EMBO/sd-character-level-ner huggingface dataset:
CHD8 subnetwork analysis in relationship to brain size and downstream CHD8-knockdown effects in vitro. A) CHD8 subnetwork analysis included all CHD8-targets from the Hc network. Network legend is the same of Figure 5: grey (downstream CHD8 target), cyan (upstream regulatory gene of brain-size relevant genes altered in ASD), red (differentially expressed in blood), green (cyan and red), diamond shape (brain size relevant gene altered in ASD), black circle (differentially expressed in ASD cortex from Voineagu et al, 2011).
Intrauterine dwarfism observed upon NSMCE2 deletion on 17.5 dpc embryos. Pregnant females were treated at 14.5 dpc for 3 days with intraperitoneal injections of 4‐OHT. The image represents the difference in size observed between Nsmce2+/+ and Nsmce2lox/lox embryos carrying the UQ.CreERT2 transgene (Nsmce2+/+ and Nsmce2lox/lox, from now on).
D. Schematic diagram of the contribution made by ROCK signaling to pancreatic cancer invasive growth.
E The chromatin compaction of the indicated regions was detected by nuclease accessibility assay. Genomic DNA was purified from MEFs infected with Flag alone and SKO plus Flag, wild-type Gadd45a or G39A Gadd45a on day 8. (*p≤0.05; **p≤0.01; n=3)
ST2 wild type or NEMO KO cells were stimulated with SF-IL-17 (500 ng/ml) as indicated or were left unstimulated and IL-17 was added post lysis. Lysates were subjected to anti-Flag immunoprecipitation to isolate IL-17RSC (C) and analyzed by immunoblotting.
B-P, Sections of testes from Dnd1flox/flox (B, E, H, K, N), Dnd1flox/flox_Tg(Oct4PE-CreERT2) (C, F, I, L, O) or Nanos2-/- (D, G, J, M, P) embryos were prepared at E16.5 and then immunostained with antibodies against pH3 (B-D), STRA8 (E-G), SYCP3 (H-J), activated-Caspase3 (K-M) or LAMININ (N-P) (green). Germ cells were immunostained with TRA98 (B-D) or DAZL (N-P) (red), and DNA was labeled with DAPI (blue). Tamoxifen was administered at E13.5. Scale bars: 50 m in B for B−D and K-P, 50 m in E for E−J. See also Fig. EV3.
Detailed structure of p62 (cartoon), colored from N to C termini in blue, cyan, green, yellow, orange then red. Dotted boxes show the different structural features of p62. Metal ions in p62 are colored gray and are numbered.
A) Volcano plot comparing the number of transposon insertions per gene of all 24 rewired libraries and two wild-type (wt) libraries. Genes that are significantly (p-value < 0.05) required (red, log2(fold change) < -1.5; blue, log2(fold change) < -1) or dispensable (green, log2(fold change > 2)) in the rewired libraries are highlighted. Genes depicted in grey are essential due to differential growth requirements in the preparation of the two wt libraries compared to the rewired strains, or correspond to genes deleted in the rewired strains.
(B) Immunoblot analysis of BAT cells stimulated with NE for 5 minutes in the presence of Rapamycin (Rapa), Torin or Wortmannin (Wrtm) for the indicated proteins.
J Analysis of Scl‐regulated key hematopoietic and cardiac genes shows that many of them can be bound also by cardiac factors, Scl, Gata4 and Hand1 (orange); Scl and Hand1 binding (green); Scl and Gata4 binding (orange); and Scl binding alone (blue).
F, I Effect of Treg-specific TRAF6-deficiency on baseline T cell activation. The frequencies of effector cells (CD44high/CD62Llow), memory cells (CD44high/CD62Lhigh) and naïve cells (CD44low/CD62Lhigh) in the CD8+ T cell compartments of Traf6fl/fl Foxp3Cre- (wild type) and Traf6fl/flFoxp3Cre+ mice were determined by flow cytometry (5 mice/group).
