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Sample records for structural core antigen

  1. Recovery of antigenically reactive HIV-2 cores.

    PubMed

    Chrystie, I L; Almeida, J D

    1989-03-01

    Negative staining studies of human immunodeficiency virus (HIV) have been hampered by the fragile nature of the particles. Although detergent treatment is capable of releasing cores from HIV-2 particles, these are unstable and do not retain morphological integrity. Addition of glutaraldehyde will stabilise these structures but, if used at too high a concentration, will destroy their antigenicity. This study shows that if both detergent and glutaraldehyde are used in correct proportions, antigenically reactive cores can be recovered from HIV-2 cell cultures. More specifically we show that a mixture of 0.1% Nonidet P40 and 0.1% glutaraldehyde produces preparations of HIV-2 cores that are suitable for immune electron microscopy. These cores reacted positively, that is, formed immune complexes, with both human HIV-2 antisera and a mouse monoclonal antibody that, although directed against p24 (HIV-1), reacts also with p25 (HIV-2).

  2. Antigenic determinants and functional domains in core antigen and e antigen from hepatitis B virus.

    PubMed Central

    Salfeld, J; Pfaff, E; Noah, M; Schaller, H

    1989-01-01

    The precore/core gene of hepatitis B virus directs the synthesis of two polypeptides, the 21-kilodalton subunit (p21c) forming the viral nucleocapsid (serologically defined as core antigen [HBcAg]) and a secreted processed protein (p17e, serologically defined as HBe antigen [HBeAg]). Although most of their primary amino acid sequences are identical, HBcAg and HBeAg display different antigenic properties that are widely used in hepatitis B virus diagnosis. To locate and to characterize the corresponding determinants, segments of the core gene were expressed in Escherichia coli and probed with a panel of polyclonal or monoclonal antibodies in radioimmunoassays or enzyme-linked immunosorbent assays, Western blots, and competition assays. Three distinct major determinants were characterized. The single conformational determinant responsible for HBc antigenicity in the assembled core (HBc) and a linear HBe-related determinant (HBe1) were both mapped to an overlapping hydrophilic sequence around amino acid 80; a second HBe determinant (HBe2) was assigned to a location in the vicinity of amino acid 138 but found to require for its antigenicity the intramolecular participation of the extended sequence between amino acids 10 and 140. It is postulated that HBcAg and HBeAg share common basic three-dimensional structure exposing the common linear determinant HBe1 but that they differ in the presentation of two conformational determinants that are either introduced (HBc) or masked (HBe2) in the assembled core. The simultaneous presentation of HBe1 and HBc, two distinctly different antigenic determinants with overlapping amino acid sequences, is interpreted to indicate the presence of slightly differently folded, stable conformational states of p21c in the hepatitis B virus nucleocapsid. Images PMID:2463383

  3. Reaching for far-flung antigen: How solid-core podosomes of dendritic cells transform into protrusive structures.

    PubMed

    Baranov, Maksim V; Ter Beest, Martin; van den Bogaart, Geert

    2014-10-01

    We recently identified a novel role for podosomes in antigen sampling. Podosomes are dynamic cellular structures that consist of point-like concentrations of actin surrounded by integrins and adaptor proteins such as vinculin and talin. Podosomes establish cellular contact with the extracellular matrix (ECM) and facilitate cell migration via ECM degradation. In our recent paper, we studied podosomes of human dendritic cells (DCs), major antigen presenting cells (APC) that take-up, process, and present foreign antigen to naive T-cells. We employed gelatin-impregnated porous polycarbonate filters to demonstrate that the mechanosensitive podosomes of DCs selectively localize to regions of low-physical resistance such as the filter pores. After degradation of the gelatin, podosomes increasingly protrude into the lumen of these pores. These protrusive podosome-derived structures contain several endocytic and early endosomal markers such as clathrin, Rab5, and VAMP3, and, surprisingly, also contain C-type lectins, a type of pathogen recognition receptors (PRRs). Finally, we performed functional uptake experiments to demonstrate that these PRRs facilitate uptake of antigen from the opposite side of the filter. Our data provide mechanistic insight in how dendritic cells sample for antigen across epithelial barriers for instance from the lumen of the lung and gut.

  4. Reaching for far-flung antigen: How solid-core podosomes of dendritic cells transform into protrusive structures

    PubMed Central

    Baranov, Maksim V; ter Beest, Martin; van den Bogaart, Geert

    2014-01-01

    We recently identified a novel role for podosomes in antigen sampling. Podosomes are dynamic cellular structures that consist of point-like concentrations of actin surrounded by integrins and adaptor proteins such as vinculin and talin. Podosomes establish cellular contact with the extracellular matrix (ECM) and facilitate cell migration via ECM degradation. In our recent paper, we studied podosomes of human dendritic cells (DCs), major antigen presenting cells (APC) that take-up, process, and present foreign antigen to naive T-cells. We employed gelatin-impregnated porous polycarbonate filters to demonstrate that the mechanosensitive podosomes of DCs selectively localize to regions of low-physical resistance such as the filter pores. After degradation of the gelatin, podosomes increasingly protrude into the lumen of these pores. These protrusive podosome-derived structures contain several endocytic and early endosomal markers such as clathrin, Rab5, and VAMP3, and, surprisingly, also contain C-type lectins, a type of pathogen recognition receptors (PRRs). Finally, we performed functional uptake experiments to demonstrate that these PRRs facilitate uptake of antigen from the opposite side of the filter. Our data provide mechanistic insight in how dendritic cells sample for antigen across epithelial barriers for instance from the lumen of the lung and gut. PMID:26843902

  5. Radioimmunoassay for hepatitis B core antigen

    SciTech Connect

    Sagnelli, E.; Pereira, C.; Triolo, G.; Vernace, S.; Paronetto, F.

    1982-02-01

    Serum hepatitis B core antigen (HBcAg) is an important marker of hepatitis B virus replication. We describe an easy, sensitive radioimmunoassay for determination of HBcAg in detergent-treated serum pellets containing Dane particles. Components of a commercial kit for anticore determination are used, and HBcAG is measured by competitive inhibition of binding of /sub 125/I-labeled antibodies to HBcAg with HBcAg-coated beads. We assayed for HBcAG in the sera of 49 patients with hepatitis B surface antigen (HBsAg)-positive chronic hepatitis, 50 patients with HBsAg-negative chronic hepatitis, and 30 healthy volunteers. HBcAg was detected in 41% of patients with HBsAg-positive chronic hepatitis but not in patients with HBsAg-negative chronic hepatitis. Hepatitis Be antigen (an antigen closely associated with the core of Dane particles) determined in the same sera by radioimmunoassay, was not detected in 50% of HBcAg-positive sera.

  6. Francisella Tularensis Blue–Gray Phase Variation Involves Structural Modifications of Lipopolysaccharide O-Antigen, Core and Lipid A and Affects Intramacrophage Survival and Vaccine Efficacy

    PubMed Central

    Soni, Shilpa; Ernst, Robert K.; Muszyński, Artur; Mohapatra, Nrusingh P.; Perry, Malcolm B.; Vinogradov, Evgeny; Carlson, Russell W.; Gunn, John S.

    2010-01-01

    Francisella tularensis is a CDC Category A biological agent and a potential bioterrorist threat. There is no licensed vaccine against tularemia in the United States. A long-standing issue with potential Francisella vaccines is strain phase variation to a gray form that lacks protective capability in animal models. Comparisons of the parental strain (LVS) and a gray variant (LVSG) have identified lipopolysaccharide (LPS) alterations as a primary change. The LPS of the F. tularensis variant strain gains reactivity to F. novicida anti-LPS antibodies, suggesting structural alterations to the O-antigen. However, biochemical and structural analysis of the F. tularensis LVSG and LVS LPS demonstrated that LVSG has less O-antigen but no major O-antigen structural alterations. Additionally, LVSG possesses structural differences in both the core and lipid A regions, the latter being decreased galactosamine modification. Recent work has identified two genes important in adding galactosamine (flmF2 and flmK) to the lipid A. Quantitative real-time PCR showed reduced transcripts of both of these genes in the gray variant when compared to LVS. Loss of flmF2 or flmK caused less frequent phase conversion but did not alter intramacrophage survival or colony morphology. The LVSG strain demonstrated an intramacrophage survival defect in human and rat but not mouse macrophages. Consistent with this result, the LVSG variant demonstrated little change in LD50 in the mouse model of infection. Furthermore, the LVSG strain lacks the protective capacity of F. tularensis LVS against virulent Type A challenge. These data suggest that the LPS of the F. tularensis LVSG phase variant is dramatically altered. Understanding the mechanism of blue to gray phase variation may lead to a way to inhibit this variation, thus making future F. tularensis vaccines more stable and efficacious. PMID:21687776

  7. Antibodies against non-structural c100/3 and structural core antigen of hepatitis C virus (HCV) in hemodialysis patients.

    PubMed

    Yoshida, C F; Takahashi, Y; Vanderborght, B O; Rouzere, C D; França, M S; Takahashi, C; Takamizawa, A; Yoshida, I; Schatzmayr, H G

    1993-01-01

    Two groups of patients undergoing hemodialysis (HD) maintenance were evaluated for their antibody response to non-structural c100/3 protein and structural core protein of hepatitis C virus (HCV). Forty-six patients (Group 1) never presented liver abnormalities during HD treatment, while 52 patients (Group 2) had either current or prior liver enzyme elevations. Prevalence rates of 32.6% and 41.3% were found for anti-c100/3 and anti-HCV core antibodies, respectively, in patients with silent infections (Group 1). The rate of anti-c100/3 in patients of Group 2 was 71.15% and reached 86.5% for anti-HCV core antibodies. The recognition of anti-c100/3 and anti-core antibodies was significantly higher in Group 2 than in Group 1. A line immunoassay composed of structural and non-structural peptides was used as a confirmation assay. HBV infection, measured by the presence of anti-HBc antibodies, was observed in 39.8% of the patients. Six were HBsAg chronic carriers and 13 had naturally acquired anti-HBs antibodies. The duration of HD treatment was correlated with anti-HCV positivity. A high prevalence of 96.7% (Group 2) was found in patients who underwent more than 5 years of treatment. Our results suggest that anti-HCV core ELISA is more accurate for detecting HCV infection than anti-c100/3. Although the risk associated with the duration of HD treatment and blood transfusion was high, additional factors such as a significant non-transfusional spread of HCV seems to play a role as well. The identification of infective patients by more sensitive methods for HCV genome detection should help to control the transmission of HCV in the unit under study.

