were analyzed by SDS-PAGE and stained with Coomassie blue. J. Analysis of Kap114p dissociation from yTBP in the presence of RanQ69L. Band intensities of Kap114p and Kap114p (Δ347-371) from the SDS-PAGE gels were used to determine the average fraction of bound protein.
D The volcano plots showing the differentially expressed genes in ageing tissues. Genes with a fold change greater than 1.5 and a P value smaller than 0.05 were considered significantly changed by ageing. The numbers and percentages of Age-DEGs in expressed genes are shown in the corresponding plots.
RNAPII CRAC were performed in the presence of the indicated versions of SEN1 expressed from its own promoter in a centromeric plasmid, upon depletion of the chromosomally-encoded version of Sen1 in a Sen1-AID strain. I) Venn diagrams illustrating the overlap between the CUTs that display statistically significant termination defects (p-value≤ 0.05, see methods for details) in the different mutants. The size of the circles is not proportional to the number of CUTs.
C. TF:proOmpA:SecB supercomplex analysis using GPC-MALS in Buffer A. TF1:proOmpA1 (10 µM each; green), SecB4 (40 µM; blue) and TF1:proOmpA1:SecB4 (10, 10 and 40 µM, respectively; black). n= 5 biological replicates; mean mass: 137 kDa (± 6 kDa) representative experiment shown; red circles: determined mass (kDa); AU: arbitrary units.
g, h, Induction of Ulk1 in the etoposide-treated Atg5-/- MEFs was assessed by qPCR (g) and by immunoblotting (h).
(F and G) Immunostaining assay of PAX6 (green) and SOX1 (red) in control and V1-PAKI cells on day 16 of dorsal neural differentiation (F), and quantiﬁcation of SOX1+ cells (G), p=0.0001. Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). *p<0.05, **p<0.01, ***p<0.001 (unpaired two-tailed Student's t-test).
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 (A-C) fixed and treated with an anti‐ubiquitin antibody, or (D) lysed, fixed and analyzed by flow cytometry. 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. (B) The percentage of D. discoideum with intact LCVs was assessed for the following number of cells: JR32, n = 132; JR32 ∆plcABC, n = 606; Corby, n = 265; Corby ∆plaACD, n = 357. (C) The percentage of D. discoideum harboring ubiquitinated L. pneumophila was assessed for the following number of cells: JR32, n = 100; JR32 ∆plcABC, n = 602; Corby, n = 281; Corby ∆plaACD, n = 389. (D) Quantification of GFP-positive bacteria of the L. pneumophila strains by flow cytometry and FlowJo software. Data shown are means and SEM from (B, C) three biological replicates and (D) a technical triplicate (two-tailed Student's t test; *P < 0.05, and **P < 0.01).
Schematic showing the role of TRPML1 in vesicular trafficking. TRPML1 is active in the membrane of late-endosomes and facilitates fusion of these vesicles with lysosomes or the plasma membrane. Channels delivered to the plasma membrane are redelivered to the late-endosomes via endocytosis. Whereas delivery of vesicles to the lysosomes is required for cholesterol de-esterification in that compartment, vesicular fusion with the plasma membrane is required for cholesterol recycling.
Left panel, indicated cells were incubated with EV from 3T3-F442A adipocytes previously loaded with BODIPY FL C16 and immediately treated, or not, with Etomoxir for 24h. Then, cells were fixed and nuclei were counterstained with DAPI before observation by confocal microscopy. Right panel, quantification of BODIPY FL C16 staining area per cell (n=3).
Alignment of the 2019-nCoV RBD (core in cyan and RBM in red) and SARS-CoV RBD (core in orange and RBM in blue) structures.
Percentage differences of F-actin and microtubule fluorescence intensities at the centrosome were compared in cells transfected either with centrin1-VCA-GFP or with centrin1-GFP. Errors bars represent standard deviations. P values were calculated with one-sample t-test (i.e. comparison to a theoretical mean of "0").
The expression of H1f1α, Snai2, Twist1/2, and Zeb1 was modulated with overexpression or sh-RNA-mediated knockdown via a retrovirus system during reprogramming with 5C medium (C). The expression of Bmi1, Ctcf, Ezh2, Kdm2b, Wdr5 was determined on day 6 with qPCR and normalized against those in MEFs. The comparisons were performed between all groups and corresponding Flag groups.
C, D, E. Quantification of the dispersion of satellite components upon depletion of Plk4 but not hSAS-6 knockdown. The results of PCM1 (C), hMsd1/SSX2IP (D) or BBS4 (E) are shown. Data represent the mean + SD (>200 cells, n=3). Statistical analysis was performed using two-tailed unpaired student's t-tests. **p<0.01, n.s. (not significant).
(I) Plasmids encoding wild-type GSDMD, GSDMDsusti. or mCherry-GSDMD-C were co-transfected with nucleocapsid into HEK293T cells, followed by immunoprecipitation with antibody against FLAG. Input and precipitates were immunoblotted with antibodies against the indicated protein tags. Data information: Experiments were repeated for three times with similar results.
