EMBO/sd-character-level-ner huggingface dataset:
b) Computer simulation on 2D lattices representing the basal layer and hair follicles. The panels show the probability for a clone to be attached to hair follicles (p(S)) as a function of its size (S). At each time-point three sets of data were figured: values detected experimentally (green squares) versus values produced by simulating the Klein model (orange circles) and values obtained from simulations of the extended model, including the periodic activation of HFs (blue circles) enhancing the rate of migration of post-mitotic cells in a circular neighborhood of 21 cells around the active HFs. It can be noted that the new model taking into account hair follicles' influence is closer to observed values.
B: In order to cover hydrophobic protein regions, the bilayer has to deform (to bend and to stretch).
E, F. Catalytically dead mutant EXOSC10 rescued EXOSC10 knockdown-induced GA increase.
(B) Canonical pathways with significant enrichment of candidate genes were identified by hypergeometric method using the Ingenuity Pathway Analysis software. Blue bars indicate the −log of the p-values (Fisher's exact test) of the enrichment (left vertical axis). The orange line indicates the percentage of the identified autophagy-regulating genes of all genes in the respective pathway (right vertical axis). The threshold line indicates the position of the P = 0.05. See Table S1 for genes associated with these pathways. AMPK, AMP-activated protein kinase; ERK, extracellular signal-regulated kinase; ROS, reactive oxygen species; ILK, integrin-linked kinase; iCOS, inducible T cell co-stimulator.
J. As in (I), but using RNF4-depleted CSF-arrested extracts reconstituted with recombinant RNF4 WT or C130A from (H).
C Cell wall and vacuolar membrane was visualized with PI (green) and MDY-64 (yellow). pER8::GFP-SAUR19 seedlings were treated with DMSO (n=60) or 10 µM β-estradiol (n=56) for 6 h in liquid medium. Mann Whitney U test (***p < 0.001). Data information: Scale bars: 5 µm.
(D, E) HEK 293 cells were transfected with the indicated siRNAs. After 48 h, the cells were transfected with mCherry-EGFP-LC3. For Bafilomycin A1 treatment, the cells were then incubated with Bafilomycin A1 (100 nM) for 24 h. For starvation treatment, the cells were cultured for 22 h and then treated with Earle's Balanced Salt Solution for 2 h. Cells were fixed and visualized using confocal microscopy. Scale bar, 5 µm. The quantification data of yellow (autophagosomes) or red (autolysosomes) are shown in Figure 6E. Data from three independent experiments represented as means ± S.E.M., *, p<0.05; **, p<0.01, one-way ANOVA.
A In quiescent LECs, VEGFR3 and β1 integrin are physically separated. ILK directly or indirectly interacts with β1 integrin and connects it to the F-actin cytoskeleton via intracellular proteins, such as α-parvin, a component of the IPP complex. B Upon mechanical stretch, the complex of β1 integrin and ILK (along with the entire IPP complex) transiently disrupts. C This releases β1 integrin, resulting in its interaction with VEGFR3, and thus in increased VEGFR3 tyrosine phosphorylation ("P" in yellow circle). As a consequence, LEC proliferation and lymphatic vascular growth are induced. D The absence of ILK results in permanent interaction between VEGFR3 and β1 integrin, leading to upregulated VEGFR3 tyrosine phosphorylation ("P" in yellow circle), LEC proliferation, and non-physiologic lymph
(C, D) Immunostaining for 53BP1 and USP28 on sagittal sections of WT embryos at E6.5 (C) or sagittal planes of whole-mount immunostaining at E5.5 (D). Quantification of the fluorescent signals in the epiblast (Ep) versus visceral endoderm (VE) are shown below. Four embryos per genotype were used for the quantifications. **** p < 0.0001, ***p<0.001 (two-tailed student's T-test). Bars represent mean ± s.d. Scale bar = 50 μm. (C) 53BP1 in Ep: 1.00 ± 0.10 (n=225 cells); 53BP1 in VE: 0.37 ± 0.06 (n=105); USP28 in Ep: 1.00 ± 0.08 (n=235); USP28 in VE: 0.17 ± 0.05 (n=90). (D) 53BP1 in Ep: 1.00 ± 0.24 (n=225); 53BP1 in VE: 0.68 ± 0.14 (n=115); USP28 in Ep: 1.00 ± 0.23 (n=280); USP28 in VE: 0.28 ± 0.00 (n=110).