A. A scheme for in vitro screening method of small molecules competing Dvl-CXXC5 binding. Briefly, purified Dvl PDZ domain was attached to the polystyrene surface of each well of 96-well plates. Then, PolyR-DBM (ployarginine conjugated Dvl binding motif tagged with FITC) (Kim et al, 2015) was added to each well and allowed to bind to the Dvl PDZ domain; 10 μM small molecule compound was added to each well, and the compounds competing with Dvl PZD-PolyR-DBM binding were measured by a microplate reader to screen the compounds reducing fluorescence signal.
F. Left panel: Schematic of the A70.2 INV-4 cell line strategy to induce RAG1/2-mediated recombination using imatinib. Right panel: A70.2 INV-4 cell lines were transduced with lentiviruses encoding the lentiCRISPRv2 expressing sgRNAs against the 53bp1, Shld1, Shld2, Shld3, and Lig4 genes. Guide RNA targeting chicken AID was used as a negative control (Ctrl). Cells were selected with puromycin and treated with 3 μM imatinib for 4 days after which GFP frequency was measured (mean ± SD of 3 biological replicates). The insertion-deletion (indel) penetrance as measured by TIDE analysis [39] of sequence for each of these sgRNA constructs is shown in Figure EV1E, and the baseline GFP frequency prior to imatinib stimulation is shown in Figure EV1F. sgRNA sequences used are shown in Table EV2.
D Electron microscopy analysis in Ttn knock-in embryos cultured for 24 h after mScrAON and mTtnAON transient transfection. mTtnAON treatment of homozygous embryos rescued myofibril formation (left, black arrows), resulting in thicker filaments (right).
(d) Completed reactions in c were subjected to density gradient flotation to isolate only the lipidated material. Floated samples were run on SDS-PAGE and imaged by Coomassie. For c and d, the samples were prepared at the same time from the same materials and run simultaneously on multiple gels, as indicated by the vertical lines. Uncropped versions of all gels are included in Supplementary Fig. 7.
(F-J) The crucial role of Ulk1 dephosphorylation at Ser637 in etoposide-induced autophagy. (I, J) The indicated MEFs were treated with or without etoposide (10 µM) for 6 hr, followed by immunostaining with an anti-LC3 antibody. Representative images are shown in (I). LC3 puncta are markedly observed in DKO MEFs transfected with wild-type HA-Ulk1. Puncta were absent and weakly observed in MEFs expressing the mutants S637D and S637A, respectively. (J) The population of cells with LC3 puncta was calculated (n > 100 cells in each experiment). Data are shown as the mean  ±  SD (n = 3 experiments). *p < 0.05, **p < 0.01.
Relative TSC1 and TSC2 mRNA expression levels determined by qRT-PCR for high MYC (-Tet) versus low MYC (+Tet) P493-6 cells treated for 24 h with tetracycline (mean ± st.dev., n=3 technical replicates) *p< 0.05; **p< 0.01; statistical relevance was determined by unpaired t-test (two-tailed).
(D-F) Hypocotyl length, root length, and root to total length is dependent on TF and exogenous TCA cycle metabolites. Radar plots presents mutant phenotypes relative to Col-0 (black). Ratio of mutant:WT traits were determined using the estimated marginal means of each genotype calculated from 16-20 seedlings per genotype per condition across two experiments.
C. qPCR analysis of Ahr expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for 4h with 20 ng/ml IL-4 and/or 10 μg/ml α-IgM. Ahr expression was normalized to Hprt1. Ahr expression among groups was normalized to Medium. n = 3 independent experiments; mean ± SEM; one-way ANOVA, Tukey's multiple comparison test.
The active fragment of mTOR was incubated with Flag-RagC WT purified from HEK-293E cells. The kinase reaction was performed in the presence or absence of mTOR inhibitor Torin or Rapamycin. Samples were analysed by Western blot for pRagC S21
Atg4BC74A-expressing cells (for Atg16L1) or control cells (for PDI, COP II and β-COP) were labelled with specific antibodies against the indicated markers. The left and right anti-Atg16L1 and anti-PDI images are from two different ER-IM complexes. Arrows, arrowheads and open arrowheads indicate the ER, IMs and VTCs, respectively. Small arrows in the image from the anti-COP II experiment indicate immunogold particles. Scale bars, 200 nm.