  8. Core assembly storage structure

    DOEpatents

    Jones, Jr., Charles E.; Brunings, Jay E.

    1988-01-01

    A structure for the storage of core assemblies from a liquid metal-cooled nuclear reactor. The structure comprises an enclosed housing having a substantially flat horizontal top plate, a bottom plate and substantially vertical wall members extending therebetween. A plurality of thimble members extend downwardly through the top plate. Each thimble member is closed at its bottom end and has an open end adjacent said top plate. Each thimble member has a length and diameter greater than that of the core assembly to be stored therein. The housing is provided with an inlet duct for the admission of cooling air and an exhaust duct for the discharge of air therefrom, such that when hot core assemblies are placed in the thimbles, the heat generated will by convection cause air to flow from the inlet duct around the thimbles and out the exhaust duct maintaining the core assemblies at a safe temperature without the necessity of auxiliary powered cooling equipment.

  9. The redefinition of Helicobacter pylori lipopolysaccharide O-antigen and core-oligosaccharide domains

    PubMed Central

    Debowski, Aleksandra W.; Nilsson, Hans-Olof; Fulurija, Alma; Dell, Anne; Stubbs, Keith A.; Marshall, Barry J.

    2017-01-01

    Helicobacter pylori lipopolysaccharide promotes chronic gastric colonisation through O-antigen host mimicry and resistance to mucosal antimicrobial peptides mediated primarily by modifications of the lipid A. The structural organisation of the core and O-antigen domains of H. pylori lipopolysaccharide remains unclear, as the O-antigen attachment site has still to be identified experimentally. Here, structural investigations of lipopolysaccharides purified from two wild-type strains and the O-antigen ligase mutant revealed that the H. pylori core-oligosaccharide domain is a short conserved hexasaccharide (Glc-Gal-DD-Hep-LD-Hep-LD-Hep-KDO) decorated with the O-antigen domain encompassing a conserved trisaccharide (-DD-Hep-Fuc-GlcNAc-) and variable glucan, heptan and Lewis antigens. Furthermore, the putative heptosyltransferase HP1284 was found to be required for the transfer of the third heptose residue to the core-oligosaccharide. Interestingly, mutation of HP1284 did not affect the ligation of the O-antigen and resulted in the attachment of the O-antigen onto an incomplete core-oligosaccharide missing the third heptose and the adjoining Glc-Gal residues. Mutants deficient in either HP1284 or O-antigen ligase displayed a moderate increase in susceptibility to polymyxin B but were unable to colonise the mouse gastric mucosa. Finally, mapping mutagenesis and colonisation data of previous studies onto the redefined organisation of H. pylori lipopolysaccharide revealed that only the conserved motifs were essential for colonisation. In conclusion, H. pylori lipopolysaccharide is missing the canonical inner and outer core organisation. Instead it displays a short core and a longer O-antigen encompassing residues previously assigned as the outer core domain. The redefinition of H. pylori lipopolysaccharide domains warrants future studies to dissect the role of each domain in host-pathogen interactions. Also enzymes involved in the assembly of the conserved core structure

  10. The redefinition of Helicobacter pylori lipopolysaccharide O-antigen and core-oligosaccharide domains.

    PubMed

    Li, Hong; Yang, Tiandi; Liao, Tingting; Debowski, Aleksandra W; Nilsson, Hans-Olof; Fulurija, Alma; Haslam, Stuart M; Mulloy, Barbara; Dell, Anne; Stubbs, Keith A; Marshall, Barry J; Benghezal, Mohammed

    2017-03-01

    Helicobacter pylori lipopolysaccharide promotes chronic gastric colonisation through O-antigen host mimicry and resistance to mucosal antimicrobial peptides mediated primarily by modifications of the lipid A. The structural organisation of the core and O-antigen domains of H. pylori lipopolysaccharide remains unclear, as the O-antigen attachment site has still to be identified experimentally. Here, structural investigations of lipopolysaccharides purified from two wild-type strains and the O-antigen ligase mutant revealed that the H. pylori core-oligosaccharide domain is a short conserved hexasaccharide (Glc-Gal-DD-Hep-LD-Hep-LD-Hep-KDO) decorated with the O-antigen domain encompassing a conserved trisaccharide (-DD-Hep-Fuc-GlcNAc-) and variable glucan, heptan and Lewis antigens. Furthermore, the putative heptosyltransferase HP1284 was found to be required for the transfer of the third heptose residue to the core-oligosaccharide. Interestingly, mutation of HP1284 did not affect the ligation of the O-antigen and resulted in the attachment of the O-antigen onto an incomplete core-oligosaccharide missing the third heptose and the adjoining Glc-Gal residues. Mutants deficient in either HP1284 or O-antigen ligase displayed a moderate increase in susceptibility to polymyxin B but were unable to colonise the mouse gastric mucosa. Finally, mapping mutagenesis and colonisation data of previous studies onto the redefined organisation of H. pylori lipopolysaccharide revealed that only the conserved motifs were essential for colonisation. In conclusion, H. pylori lipopolysaccharide is missing the canonical inner and outer core organisation. Instead it displays a short core and a longer O-antigen encompassing residues previously assigned as the outer core domain. The redefinition of H. pylori lipopolysaccharide domains warrants future studies to dissect the role of each domain in host-pathogen interactions. Also enzymes involved in the assembly of the conserved core structure

  11. Immunological Properties of Hepatitis B Core Antigen Fusion Proteins

    NASA Astrophysics Data System (ADS)

    Francis, Michael J.; Hastings, Gillian Z.; Brown, Alan L.; Grace, Ken G.; Rowlands, David J.; Brown, Fred; Clarke, Berwyn E.

    1990-04-01

    The immunogenicity of a 19 amino acid peptide from foot-and-mouth disease virus has previously been shown to approach that of the inactivated virus from which it was derived after multimeric particulate presentation as an N-terminal fusion with hepatitis B core antigen. In this report we demonstrate that rhinovirus peptide-hepatitis B core antigen fusion proteins are 10-fold more immunogenic than peptide coupled to keyhole limpet hemocyanin and 100-fold more immunogenic than uncoupled peptide with an added helper T-cell epitope. The fusion proteins can be readily administered without adjuvant or with adjuvants acceptable for human and veterinary application and can elicit a response after nasal or oral dosing. The fusion proteins can also act as T-cell-independent antigens. These properties provide further support for their suitability as presentation systems for "foreign" epitopes in the development of vaccines.

  12. The potential role of HCV core antigen testing in diagnosing HCV infection.

    PubMed

    Dawson, George J

    2012-01-01

    The potential uses of serological tests that detect HCV core antigens in biological fluids are highlighted. The most common serological tests utilized to detect exposure to HCV rely on the detection of antibodies to HCV. However, these tests cannot distinguish between individuals who have resolved their infection and those who remain actively infected with HCV. By contrast, the HCV core antigen test detects circulating HCV core antigen and identifies individuals who are actively infected with HCV. There is increasing interest in using the HCV core antigen test as a reflex test for seropositive individuals to identify individuals who are actively infected with HCV. In addition, the HCV core antigen test can be utilized to detect the early phase of HCV infection prior to the development of antibodies, both in the blood bank setting and in the diagnostic laboratory. Lastly, quantitative versions of the HCV core antigen test can be used to monitor the effectiveness of antiviral therapy.

  13. Red cell antigens: Structure and function

    PubMed Central

    Pourazar, Abbasali

    2007-01-01

    Landsteiner and his colleagues demonstrated that human beings could be classified into four groups depending on the presence of one (A) or another (B) or both (AB) or none (O) of the antigens on their red cells. The number of the blood group antigens up to 1984 was 410. In the next 20 years, there were 16 systems with 144 antigens and quite a collection of antigens waiting to be assigned to systems, pending the discovery of new information about their relationship to the established systems. The importance of most blood group antigens had been recognized by immunological complications of blood transfusion or pregnancies; their molecular structure and function however remained undefined for many decades. Recent advances in molecular genetics and cellular biochemistry resulted in an abundance of new information in this field of research. In this review, we try to give some examples of advances made in the field of ‘structure and function of the red cell surface molecules.’ PMID:21938229

  14. Common antigen structures of HL-A antigens

    PubMed Central

    Miyakawa, Y.; Tanigaki, N.; Yagi, Y.; Pressman, D.

    1973-01-01

    Antigenic determinants recognizable by rabbits were found to be present on the molecular fragments (48,000 Daltons) which were obtained by papain-solubilization of the membrane fractions of cultured human lymphoid cells and which carried the HL-A determinants. Results were obtained which suggest that these antigenic determinants are present in common on these molecular fragments carrying HL-A determinants regardless of their HL-A specificity and are restricted to the molecular fragments which carry HL-A determinants. The study was made by use of radioimmune methods involving the binding of radioiodine-labelled soluble HL-A antigen preparations by anti-HL-A alloantisera and by rabbit antisera raised against the membrane fractions of cultured human lymphoid cells. PMID:4119543

  15. Structure of the core oligosaccharide in the serotype O8 lipopolysaccharide from Klebsiella pneumoniae.

    PubMed Central

    Severn, W B; Kelly, R F; Richards, J C; Whitfield, C

    1996-01-01

    Two classes of mutants with O-antigen-deficient lipopolysaccharides were isolated from the serotype O8 reference strain, belonging to Klebsiella pneumoniae subspecies ozaenae. These mutants were selected by resistance to bacteriophage KO1-2, which recognizes and lyses strains with lipopolysaccharide molecules containing the D-galactan II O antigen. Strain RFK-11 contains a defect in O-antigen synthesis and has a complete core, including the attachment site for O antigen. This mutation is complemented by a plasmid carrying the rfb (O-antigen biosynthesis) gene cluster from the related K. pneumoniae serotype O1. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the lipopolysaccharide from strain RFK-9 has a mobility typical of deep-rough lipopolysaccharide. RFK-9 lipopolysaccharide lacks the attachment site for O antigen. Lipopolysaccharides from strains RFK-9 and RFK-11 were isolated, and their structures were determined by methylation analyses, muclear magnetic resonance spectroscopy, and mass spectroscopy. The deduced O8 core oligosaccharide includes the partial core structure reported for the K. pneumoniae subspecies pneumoniae serotype O1 lipopolysaccharide (M. Süsskind, S. Müller-Leonnies, W. Nimmich, H. Brade, and O. Holst, Carbohydr. Res. 269:C1-7, 1995), consistent with the possibility of a conserved core structure within the species. The core oligosaccharide differs from those of the genera Salmonella and Escherichia by the absence of a hexose-containing outer core, the lack of phosphate residues in the inner core, and the presence of galacturonic acid residues. PMID:8626303

  16. Characterization of the core oligosaccharide and the O-antigen biological repeating unit from Halomonas stevensii lipopolysaccharide: the first case of O-antigen linked to the inner core.