C, D Time course analysis of the splicing patterns of CLK1 and TAF1D intron-retaining RNAs in control and HSATIII knockdown cells by semi-quantitative RT-PCR. Arrows indicate the positions of primers for RT-PCR. GAPDH mRNA was used as an internal control. The experiment was performed in triplicate. Quantification of the data shown in (C),
EMT-related markers, stemness markers and drug resistance genes were assessed by real-time PCR (C) in SNU719 and YCCEL1 cells transfected with circLMP2A or vector.
A. Detection of Sufu and Skp1 after immunoprecipitation of the indicated Flag-tagged F-Box Proteins (FBPs). An Empty Vector (EV) was used as a negative control. HEK293T cells were treated with MLN4924 (2 M) for 5 hours prior collection.
F cGAS-G3BP1 interaction analysis. cGAS was precipitated using anti-cGAS antibodies in U937 cells treated with EGCG as indicated. IgG served as control. The cGAS-G3BP1 interaction was further analyzed by immunoblotting. Data information: Representative images are shown WCL, whole cell lysate. IP, immunoprecipitation.
E. Isometric force from soleus muscles of WT and sgk1-/- mice during repetitive electrical stimulations for 500 ms. Amplitudes of isometric force from soleus muscles at two stimulation frequencies. Specific force is plotted in all cases. Mean values ± SD from n = 9 (sgk1−/−) and n = 10 (WT) independent animals (p = 0.01).
E The interface (red circle) for interaction between C-terminal domain of β-catenin (helix C) and α-interface of KRAS represented by a ribbon diagram
(C) Detection of Dyn2 PHD-stalk interactions by FRET using IAEDANS-labeled Dyn2L354C.
(F) Proliferation assay of Stat3+/+ and Stat3-/- cells cultured in presence of LIF showing the reduction of proliferation after 48hours treatment with increasing concentrations of Antimycin A (50nM, 100nM or 200nM). See also Appendix Figure S4F. Scores were normalized to WT cells treated with a vehicle (EtOH). Mean and s.e.m. of two independent experiments is shown. Unpaired t-test: ** P<0.01. See also Appendix Figure S4E.
(C) Quantitative analysis of oxidative stress in post-natal pups of indicated age (in days) using the peroxide linked oxidative stress marker DHR-123, as described in methods (mean ± SD, : p<0.01; N=8).
(E) Beeswarm plots of the echocardiographic parameter (ejection fraction) from CLIP-170 S311D overexpressing mice and the control. Number of mice, (Control, S311D), Tx 2w (3, 4), Tx 8w (5, 11), Tx 26w (4, 11). Data means ±S.D. There was no significant difference.
Clustering and heatmap showing the relationship between the codon ratios and exon lengths in large exons (> 180 nt) in 265 species. The codon enrichment was estimated by linear regression between the codon ratios and exon lengths in large exons (> 180 nt). A regression coefficient with p < 0.01 is indicated by a heatmap, whereas a regression coefficient without statistical significance is indicated in gray. Codons preferentially used in large exons are color-coded in blue. Enlarged view with species names is shown in Appendix Fig S5.
(D) ISG20 secretion in the positive clone supernatant significantly decreased ZIKV infection in trophoblast cells. Supernatants from negative and positive clones were collected and added to ISG20-/- Sw.71 trophoblast cells together with ZIKA virus (MOI=2) for 1 h, followed by refreshing with new growth media for 48 h. RNA was then collected to determine viral titers by qRT-PCR. Data represent as mean ± SEM; n=3 biological replicates; **p < 0.01 by Student's t-test.
Frequency of IL-22+ γδ T cells following culture with IL-1β, IL-23 or nothing. Each symbol represents one experiment. Open circles = Cre+ (each color represents a different culture condition).
C) Scatter plots show the numbers of γ-tubulin molecules per centrosome determined by calibrations using either SRM measurements (n=46 cells) or EGFP-VLP2/6 fluorescence (n=40 cells). The black lines represent mean values; numbers ± SEM are indicated on top of each scatter plot.
