gebhart/patrepeval huggingface dataset:
Interaction of folate receptor with signaling molecules lyn and Gαi-3 in detergent-resistant complexes from the ovary carcinoma cell line IGROV1 (2000)

Using as a model the ovary carcinoma cell line IGROV1, we analyzed the partitioning of the glycosyl-phosphatidylinositol-anchored folate receptor into lipid rafts based on its relative detergent insolubility, with a focus on physically and functionally associated signaling molecules. A variable amount (40-60%) of folate receptor was found in low-density Triton X-100 insoluble complexes together with subunits of heterotrimeric G-proteins and the src-family non-receptor tyrosine kinases p53-56 lyn. In the same fraction the structural component of caveolae, caveolin, was not detected at the protein level, although the corresponding mRNA was detected in trace amounts. Comodulation of folate receptor and signalling molecules was observed in the detergent-insoluble complexes during cell proliferation or induced by phosphatidylinositol-specific phospholipase C treatment or by interaction with anti-folate receptor monoclonal antibodies. Moreover, complexes of folate receptor, lyn and the G(&agr;)(i-3) subunit were immunoprecipitated using either anti-folate receptor or anti-lyn antibodies. In vitro kinase assay of the immunoprecipitates revealed stimulation of phosphorylation of common and specific proteins. In particular, the p53 form of lyn appeared to be enriched and phosphorylated in the anti-folate receptor MOv19 monoclonal antibody immunoprecipitate, whereas a 40 kDa band common to anti-folate receptor and anti-lyn immunoprecipitates was the phosphorylated form of the G(&agr;)(i-3) subunit. These findings point to the functional interaction between folate receptor and associated signaling molecules.
Expression of XCR1 Characterizes the Batf3-Dependent Lineage of Dendritic Cells Capable of Antigen Cross-Presentation (2012)

Cross-presentation of antigen by dendritic cells (DCs) to CD8(+) T cells is a fundamentally important mechanism in the defense against pathogens and tumors. Due to the lack of an appropriate lineage marker, cross-presenting DCs in the mouse are provisionally classified as "Batf3-IRF-8-Id2-dependent DCs" or as "CD8(+) DCs" in the spleen, and as "CD103(+)CD11b(-) DCs" in the periphery. We have now generated a mAb to XCR1, a chemokine receptor which is specifically expressed on CD8(+) DCs and a subpopulation of double negative DCs in the spleen. Using this antibody, we have determined that only XCR1(+)CD8(+) (around 80% of CD8(+) DCs) and their probable precursors, XCR1(+)CD8(-) DCs, efficiently take up cellular material and excel in antigen cross-presentation. In lymph nodes (LNs) and peripheral tissues, XCR1(+) DCs largely, but not fully, correspond to CD103(+)CD11b(-) DCs. Most importantly, we demonstrate that XCR1(+) DCs in the spleen, LNs, and peripheral tissues are dependent on the growth factor Flt3 ligand and are selectively absent in Batf3-deficient animals. These results provide evidence that expression of XCR1 throughout the body defines the Batf3-dependent lineage of DCs with a special capacity to cross-present antigen. XCR1 thus emerges as the first surface marker characterizing a DC lineage in the mouse and potentially also in the human.
Klotho is a substrate for α‐, β‐ and γ‐secretase (2009)

Klotho is an anti-aging protein with different functions of the full-length membrane protein and the secreted hormone-like form. Using overexpression and knock-down approaches as well as embryonic fibroblasts of knock-out mice we present evidence that Klotho is shedded by the alpha-secretases ADAM10 and 17 as well as by the beta-secretase beta-APP cleaving enzyme 1. The remaining membrane-bound fragment is a substrate for regulated intramembrane proteolysis by gamma-secretase. Our data suggest that therapeutic approaches targeting these proteases should be carefully analyzed for potential side effects on Klotho-mediated physiological processes.
Regulation of Phagocyte Oxygen Radical Production by the GTP-Binding Protein Rac 2 (1991)