    PubMed

    Pieretti, Giuseppina; Carillo, Sara; Lindner, Buko; Kim, Kwang Kyu; Lee, Keun Chul; Lee, Jung-Sook; Lanzetta, Rosa; Parrilli, Michelangelo; Corsaro, Maria Michela

    2012-03-19

    A novel core structure among bacterial lipopolysaccharides (LPS) that belong to the genus Halomonas has been characterized. H. stevensii is a moderately halophilic microorganism, as are the majority of the Halomonadaceae. It brought to light the pathogenic potential of this genus. On account of their role in immune system elicitation, elucidation of LPS structure is the mandatory starting point for a deeper understanding of the interaction mechanisms between host and pathogen. In this paper we report the structure of the complete saccharidic portion of the LPS from H. stevensii. In contrast to the finding that the O-antigen is usually covalently linked to the outer core oligosaccharide, we could demonstrate that the O-polysaccharide of H. stevensii is linked to the inner core of an LPS. By means of high-performance anion-exchange chromatography with pulsed amperometric detection we were able to isolate the core decasaccharide as well as a tridecasaccharide constituted by the core region plus one O-repeating unit after alkaline degradation of the LPS. The structure was elucidated by one- and two-dimensional NMR spectroscopy, ESI Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry, and chemical analysis.

  17. The structures of core regions from enterobacterial lipopolysaccharides - an update.

    PubMed

    Holst, Otto

    2007-06-01

    To the major virulence factors of Gram-negative bacteria belong the lipopolysaccharides (endotoxins), which are very well characterized for their immunological, pharmacological and pathophysiological effects displayed in eucaryotic cells and organisms. In general, these amphiphilic lipopolysaccharides comprise three regions, which can be differentiated by their structures, function, genetics and biosynthesis: lipid A, the core region and a polysaccharide portion, which may be the O-specific polysaccharide, Enterobacterial Common Antigen (ECA) or a capsular polysaccharide. In the past, much emphasis has been laid on the elucidation of the structure-function relation. The lipid A was proven to represent the toxic principle of endotoxic active lipopolysaccharides, however, its toxicity depends not only on its structure but also on that of the core region, which is covalently linked to lipid A. Thus, and since the core region possesses immunogenic properties, complete structural analyses of lipopolysaccharides core regions and of structure-function relation are highly important for a better understanding of lipopolysaccharides action. To date, quite a number of core structures from lipopolysaccharides of various Gram-negative bacteria have been published and summarized in several overviews. This short review adds to this knowledge those structures of enterobacterial lipopolysaccharides that were published between January 2002 and October 2006.

  18. Hepatitis B virus nucleocapsid but not free core antigen controls viral clearance in mice.

    PubMed

    Lin, Yi-Jiun; Wu, Hui-Lin; Chen, Ding-Shinn; Chen, Pei-Jer

    2012-09-01

    We have recently shown that hepatitis B virus (HBV) core antigen (HBcAg) is the major viral factor for HBV clearance using a hydrodynamics-based mouse model. Knockout of HBcAg hampers the development of antiviral immune responses and thus promotes HBV persistence. Here, we further demonstrated that only in the capsid form, but not the free or dimer form, can HBcAg exert its contributory role in HBV clearance. HBcAg is the main structural protein of HBV icosahedral nucleocapsid. A mutant HBV DNA which expresses an assembly-defective HBcAg, HBcAgY132A, surprisingly prolonged HBV surface antigenemia in both C57BL/6 and BALB/c mice without affecting viral transcription and translation. This result was not due to a loss of the possible immune epitope caused by the single-amino-acid substitution of HBcAg. Moreover, the particular HBV mutant failed to induce robust humoral and cellular immunity against HBV. These data revealed the requirement of capsid structure for inducing adequate immunity that leads to HBV clearance in mice.

  19. [Hepatitis B virus core antigen as a carrier for virus-like partical vaccine: a review].

    PubMed

    Yang, Xing-Yu; Bo, Hong; Shu, Yue-Long

    2012-05-01

    Hepatitis B virus core antigen (HBcAg) is a major viral nucleocapsid protein of HBV. It is a 21-22kD protein consisting of 183-185 amino acids. Because of its easy purification, strong immunogenicity, high expression level, and self-assembles into the virus-like particles (VLP), HBcAg could be an efficient and safe VLP carrier for developing vaccines for various pathogens. Up to now, HBcAg VLP carrier has been an important system to develop novel vaccines and many antigen epitope genes from viruses, bacteria and parasites were expressed successfully using the system.

  20. MHC structure and function – antigen presentation. Part 1

    PubMed Central

    Goldberg, Anna Carla; Rizzo, Luiz Vicente

    2015-01-01

    The setting for the occurrence of an immune response is that of the need to cope with a vast array of different antigens from both pathogenic and non-pathogenic sources. When the first barriers against infection and innate defense fail, adaptive immune response enters the stage for recognition of the antigens by means of extremely variable molecules, namely immunoglobulins and T-cell receptors. The latter recognize the antigen exposed on cell surfaces, in the form of peptides presented by the HLA molecule. The first part of this review details the central role played by these molecules, establishing the close connection existing between their structure and their antigen presenting function. PMID:25807245

  1. Engineered Magnetic Core-Shell Structures.

    PubMed

    Alavi Nikje, Mir Mohammad; Vakili, Maryam

    2015-01-01

    In recent years, engineered magnetic core-shell structures are playing an important role in the wide range of various applications. These magnetic core-shell structures have attracted considerable attention because of their unique properties and various applications. Also, the synthesis of engineered magnetic core-shell structures has attracted practical interest because of potential applications in areas such as ferrofluids, medical imaging, drug targeting and delivery, cancer therapy, separations, and catalysis. So far a large number of engineered magnetic core-shell structures have been successfully synthesized. This review article focuses on the recent progress in synthesis and characterization of engineered magnetic core-shell structures. Also, this review gives a brief description of the various application of these structures. It is hoped that this review will play some small part in helping future developments in important field.

  2. Identification of the Drosophila core 1 beta1,3-galactosyltransferase gene that synthesizes T antigen in the embryonic central nervous system and hemocytes.

    PubMed

    Yoshida, Hideki; Fuwa, Takashi J; Arima, Mikiko; Hamamoto, Hiroshi; Sasaki, Norihiko; Ichimiya, Tomomi; Osawa, Ken-Ichi; Ueda, Ryu; Nishihara, Shoko

    2008-12-01

    T antigen (Galbeta1-3GalNAcalpha1-Ser/Thr), the well-known tumor-associated antigen, is a core 1 mucin-type O-glycan structure that is synthesized by core 1 beta1,3-galactosyltransferase (C1beta3GalT), which transfers Gal from UDP-Gal to Tn antigen (GalNAcalpha1-Ser/Thr). Three putative C1beta3GalTs have been identified in Drosophila. However, although all three are expressed in embryos, their roles during embryogenesis have not yet been clarified. In this study, we used P-element inserted mutants to show that CG9520, one of the three putative C1beta3GalTs, synthesizes T antigen expressed on the central nervous system (CNS) during embryogenesis. We also found that T antigen was expressed on a subset of the embryonic hemocytes. CG9520 mutant embryos showed the loss of T antigens on the CNS and on a subset of hemocytes. Then, the loss of T antigens was rescued by precise excision of the P-element inserted into the CG9520 gene. Our data demonstrate that T antigens expressed on the CNS and on a subset of hemocytes are synthesized by CG9520 in the Drosophila embryo. In addition, we found that the number of circulating hemocytes was reduced in third instar larvae of CG9520 mutant. We, therefore, named the CG9520 gene Drosophila core 1 beta1,3-galactosyltransferase 1 because it is responsible for the synthesis and function of T antigen in vivo.

  3. Fine structure of A and M antigens from Brucella biovars.

    PubMed

    Meikle, P J; Perry, M B; Cherwonogrodzky, J W; Bundle, D R

    1989-09-01

    Brucella A and M epitopes were found on single O-polysaccharide chains of all biotype strains of this species. Lipopolysaccharides from the type and reference strains of five of the six Brucella species, B. abortus, B. melitensis, B. suis, B. canis, and B. neotomae, were extracted and purified. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, in conjunction with silver staining and immunoblotting developed by monoclonal antibodies, showed bands characteristic of A, M, or mixed A and M antigens. The A antigen previously described as an exclusively alpha 1,2-linked homopolymer of 4,6-dideoxy-4-formamido-D-mannopyranose was shown by 1H and 13C nuclear magnetic resonance spectroscopy to possess a fine structure consistent with the low-frequency occurrence of alpha 1, 3-linked 4,6-dideoxy-4-formamido-D-mannopyranose residues. This feature was previously attributed only to the M antigen, which is also a homopolymer of the same sugar. B. melitensis biotype 3 and B. suis biotype 4 lipopolysaccharides showed characteristics of mixed A and M antigens. Immunoabsorption of these O polysaccharides on a column of immobilized A-antigen-specific monoclonal antibody enriched polymer chains with A-antigen characteristics but did not eliminate M epitopes. Composite A- and M-antigen characteristics resulted from O polysaccharides in which the frequency of alpha 1,3 linkages, and hence, M-antigen characteristics, varied. All biotypes assigned as A+ M- expressed one or two alpha 1,3-linked residues per polysaccharide O chain. M antigens (M+ A-) also possessed a unique M epitope as well as a tetrasaccharide determinant common to A-antigen structures. B. canis and B. abortus 45/20, both rough strains, expressed low-molecular-weight A antigen.