(P-Q). Representative images (P) and quantification (Q) of p-HSL DAB staining in gWAT and iWAT of male mice after 11 weeks of AKG supplementation (n = 9 per group).
F Correlation between editing efficiency (total indel rate) and levels of phosphorylated IκBα in CD4 T cells (normalised to the mean fluorescence intensity in NTC; n=9, linear regression).
A) Confocal images at the lateral plane showing the immunostaining of the medium threshold Hh target Collier (Col) of wild type wing discs and discs after inhibition of vesicle fusion (α-Snap RNAi), vesicle trafficking (Hrs RNAi) or in over-expression of the Tsp96F-HA. Quantification of gradient lengths (μm) using Collier signal and normalized to the wing pouch size, showing the proportion of wing pouch covered by signal (1=total coverage). Quantification was performed for wild type condition as well as in temporally regulated RNAi expression for the ESCRT complex proteins Hrs, Tsg101, Shrub and Vps4 and for the SNARE proteins Syb, Snap24, α-Snap, as well as in transient over-expression of the Tsp96F-HA. Central horizontal lines show median values of N=7-22 , box shows lower and upper quartiles and the whiskers show the maximum and minimum excluding outliers. Note a slight but significant increase in the length of Col signal for all treatment compared to the wild type condition.
(D) Eighteen hours after infant rabbits were infected with WT (middle panel) or vgpAL10A (lower panel) V. parahaemolyticus, fixed sections from the small intestine were stained with antibodies to c-Myc (green), EBP2 (red), and DAPI (blue). Uninfected rabbits were processed similarly and were included as a control (upper panel). White arrows indicate co-localization of c-Myc and EBP2 (middle panel).
E. Viral load in the brain of mice from different experimental groups. The samples were either collected at the time of death, or at 100 dpi for the survivors.
B Luciferase activity of the reporter constructs shown in (A) were measured in KGN cells after transfection with an miR-1236 mimic for 48 h. The black arrow indicates the position of 402C>G mutation site.
A SSX2IP interacts with OCRL. Plasmids carrying GFP-OCRL-WT, GFP-OCRL-△RhoGAP and GFP-OCRL-△ASH+RhoGAP were transfected into RPE-1 cells. Immunoprecipitation was performed with GFP-Trap, followed by blotting with the indicated antibodies.
(G) Centriole number was quantified with respect to the number of nuclei per cell in wt and Pidd1-/- livers at the time points described in (E); n=3 biological replicates.
(C) Metagene analysis reveals features of active translation in uORFs classified as translated. Metagene plots display normalized ribosome protected fragment density surrounding uORF start and stop codons, colored according to frame relative to the ORF being translated. CDS regions with and without uORFs are also shown for comparison. Note the clear phasing of ribosome-protected fragments within high and medium confidence uORFs, and the characteristic start and stop RPF peaks across all classes of uORFs.
RAW264.7 WT, LRRK2 KO or Rab8A macrophages pre-treated with 1 μM GSK2578215A (GSK inh) were treated with 1 mM LLOMe for 30 min. CHMP4B vesicle numbers were analysed by immunofluorescence and high content imaging. Scale bar = 20 μm. Right panels show the quantification of number of CHMP4B positive vesicles per cell. Mean ± SEM of three independent biological experiments. ns=non-significant, *p≤0.05, **p≤0.01 by One-way ANOVA followed by Sidak's multiple comparisons test.
D. Representative images of the intestine of Casp8WT and Casp8ECko mice, with mild and severe hemorrhages at a late disease stage.
(G) Western blot for TIP30 and Actin in mouse hearts with AAV9 mediated overexpression of TIP30 (AAV-TIP30) or from mice treated with a control AAV9 construct (AAV-Con) followed by 2 weeks of TAC surgery.
(A) Five weeks-old Arabidopsis Col-0 wild type (WT), atg5, atg7 and nbr1 mutant plants were placed into a growth chamber with approximately 50% humidity. The photograph of representative plants was taken 10 days after withholding watering. The experiment was repeated twice with similar results.