A major action of the microbicidal system of human neutrophils is the formation of superoxide anion (O2-) by a multicomponent oxidase that transfers electrons from the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) to molecular oxygen. The mechanism of assembly and activation of the oxidase from its cytosolic and membrane-bound components is unknown, but may require the activity of a guanosine 5'-triphosphate (GTP)-binding component. A cytosolic GTP-binding protein (Gox) that regulates the NADPH oxidase of neutrophils was identified. Gox was purified and shown to augment the rate of O2- production in a cell-free oxidase activation system. Sequence analysis of peptide fragments from Gox identified it as Rac 2, a member of the Ras superfamily of GTP-binding proteins. Antibody to a peptide derived from the COOH-terminus of Rac 2 inhibited O2- generation in a concentration-dependent manner. These results suggest that Rac 2 is a regulatory component of the human neutrophil NADPH oxidase, and provide new insights into the mechanism by which this oxygen radical-generating system is regulated.
Identification and behavior of epithelial stem cells in the Drosophila ovary (1995)

Throughout their lives, adult Drosophila females continuously produce oocytes, each surrounded by an epithelial monolayer of follicle cells. To characterize the somatic stem cells that give rise to ovarian follicle cells, we marked dividing cells using FLP-catalyzed mitotic recombination and analyzed the resulting clones. Each ovariole in young females contains, on average, two somatic stem cells located near the border of germarium regions 2a and 2b. The somatic stem cells do not coordinate their divisions either with each other or with the germline stem cells. As females age, initially mosaic ovarioles become monoclonal, indicating that functional somatic stem cells have a finite life span. Analysis of agametic flies revealed that somatic cells continue to divide in the absence of a germline. Under these conditions, the somatic stem cells develop near the tip of the ovariole (the normal site of the germline stem cells), and a subpopulation of somatic cells that normally separates the germline and somatic stem cells is missing.
Sites in the third intracellular loop of the alpha 2A-adrenergic receptor confer short term agonist-promoted desensitization. Evidence for a receptor kinase-mediated mechanism. (1992)

To investigate the mechanisms of agonist-promoted desensitization of the alpha 2-adrenergic receptor (alpha 2AR), the human alpha 2AAR and a mutated form of the receptor were expressed in CHW cells. After cells were exposed to epinephrine for 30 min, the ability of the wild type alpha 2AAR to mediate inhibition of forskolin-stimulated adenylyl cyclase was depressed by approximately 78%. To assess the role of receptor phosphorylation during desensitization, cells were incubated with 32Pi, exposed to agonist, and alpha 2AAR purified by immunoprecipitation with a fusion protein antibody. Agonist-promoted desensitization was found to be accompanied by phosphorylation of the alpha 2AAR in vivo. The beta-adrenergic receptor kinase (beta ARK) is known to phosphorylate purified alpha 2AAR in vitro. We found that heparin, a beta ARK inhibitor, ablated short term agonist-induced desensitization of alpha 2AAR, while such desensitization was unaffected by inhibition of protein kinase A. To further assess the role of beta ARK, we constructed a mutated alpha 2AAR which has a portion of the third intracellular loop containing 9 serines and threonines (potential phosphorylation sites) deleted. This mutated alpha 2AAR failed to undergo short term agonist-induced desensitization. Agonist promoted in vivo phosphorylation of this mutated receptor was reduced by 90%, consistent with the notion that receptor phosphorylation at sites in the third intracellular loop plays a critical role in alpha 2AAR desensitization. After 24 h of agonist exposure, an even more profound desensitization of alpha 2AAR occurred, which was not accompanied by a decrease in receptor expression. Rather, long term agonist-induced desensitization was found to be due in part to a decrease in the amount of cellular Gi, which was not dependent on receptor third loop phosphorylation sites.
Protein Expression in Mammalian Cells (2011)

Through all of the recent progress provided by high throughput DNA sequencing technologies, it has become clearer and clearer that the study of proteins and protein organelles will be the key to unloc
The Lattice-Boltzmann Method for Gaseous Phenomena (2003)