(E) The endpoint analysis of % cells with NET formation was detected with dPMNs that were transfected with plasmids of either wildtype lamin B (WT control), or mutants with single or multiple defined point mutations at PKCα-consensus-phosphorylation sites (S395A, S405A, S408A) of lamin B, and treated for 3 h by 10 μM PAF in medium containing cell-permeable dye SYTO Red (500 nM) for the total cell count, while the cells with NET formation were stained by cell impermeable dye SYTOX Blue (5 μM). Then the images were taken with Olympus confocal microscopy, followed by automated quantification of NETs using ImageJ for quantification of % cells with NET formation. percentage of cells with NET formation by immunofluorescent imaging quantification using ImageJ (E)
Cells were cultured under normal or hypoxic condition. Relative levels of the HIF1A-AS transcripts in subcellular fractions (G), were determined by qRT-PCR.
A. Uptake of FITC-insulin and CAV1 expression in primary human umbilical venous ECs (HUVECs) upon Notch induction. Scale bar 20 µm.
Forebrain slices from WT (A-F) and S1928A KI mice (G-L) were treated with vehicle (water) or 10 M isoproterenol (ISO) for 0.5 - 10 min before solubilization, ultracentrifugation, IP of α11.2 (A-C, G-I) or β2AR (D-F, J-L), and sequential IB for pS1928, pS1700, and α11.2, for GluA1, or for β2AR, of corresponding regions of the blots, as indicated. All the α11.2 IPs in A-C and G-I were from the same samples (which were split in half for parallel IP) as the β2AR IPs in D-F and J-L, respectively (for quantification of coIP of β2AR with α11.2 see Figure EV1F,G).(A-F) In WT, the time-dependent increase in S1928 and S1700 phosphorylation (A-C) paralleled the decrease in coIP of β2AR with α11.2 (A bottom, Figure EV1F) and of α11.2 with β2AR (D-F).(G-L) In S1928A KI mice, ISO induced S1700 phosphorylation (G,I) but did not disrupt the α11.2 - β2AR interaction (G bottom, J-L, Figure EV1G).(B,C,H,I) For quantification of α11.2 phosphorylation, pS1928 and pS1700 signals were normalized to α11.2 (**p<0.01, ***p<0.001, ANOVA).(E,F,K,L) For quantification of coIP, α11.2 and GluA1 signals were normalized to β2AR (***p<0.001, One Way ANOVA).
(D) MCF7 cells stably infected with lentivirus expressing control (shLuc), Ulk1 or ZIPK shRNA were cultured in nutrient‐rich DMEM medium (F) or EBSS (S) for 2 h. Effects of Ulk1 and ZIPK knockdown on starvation‐induced myosin II activation were analysed by immunoblotting with antibodies as indicated. Data are mean±s.e. of triplicates.
F. Expression of CAV1 in HUVECs upon Notch manipulation and HEY1 induction. n=3, data represent mean ± SEM, unpaired t-test.
(G and H) Both the association with α-catenin and the functional WW domain are required for the STXBP4's tumor suppressive function in 786-O cells. Overexpression of STXBP4, but not the indicated STXBP4 missense mutants, significantly suppressed the 786-O cell xenograft tumor formation. Xenograft tumors are shown in (G), and the tumor weight is quantified in (H) (n = 5 mice, mean ± s.d.). ** p < 0.01 (Student's t-test). Scale bar, 1 cm.
A Enzyme-linked immunosorbent assay (ELISA) for Activin A expression in the supernatant of C57#1 and C57#3 DLP mouse prostate organoid lines, upon acute A83-01 removal (48 hours) or long-term adaptation (n = 6 biological replicates). Two-way ANOVA, Sidak's test, p-value *** (<0.001), **** (<0.0001).
