EMBO/sd-character-level-ner huggingface dataset:
Asphyxiating thoracic dystrophy (ATD) probands R05-365A and Cmh001543-01.Figure 1(A) AP radiograph demonstrates characteristic findings of ATD in the R05-365A proband. Note the shortened humeri (closed arrowhead) and elongated clavicles (arrow). (B) Radiographs of the Cmh001543-01 proband showing similar findings. (C) Family R05-365A pedigree; * indicates common ancestors. CHD, congenital heart disease, SAB, spontaneous abortion. Abn, abnormalities
Figure 5A. Representative FACS plots of splenocytes from diseased secondary recipients that were transplanted with 104 to 105 flow-sorted myeloid leukemia blasts (ML: CD11b+Gr1+/CD3-CD4-CD8-) from sick primary Myc/Bcl2+LSK-, GMP- or DN2-transplanted mice. Cell percentages in indicated gates are shown. B. Table summarizing the phenotype frequencies within the spleens of secondary recipients that were retransplanted with Myc/Bcl2+LSK-, GMP- or DN2-derived myeloid blasts as described in A. T-lymphoid leukemia: (TL: CD11b-Gr1-/CD3+CD4+CD8+), biphenotypic leukemia: BL (CD11b+Gr1+/CD3+CD4+CD8+), myeloid leukemia: ML (CD11b+Gr1+/CD3-CD4-CD8-). Numbers before the dash represent mice holding the indicated leukemia fraction; numbers after the dash indicate the total mouse count analyzed. C. Single myeloid blasts from 4 different Myc/bcl2+ DN2-derived leukemias were flow-sorted from transplanted mice and grown on irradiated OP9:OP9DL1 stroma. The clones were analyzed at two different time points. FACS plots of two representative clones, one with strong (top) and one with weak (bottom) lineage switching potential are shown. D. Table summarizing the lineage switching outcome of 20 independent clones that were grown from single DN2-derived myeloid blasts of 4 different leukemias. Percentages at the right indicate the relative amounts of cells with T-lymphoid (TL), biphenotypic (BL) or myeloid (ML) phenotype as analyzed by FACS at the end of the experiment. E. FACS plot of DN2-derived primary leukemic cells transduced with a retrovirus carrying GFP alone or GFP together with PU.1 as a bicistronic RNA. The transduced cells were grown on OP9/OP9Dll1 1:1 layer for 8-13 days and analyzed using a GFP-gate. The data are representative of 3 different experiments with similar outcome.
Human S100A9 inhibits HIV-1 reverse transcriptase activity and uncoating.Figure 10Colorimetric HIV-1 RT activity assay was adapted from manufacturer's protocol using constant amount of HIV-1 RT (0.5ng) and increasing amounts of lysates from (A) E2C- and S100A9-expressing HEK293T and (B) E2C- and S100A9-expressing Jurkat cells. Means ± SD colorimetric data obtained from at least two independent experiments were normalized to E2C-expressing lysates and shown on graphs. Schematic description of fate-of-capsid assay is displayed above. HEK293T expressing E2C or S100A9 were transduced with HIV-Luc (10ng p24) for 4 h. Cells were then subjected to the fate of capsid assay (see methods) in order to pull-down intact cores (CA cores) (recovered in the pellet). Equal volumes from the soluble (top fraction) and pelleted (down fraction) materials were analyzed by western blotting in order to evaluate the presence of p24 (CA), CypA, S100A9 and E2C proteins.
Figure 6Representative blots showing expression levels of LATS1/2, CCNE1, CCND1 and YAP in hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells. Cells were collected at passage four (P4) and Passage seven (P7). Actin was used as internal control. mRNA levels of LATS1, LATS2 and YAP in hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells. Cells were collected at passage seven and protein levels were analyzed using quantitative real-time PCR. Representative gel photographs showing mRNA levels of LATS1, LATS2, and YAP in the LATS2-knockout hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells examined using semi-quantitative RT-PCR at passage seven. Representative images showing the morphologic changes and SA-β-gal staining in control and LATS2-knockout hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells. Quantitative data showing the ratio of SA-β-gal positive cells in the control and LATS2-knockout hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells at the seventh passage. Growth curves of the control and LATS2-knockout hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells.