We present a physically-based, yet fast and simple method to simulate gaseous phenom-ena. In our approach, the incompressible Navier-Stokes (NS) equations governing fluid motion have been modeled in a novel way to achieve a realistic animation. We introduce the Lattice Boltzmann Model (LBM) which simulates the microscopic movement of fluid particles by lin-ear and local rules on a grid of cells, so that the macroscopic averaged properties obey the desired NS equations. The LBM is defined on a 2D or 3D discrete lattice, which is used to solve fluid animation based on different boundary conditions. The LBM simulation generates in real-time an accurate velocity field and can incorporate an optional temperature field to ac-count for the buoyancy force of hot gas. Because of the linear and regular operations on each local cell of the LBM grid, we implement the computation in commodity texture hardware, further improving the simulation speed. Finally, textured splats are used to add small scale tur-bulent details, achieving high-quality real-time rendering. Our method can also simulate the physically correct action of stationary or mobile obstacles on gaseous phenomena in real-time, while still maintaining highly plausible visual details.
5-(Haloalkyl)-2'-deoxyuridines: a novel type of potent antiviral nucleoside analog (1985)

Syntheses of 5-(2-haloethyl)-2'-deoxyuridines, 5-(3-chloropropyl)-2'-deoxyuridines, and 5-(2-chloroethyl)-2'-deoxycytidine are described. The antiviral activities of these compounds were determined in cell culture against herpes simplex virus types 1 and 2. All compounds were shown to possess significant and selective antiviral activity. The most potent derivative, 5-(2-chloroethyl)-2'-deoxyuridine (CEDU), inhibited HSV-1 at concentrations below 0.1 microgram/mL. It exerted measurable inhibitory effects on cell proliferation only at concentrations higher than 100 micrograms/mL. In vivo CEDU reduced the mortality rate of HSV-1-infected mice at concentrations lower than 5 mg/kg per day when given intraperitoneally and orally. Thus, it proved to be more effective in this in vivo model than the reference compounds (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) and 9-[(2-hydroxyethoxy)methyl]guanine (ACV).
Simultaneous Reduction and Surface Functionalization of Graphene Oxide by Mussel‐Inspired Chemistry (2010)

Abstract This study presents a method of simultaneous reduction and surface functionalization of graphene oxide by a one‐step poly(norepinephrine) functionalization. The pH‐induced aqueous functionalization of graphene oxide by poly(norepinephrine), a catecholamine polymer inspired by the robust adhesion of marine mussels, chemically reduced and functionalized graphene oxide. Moreover, the polymerized norepinephrine (pNor) layer provided multifunctionality on the reduced graphene oxide that includes surface‐initiated polymerization and spontaneous metallic nanoparticle formation. This facile surface modification strategy can be a useful platform for graphene‐based nano‐composites.
p53 Mediates Nontranscriptional Cell Death in Dopaminergic Cells in Response to Proteasome Inhibition (2006)

Proteasome dysfunction has been demonstrated in Parkinson disease (PD), and proteasome inhibitors have been shown to induce degeneration of dopaminergic neurons in vitro and in vivo. The mechanism whereby proteasome dysfunction leads to dopaminergic cell death, however, is unknown. In this study, we show that proteasome inhibition in both PC12 cells and dopaminergic neurons derived from embryonic stem cells is associated with mitochondrial membrane permeabilization, activation of caspase-3, and nuclear changes consistent with apoptosis. Prior to the emergence of apoptotic features, we found that proteasome inhibition induced increased levels of phosphorylated p53. Inhibition of p53 by pifithrin-alpha or by RNA interference prevented mitochondrial membrane permeabilization and cytotoxicity. There was no increase in p53 mRNA in proteasome-inhibited cells, suggesting that p53 was increased in a transcription-independent manner. Further, there was no increase in Puma or Bax mRNA and p53 co-immunoprecipitated with Bcl-xL and Mdm2. These findings suggest that p53 mediates cell death by way of a direct mitochondrial effect in this model. We also observed increased levels of phosphorylated p53 in dopamine neurons of the substantia nigra pars compacta of mice following systemic administration of a proteasome inhibitor. These changes preceded degeneration of dopaminergic neurons. Increased phosphorylated p53 was also demonstrated in the substantia nigra pars compacta of post-mortem PD brains. These results suggest that abnormalities in p53 signaling play a role in dopaminergic cell death induced by proteasome inhibition and may be relevant to neurodegeneration in PD.
Measurement of Cremophor EL Following Taxol: Plasma Levels Sufficient to Reverse Drug Exclusion Mediated by the Multidrug-Resistant Phenotype (1993)