(a,b) Representative immunohistochemistry and quantitative assessment of (a) tumour-infiltrating CD3ε-positive T cells and (b) FoxP3+ Tregs in lung tumours from KRas;Atg5fl/+ and KRas;Atg5fl/fl littermates 6 weeks after AdCre inhalation. Data are shown as mean percentages (±s.e.m.) of the indicated cell types per total cell numbers in the tumour areas. Only cells within tumours were scored. At least six mice per genotype were analysed. Scale bars, 50 μm. ***P0.001(χ2-test assessing the genotype effect in a generalized linear model with logit link).
Actinin, ANP and Troponin Iimmunofluorescence staining of differentiation cultures derived from wild-type and knockout ESCs.
(B) Luciferase assay on ES cells transfected with D-loop-Lux reporter plasmid and Stat3 in the presence or in the absence of LIF for 48 hours; p53 was previously shown to activate a similar reporter construct (Heyne et al, 2004) and therefore was used as positive control. Increased expression of Stat3 enhances Luciferase activity. Mean and sem of 4 independent experiments. Unpaired t-test: * P<0.05.
E Schematic description of the experimental CRISPR-Cas9 approach: Cas-9 expressing-RKO cells were transduced with a genome-wide pooled knockout CRISPR library and passaged in the presence of either IMT1 or DMSO for guide selection. After cell collection and DNA isolation, the guides were sequenced and quantified in each population.
A) Alignment of yeast and human Ykt6 protein sequence. The SNARE domain is labelled in yellow, phosphorylation sites are marked in green and red. Red phosphorylation sites match the Atg1 kinase consensus.
Immunoblot of mGPDH, myogenin and MyHC in C2C12 myocytes transfected with siRNA targeting mGPDH. Quantificatio represents the levels of indicated protein normalized to β-actin at indicated day after differentiation
G. HeLa cells expressing LCS-GR mock or GOLPH3-KD were treated and stained as in D. Black arrowheads indicate GM130; peri-Golgi vesicles containing LCS-GR are marked by red arrowheads. LCS-GR in the TGN is marked by blue arrowheads. Scale bar, 150 nm.
E. LORE is an active tyrosine kinase. The α-pY antibody was used to probe tyrosine phosphorylation in recombinant protein MBP-tagged LORE-CD (cytosolic domain). The LORE activation loop conserved K516 was mutated to E, and D613 was mutated to V. The bottom gel showing protein abundance stained by Coomassie Brilliant Blue (CBB).
Several proteins coordinating the usage of two ends of a DSB suppress BIR: (1) Mre11-Rad50-Xrs2 complex (MRX) that promotes synchronous resection of two ends of a DSB, (2) D-loop unwinding helicase Mph1 that stimulates SDSA, and (3) ssDNA annealing proteins Rad52 and Rad59 that promote second end capture. All of these proteins are particularly important to reduce BIR when recombination occurs between short repetitive sequences.
Immunoblots and quantification of p-IKK/IKK, p65 and p-IκB/IκB protein in adrenal chromaffin cells cultured with vehicle, AKG (100 μM), IKK inhibitor IKK16 or AKG + IKK16 for 3 hrs.
B. ATP amounts in DIV18 CNs, untreated or complemented with 30 U/mL rIFN-β. Error bars equal SEM from 5 (untreated cells) or 3 (treated cells) independent experiments.
F uPARR83/89A is not cleaved by uPA and plasmin. 293/uPARWT and 293/uPARR83/89A cells were seeded on FN-coated tissue culture plates and allowed to adhere before treatment with the indicated reagents: 10 nM sc-uPA and tc-uPA, 30 nM Plg and Pli. After 1 h, cells were lysed, resolved by SDS-PAGE and analysed by immunoblotting using monoclonal antibodies recognizing different epitopes in uPAR [51]. R2 binds an epitope in D3 of uPAR and recognizes the full-length receptor (uPAR) as well as the truncated form lacking D1 (D2D3). R3 binds an epitope in D1 and only recognizes full-length uPAR. The blot is from a representative experiment and the mobility of molecular weight standards is shown.