MICU2 Ca2+-free and partial Ca2+-bound states.Figure 2A Close-up view of Ca2+-free MICU1-MICU2 interfaces I (left and middle) and II (right). The atomic interactions at the interface I consist of mainly electrostatic (left) and weak hydrophobic (middle) interactions, while interface II mainly contains hydrophobic interactions (right) B MICU1 interacts with MICU2 at two major interfaces. C Close-up views of the partial Ca2+-bound MICU1-MICU2 interface II. The atomic interactions at interface II consist of weak electrostatic (left) and strong hydrophobic (middle) interactions. The red, green, and orange spheres represent Ca2+, N-, and C-terminus. D The surface-rendered MICU2 hydrophobic pocket shows the interaction at interface II.
Figure 2A A schematic of the injections into the sciatic nerve followed by ipsilateral DRG and dorsal spinal cord tissue analysis. B von Frey testing in female rats (n=6/group) at 1-21 days after injections of OC43p peptide, respective control scrambled OC43p-SCR, OC43p-S2 (10 μg in 5 μl, each) peptides, and PBS vehicle. Responses were recorded in ipsilateral hind paws. Mean tactile withdrawal thresholds are in gram force (g) ± standard deviation; Two-way analysis of variance (ANOVA) with Bonferroni posthoc test: **, p≤0.005; ***, p≤0.0005; ****, p≤0.00005. C Areas under the curve (AUC) were calculated for days 1-21 (n=6 animals/group). Bars show the mean AUC and standard deviations (error bars) for each injection group. Data were analyzed by two-way ANOVA with Tukey posthoc test: ***, p≤0.0005; ****, p≤0.00005. D Observational assays of unstimulated pain-like behavior. Assays were conducted in female rats (n=6/group) after injection of OC43p (red), OC43p-SCR (purple), or PBS (green) on days 4, 14, and 20 post-injection. Each animal was video recorded for 2 min three times within a 2 h period of time. Hind paw positions were scored to calculate unstimulated pain-like behavior indices. Index means and standard deviation are shown; Two-way ANOVA with Tukey's posthoc test was used for groups comparisons.
Beclin 1 is a new substrate of DAPK.Figure 2(A) Flag‐tagged DAPK (100 ng) was incubated with GST (900 ng) or GST-beclin‐1 (750 ng) in the presence of Ca2+, calmodulin and [γ‐33P]ATP for 30 min or 60 min. Phosphorylated proteins were visualized by X‐ray film exposure, and GST/GST-beclin‐1 levels were visualized by Ponceau S staining. The autophosphorylation of DAPK indicates that its catalytic activity was intact in all samples. (B) Flag‐tagged DAPK (60 ng) was incubated with Flag‐tagged beclin 1 (250 ng), which was purified from HEK293T cells, and a kinase assay was performed for 60 min. Where indicated (+LiCl), beclin‐1‐bound beads were first washed stringently in 0.5 M LiCl and 0.5 M KCl. Phosphorylated proteins were visualized by X‐ray film exposure, and the levels of beclin 1 were visualized by Western blot analysis using beclin 1 antibodies. DAPK, death‐associated protein kinase; GST, glutathione S‐transferase; HEK, human embryonic kidney.