B Comparison of the lists of genes significantly changed by Rosi in wild type cells (Cited4+/+: Rosi vs. Ctrl, P<0.01) or by Cited4-knockout under Rosi treatment (Rosi: Cited4-/- vs. Cited4+/+, P<0.01) in expression profiles from female Lin-Sca1+ progenitors 2 days after induction of differentiation with 100 nM Rosi or vehicl C Comparison of the lists of gene sets significantly enriched by Rosi in wild type cells (Cited4+/+: Rosi vs. Ctrl, false discovery rate (FDR) <0.1) or by Cited4-knockout under Rosi treatment (Rosi: Cited4-/- vs. Cited4+/+, FDR<0.1) in GSEA (KEGG) (n=3)
Adhesion of FITC-labelled A909 strains to human CC1- expressing or control CHO transfectants at MOI of 10. Cell lines were detached and then incubated with FITC-labelled A909 strains for 30 mins at 4oC. Mean and SD for each population for n = 6 independent replicates is displayed
D. Immunoblot analysis with the indicated antibodies of PANC-1 cells transfected with control siRNA (CNT) or hMENA(t) siRNA, showing that the knock‐down of total hMENA isoforms, (hMENA(t)) inhibits GAS6-mediated pAXL and pAKT expression. Cells were serum starved overnight and subsequently stimulated with DMSO (0.02%) in control culture medium (-) or rGAS6 (200 ng/mL), for 30 and 60 min. The fold change of pAXL or pAKT expression respect to siCNT untreated cells is reported.
A, HCT116 cells were treated with either vehicle alone (-), 1 µM MPA, 10 µM MPA or 5 nM ActD for 24 hrs and mRNA levels of p21 were quantified by real-time qPCR in 2 independent experiments carried out in triplicate and normalized to 28S rRNA. Data information: , data are presented as mean ± SD, relative to control. *p<0.05, **p<0.01, ***p<0.001, by two tail T-Student's test.
Quantification of the relative binding of the truncated forms with the clathrin complex or β-catenin complex; the red frame indicates the common domains of BCL9 for binding of both complexes.
E Heatmap showing the AUC score of regulons enriched in each cluster. Z-score (column scaling) was calculated. Representative regulons were highlighted on the top.
Ccny/l1 stimulate cyclin-dependent kinases (CDK) 14 and 16 predominantly during G2/M (not shown) to phosphorylate and activate LRP6. This co-receptor activation leads to a peak of WNT/STOP signalling and GSK3 inhibition in mitosis. Mitotic WNT signalling has two consequences: First, it increases asymmetric AP division via unknown effectors, which leads to more basal progenitors and hence post-mitotic neurons; Second, it protects Sox proteins from proteasomal degradation. Sox4 stabilization in mitotic APs leads to increased BP generation, and its stabilization in mitotic BPs may promote BP self-renewal and/or differentiation. Sox11 is stabilized in both mitotic and non-mitotic cells of the SVZ, which leads to increased post-mitotic neuron generation. WNT/β-catenin signalling primarily promotes AP self-renewal.
F. pDPCSUMO was subjected to sequential extract addition as depicted in (D). Recombinant UBC9DN was added to NPE where indicated to block de novo SUMOylation. At the indicated time points following addition of CSF-arrested egg extract, the plasmid was recovered via DPC pull-down and immunoblotted against M.HpaII.
A. SIM of exponential B. subtilis cells. RNase J1 was fused to GFP (green), RNAP to mCherry (red). The graph shows relative fluorescence intensities at the cell midsection (along the long axis); SIM of the cell is below. Yellow indicates colocalization of the two proteins.
Binding was measured by fluorescence polarization using N-terminally TAMRA-labeled monoubiquitin. The dissociation constants for ubiquitin binding to USP4 WT and C311A are 92 ± 21 nM (Clerici et. al, 2014) and 0.60 ± 0.17 nM, respectively. Error bars are s.d. calculated on five measurements per point.
B Cellular and molecular consequences of heme deficiency on GATA-1 function. Type I incoherent feed-forward loop [88] under normal heme conditions that controls heme biosynthesis and globin chain production. This loop also activates a p62-dependent pathway that can induce Nrf2 and confer cytoprotection [70], and promote autophagy, a process vital for erythroid cell maturation [89-92]. In heme deficiency, Bach1-sensitive and -insensitive (X?) mechanisms disrupt multiple mechanistic steps, thus impairing hemoglobin biosynthesis, cytoprotection, and autophagy. As impaired autophagy and associated molecular defects would compromise cell survival and/or maturation, this underscores the critical implications of the heme mechanism to amplify GATA-1 activity described herein. The red arrows indicate relationships derived from this study. The black arrows indicate relationships that were either known or predicted from existing knowledge.