  4. Changes in structural and antigenic properties of proteins by radiation

    NASA Astrophysics Data System (ADS)

    Kume, Tamikazu; Matsuda, Tsukasa

    1995-08-01

    Radiation effect on structural and antigenic properties of proteins (0.2% in 0.01 M phosphate buffer, pH 7.4) were investigated using ovalbumin (OVA) and bovine serum albumin (BSA). Aggregation of OVA and BSA was induced by radiation and the molecular mass increased significantly in N 2. Significant changes in surface hydrophobicity and [ θ] 222 nm of CD were also observed by radiation showing the destruction of secondary structure of proteins. Antigenicity of irradiated OVA measured by the method of immunodiffusion was decreased by radiation, and the reactivity to anti-OVA antibody was almost diminished at 8 kGy in N 2 and 4 kGy in O 2, respectively. The reactivity of BSA was diminished at 4 kGy both in N 2 and O 2. Changes in hydrophobicity of OVA did not correspond to the decrease in antigenicity, whereas the changes in [ θ] 222 nm relatively well corresponded to the antigenicity. The SDS-PAGE and immunoblotting analysis showed that radiation at higher doses induced the production of protein aggregates and degraded fragments with reactivity to the specific antibodies. These results suggest that the main part of conformation-dependent antigenic structure (conformational epitope) is easily lost by radiation, but some antigenicity, which is mostly due to the amino acid sequence-dependent antigenic structures (sequential epitopes), remains even at higher dose.

  5. Atomic structure of anthrax protective antigen pore elucidates toxin translocation.

    PubMed

    Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed.

  6. Characterizing Facesheet/Core Disbonding in Honeycomb Core Sandwich Structure

    NASA Technical Reports Server (NTRS)

    Rinker, Martin; Ratcliffe, James G.; Adams, Daniel O.; Krueger, Ronald

    2013-01-01

    Results are presented from an experimental investigation into facesheet core disbonding in carbon fiber reinforced plastic/Nomex honeycomb sandwich structures using a Single Cantilever Beam test. Specimens with three, six and twelve-ply facesheets were tested. Specimens with different honeycomb cores consisting of four different cell sizes were also tested, in addition to specimens with three different widths. Three different data reduction methods were employed for computing apparent fracture toughness values from the test data, namely an area method, a compliance calibration technique and a modified beam theory method. The compliance calibration and modified beam theory approaches yielded comparable apparent fracture toughness values, which were generally lower than those computed using the area method. Disbonding in the three-ply facesheet specimens took place at the facesheet/core interface and yielded the lowest apparent fracture toughness values. Disbonding in the six and twelve-ply facesheet specimens took place within the core, near to the facesheet/core interface. Specimen width was not found to have a significant effect on apparent fracture toughness. The amount of scatter in the apparent fracture toughness data was found to increase with honeycomb core cell size.

  7. A Novel Protective Vaccine Antigen from the Core Escherichia coli Genome

    PubMed Central

    Moriel, Danilo G.; Tan, Lendl; Goh, Kelvin G. K.; Ipe, Deepak S.; Lo, Alvin W.; Peters, Kate M.

    2016-01-01

    ABSTRACT Escherichia coli is a versatile pathogen capable of causing intestinal and extraintestinal infections that result in a huge burden of global human disease. The diversity of E. coli is reflected by its multiple different pathotypes and mosaic genome composition. E. coli strains are also a major driver of antibiotic resistance, emphasizing the urgent need for new treatment and prevention measures. Here, we used a large data set comprising 1,700 draft and complete genomes to define the core and accessory genome of E. coli and demonstrated the overlapping relationship between strains from different pathotypes. In combination with proteomic investigation, this analysis revealed core genes that encode surface-exposed or secreted proteins that represent potential broad-coverage vaccine antigens. One of these antigens, YncE, was characterized as a conserved immunogenic antigen able to protect against acute systemic infection in mice after vaccination. Overall, this work provides a genomic blueprint for future analyses of conserved and accessory E. coli genes. The work also identified YncE as a novel antigen that could be exploited in the development of a vaccine against all pathogenic E. coli strains—an important direction given the high global incidence of infections caused by multidrug-resistant strains for which there are few effective antibiotics. IMPORTANCE E. coli is a multifaceted pathogen of major significance to global human health and an important contributor to increasing antibiotic resistance. Given the paucity of therapies still effective against multidrug-resistant pathogenic E. coli strains, novel treatment and prevention strategies are urgently required. In this study, we defined the core and accessory components of the E. coli genome by examining a large collection of draft and completely sequenced strains available from public databases. This data set was mined by employing a reverse-vaccinology approach in combination with proteomics

  8. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide

    PubMed Central

    Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M.; Corsaro, Maria Michela

    2017-01-01

    Erwinia amylovora (E. amylovora) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry. PMID:28273861

  9. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide.

    PubMed

    Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M; Corsaro, Maria Michela

    2017-03-04

    Erwinia amylovora (E. amylovora) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry.

  10. Effect of deletion of genes involved in lipopolysaccharide core and O-antigen synthesis on virulence and immunogenicity of Salmonella enterica serovar typhimurium.

    PubMed

    Kong, Qingke; Yang, Jiseon; Liu, Qing; Alamuri, Praveen; Roland, Kenneth L; Curtiss, Roy

    2011-10-01

    Lipopolysaccharide (LPS) is a major virulence factor of Salmonella enterica serovar Typhimurium and is composed of lipid A, core oligosaccharide (C-OS), and O-antigen polysaccharide (O-PS). While the functions of the gene products involved in synthesis of core and O-antigen have been elucidated, the effect of removing O-antigen and core sugars on the virulence and immunogenicity of Salmonella enterica serovar Typhimurium has not been systematically studied. We introduced nonpolar, defined deletion mutations in waaG (rfaG), waaI (rfaI), rfaH, waaJ (rfaJ), wbaP (rfbP), waaL (rfaL), or wzy (rfc) into wild-type S. Typhimurium. The LPS structure was confirmed, and a number of in vitro and in vivo properties of each mutant were analyzed. All mutants were significantly attenuated compared to the wild-type parent when administered orally to BALB/c mice and were less invasive in host tissues. Strains with ΔwaaG and ΔwaaI mutations, in particular, were deficient in colonization of Peyer's patches and liver. This deficiency could be partially overcome in the ΔwaaI mutant when it was administered intranasally. In the context of an attenuated vaccine strain delivering the pneumococcal antigen PspA, all of the mutations tested resulted in reduced immune responses against PspA and Salmonella antigens. Our results indicate that nonreversible truncation of the outer core is not a viable option for developing a live oral Salmonella vaccine, while a wzy mutant that retains one O-antigen unit is adequate for stimulating the optimal protective immunity to homologous or heterologous antigens by oral, intranasal, or intraperitoneal routes of administration.

  11. Effect of Deletion of Genes Involved in Lipopolysaccharide Core and O-Antigen Synthesis on Virulence and Immunogenicity of Salmonella enterica Serovar Typhimurium▿

    PubMed Central

    Kong, Qingke; Yang, Jiseon; Liu, Qing; Alamuri, Praveen; Roland, Kenneth L.; Curtiss, Roy

    2011-01-01

    Lipopolysaccharide (LPS) is a major virulence factor of Salmonella enterica serovar Typhimurium and is composed of lipid A, core oligosaccharide (C-OS), and O-antigen polysaccharide (O-PS). While the functions of the gene products involved in synthesis of core and O-antigen have been elucidated, the effect of removing O-antigen and core sugars on the virulence and immunogenicity of Salmonella enterica serovar Typhimurium has not been systematically studied. We introduced nonpolar, defined deletion mutations in waaG (rfaG), waaI (rfaI), rfaH, waaJ (rfaJ), wbaP (rfbP), waaL (rfaL), or wzy (rfc) into wild-type S. Typhimurium. The LPS structure was confirmed, and a number of in vitro and in vivo properties of each mutant were analyzed. All mutants were significantly attenuated compared to the wild-type parent when administered orally to BALB/c mice and were less invasive in host tissues. Strains with ΔwaaG and ΔwaaI mutations, in particular, were deficient in colonization of Peyer's patches and liver. This deficiency could be partially overcome in the ΔwaaI mutant when it was administered intranasally. In the context of an attenuated vaccine strain delivering the pneumococcal antigen PspA, all of the mutations tested resulted in reduced immune responses against PspA and Salmonella antigens. Our results indicate that nonreversible truncation of the outer core is not a viable option for developing a live oral Salmonella vaccine, while a wzy mutant that retains one O-antigen unit is adequate for stimulating the optimal protective immunity to homologous or heterologous antigens by oral, intranasal, or intraperitoneal routes of administration. PMID:21768282

  12. Monitoring response to antiviral therapy for patients with chronic hepatitis C virus infection by a core-antigen assay.

    PubMed

    Rebucci, Chiara; Cerino, Antonella; Cividini, Agostino; Timo, Letizia; Furione, Milena; Mondelli, Mario U

    2003-08-01

    A recently released immunoassay detecting total serum hepatitis C virus (HCV) core antigen was used to prospectively monitor virological responses to antiviral treatment in patients with chronic HCV infection. Sustained responders cleared core protein from serum within the first month of therapy and maintained stably negative values for the entire duration of follow-up after treatment discontinuation. However, patients who relapsed or failed to respond showed transient negative values and could not be accurately discriminated either because of the intrinsic lower sensitivity of the core-antigen assay than those of molecular assays or because of differentially regulated secretion of immunoreactive core protein from infected hepatocytes.

  13. Structure and Dynamics of Antigenic Peptides in Complex with TAP

    PubMed Central

    Lehnert, Elisa; Tampé, Robert

    2017-01-01

    The transporter associated with antigen processing (TAP) selectively translocates antigenic peptides into the endoplasmic reticulum. Loading onto major histocompatibility complex class I molecules and proofreading of these bound epitopes are orchestrated within the macromolecular peptide-loading complex, which assembles on TAP. This heterodimeric ABC-binding cassette (ABC) transport complex is therefore a major component in the adaptive immune response against virally or malignantly transformed cells. Its pivotal role predestines TAP as a target for infectious diseases and malignant disorders. The development of therapies or drugs therefore requires a detailed comprehension of structure and function of this ABC transporter, but our knowledge about various aspects is still insufficient. This review highlights recent achievements on the structure and dynamics of antigenic peptides in complex with TAP. Understanding the binding mode of antigenic peptides in the TAP complex will crucially impact rational design of inhibitors, drug development, or vaccination strategies. PMID:28194151

  14. Role of Escherichia coli K-12 rfa genes and the rfp gene of Shigella dysenteriae 1 in generation of lipopolysaccharide core heterogeneity and attachment of O antigen.