BDNF secretion induced by KCl treatment assessed by in-situ BDNF ELISA in cultured hippocampal neurons infected with scrambled or Tardbp shRNA lentiviruses. Histogram bars show average ± SEM BDNF levels normalized to a standard curve (N=3 independent experiments; n=3 wells per condition in each experiment). *, p<0.05; ***, p<0.001. Data information: Results are presented as average ± standard error of the mean (SEM). All statistical tests were performed using 2-way ANOVA with Sidak post hoc analysis.
(j-o) Direct visualization of IL-17A on Candida freshly harvested from human vagina. Same experiment as in (a-g) on cells previously stained with Con A (j,m, green) and incubated with PE-anti-human IL-17A (k,n, red) and double stained in the merged images (l,o). Scale bars, 10 μm. Shown is one representative experiment out of three.
(D) Schematic depicting the function of UHMK1 in GC. H. pylori-induced upregulation of UHMK1 or human GC-associated UHMK1 mutation enhances the level of NCOA3 phosphorylation at S1062/T1067; this event greatly increases the association of NCOA3 with ATF4, which activates the de novo purine biosynthesis pathway and promotes the development of GC. Interestingly, activated ATF4 transcriptionally upregulated UHMK1 expression.
(A) After 4 h of starvation in 1% K‐acetate medium in the presence of PMSF, autophagic vesicles can be visualized in vacuoles of wild‐type and pep4prb1 cells using Normaski optics. In aut2Δ and aut7Δ cells no autophagic vesicles can be seen. Bar represents 20 μm.
(C) Schematic of stall and bypass products generated by SwaI and BamHI cleavage (D and E).
A, B. Immunoblotting were performed to validate Mettl3 or Mettl14 expression levels in CT26 and B16 cells as indicated. Gapdh served as a loading control.
(G) qRT-PCR of Irf7 and Irf9 downregulation in parental RM1 cells, RM1 cells from bone metastases (RM1 BD) in WT and Ifnar1 deficient (-/-) mice, with naïve BM from WT and Ifnar1 (-/-) animals for reference. (n = 3 mice per group; n = 1 for -/- BM control). p values represented as * < 0.05 and ** < 0.005 (Student's t test).
B, C. Immunisation with cGAMP-S-VLPs augments anti-Spike and anti-RBD antibody titres. Mice were immunised via the intra-muscular route with 5x105 IU of cGAMP-S-VLPs, Empty-S-VLPs, or PBS as a control. Three weeks after immunisation, sera were collected, heat-inactivated, and titres of antibodies capable of binding to SARS-CoV-2 S (B) or its RBD (C) were determined by ELISA. The antibody response was expressed as Endpoint titre defined as the reciprocal of the highest serum dilution that gives a positive signal (blank+10SD). The dotted line shows the limit of detection (LOD).
Changed metabolic pathways in muscle of PEO (G) patients. Data information: Top 10 pathways with ≥ 10% of detected metabolites per pathway are shown. bio., biosynthesis; deg., degradation; metab., metabolism.
(A) Average plots of Med8 cleavages around SAGA- and TFIID-dependent gene TSSs stratified into quintiles by the level of NET-seq signal in a 200 bp window downstream of the TSS.
B. Schematic representation of Casp8 deletion in PDGFb-CreERT2 x Casp8fl/fl mice (Casp8BECko) indicating the time points for tamoxifen treatment and analysis.
A-J)Ten per group female C57Bl/6 mice heterozygous for the PyMT-MMTV started high fat diet (HFD) when 6-7 weeks old (prior of mammary tumour development) together with control mice on normal diet (ND; n=10). Mice were administered amlexanox (17 mM) or vehicle control daily by oral gavage (Reilly et al, 2013). A control group (wild-type mice) was also included to confirm the efficacy of the diet and to control for possible unpredicted interactions of the MMTV-PyMT gene. Mammary tumours are developing earlier in PyMT-MMTV+/- mice on HFD compared to ND mice. Amlexanox does not affect tumour development in PyMT-MMTV+/- mice on ND, but delays tumour formation in J) HFD mice.
(A) Domain organization of PPM1H, PPM1J, and PPM1A. The annotation of regions (anchor, flap domain) is discussed in the text. The loop deletion (188-226) that was engineered to improve diffraction is indicated.