J IHC for hCK7, in brown, of cross-sectioned "humanized" mouse milk duct mammary glands at day 20 of pregnancy. Arrow heads point to mouse alveoli, stars highlight lumina filled with secretions. Scale bar, 100 μm.
H. Quantification of data in (F) by quantitative image-based cytometry (QIBC) (n≥3000 cells per condition; data from a representative experiment are shown). See also Fig EV1G.
(B) Quantification of these changes by BRET analysis. The PI4P-Rab7 BRET sensor construct was transfected into the respective cell lines and the cells treated with OSW1 (20 nM) for the indicated times. The BRET ratios were expressed relative to those of DMSO treated cells. Data information: Means ± S.E.M. are shown from three experiments performed in triplicates.
H- ERK7 expressing, GFP-marked, fat body clone (H, marked by yellow dotted line; scale bar: 50 µm) visualized by LipidTOX staining (N=11 for control and 4 for ERK7 overexpression).
(C) K-fibers extend to spindle poles. The length of K-fibers and distance between kinetochores and a spindle pole (KT-to-Pole distance) were measured. K-fiber length relative to the KT-to-Pole distance was calculated (n=90 K-fibers of 5 oocytes from 2 independent experiments).
K-L. Quantification of dextran positive axons shows that AAV-HDAC3mut promotes DRG regenerative growth across and beyond the spinal lesion site. Data is expressed as percentage of dextran+ axons at each distance vs dextran+ axons at -700μm from the lesion margin (K) or distance from the caudal margin of the lesion to the most rostral dextran+ axon tip for each animal (L). N= 10 animals per condition, ± s.e.m. *p<0.05, **p<0.01, ***p<0.005, ****p<0.001 indicate a significant difference (ANOVA followed by Bonferroni test).
(D) Simplification of lysate (collecting only the flow-through from anion exchange chromatography) prior to SEC separation allows class-averaging of structural signatures from complex fractions that were previously too low abundant. Proteins identified in this simplified fraction are found in Table S4.
E: Western blot analysis of PITRM1 in primary fibroblasts (left) and skeletal muscle (right) of controls (CTR) and subject II-2. Densitometric quantification using the Genetools software is shown below the blots. In blue is PITRM1WT and in red PITRM1R183Q.
(D) Proliferation was measured in primary fibroblasts treated with TGFα (20ng/mL) and indicated doses of barasertib for 48hrs.. **P<0.005, 1-way ANOVA, (n=9-11).
(A) diagram of the genomic rescue constructs in which wild type Btz (Btz-WT) or Btz with the H215A and D216A mutations (Btz-HD) is C-terminally tagged with GFP and driven by its endogenous regulatory sequences.
(C) Viral titers in siRNA-treated NSC-34 cells. Cells were transfected with various concentrations of siRNA specific to the indicated target genes. The efficiency of siRNA-mediated knockdown at 48h.p.t. was validated by Western blot while cytotoxicity was determined by AlamarBlue assay siRNA- or siNTC-transfected cells were infected with EV-A71 S41 at MOI 10, and the viral titers were determined at 48h.p.i.
F, G C57BL/6 mice received pleural KPM1 cells followed by a single intrapleural injection of liposomes containing 1% DMSO or 15 mg/Kg deltarasin in 1% DMSO at day 9 post-tumor cells. Shown are data summaries of MPE volume (n = 8 and 7 DMSO and deltarasin-treated mice/group, respectively) and pleural fluid nucleated cells at day 19 post-KPM1 cells (F), as well as representative images of pleural effusions (dashed lines) and tumors (t in (G)).
(K) ALG‐2::GFP forms a few aggregates in epg‐6 mutant embryos. (L) ALG‐2::GFP forms a large number of aggregates in epg‐6 mutant embryos under stress conditions. GFP, green fluorescent protein; s.d., standard deviation.