    PubMed Central

    Klena, J D; Ashford, R S; Schnaitman, C A

    1992-01-01

    The rfp gene of Shigella dysenteriae 1 and the rfa genes of Escherichia coli K-12 and Salmonella typhimurium LT2 have been studied to determine their relationship to lipopolysaccharide (LPS) core heterogeneity and their role in the attachment of O antigen to LPS. It has been inferred from the nucleotide sequence that the rfp gene encodes a protein of 41,864 Da which has a structure similar to that of RfaG protein. Expression of this gene in E. coli K-12 results in the loss of one of the three bands seen in gel analysis of the LPS and in the appearance of a new, more slowly migrating band. This is consistent with the hypothesis that Rfp is a sugar transferase which modifies a subset of core molecules so that they become substrates for attachment of S. dysenteriae O antigen. A shift in gel migration of the bands carrying S. dysenteriae O antigen and disappearance of the Rfp-modified band in strains producing O antigen suggest that the core may be trimmed or modified further before attachment of O antigen. Mutation of rfaL results in a loss of the rough LPS band which appears to be modified by Rfp and prevents the appearance of the Rfp-modified band. Thus, RfaL protein is involved in core modification and is more than just a component of the O-antigen ligase. The products of rfaK and rfaQ also appear to be involved in modification of the core prior to attachment of O antigen, and the sites of rfaK modification are different in E. coli K-12 and S. typhimurium. In contrast, mutations in rfaS and rfaZ result in changes in the LPS core but do not affect the attachment of O antigen. We propose that these genes are involved in an alternative pathway for the synthesis of rough LPS species which are similar to lipooligosaccharides of other species and which are not substrates for O-antigen attachment. All of these studies indicate that the apparent heterogeneity of E. coli K-12 LPS observed on gels is not an artifact but instead a reflection of functional differences among

  15. Detection of antibodies against hepatitis B virus surface antigen and hepatitis C virus core antigen in plasma with a waveguide-mode sensor.

    PubMed

    Shimizu, Takenori; Tanaka, Torahiko; Uno, Shigeyuki; Ashiba, Hiroki; Fujimaki, Makoto; Tanaka, Mutsuo; Awazu, Koichi; Makishima, Makoto

    2017-02-09

    In large-scale disasters, such as huge significant earthquakes, on-site examination for blood typing and infectious disease screening will be very helpful to save lives of victims who need surgical treatment and/or blood transfusion. However, physical damage, such as building collapse, electric power failure and traffic blockage, disrupts the capacity of the medical system. Portable diagnostic devices are useful in such cases of emergency. In this study, we evaluated a waveguide-mode sensor for detection of anti-hepatitis virus antibodies. First, we examined whether we can detect antigen-antibody interaction on a sensor chip immobilized hepatitis B virus surface (HBs) antigen and hepatitis C virus (HCV) core antigen using monoclonal mouse antibodies for HBs antigen and HCV core antigen. We obtained significant changes in the reflectance spectra, which indicate specific antigen-antibody interaction for anti-HBs antibody and anti-HCV antibody. Next, we examined the effect of horseradish peroxidase-conjugated secondary antibody using aminoethyl carbazole as the peroxidase substrate and found that the colorimetric reaction increases detection sensitivity for anti-HBs antibody more than 300 times. Finally, we successfully detected anti-HBs antibody in human blood samples with an enhancing method using a peroxidase reaction. Thus, a portable device utilizing a waveguide-mode sensor may be applied to on-site blood testing in emergency settings.

  16. Structural and antigenic analysis of meningococcal piliation.

    PubMed Central

    Olafson, R W; McCarthy, P J; Bhatti, A R; Dooley, J S; Heckels, J E; Trust, T J

    1985-01-01

    Pilin with an Mr of 16,500 was purified to homogeneity from Neisseria meningitidis SP3428. Procedures which provided useful separation during purification included high-pressure liquid chromatography with a TSK size exclusion column, Sephacryl S-200 column chromatography, ion-exchange chromatography with SP-Sephadex, and preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The amino acid composition of this pilin was similar to that previously reported for this species. The sequence of N-terminal 51 amino acids was also determined. The protein lacked a modified phenylalanine at the amino terminus and displayed six residues which were different from Neisseria gonorrhoeae in that region of the molecule determined to be the lectin-binding domain. Monoclonal antibody raised to this pilin was employed, along with a monoclonal antibody to an epitope common to all gonococcal pilins, to analyze the intra- and interstrain heterogeneity of meningococcal piliation. The results indicate that N. meningitidis displays considerable intra- and interstrain heterogeneity with respect to both pilus subunit size and antigenicity. The Mr of subunits ranged from 13,000 to 20,000. Images PMID:2580788

  17. Immunofluorescent Staining for the Detection of the Hepatitis B Core Antigen in Frozen Liver Sections of Human Liver Chimeric Mice.

    PubMed

    Allweiss, Lena; Lütgehetmann, Marc; Dandri, Maura

    2017-01-01

    The hepatitis B virus (HBV) is the causative agent for chronic hepatitis B infection, which affects an estimate of 240 million people worldwide and puts them at risk of developing terminal liver disease. The life cycle of the virus and its interactions with the host immune system are still incompletely understood, and currently available treatment options rarely achieve a cure. Therefore, basic research and new drug development are needed. One parameter for measuring the intrahepatic activity of the virus is monitoring the production of the HBV core antigen (HBcAg), which not only serves as the main structural protein of its nucleocapsid but is also recruited to the covalently closed circular DNA (cccDNA), the nuclear HBV genome responsible for infection persistence. Here, we report a sensitive immunofluorescence staining method to detect HBcAg in cryopreserved liver sections. The method combines conventional immunofluorescence staining procedures with the Tyramide Signal Amplification (TSA) system.

  18. Improvement in the specificity of assays for detection of antibody to hepatitis B core antigen.

    PubMed Central

    Weare, J A; Robertson, E F; Madsen, G; Hu, R; Decker, R H

    1991-01-01

    Reducing agents dramatically alter the specificity of competitive assays for antibody to hepatitis B core antigen (anti-HBc). A specificity improvement was demonstrated with a new assay which utilizes microparticle membrane capture and chemiluminescence detection as well as a current radioimmunoassay procedure (Corab: Abbott Laboratories, Abbott Park, Ill.). The effect was most noticeable with elevated negative and weakly reactive samples. In both systems, reductants increased separation of a negative population (n = 160) from assay cutoffs. With a selected population (n = 307), inclusion of reductant eliminated apparent anti-HBc activity in 54 of 81 samples in the 30 to 70% inhibition range. Reductant-stable anti-HBc samples were strongly associated with the presence of antibody to hepatitis B surface antigen (21 of 27). The association persisted below the detection limits of current assays to 0.3 to 0.4 Paul Ehrlich Institute units per ml. Only 1 of 54 reduction-sensitive borderline samples was confirmed to be positive for antibody to hepatitis B surface antigen. The modified procedures had unchanged or slightly improved sensitivity for immunoglobulin G (IgG)-associated anti-HBc activity. Although IgM anti-HBc detection was reduced from four- to eightfold in the presence of reductants, sensitivities remained at least twofold greater than tha of an enzyme immunoassay (Corzyme M; Abbott) designed to detect acute-phase levels of IgM anti-HBc. The use of reducing agents should significantly improve the reliability of anti-HBc testing, especially near assay cutoffs. PMID:2037678

  19. Hepatitis B viral antigenic structure: signature analysis by monoclonal radioimmunoassays.

    PubMed Central

    Wands, J R; Wong, M A; Shorey, J; Brown, R D; Marciniak, R A; Isselbacher, K J

    1984-01-01

    An approach has been developed for the analysis of hepatitis B viral (HBV) antigenic structure that creates numerical "signatures" of HBV strains. This technique employs high-affinity IgM and IgG monoclonal antibodies (anti-HBsAg) directed toward distinct and separate determinants on hepatitis B surface antigen (HBsAg). Such antibodies have been used to develop sensitive and specific radioimmuno-assays for measurement of HBsAg-associated determinants in serum. In performing "signature" analysis separate binding curves for each monoclonal anti-HBsAg are generated by measuring immunoreactivity in serial dilutions of HBsAg-positive serum. Since the HBsAg concentration in serum is unknown, the binding profiles of groups of samples from the same "classic" HBV subtype are aligned by an iterative maximum likelihood procedure to give the numerical signature of that HBV subtype. By using this approach, HBsAg shows far more antigenic heterogeneity than previously recognized by polyvalent anti-HBsAg antibodies. Indeed, there are subgroups within the classic HBsAg subtypes. In addition, the a domain (common to all known subtypes or strains of HBV) has been shown to be multideterminant. Thus, these studies have demonstrated heretofore unrecognized differences in HBV subtypes. This approach also has broader significance for the study of subtle or major antigenic changes among other viral agents since it is not necessary to know the concentration of virus or viral protein in complex protein mixtures. PMID:6585796

  20. Vortex Core Structure in Multilayered Rashba Superconductors

    NASA Astrophysics Data System (ADS)

    Higashi, Y.; Nagai, Y.; Yoshida, T.; Yanase, Y.

    2014-12-01

    We numerically study the electronic structure of a single vortex in two dimensional superconducting bilayer systems within the range of the mean-field theory. The lack of local inversion symmetry in the system is taken into account through the layer dependent Rashba spin-orbit coupling. The spatial profiles of the pair potential and the local quasiparticle density of states are calculated in the clean spin-singlet superconductor on the basis of the quasiclassical theory. In particular, we discuss the characteristic core structure in the pair-density wave state, which is spatially modulated exotic superconducting phase in a high magnetic field.

  1. Low Cost Large Core Vehicle Structures Assessment

    NASA Technical Reports Server (NTRS)

    Hahn, Steven E.