The efficacy of paclitaxel against some tumors may be aided by its administration in a vehicle solution containing Cremophor in quantities that reach concentrations in the plasma sufficient to reverse multidrug resistance of neoplastic cells.
Characterization of a Conformationally Sensitive Murine Monoclonal Antibody Directed to the Metal Ion-Dependent Adhesion Site Face of Integrin CD11b (2002)

Integrin binding to physiologic ligands requires divalent cations and an inside-out-driven switch of the integrin to a high-affinity state. Divalent cations at the metal ion-dependent adhesion site (MIDAS) face of the alpha subunit-derived A domain provide a direct bridge between ligands and the integrin, and it has been proposed that activation dependency is caused by reorientation of the surrounding residues relative to the metal ion, forming an optimal binding interface. To gain more insight into the functional significance of the protein movements on the MIDAS face, we raised and characterized a murine mAb 107 directed against the MIDAS face of the A domain from integrin CD11b. We find that mAb 107 behaves as a ligand mimic. It binds in a divalent-cation-dependent manner to solvent-exposed residues on the MIDAS face of CD11b, blocks interaction of 11bA or the holoreceptor with ligands, and inhibits spreading and phagocytosis by human neutrophils. However, in contrast to physiologic ligands, mAb 107 preferentially binds to the inactive low-affinity form of the integrin, suggesting that its antagonistic effects are exerted in part by stabilizing the receptor in the low-affinity state. These data support a functional relevance of the protein movements on the MIDAS face and suggest that stabilizing the A domain in the low-affinity state may have therapeutic benefit.
The Action Pattern of Porcine Pancreatic α-Amylase in Relationship to the Substrate Binding Site of the Enzyme (1970)

Abstract The position specificity of porcine pancreatic α-amylase action on maltotriose (G3) through maltooctaose (G8) has been studied with maltodextrins specifically labeled in the reducing glucose unit with 14C. The initial relative rates of formation of the labeled products were determined for each substrate. As the size of the maltodextrin increases, the point of maximum frequency of attack shifts from the first bond from the reducing end (bond 1) in G3 to bond 2 in G4 through G7 and to bond 3 in G8. All of the dextrins had more than one bond cleaved except G5, which was cleaved only at bond 2 giving labeled G2 (G2*). Further, neither bond 1 nor the nonreducing terminal bond was cleaved for G5 and higher dextrins in the series. The action patterns on G3 and G4 were observed to be concentration-dependent. At low concentrations of G3* (2.5 mm), G1* was formed at a faster rate than G2*; at 44 mm, the rates of formation of G1* and G2* were equal, and at 100 mm the rate of formation of G2* exceeded G1*. By kinetic analysis and specific labeling experiments, it has been shown that, at low concentrations of G3 the formation of products is due to hydrolysis. At high concentrations, the products are due to a condensation reaction in which 2 molecules of G3 condense to give G6 with subsequent hydrolysis and change in product distribution. The data are consistent with a five-glucose binding site, in which the catalytic groups are located at bond 2.
A dynamic model of the hypoxia-inducible factor 1-alpha (HIF-1α) network (2013)

Activation of the hypoxia-inducible factor (HIF) pathway is a critical step in the transcriptional response to hypoxia. Although many of the key proteins involved have been characterised, the dynamics of their interactions in generating this response remain unclear. In the present study, we have generated a comprehensive mathematical model of the HIF-1α pathway based on core validated components and dynamic experimental data, and confirm the previously described connections within the predicted network topology. Our model confirms previous work demonstrating that the steps leading to optimal HIF-1α transcriptional activity require sequential inhibition of both prolyl- and asparaginyl-hydroxylases. We predict from our model (and confirm experimentally) that there is residual activity of the asparaginyl-hydroxylase FIH (factor inhibiting HIF) at low oxygen tension. Furthermore, silencing FIH under conditions where prolyl-hydroxylases are inhibited results in increased HIF-1α transcriptional activity, but paradoxically decreases HIF-1α stability. Using a core module of the HIF network and mathematical proof supported by experimental data, we propose that asparaginyl hydroxylation confers a degree of resistance upon HIF-1α to proteosomal degradation. Thus, through in vitro experimental data and in silico predictions, we provide a comprehensive model of the dynamic regulation of HIF-1α transcriptional activity by hydroxylases and use its predictive and adaptive properties to explain counter-intuitive biological observations.
Targeting Mutant BRAF in Relapsed or Refractory Hairy-Cell Leukemia (2015)