A, Long-range BIR/RMD with identical repeats or divergent repeats. The frequency of BIR/RMD in mES cells carrying the RMD-GFP reporter with identical repeats (0%) or repeats with 1% and 3% divergence was determined after cleavage at L17/R3.3k or L17/R28.4k.
(c) Quantification of width of Dorsal Oblique 3 (DO3) muscle in larvae carrying tumors of RasV12; ctrl at day 6 (n=29) and RasV12; scrib-/-at days 6 (n=29) and day 10 (n=31).
A Western blot analysis showing dynamic expression patterns of POU5F1 and METTL5 during the indicated time points of EB induction. α-TUBULIN was used as a loading control.
(H) Brucella replication in BMMs treated with either non-targeting siRNAs (siNT), or siRNAs against Stx6 (siStx6) and infected for 24 h with either wild type (2308), ΔbspF, or complemented ∆bspF (ΔbspF::bspF) bacteria. Data are means ± SD of n=3 independent experiments, in which at least 100 cells were analyzed per experiment. Grey dots represent individual cells analyzed (n>300); black dots indicate means of individual experiments. Asterisks indicate statistically significant differences (P<0.05, one-way ANOVA followed by Dunnett's multiple comparisons test) between test and control conditions.
(C) Distribution of MTR FI (given in Δψm) of AP‐localized mitochondria at different times before autophagy. Values are relative to cell's average MTR FI. In the x‐axis, a zero value represents the average Δψm and positive values represent depolarized mitochondria.
Ronin is dispensable for the development of the pluripotent lineage during the "quiet" pre-implantation embryogenesis, but it is critical for exit of embryo dormancy and for providing enough metabolic capacity for the post-implantation epiblast to support cell proliferation and morphogenesis.
HER-2-E0771 mammary tumour cells (2x105) were injected into the fourth inguinal mammary fat pads of female HER-2 TG mice. Six days after tumour injection HER-2 TG mice received total body irradiation (4 Gy) followed by the adoptive transfer of 10x106 control HER-2 CAR-T cells or those in which PTPN2 had been deleted by CRISPR RNP. Mice were injected with IL-2 (50,000 IU/day) on days 0-4 post adoptive CAR-T cell transfer and tumour growth monitored. g) CD45+ CD8+ mCherry+ CAR-T cells numbers were determined in HER-2-E0771 tumours by flow cytometry 19 days post adoptive transfer.
A. Quantification of the mTFP/Venus fluorescence ratio of laconic (lactate sensor) showing concentration-dependent lactate uptake in HBVPs. (n=8 from 3 independent experiments. Error bars indicate the standard error of the mean (SEM)) B. Representative images showing mTFP (blue) and Venus (yellow) fluorescence in control and lactate (20mM) treated HBVPs.
Apo-Bd1971 was supplemented with 10 mM MgCl2 or CaCl2 in conjunction with saturating concentrations (2.5 mM) of cAMP, cGMP or no nucleotide and phosphodiesterase activity with respect to the generic substrate PNPP (5 mM) was measured spectrophotometrically. Values are the average of three repeats, error bars represent standard deviation.
I-M. Time course of mRNA expression of NRP1 ligands in mouse RPE-choroid-sclera complexes relative to naïve (no burn), 3 (D3), 7 (D7), 10 (D10), and 14 (D14) days after burn for Vegfa (I); n = 11 (No burn), 6 (D3) , 7 (D7) , 4 (D10 and D14), Sema3a (J); n = 17 (No burn), 6 (D3) , 4 (D7) , 3 (D10 and D14), Tgfb1 (K); n = 14 (No burn), 3 (D3) , 7 (D7) , 3 (D10), 6 (D14), Pdgfb (L); n = 9 (No burn), 5 (D3 and D7), 4 (D10 and D14), Pgf (M); n = 6 (No burn), 4 (D3) , 3 (D7) , 6 (D10), 3 (D14).
C Pictures of representative subcutaneous xenograft tumors dissected from immunodeficient mice 20 days after injection with primary hepatocytes from P240 PR-SET7ΔHepA livers or Hepa 1-6 cells. Right panel shows average tumor volumes (n = 3) dissected at the indicated time points following injection.
F, G. U2OS cells were arrested in G1 and treated with control or Plk4 siRNA, followed by immunofluorescence microscopy by using indicated antibodies. Enlarged images (marked by arrowheads) are shown on the right. Quantification of PCM1 distribution is shown in G. >200 cells were counted and classified into two categories: normal (around and away from the centrosome) or dispersed. Data represent the mean + SD (n=3). Statistical analysis was performed using two-tailed unpaired student's t-tests. **p<0.01. Scale bar, 1 μm (F, right), 10 μm (F).
The cellular levels of Ca2+ ions after ligand (C10ORF99) stimulation of the indicated GPR15 receptors (human, mouse, Japanese quail GPR15). A plasmid encoding human NTSR1 and the parental pcDNA plasmid were transfected as positive and negative controls, respectively. The fold-change in calcium levels was calculated based on the fluorescence intensity (excitation and emission wavelengths: 490 and 520 nm, respectively). Calcium RLU (relative light unit) fold was calculated using no stimulation data as standard value.