    1998-01-01

    Boeing Information, Space, and Defense Systems executed a Low Cost Large Core Vehicle Structures Assessment (LCLCVSA) under contract to NASA Marshall Space Flight Center (MSFC) between November 1997 and March 1998. NASA is interested in a low-cost launch vehicle, code named Magnum, to place heavy payloads into low earth orbit for missions such as a manned mission to Mars, a Next Generation Space Telescope, a lunar-based telescope, the Air Force's proposed space based laser, and large commercial satellites. In this study, structural concepts with the potential to reduce fabrication costs were evaluated in application to the Magnum Launch Vehicle (MLV) and the Liquid Fly Back Booster (LFBB) shuttle upgrade program. Seventeen concepts were qualitatively evaluated to select four concepts for more in-depth study. The four structural concepts selected were: an aluminum-lithium monocoque structure, an aluminum-lithium machined isogrid structure, a unitized composite sandwich structure, and a unitized composite grid structure. These were compared against a baseline concept based on the Space Shuttle External Tank (ET) construction. It was found that unitized composite structures offer significant cost and weight benefits to MLV structures. The limited study of application to LFBB structures indicated lower, but still significant benefits. Technology and facilities development roadmaps to prepare the approaches studied for application to MLV and LFBB were constructed. It was found that the cost and schedule to develop these approaches were in line with both MLV and LFBB development schedules. Current Government and Boeing programs which address elements of the development of the technologies identified are underway. It is recommended that NASA devote resources in a timely fashion to address the specific elements related to MLV and LFBB structures.

  2. Ciliary microtubule capping structures contain a mammalian kinetochore antigen

    PubMed Central

    1990-01-01

    Structures that cap the plus ends of microtubules may be involved in the regulation of their assembly and disassembly. Growing and disassembling microtubules in the mitotic apparatus are capped by kinetochores and ciliary and flagellar microtubules are capped by the central microtubule cap and distal filaments. To compare the ciliary caps with kinetochores, isolated Tetrahymena cilia were stained with CREST (Calcinosis/phenomenon esophageal dysmotility, sclerodactyly, telangiectasia) antisera known to stain kinetochores. Immunofluorescence microscopy revealed that a CREST antiserum stained the distal tips of cilia that contained capping structures but did not stain axonemes that lacked capping structures. Both Coomassie blue- stained gels and Western blots probed with CREST antiserum revealed that a 97-kD antigen copurifies with the capping structures. Affinity- purified antibodies to the 97-kD ciliary protein stained the tips of cap-containing Tetrahymena cilia and the kinetochores in HeLa, Chinese hamster ovary, and Indian muntjak cells. These results suggest that at least one polypeptide found in the kinetochore is present in ciliary microtubule capping structures and that there may be a structural and/or functional homology between these structures that cap the plus ends of microtubules. PMID:2106524

  3. Structure and serology of O-antigens as the basis for classification of Proteus strains.

    PubMed

    Knirel, Yuriy A; Perepelov, Andrei V; Kondakova, Anna N; Senchenkova, Sof'ya N; Sidorczyk, Zygmunt; Rozalski, Antoni; Kaca, Wieslaw

    2011-02-01

    This review is devoted to structural and serological characteristics of the O-antigens (O-polysaccharides) of the lipopolysaccharides of various Proteus species, which provide the basis for classifying Proteus strains to O-serogroups. The antigenic relationships of Proteus strains within and beyond the genus as well as their O-antigen-related bioactivities are also discussed.

  4. Reinvestigation of the structure of Brucella O-antigens.

    PubMed

    Kubler-Kielb, Joanna; Vinogradov, Evgeny

    2013-08-30

    O-Specific polysaccharides of Brucella contain two antigenic determinants, called A and M. Most of the strains express epitope A with a small amount of epitope M, whereas Brucella melitensis strain 16 M expresses longer polymer consisting mostly of M-type epitopes. Proposed explanation was that epitope A is defined by 1-2-linked homopolymer of N-formylperosamine (Rha4NFo), while epitope M is a pentasaccharide with four 2- and one 3-substituted Rha4NFo. We reinvestigated both types of structures by 2D NMR and showed that M-epitope is a tetrasaccharide, missing one of the 2-linked Rha4NFo as compared to the previously proposed structure. Polysaccharide from B. melitensis 16 M contains a fragment of 1-2-linked polymer, capped with M-type polymer. Other strains contain one or two M-type units at the non-reducing end of the 1-2-linked O-chain.

  5. Proteaselike sequence in hepatitis B virus core antigen is not required for e antigen generation and may not be part of an aspartic acid-type protease.

    PubMed Central

    Nassal, M; Galle, P R; Schaller, H

    1989-01-01

    The hepatitis B virus (HBV) C gene directs the synthesis of two major gene products: HBV core antigen (HBcAg[p21c]), which forms the nucleocapsid, and HBV e antigen (HBeAg [p17e]), a secreted antigen that is produced by several processing events during its maturation. These proteins contain an amino acid sequence similar to the active-site residues of aspartic acid and retroviral proteases. On the basis of this sequence similarity, which is highly conserved among mammalian hepadnaviruses, a model has been put forward according to which processing to HBeAg is due to self-cleavage of p21c involving the proteaselike sequence. Using site-directed mutagenesis in conjunction with transient expression of HBV proteins in the human hepatoma cell line HepG2, we tested this hypothesis. Our results with HBV mutants in which one or two of the conserved amino acids have been replaced by others suggest strongly that processing to HBeAg does not depend on the presence of an intact proteaselike sequence in the core protein. Attempts to detect an influence of this sequence on the processing of HBV P gene products into enzymatically active viral polymerase also gave no conclusive evidence for the existence of an HBV protease. Mutations replacing the putatively essential aspartic acid showed little effect on polymerase activity. Additional substitution of the likewise conserved threonine residue by alanine, in contrast, almost abolished the activity of the polymerase. We conclude that an HBV protease, if it exists, is functionally different from aspartic acid and retroviral proteases. Images PMID:2657101

  6. Cellular Antigens in the Structure of Venezuelan Equine Encephalomyelitis Virus

    DTIC Science & Technology

    1975-02-28

    the previously described method. 𔄁xzracts of the Dolichos biflorus L seeds (to calculate antigen A) and Cytisus sessilifolius L. seeds (to calculate...find the group antigen A and phytohemagglutinins "from seeds Cytisus sessilefolius L. in order to calculate antigen H. As h -6- "Fable 4 shows virus

  7. Tandem Fusion of Hepatitis B Core Antigen Allows Assembly of Virus-Like Particles in Bacteria and Plants with Enhanced Capacity to Accommodate Foreign Proteins

    PubMed Central

    Peyret, Hadrien; Gehin, Annick; Thuenemann, Eva C.; Blond, Donatienne; El Turabi, Aadil; Beales, Lucy; Clarke, Dean; Gilbert, Robert J. C.; Fry, Elizabeth E.; Stuart, David I.; Holmes, Kris; Stonehouse, Nicola J.; Whelan, Mike; Rosenberg, William; Lomonossoff, George P.; Rowlands, David J.

    2015-01-01

    The core protein of the hepatitis B virus, HBcAg, assembles into highly immunogenic virus-like particles (HBc VLPs) when expressed in a variety of heterologous systems. Specifically, the major insertion region (MIR) on the HBcAg protein allows the insertion of foreign sequences, which are then exposed on the tips of surface spike structures on the outside of the assembled particle. Here, we present a novel strategy which aids the display of whole proteins on the surface of HBc particles. This strategy, named tandem core, is based on the production of the HBcAg dimer as a single polypeptide chain by tandem fusion of two HBcAg open reading frames. This allows the insertion of large heterologous sequences in only one of the two MIRs in each spike, without compromising VLP formation. We present the use of tandem core technology in both plant and bacterial expression systems. The results show that tandem core particles can be produced with unmodified MIRs, or with one MIR in each tandem dimer modified to contain the entire sequence of GFP or of a camelid nanobody. Both inserted proteins are correctly folded and the nanobody fused to the surface of the tandem core particle (which we name tandibody) retains the ability to bind to its cognate antigen. This technology paves the way for the display of natively folded proteins on the surface of HBc particles either through direct fusion or through non-covalent attachment via a nanobody. PMID:25830365

  8. Expression of the Yersinia enterocolitica O:3 LPS O-antigen and outer core gene clusters is RfaH-dependent.

    PubMed

    Leskinen, Katarzyna; Varjosalo, Markku; Li, Zhilin; Li, Chun-Mei; Skurnik, Mikael

    2015-06-01

    The antiterminator RfaH is required for the expression of LPS, capsule, haemolysin, exotoxin, haemin uptake receptor and F pilus. As these structures are critical for bacterial virulence, loss of RfaH usually leads to attenuation. Here, we inactivated the rfaH gene of Yersinia enterocolitica O:3 to study its role in this enteropathogen. RNA sequencing of the WT and ΔrfaH strain transcriptomes revealed that RfaH acted as a highly specific regulator that enhanced the transcription of the operons involved in biosynthesis of LPS O-antigen and outer core (OC), but did not affect the expression of enterobacterial common antigen. Interestingly, the transcriptome of the ΔrfaH strain was very similar to that of an O-antigen-negative mutant. This indicated that some of the changes seen in the ΔrfaH strain, such as the genes involved in outer membrane homeostasis or in the stress-response-associated Cpx pathway, were actually due to indirect responses via the loss of O-antigen. The decreased amount of LPS on the ΔrfaH strain cell surface resulted in an attenuated stress response, and lower resistance to compounds such as SDS and polymyxin B. However, the ΔrfaH strain was significantly more resistant to complement-mediated killing by normal human serum. Taken together, our results revealed a novel role of RfaH acting as a highly specific regulator of O-antigen and OC of LPS in Y. enterocolitica O:3. It may be speculated that RfaH might have an in vivo role in controlling tissue-specific expression of bacterial surface oligo/polysaccharides.

  9. Japanese reference panel of blood specimens for evaluation of hepatitis C virus RNA and core antigen quantitative assays.

    PubMed

    Murayama, Asako; Sugiyama, Nao; Watashi, Koichi; Masaki, Takahiro; Suzuki, Ryosuke; Aizaki, Hideki; Mizuochi, Toshiaki; Wakita, Takaji; Kato, Takanobu

    2012-06-01

    An accurate and reliable quantitative assay for hepatitis C virus (HCV) is essential for measuring viral propagation and the efficacy of antiviral therapy. There is a growing need for domestic reference panels for evaluation of clinical assay kits because the performance of these kits may vary with region-specific genotypes or polymorphisms. In this study, we established a reference panel by selecting 80 donated blood specimens in Japan that tested positive for HCV. Using this panel, we quantified HCV viral loads using two HCV RNA kits and five core antigen (Ag) kits currently available in Japan. The data from the two HCV RNA assay kits showed excellent correlation. All RNA titers were distributed evenly across a range from 3 to 7 log IU/ml. Although the data from the five core Ag kits also correlated with RNA titers, the sensitivities of individual kits were not sufficient to quantify viral load in all samples. As calculated by the correlation with RNA titers, the theoretical lower limits of detection by these core Ag assays were higher than those for the detection of RNA. Moreover, in several samples in our panel, core Ag levels were underestimated compared to RNA titers. Sequence analysis in the HCV core region suggested that polymorphisms at amino acids 47 to 49 of the core Ag were responsible for this underestimation. The panel established in this study will be useful for estimating the quality of currently available and upcoming HCV assay kits; such quality control is essential for clinical usage of these kits.