A short oral course of vemurafenib was highly effective in patients with relapsed or refractory hairy-cell leukemia. (Funded by the Associazione Italiana per la Ricerca sul Cancro and others; EudraCT number, 2011-005487-13; ClinicalTrials.gov number NCT01711632.).
A rat anti-mouse T4 monoclonal antibody (H129.19) inhibits the proliferation of Ia-reactive T cell clones and delineates two phenotypically distinct (T4+, Lyt-2,3-, and T4-, Lyt-2,3+) subsets among anti-Ia cytolytic T cell clones. (1984)

Hybridoma H129 .19 was derived by fusion between spleen cells of a Lou / Ws1 rat immunized with an Lyt-1+,2- anti-I-Ak cytolytic T lymphocyte (CTL) clone and the nonsecreting myeloma X63-Ag8.653. The monoclonal antibody (mAb) H129 .19 (IgG2a, kappa) was selected for its capacity to inhibit the lytic potential of the immunizing clone. H129 .19 identified a monomorphic determinant on a 55 m.w. murine T cell differentiation antigen, which appeared to be homologous to the human T4 molecule in that: 1) H129 .19 reacted with 80% adult thymocytes, with a subset of splenic T cells, and with the interleukin 2 (IL 2)-producing EL4 thymoma; 2) The mAb bound to and inhibited the IL 2 production and the proliferation of various allo- or soluble antigen-reactive T cell clones that recognized restriction or activating determinants on the I-A or I-E molecules, respectively; 3) H129 .19 did not inhibit the proliferation and/or cytolysis of Lyt-2,3+ T cells specific for class I MHC antigen; and 4) Among six anti-Iak CTL clones examined in this study, the mAb H129 .19 reacted with two I-Ak-specific, Lyt-2,3- clones on which it exerted strong cytolysis inhibiting effect at the effector cell level. By contrast, two other anti-I-Ak and two anti-I-Ek CTL clones were found to express the Lyt-2,3+,T4- cell surface phenotype. The cytolytic potential of the latter clones was not inhibited by anti-Lyt-2,3 mAb. These studies strongly suggest that the mouse T4 molecule facilitates the recognition of class II MHC antigen by most but not all T cells.
The Synthesis of 3'-Fluoro-dl-thyronine and Some of its Iodinated Derivatives (1941)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Synthesis of 3'-Fluoro-dl-thyronine and Some of its Iodinated DerivativesCarl Niemann, James F. Mead, and Andrew A. BensonCite this: J. Am. Chem. Soc. 1941, 63, 2, 609–611Publication Date (Print):February 1, 1941Publication History Published online1 May 2002Published inissue 1 February 1941https://pubs.acs.org/doi/10.1021/ja01847a072https://doi.org/10.1021/ja01847a072research-articleACS PublicationsRequest reuse permissionsArticle Views112Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Biological Activity of a C-Terminal Fragment ofPasteurella multocidaToxin (2001)

The protein toxin of Pasteurella multocida PMT is a potent mitogen and activator of phospholipase Cbeta. In this study different toxin fragments were investigated. A C-terminal fragment encompassing amino acids 581 through 1285 (PMT581C) was constructed, which was inactive toward intact embryonic bovine lung (EBL) cells after addition to culture medium but caused reorganization of the actin cytoskeleton and rounding up of cells when introduced into the cells by electroporation. As the holotoxin, the toxin fragment PMT581C induced an increase in total inositol phosphate levels after introduction into the cell by electroporation. A C-terminal fragment shorter than PMT581C as well as N-terminal fragments were inactive. Exchange of cysteine-1165 for serine in the holotoxin resulted in a complete loss of the ability to increase inositol phosphate levels. Correspondingly, the mutated toxin fragment PMT581C.C1165S was inactive after cell introduction by electroporation, suggesting an essential role of Cys-1165 in the biological activity of the toxin.