Sir3-Sae2 interaction prevents Sae2 function and promotes NHEJ A.Figure 5A. Survival frequencies after DSB induction at LYS2 locus in WT or sae2Δ strains where the Sir3SaID or Sir3SaIDT557I domains are overexpressed from a GPD promoter at the SIR3 locus. Error bars indicate survival standard error (SEM) of at least three independent experiments. Data information: Significance was determined using 2-tailed, unpaired Student's t test. *P-value 0.01 to 0.05, significant; **P-value 0.001 to 0.01, very significant; ****P < 0.0001, extremely significant; P ≥ 0.05, not significant (ns). B. Representative images of Sae2-GFP in WT cells and in cells overexpressing either full-length Sir3 or the sir3SaID domain. Scale bars are 2 μm. C. Survival frequencies after DSB induction at LYS2 locus in the indicated strains. Error bars indicate survival standard error (SEM) of at least three independent experiments. Data information: Significance was determined using 2-tailed, unpaired Student's t test. *P-value 0.01 to 0.05, significant; **P-value 0.001 to 0.01, very significant; ****P < 0.0001, extremely significant; P ≥ 0.05, not significant (ns). D. Representative images of Sir3-mCherry and Sae2-GFP signal in cells overexpressing Sir3 and sir3T557I . Scale bars are 2 μm. E. Telomeric silencing assay at TEL7L in WT, sir4Δ, sir3T557I cells, cells overexpressing SIR3 (oeSIR3) or sir3T557I (oesir3T557I). Growth on 5-FOA plates reflects telomeric silencing. F. Representative silver-stained gels of in vitro GST-pulldown of GST or GST-Sir3SaID, GST-sir3-T557ISaID and Sae2C purified peptides. Control: Sae2C (300 ng, lane 6). G. Co-immunoprecipitation between Sae2-GFP and Sir3 from untagged, Sae2-GFP WT cells, and Sae2-GFP cells overexpressing WT Sir3 (oeSir3, WT), Sae2-GFP sir3Δ or Sae2-GFP overexpressing the sir3-T557I mutant (oeSir3, T557I) using antibodies against Sae2-GFP, analysed by Western blot with anti-GFP and anti-Sir3 antibodies.
Figure 1A Tumor models were derived at DX and REL following treatment. Mitochondria-rich fractions were exposed to tBid or BimBH3 peptide and cytochrome c release measured as a surrogate for apoptotic commitment. Cyto c, cytochrome c; mito, mitochondria. B Maximal cytochrome c release in response to tBid or BimBH3 peptide for each replicate of a DX/REL tumor pair (1-9 biological replicates per DX/REL pair; n=44 total). Cyto c, cytochrome c C Maximal cytochrome c release for all DX/REL pairs with ≥3 biological replicates); box-whisker plots summarize data (box 25%-75%; belt=median; dot=mean; whiskers=minimum and maximum values). Statistical analyses were performed using an unpaired two-sided Student's t-test, with significance p<0.05 (trend p<0.10). Cyto c, cytochrome c D Bak oligomerization in response to escalating tBid concentration for DX/REL pairs. Relative mitochondrial protein loading per lane is assessed by densitometry, showing ration of loading control in REL lane with patient-matched DX lane at same tBid exposure (no REL lane is underloaded compared to DX lane).
Intracellular localization of Ret is altered in the absence of FAK in SCC cells.Figure 1(A) FAK+/+ and FAK−/− murine SCC cells were lysed and FAK, Ret or Src immunoprecipitated and immunoblotting carried out using anti‐FAK, anti‐Ret, anti‐Src and anti‐actin. (B) Cells were fixed and stained with either anti‐Ret (green in the upper left panels) or anti‐Ret PY1062 (green in the lower left panels) and DAPI (blue). Merged and zoomed images are shown. Solid arrows indicate localization at adhesions while broken arrows show localization in puncta. Quantification of percentage of cells that contained Ret in intracellular puncta is shown. Data are presented as mean±s.d. and the significance calculated using a Student's t‐test (n=3). Lysates were immunoblotted with anti‐Ret PY1062 and anti‐actin (lower right panels). (C) Cells were fixed and stained with anti‐Ret (green) and anti‐FAK (red). Merged images are also shown. Solid arrows indicate co‐localization between Ret and FAK at adhesions, while broken arrows indicate its absence in puncta. Scale bars, 20 μM. DAPI, 4,6‐diamidino‐2‐phenylindole; FAK, focal adhesion kinase; Ret, rearranged during transfection; SCC, squamous cell carcinoma.