K. Phase plots of a representative AP of a human iPSC-derived neuron treated with Centrinone-B and a control neuron of 13 and 14 days, respectively.
G Gel filtration chromatography of the recombinant PTAR1-RabGGTβ complex purified from Sf9 insect cells on a Superdex 200 column. Inset shows SDS-PAGE and Coomassie staining analysis of the purified complex.
The MBP DNA promoter was inserted into the pGL4.1 luciferase report vector and was co-expressed with N-terminal MYRF (nMYRF) and mHTT to assess its transcription activity via the luciferase assay. MYRF markedly enhanced the MBP promoter activity. N-terminal mutant HTT significantly inhibited the reporter activity, ***P< 0.001; which was reversed by LAQ (5 μM) treatment, **P< 0.01. The ratios were obtained from 3 independent experiments. One-way ANNOVA followed with Tukey's test. Data are mean ±SEM.
(I) HCT116XIAP WT and XIAP KO cells were treated with 20 ‐μM Z‐VAD‐FMK or DMSO for 2 h. Cell lysates were then analysed by western blotting. The data are representative of three biological replicates. The ratio of LCII/LC3I to actin is presented in Supplementary Figure S1F.
Figure 3. Differential lysine acetylation and protein expression in Arabidopsis leaves after inhibitor treatment. Vacuum-infiltration of leaf strips with solutions containing either of the two deacetylase inhibitors apicidin (A, C)versus a buffer control for 4 hours leads to differential accumulation of lysine acetylation sites. Volcano plots depict protein ratios (C, D) for inhibitor treatment vs. control, with p-values determined using the LIMMA package. Orange, protein with nuclear localization according to SUBA4 database. Blue, proteins with lysine acetylation sites identified. Dashed lines indicate significance thresholds of either uncorrected p-values < 5 % or Benjamini-Hochberg corrected FDR < 5 %. A missing line indicates that the significance threshold was not reached by any of the data points. cancel
D. Co-expression of SidP with MavQ in HeLa cells does not influence the production of PtdIns3P caused by MavQ. The association of the fluorescence probe GFP-2xFYVEHrs with vesicle-like structures was used to indicate the distribution of PtdIns3P in cells. At least 100 cells were scored in each sample (n≥100) (left panel). Wort, wortmannin. Expression of MavQ and SidP in the samples were shown in the right panel. EV represents empty vector.
B. Similar to A indicating 13 major cell populations based on unsupervised clustering. Each cell is colored based on cluster.
NK cell medium was incubated with either euploid control or ArCK cells for 12 hours. At the time of NK cell addition, media were switched between ArCK and euploid control cells (Ctrl). NK cell killing was measured as described in Figure 1C. For reference, NK cell killing of ArCK and euploid control cells (Ctrl) without medium switch were performed side by side and plotted on the graph. Black, euploid control cells without medium switch; red, ArCK cells without medium switch; blue, euploid control cells in ArCK cell condition medium; green, ArCK cells in euploid control cell condition medium. n=3 biological replicates; mean± SEM. Ctrl vs. ArCK, p< 0.0001; Ctrl vs. Ctrl in ArCK med, p< 0.0001; Ctrl vs. ArCK in Ctrl med, p< 0.0001; ArCK vs. ArCK in Ctrl med, p= 0.0002; KS test.
(E) NF-κB luciferase assay in HEK293T WT and NOD1/2 KO NF-κB reporter cells upon cytosolic S1P stimulation.
A. Deep analysis of netrin-3 gene expression in lung cancer cell lines (n=76; RNA-Seq).
(F) Jurkat TAg cells transfected with YFP vector or YFP-T1B were stimulated with 10μg/ml anti-CD3 for indicated times, then lysed and immunoprecipitated with anti-TAK1, followed by immunoblotting with the indicated antibodies.
L929 cells stably transfected with control shRNA or ZDHHC18 shRNA efficiency of ZDHHC18 is shown by western blotting (F) results. Data information: NC: negative control.
A) Motif counts for abundant TF binding sites at the specific DHSs in TM, TB and TB+.
c, Pairwise correlation between cell cycle phase durations of RPE cells overexpressing Myc. Number of cells: Myc, n = 116