(f) Phagophore formation in mCherry-ULK1. Scale bar, 10 μm. (g) mCherry-ATG5-expressing U2OS cells after 24 h in the presence (+Q) or absence (−Q) of glutamine. Scale bar, 10 μm.
A Equal numbers of CTC-ITB-01 cells were seeded on 6-well culture plates and grown in the presence or absence of different 17-β-estradiol concentrations as indicated. After 10 days cells were fixed and stained with Coomassie blue staining (right panel). Macroscopic photos are shown of the fixed cell colonies from cells grown in the absence or presence of the indicated E2 concentrations (right panel). Scale bar 200 µm.
(D) HeLa cells treated with siControl or siTom70 were fractionated into cytosolic and mitochondrial fractions and then immunoblotted with anti-lactate dehydrogenase (LDH), anti-Tom20, and anti-Flag antibodies. LDH was used as a cytosolic marker. Although some MITOL detached from mitochondria during fractionation, sufficient amounts of MITOL were collected in the mitochondria-enriched fraction in control cells. In contrast, almost all of the MITOL was collected in the cytosolic fraction in siTom70-treated cells.
(F) qRT-PCR of cest-2.2 mRNA expression in nuo-6(qm200) animals grown on control and cest-2.2 RNAi (unpaired t-test, n=3 biological replicates). Data information: mean± SEM Across experiments, p value summary is ns= not significant, *p<0.05, **p < 0.01; ***p < 0.001, ****p<0.0001.
(F) Representative images of P90 SOD1G93A and WT sciatic nerves. Red: denotes NFH, Blue: denotes GFAP and green denotes CRMP4, Yellow: denotes the Z projection of 3D Imaris co-localization of CRMP4 and NFH. Scale bar: 5 μm. (G) Quantification of the co-localization area of CRMP4 with NFH in the sciatic nerve in 3 SOD1G93A mice compared to 3 WT mice using Imaris analysis. 14 WT sciatic nerve sections and 11 SOD1G93A sections were monitored. Data presented as mean ±SE. Student's t-test, n=3, ****p<0.0001.
Hematoxylin-eosin (H&amp;amp;E) and p-ERK stainings on FFPE material of all metastases showed that all vemurafenib-resistant tumors had reactivation of the MAPK pathway. Scale bar represents 100 μm
(C) Western blotting of phospho-Thr389-p70S6K (pS6K), total p70S6K (S6K), phospho-Ser235/236-S6 (pS6) and total S6. Quantification represents the pS6K/S6K and pS6/S6 ratios relative to the NT control. Data information: All quantifications are of three independent experiments (n = 3) and error bars represent the SEM. Significance between means was first determined using ANOVA. Significance p-values were calculated using Fisher"s LSD. *, p < 0.05; **, p < 0.01 from non-treated (NT) controls; †, p < 0.05; ††, p < 0.01 from IFNγ/TNFα treated controls
(B) Fluorescence microscopy. p62-deficient MEFs were co-transfected with mCherry-GFP-p62 in combination with wild-type NBR1 or NBR1 D50R mutant. 48 hrs after the transfection, fluorescence images were observed. Bars: 10 µm. The number of puncta positive for only red-signal in each MEFs was counted in more than 100 cells. Bar graphs are represented as means ± s.e. ***P < 0.001 as determined by Welch's t-test.
A HUVEC were transduced with increasing titers of adenovirus expressing human SHP2. VE-cadherin was immunoprecipitated from cell lysates and precipitates as well as total cell lysates were analyzed by immunoblots for indicated antigens.
(A) Tri‐ and tetrasomic cells accumulate p62‐positive foci. This effect was further increased by treatment with Bafilomycin A1. Right panel: Quantification of the fluorescence intensity changes; significance was evaluated by non‐parametric T‐test (***P<0.001), '+' designates addition of Bafilomycin A1.
C A 3D representation of simulation waves under high (left) and low (right) threshold waves propagating in time.
(A) Recombinant proteins were mixed, as indicated, in the presence (lane 5) or absence (lane 4) of ATP and incubated for 1 h at 30°C before being separated by SDS-PAGE and analyzed by western blotting using the α-His antibody. Components present (+) or absent (−) from the assay are indicated.