F. Confocal images of JC-1 monomers (green) and aggregates (red) of GV and MII oocytes from wild-type (WT) and Erk1/2oo-/- oocytes (n=3 mice in each group). Erk1/2oo-/- oocytes exhibited big and multiple polar bodies, indicated by red arrows. Hoechst 33342 (blue) was co-stained to represent nucleus or chromosome. Scale bar=10 µm.
(E) Figure shows most strongly enriched DNA binding motifs within 3 specific peak sets; SOX3 and SOX9 bound regions around astrocyte specific genes, SOX9 and SOX10 bound regions around astrocyte specific genes, and SOX9 and SOX10 bound regions around oligodendrocyte specific genes
g, LC3 immunoblot of MDMs transduced with the indicated shRNA at day 0 and day 10 after HIV-1 infection. *P  0.05; **P  0.01; ***P  0.001; t-test.
(j) Density phase plots from instantaneous Hilbert phase reconstruction at multiple timepoints over a 12-14h period; dots indicate the phase angle in Cell 1 and Cell 2 from 14 pairs collected from 3 experiments; colormap indicates probability density showing accumulation of phase values predominantly along the (0,0) and (2π, 2π) diagonal; light colours indicate most frequent.
The percentage of Ki67-positive tumor cells in the 45 samples considered are illustrated by the bar graphs. Each value represents the mean ± SE of at least five separate fields for each experimental sample. *Significantly lower than the corresponding vehicle-treated control (P-value < 0.05, Student's t-test). **Significantly lower than the corresponding vehicle-treated control (P-value < 0.01, Student's t-test).
(E) Density figure showing the comparison of defense-responsive genes between LP treatment and RALF23 treatment (n = 3, n refers to technical replicates). The x- and y-axes represent changes in transcription level, and the red area indicates high density. Spearman correlations were used for the correlation analysis. Data information: All experiments were repeated three times with similar results.
(B) Immunoprecipitation of exogenous expressed Hsc70 and Htt-552-18Q. Hella cells were transfected with wt and mutant Htt-18Q for 48 h. The lysates were subjected to immunoprecipitation with anti-Hsc70 antibody or no primary antibody. Mutation of Htt-552-18Q at 99-103 was labeled with ▴ and mutation of Htt-552-18Q at 248-252 was labeled with ▪. Ab: Antibody.
(D) The relocation of CMA-active lysosomes toward the nuclear regions in PC12 cells. Cells were maintained in the presence or absence of serum. After 12 h, cells were fixed and subjected to immunofluorescence for LAMP-2A. Representative cells for each condition. N: nucleus. Thin arrows point to lysosomes. The scale bar represents 10 µm.
A. Chromatograms showing the confirmation a 1-nucleotide insertion mutation by Sanger sequencing.
Experimental design for blocking JNK/c-Jun signaling in the IMQ-induced skin inflammation model. c-Jun fl/fl, c-JunΔ/ΔCD11c-Cre, Tlr7-/- and Tlr7-/- c-JunΔ/ΔCD11c-Cre mice were treated with IMQ and JNK inhibitor SP600125 (JNKi, 15 mg/kg, i.p.) or vehicle for 5 consecutive days. Data information: Data are shown as mean ± SEM. P‐values were calculated by one-way ANOVA with Tukey Statistical significance: ns > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001, **** P < 0.0001. See Appendix Table S3 for exact P‐values.
(E) SIRT5 protects HEK293T cells from ROS-induced cell death. The indicated stable HEK293T cells were treated as mentioned above in (D), and then cell viability was determined by counting the remaining adherent cells. The results are average ± SD of 3 independent experiments **p<0.01 (two-tailed unpaired t-test).
H) Relative cellular viability was measured after NMN treatment, with or without MMS pretreatment, in WT and Ews-/- cells. Error bars represent as mean ±SEMs, and technical repeats (n=3). Significance determined by Two-way ANOVA, ***P < 0.001.
C, D. Titration of shRNA #1 (C) and of shRNA #2 (D) LVs (lentiviral vectors) on WT Schwann cell/DRG neuron co-cultures analyzed after 7 days of ascorbic acid treatment, with quantification of the mean number of Mbp positive segments and Schwann cell number. In (C) n= 20 (SCR, Scramble), n= 11 (LV #sh1, 12.5%), n= 16 (LV #sh1, 25%), n= 9 (LV #sh1, 50%) DRG/coverslips from two independent experiments. Results are mean ± SEM, p<0.0001, nonparametric one-way ANOVA, followed by Dunn's post hoc test. In (D) n= 14 (SCR), n= 10 (LV #sh2, 12.5%), n= 12 (LV #sh2, 25%), n= 79 (LV #sh2, 50%) DRG/ coverslips, representative of two independent experiments. Results are mean ± SEM, p<0.0001, nonparametric one-way ANOVA, followed by Dunn's post hoc test.