  10. Material with core-shell structure

    DOEpatents

    Luhrs, Claudia [Rio Rancho, NM; Richard, Monique N [Ann Arbor, MI; Dehne, Aaron [Maumee, OH; Phillips, Jonathan [Rio Rancho, NM; Stamm, Kimber L [Ann Arbor, MI; Fanson, Paul T [Brighton, MI

    2011-11-15

    Disclosed is a material having a composite particle, the composite particle including an outer shell and a core. The core is made from a lithium alloying material and the outer shell has an inner volume that is greater in size than the core of the lithium alloying material. In some instances, the outer mean diameter of the outer shell is less than 500 nanometers and the core occupies between 5 and 99% of the inner volume. In addition, the outer shell can have an average wall thickness of less than 100 nanometers.

  11. Sandwiched structural panel having a bi-directional core structure

    NASA Technical Reports Server (NTRS)

    Weddendorf, Bruce (Inventor)

    1995-01-01

    A structural panel assembly has a bi-directional core structure sandwiched between and secured to a pair of outer side wall members. The core structure is formed from first and second perpendicular series of elongated strip members having crenelated configurations. The strip members in the first series thereof are transversely interwoven with the strip members in the second series thereof in a manner such that crest portions of the strip members in the first series overlie and oppose trough portions of the strip members in the second series, and trough portions of the strip members in the first series underlie and oppose crest portions of the strip members in the second series. The crest portions of all of the strip members lie generally in a first plane and are secured to the inner side of one of the panel assembly outer side walls, and the trough portions of all of the strip members lie generally in a second plane and are secured to the inner side of the other panel assembly outer side wall.

  12. Heat treatment of unclarified Escherichia coli homogenate improved the recovery efficiency of recombinant hepatitis B core antigen.

    PubMed

    Ng, Michelle Y T; Tan, Wen Siang; Abdullah, Norhafizah; Ling, Tau Chuan; Tey, Beng Ti

    2006-10-01

    Heat precipitation procedure has been regularly incorporated as a selective purification step in various thermostable proteins expressed in different hosts. This method is efficient in precipitation of most of the host proteins and also deactivates various host proteases that can be harmful to the desired gene products. In this study, introduction of heat treatment procedure in the purification of hepatitis B core antigen (HBcAg) produced in Escherichia coli has been investigated. Thermal treatment of the cell homogenate at 60 degrees C for 30 min prior to subsequent clarification steps has resulted in 1.4 times and 18% higher in purity and recovery yield, respectively, compared to the non-heat-treated cell homogenate. In direct capture of HBcAg by using anion-exchangers from unclarified feedstock, pre-conditioning the feedstock by heat treatment at 60 degrees C for 45 min has increased the recovery yield of HBcAg by 2.9-fold and 42% in purity compared to that treated for 10 min. Enzyme-linked immunosorbent assay (ELISA) analysis showed that the antigenicity of the core particles was not affected by the heat treatment process.

  13. The Structural Diversity of Carbohydrate Antigens of Selected Gram-Negative Marine Bacteria

    PubMed Central

    Nazarenko, Evgeny L.; Crawford, Russell J.; Ivanova, Elena P.

    2011-01-01

    Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens) found in cell walls of Gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobactera phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria. PMID:22073003

  14. Modelling of crack deflection at core junctions in sandwich structures

    NASA Astrophysics Data System (ADS)

    Jakobsen, J.; Andreasen, J. H.; Thomsen, O. T.

    2009-08-01

    The paper treats the problem of crack propagation in sandwich panels with interior core junctions. When a face-core interface crack approaches a trimaterial wedge, as it may occur at a sandwich core junction, two options exist for further crack advance; one is for the interface crack to penetrate the wedge along the face-core interface, and the second is deflection along the core junction interface. Crack deflection is highly relevant and a requirement for the functionality of a newly developed peel stopper for sandwich structures. The physical model presented in this paper enables the quantitative prediction of the ratio of the toughnesses of the two wedge interfaces required to control the crack propagation, and the derived results can be applied directly in future designs of sandwich structures. The solution strategy is based on finite element analysis (FEA), and a realistic engineering practice example of a tri-material composition corresponding to face and core materials is presented.

  15. Echinococcus granulosus Antigen B Structure: Subunit Composition and Oligomeric States

    PubMed Central

    Monteiro, Karina M.; Cardoso, Mateus B.; Follmer, Cristian; da Silveira, Nádya P.; Vargas, Daiani M.; Kitajima, Elliot W.; Zaha, Arnaldo; Ferreira, Henrique B.

    2012-01-01

    Background Antigen B (AgB) is the major protein secreted by the Echinococcus granulosus metacestode and is involved in key host-parasite interactions during infection. The full comprehension of AgB functions depends on the elucidation of several structural aspects that remain unknown, such as its subunit composition and oligomeric states. Methodology/Principal Findings The subunit composition of E. granulosus AgB oligomers from individual bovine and human cysts was assessed by mass spectrometry associated with electrophoretic analysis. AgB8/1, AgB8/2, AgB8/3 and AgB8/4 subunits were identified in all samples analyzed, and an AgB8/2 variant (AgB8/2v8) was found in one bovine sample. The exponentially modified protein abundance index (emPAI) was used to estimate the relative abundance of the AgB subunits, revealing that AgB8/1 subunit was relatively overrepresented in all samples. The abundance of AgB8/3 subunit varied between bovine and human cysts. The oligomeric states formed by E. granulosus AgB and recombinant subunits available, rAgB8/1, rAgB8/2 and rAgB8/3, were characterized by native PAGE, light scattering and microscopy. Recombinant subunits showed markedly distinct oligomerization behaviors, forming oligomers with a maximum size relation of rAgB8/3>rAgB8/2>rAgB8/1. Moreover, the oligomeric states formed by rAgB8/3 subunit were more similar to those observed for AgB purified from hydatid fluid. Pressure-induced dissociation experiments demonstrated that the molecular assemblies formed by the more aggregative subunits, rAgB8/2 and rAgB8/3, also display higher structural stability. Conclusions/Significance For the first time, AgB subunit composition was analyzed in samples from single hydatid cysts, revealing qualitative and quantitative differences between samples. We showed that AgB oligomers are formed by different subunits, which have distinct abundances and oligomerization properties. Overall, our findings have significantly contributed to increase the

  16. STUDIES ON THE ANTIGENIC STRUCTURE OF SOME MAMMALIAN SPERMATOZOA

    PubMed Central

    Henle, Werner; Henle, Gertrude; Chambers, Leslie A.

    1938-01-01

    1. A method has been described for separation of heads and tails of mammalian spermatozoa. 2. By means of absorption technique applied to homologous spermatozoal sera, head-specific and tail-specific antigens could be demonstrated. Both are heat-labile. 3. A heat-stable antigen was found to be common to both heads and tails. This substance is species-specific. 4. Antibodies against the head- and tail-specific antigens led to two different types of agglutination as shown by the slide method. 5. Using heterologous antisera against spermatozoa three different cross-reacting antigens could be observed, two in the heads, one in the tails. 6. One of the head-antigens is not active in the native cell; it comes to action only after breaking the cell. Antibodies against this substance were not found in antisera against native bull spermatozoa but were formed when vibrated spermatozoa or heads were injected into rabbits. 7. The cross-reactions can be removed from an antiserum leaving the head- as well as the tail-specific reaction intact. PMID:19870792

  17. MHC structure and function − antigen presentation. Part 2

    PubMed Central

    Goldberg, Anna Carla; Rizzo, Luiz Vicente

    2015-01-01

    The second part of this review deals with the molecules and processes involved in the processing and presentation of the antigenic fragments to the T-cell receptor. Though the nature of the antigens presented varies, the most significant class of antigens is proteins, processed within the cell to be then recognized in the form of peptides, a mechanism that confers an extraordinary degree of precision to this mode of immune response. The efficiency and accuracy of this system is also the result of the myriad of mechanisms involved in the processing of proteins and production of peptides, in addition to the capture and recycling of alternative sources aiming to generate further diversity in the presentation to T-cells. PMID:25807243

  18. Star cell type core configuration for structural sandwich materials

    DOEpatents

    Christensen, Richard M.

    1995-01-01

    A new pattern for cellular core material used in sandwich type structural materials. The new pattern involves star shaped cells intermixed with hexagonal shaped cells. The new patterned cellular core material includes star shaped cells interconnected at points thereof and having hexagonal shape cells positioned adjacent the star points. The new pattern allows more flexibility and can conform more easily to curved shapes.

  19. The mouse B-cell antigen receptor: definition and assembly of the core receptor of the five immunoglobulin isotypes.

    PubMed

    Neuberger, M S; Patel, K J; Dariavach, P; Nelms, K; Peaker, C J; Williams, G T

    1993-04-01

    We have shown that the core antigen receptor of all five isotypes is composed of immunoglobulin in association with a common heterodimeric alpha/beta sheath. The stoichiometry of the association is unknown although preliminary evidence points to it being an IgH2L2 [alpha/beta]2 association. Studies with chimaeric molecules indicate that much of the immunoglobulin-sheath interaction must occur through the carboxyterminal end of the molecule with particular importance being given to the linker-transmembrane region. The glycosylation of the alpha chain differs according to the isotype with which it is associated. There are two sites for N-linked glycosylation on the alpha chain (Asn-30 and Asn-40); both sites are used. Mutation of Asn-30 alone decreases but does not abolish surface expression of the antigen receptor complex. Mutation of both sites prevents expression of the surface IgM[alpha/beta] complex but not of a surface IgD[alpha/beta] complex. Moreover, the pattern of alpha glycosylation is considerably affected by changes in the linker region between C mu 4 and the transmembrane, giving further support to the importance of this region in immunoglobulin-sheath interaction. Unlike IgM, IgD and IgG2b do not require alpha/beta for transport to the cell surface and can be expressed on the surface without either sheath or glycosyl phosphatidylinositol anchor. This finding may reflect that the IgD transmembrane region is significantly less hydrophobic than that of IgM; however, it should be noted that is not clear whether naked IgD exists in vivo. In fact, we have found that the alpha/beta sheath is necessary in order to facilitate efficient internalization and presentation of antigen by membrane immunoglobulin. The sheath presumably also plays a major role in potentiating transmembrane signalling. However, mutant receptors that do not associate with the alpha/beta sheath are nevertheless able to trigger phosphorylation of cellular proteins on tyrosine residues

  20. Structural proteins of ribonucleic acid tumor viruses. Purification of envelope, core, and internal components.

    PubMed

    Strand, M; August, J T

    1976-01-25

    Murine type C virus structural proteins, the envelope glycopeptides, 30,000 dalton major core protein, and 15,000 dalton internal protein have each been purified to near homogeneity and in high yield from the smae batch of virus by use of phosphocellulose column chromatography and gel filtration procedures. Evidence that these proteins are specified by the viral genome was obtained by competition radioimmunoassay analysis, comparing these polypeptides from Rauscher virus cultivated in a variety of mammalian cell lines; all of the reactive antigenic determinants of these proteins appeared to be virus-specific.