Figure 4(A) Cryo-EM density map of tetrameric Ams1 in complex with Nbr1-ZZ1 at 2.4 Å. Ams1 subunits 1 to 4 are colored in green, blue, cyan, and yellow. Nbr1-ZZ1 molecules are all colored in orange. (B) Ribbon representation of the Ams1-ZZ1 complex structure. (C) Structure of the Nbr1-ZZ1 domain. The N and C-termini and the Zn-coordinating residues are labeled. (D) Nbr1-ZZ1 uses an acidic pocket to bind the N-terminus of Ams1. Nbr1-ZZ1 is shown as an electrostatic potential surface where the positively to negatively charged regions are colored from blue to red. The N-terminal dipeptide of Ams1 are shown as sticks. The structure has the same orientation as C. (E-F) Binding interface between Nbr1-ZZ1 and Ams1. Nbr1-ZZ1 corresponds to the top left Nbr1-ZZ1 molecule in (A). Ams1_1 is shown as electrostatic potential surface (E) or ribbons (F). Ams1_3 (cyan) and Nbr1-ZZ1 (orange) are shown as ribbons. Residues involved in interactions are labeled. (G) Interactions between Nbr1-ZZ1 (orange) and the N-terminal dipepetide of Ams1 (cyan). Hydrogen bonds are denoted by black dashed lines.
Correlation matrix of gene expression levels among TFs showing TF‐binding sites (TFBS) enrichment at PD‐hypermethylated enhancers.Figure 6Pearson correlation coefficients and correlation P‐values were calculated evaluating TF gene expression levels in iPSC‐derived DAn from PD patients and controls (n = 14) under a 2‐tailed Student's t‐test. Among TFs showing coordinated expression, maximal correlation was observed for FOXA1, FOXA2, NR3C1, HNF4A, and FOSL2.
ABCG2 is involved in multidrug tolerance in melanoma cellsA.Figure 4A. qRT-PCR analysis showing average TBP-normalized expression of ABCB1, ABCC3 and ABCG2 in the indicated cells. Data information: data are presented as mean values + SD for six replicates (n=6). B. Protein lysates from the indicated cells were immuno-blotted for the indicated proteins. Molecular masses of the proteins are indicated in kDa. The numbers below the gel lanes represent relative protein level, which was determined from the band intensity using ImageJ software, and normalized to each relative βTUBULIN control. C-D. MM099 (c) and MM029 (d) were pre-treated with either siCTL or siABCG2 as indicated and treated with increasing concentrations of THZ1 for 72h. Mean growth is shown relative to vehicle (DMSO)-treated cells. E-F. MM099 (e) and MM029 (f) were pre-treated with either siCTL or siABCG2 as indicated and treated with increasing doses of Vemurafenib for 72h. Mean growth is shown relative to vehicle (DMSO)-treated cells. D Data information: data are presented as mean values + SD for three replicates (n=3). IC50 for each cell line is indicated.
Figure 2Immunopurification and mass spectrometric analysis of CRTH2-containing protein complex in NIH 3T3 cells. Cellular extracts from NIH 3T3 cells stably expressing myc-CRTH2 protein, were immunopurified with anti-myc affinity beads and eluted with myc peptide. The eluates were used for SDS-PAGE and the gels were silver stained and analyzed using mass spectrometry. Representative mass spectrogram of CRTH2 from CRTH2-containing protein complex in NIH 3T3 cells. , Representative mass spectrogram of , LARP6 (C) and GRP78 (D) from CRTH2-containing protein complex in NIH 3T3 cells. Co-immunoprecipitation analysis of association of CRTH2 with LARP6. HEK293T cells were co-transfected with Myc-CRTH2 and Flag-LARP6 expressing plasmids. Whole cell lysates from HEK293T cells were immunoprecipitated and then immunoblotted with the indicated antibodies. Subcellular localization of CRTH2 and LARP6 in NIH 3T3 cells. NIH 3T3 cells were transfected with GFP-fused CRTH2 expressing plasmid, and fixed and immunostained with antibodies against the indicated proteins. Red arrow indicates colocalization of CRTH2 and LARP6 in the ER. Scale bar, 20 μm. , Co-IP analysis of association of CRTH2 with GPR78. HEK293T cells were co-transfected with Flag-CRTH2 expressing plasmids. Co-IP analysis of association of CRTH2 with GPR78. HEK293T cells were co-transfected with Myc-GPR78 expressing plasmids. Colocalization of CRTH2, LARP6 and GRP78 in NIH 3T3 cells. White arrow indicates colocalization of CRTH2, LARP6 and GRP78. Scale bar, 20 μm. , Schematic diagram depicting different domains of CRTH2 involved in the interaction with LARP6 and GRP78 in the endoplasmic reticulum membrane.
Figure 8(A-B) CD4+ naïve T cells were sorted from Foxp3-IRES-eGFP reporter mice and differentiated into iTreg cells with TGFβ alone or TGFβ + RA + VitC in the presence of 100 U/ml IL-2 in cultures. On day 6, cells were restimulated without IL-2 or with 3, 5, 10 and 100 U/ml IL-2 at 37°C for 1hr, and stained for phospho-STAT5. Representative histogram overlay of phospho-STAT5 staining for TGFβ and TGFβ + RA + VitC iTregs after IL-2 restimulation (A). Graph depicting the geometric mean fluorescent intensity (MFI) of phospho-STAT5 in TGFβ and TGFβ + RA + VitC iTregs after IL-2 restimulation; each dot represents cells from an individual mouse (B). Data are from seven biological replicates. P-values are calculated using two-tailed paired Student's t test and error bars show mean ± S.D. (C) ChIP-qPCR showing STAT5 occupancy at Foxp3 CNS2 and IL2Rα IN1b regions in TGFβ and TGFβ + RA + VitC iTregs without or with 3 U/ml IL-2 restimulation. GMPR is a negative control region. Data are from two biological replicates. (D-E) Representative histogram overlay (D) and geometric MFI (E) of IL2Rα staining for TGFβ and TGFβ + RA + VitC iTregs on day 3 to day 6 after differentiation in the presence of 100U/ml IL-2. Data are from three biological replicates. P-values are calculated using two-tailed paired Student's t test and error bars show mean ± S.D.
Figure 4(A) (Ai) Western blot analysis was used to confirm UHMK1 overexpression and ATF4 knockdown in BGC823 cells. (Aii) Silencing ATF4 significantly decreased the levels of the indicated metabolites in BGC823 cells overexpressing UHMK1(three biological replicates). (Aiii) Silencing ATF4 significantly decreased the levels of RNA and DNA containing U-14C-glycine in BGC823 cells overexpressing UHMK1(three biological replicates). (B) LC-MS/MS was used to examine the metabolites in SGC7901 cells with or without UHMK1 knockdown or ATF4 reintroduction. The data are shown in the heatmap. (C) Silencing ATF4 significantly decreased the levels of the indicated genes in BGC823 cells overexpressing UHMK1. Data were presented as mean ± standard deviation from three replicates. Unpaired, two-tailed statistical significance was assessed by Student's t‐test. (D) (Di) qRT-PCR was used to measure the expression of ATF4 in BGC823 cells overexpressing UHMK1. (Dii) UHMK1 overexpression enhanced the nuclear translocation of ATF4 in BGC823 cells. (Diii) ChIP assays on the ATIC and PPAT promoters were performed in BGC823 cells with the indicated antibody. Data were presented as mean ± standard deviation from three replicates. Unpaired, two-tailed statistical significance was assessed by Student's t‐test. Data information: *P< 0.05, **P< 0.01, ***P< 0.001, # marked no significance. (E) Silencing ATF4 markedly decreased the proliferation of BGC823 cells overexpressing UHMK1. (left panel) The quantitative number of colonies formed in scramble+Flag, scramble+Flag-UHMK1, siATF4+Flag and siATF4+Flag-UHMK1 group. Data were presented as mean ± standard deviation from three replicates. Unpaired, two-tailed statistical significance was assessed by Student's t‐test. (right panel) Representative images of colonies are shown. Scale bars=5mm. Data information: *P< 0.05, **P< 0.01, ***P< 0.001, # marked no significance. (F) Silencing ATF4 markedly decreased the migration of BGC823 cells with UHMK1 overexpression. (left panel) The quantitative number of migrated cells in scramble+Flag, scramble+Flag-UHMK1, siATF4+Flag and siATF4+Flag-UHMK1 group. Data were presented as mean ± standard deviation from three replicates. Unpaired, two-tailed statistical significance was assessed by Student's t‐test. (right panel) Representative images of migrated cells in each group are shown. Scale bars=100μm. Data information: *P< 0.05, **P< 0.01, ***P< 0.001, # marked no significance. (G) Silencing ATF4 markedly decreased the invasion of UHMK1 overexpressing BGC823 cells. (left panel) The quantitative number of invaded cells in scramble+Flag, scramble+Flag-UHMK1, siATF4+Flag and siATF4+Flag-UHMK1 group. Data were presented as mean ± standard deviation from three replicates. Unpaired, two-tailed statistical significance was assessed by Student's t‐test. (right panel) Representative images of invaded cells in each group are shown. Scale bars=100μm. Data information: *P< 0.05, **P< 0.01, ***P< 0.001, # marked no significance.
Binary heatmap of mutation status of important breast cancer pathways in 3,217 samplesBinary heatmap of mutation status of important BC pathways in 3,217 samples.Figure 4Binary heatmap of mutation status of important BC pathways in 3,217 samples. Samples with wild-type (wt) pathway status (defined as all member genes being wt) are colored blue, those with mutated pathways (at least one member gene mutated) are colored red.
Figure 3DC(WT) and DC(NLRC3-KO) mice were immunized with MOG(35-55) peptide in CFA adjuvant and pertussis toxin to induce EAE. Mean clinical scores of EAE in immunized DC(WT) (n= 5) and DC(NLRC3-KO) mice (n= 5). DC(WT) and DC(NLRC3-KO) mice were immunized with MOG(35-55) peptide in CFA adjuvant and pertussis toxin to induce EAE. Representative flow cytometry data showing intracellular production of IFN-γ and IL-17A by CD4+ T cells in the spinal cord and brain from DC(WT) and DC(NLRC3-KO) mice 26 d after EAE induction after restimulation with MOG(35-55) peptide. DC(WT) and DC(NLRC3-KO) mice were immunized with MOG(35-55) peptide in CFA adjuvant and pertussis toxin to induce EAE. Recall response to MOG(35-55) by splenocytes isolated from DC(WT) and DC(NLRC3-KO) mice 26 d after EAE induction. DC(WT) and DC(NLRC3-KO) mice were immunized with MOG(35-55) peptide in CFA adjuvant and pertussis toxin to induce EAE. Expression of Il12, Il6, Il23 and Il27 mRNA in DCs sorted from DC(WT) and DC(NLRC3-KO) mice 26 d after EAE induction, presented relative to that of Gapdh. DC(WT) and DC(NLRC3-KO) mice were immunized with MOG(35-55) peptide in CFA adjuvant and pertussis toxin to induce EAE. CFSE proliferation assay of naive 2D2 CD4+ T cells stimulated with MOG(35-55) plus DCs sorted from DC(WT) and DC(NLRC3-KO) mice 26 d after EAE induction. DC(WT) and DC(NLRC3-KO) mice were immunized with MOG(35-55) peptide in CFA adjuvant and pertussis toxin to induce EAE. cytokine secretion of naive 2D2 CD4+ T cells stimulated with MOG(35-55) plus DCs sorted from DC(WT) and DC(NLRC3-KO) mice 26 d after EAE induction.