  1. Aluminum core structures brazed without use of flux

    NASA Technical Reports Server (NTRS)

    1966-01-01

    Aluminum alloy face sheets are brazed to aluminum alloy honeycomb cores without using corrosive flux by means of one or three methods. The completed brazed structure has the high-strength characteristics of heat treated aluminum alloys.

  2. Core-shell CdS/Cd(OH)2 quantum dots: synthesis and bioconjugation to target red cells antigens.

    PubMed

    de Farias, P M Albuquerque; Santos, B Saegesser; de Menezes, F Duarte; Ferreira, R de Carvalho; Barjas-Castro, M de Lourdes; Castro, V; Lima, P R Moura; Fontes, A; Cesar, C L

    2005-09-01

    We report a new and efficient methodology of labelling red blood cells, in order to investigate the expression of anti-A antigen, employing luminescent semiconductor nanocrystals. Highly luminescent and stable core-shell cadmium sulphide/cadmium hydroxide [CdS/CdS(OH)2] colloidal particles were obtained in the nanometre size range. The surface of these particles was characterized by using a monoclonal anti-A antibody via a one-step glutaraldehyde cross-linking procedure, followed by conjugation of the particles to red cells of blood groups A+, and O+. Laser scanning confocal microscopy images indicated that after conjugation for 30 min, A+ and erythrocytes presented different patterns of dual bright emission whereas the O+ group cells showed no emission. We suggest that this labelling procedure may be applied as a quantitative tool to investigate the distribution and expression of alloantigen in red blood cells.

  3. Process to make core-shell structured nanoparticles

    DOEpatents

    Luhrs, Claudia; Phillips, Jonathan; Richard, Monique N

    2014-01-07

    Disclosed is a process for making a composite material that contains core-shell structured nanoparticles. The process includes providing a precursor in the form of a powder a liquid and/or a vapor of a liquid that contains a core material and a shell material, and suspending the precursor in an aerosol gas to produce an aerosol containing the precursor. In addition, the process includes providing a plasma that has a hot zone and passing the aerosol through the hot zone of the plasma. As the aerosol passes through the hot zone of the plasma, at least part of the core material and at least part of the shell material in the aerosol is vaporized. Vapor that contains the core material and the shell material that has been vaporized is removed from the hot zone of the plasma and allowed to condense into core-shell structured nanoparticles.

  4. Finding an average core structure: Application to the globins

    SciTech Connect

    Altman, R.B.; Gerstein, M.

    1994-12-31

    We present a procedure for automatically identifying from a set of aligned protein structures a subset of atoms with only a small amount of structural variation, i.e., a core. We apply this procedure to the globin family of proteins. Based purely on the results of the procedure, we show that the globin fold can be divided into two parts. The part with greater structural variation consists of the residues near the heme (the F helix and parts of the G and H helices), and the part with lesser structural variation (the core) forms a structural framework similar to that of the repressor protein (A, B, and E helices and remainder of the G and H helices). Such a division is consistent with many other structural and biochemical findings. In addition, we find further partitions within the core that may have biological significance. Finally, using the structural core of the globin family as a reference point, we have compared structural variation to sequence variation and shown that a core definition based on sequence conservation does not necessarily agree with one based on structural similarity.

  5. Dislocation core structures in Si-doped GaN

    SciTech Connect

    Rhode, S. L. Fu, W. Y.; Sahonta, S.-L.; Kappers, M. J.; Humphreys, C. J.; Horton, M. K.; Pennycook, T. J.; Dusane, R. O.; Moram, M. A.

    2015-12-14

    Aberration-corrected scanning transmission electron microscopy was used to investigate the core structures of threading dislocations in plan-view geometry of GaN films with a range of Si-doping levels and dislocation densities ranging between (5 ± 1) × 10{sup 8} and (10 ± 1) × 10{sup 9} cm{sup −2}. All a-type (edge) dislocation core structures in all samples formed 5/7-atom ring core structures, whereas all (a + c)-type (mixed) dislocations formed either double 5/6-atom, dissociated 7/4/8/4/9-atom, or dissociated 7/4/8/4/8/4/9-atom core structures. This shows that Si-doping does not affect threading dislocation core structures in GaN. However, electron beam damage at 300 keV produces 4-atom ring structures for (a + c)-type cores in Si-doped GaN.

  6. Antigenic structures stably expressed by recombinant TGEV-derived vectors.

    PubMed

    Becares, Martina; Sanchez, Carlos M; Sola, Isabel; Enjuanes, Luis; Zuñiga, Sonia

    2014-09-01

    Coronaviruses (CoVs) are positive-stranded RNA viruses with potential as immunization vectors, expressing high levels of heterologous genes and eliciting both secretory and systemic immune responses. Nevertheless, its high recombination rate may result in the loss of the full-length foreign gene, limiting their use as vectors. Transmissible gastroenteritis virus (TGEV) was engineered to express porcine reproductive and respiratory syndrome virus (PRRSV) small protein domains, as a strategy to improve heterologous gene stability. After serial passage in tissue cultures, stable expression of small PRRSV protein antigenic domains was achieved. Therefore, size reduction of the heterologous genes inserted in CoV-derived vectors led to the stable expression of antigenic domains. Immunization of piglets with these TGEV vectors led to partial protection against a challenge with a virulent PRRSV strain, as immunized animals showed reduced clinical signs and lung damage. Further improvement of TGEV-derived vectors will require the engineering of vectors with decreased recombination rate.

  7. Microarray Analysis of Antibodies Induced with Synthetic Antitumor Vaccines: Specificity against Diverse Mucin Core Structures.

    PubMed

    Pett, Christian; Cai, Hui; Liu, Jia; Palitzsch, Björn; Schorlemer, Manuel; Hartmann, Sebastian; Stergiou, Natascha; Lu, Mengji; Kunz, Horst; Schmitt, Edgar; Westerlind, Ulrika

    2017-03-17

    Glycoprotein research is pivotal for vaccine development and biomarker discovery. Many successful methodologies for reliably increasing the antigenicity toward tumor-associated glycopeptide structures have been reported. Deeper insights into the quality and specificity of the raised polyclonal, humoral reactions are often not addressed, despite the fact that an immunological memory, which produces antibodies with cross-reactivity to epitopes exposed on healthy cells, may cause autoimmune diseases. In the current work, three MUC1 antitumor vaccine candidates conjugated with different immune stimulants are evaluated immunologically. For assessment of the influence of the immune stimulant on antibody recognition, a comprehensive library of mucin 1 glycopeptides (>100 entries) is synthesized and employed in antibody microarray profiling; these range from small tumor-associated glycans (TN , STN , and T-antigen structures) to heavily extended O-glycan core structures (type-1 and type-2 elongated core 1-3 tri-, tetra-, and hexasaccharides) glycosylated in variable density at the five different sites of the MUC1 tandem repeat. This is one of the most extensive glycopeptide libraries ever made through total synthesis. On tumor cells, the core 2 β-1,6-N-acetylglucosaminyltransferase-1 (C2GlcNAcT-1) is down-regulated, resulting in lower amounts of the branched core 2 structures, which favor formation of linear core 1 or core 3 structures, and in particular, truncated tumor-associated antigen structures. The core 2 structures are commonly found on healthy cells and the elucidation of antibody cross-reactivity to such epitopes may predict the tumor-selectivity and safety of synthetic vaccines. With the extended mucin core structures in hand, antibody cross-reactivity toward the branched core 2 glycopeptide epitopes is explored. It is observed that the induced antibodies recognize MUC1 peptides with very high glycosylation site specificity. The nature of the

  8. Modeling of residual stresses in core shroud structures

    SciTech Connect

    Zhang, J.; Dong, P.; Brust, F.W.; Mayfield, M.; McNeil, M.; Shack, W.J.

    1997-10-01

    A BWR core shroud is a cylindrical shell that surrounds the reactor core. Feedwater for the reactor is introduced into the annulus between the reactor vessel wall and the shroud. The shroud separates the feedwater from the cooling water flowing up through the reactor core. The shroud also supports the top guide which provides lateral support to the fuel assemblies and maintains core geometry during operational transients and postulated accidents to permit control rod insertion and provides the refloodable volume needed to ensure safe shutdown and cooling of the core during postulated accident conditions. Core shrouds were fabricated from welded Type 304 or 304L stainless steel plates and are supported at the top and bottom by forged ring support structures. In 1990, cracking was reported in the core shroud of a non-U.S. BWR. The cracks were located in the heat-affected zone (HAZ) of a circumferential core shroud weld. Subsequent inspections in U.S. BWRs have revealed the presence of numerous flaw indications in some BWR core shrouds, primarily in weld HAZs. In several instances, this cracking was quite extensive, with the cracks extending 75% or more around the circumference of some welds. However, because the applied stresses on the shroud are low during operation and postulated accidents and because of the high fracture toughness of stainless steel, adequate structural margins can be preserved even in the presence of extensive cracking. Although assessments by the USNRC staff of the potential significance of this cracking have shown that core shroud cracking does not pose a high degree of risk in the short term, the staff concluded that the cracking was a safety concern for the long term because of the uncertainties associated with the behavior of core shrouds with complete 360{degrees} through-wall cracks under accident conditions and because it could eliminate a layer of defense-in-depth.

  9. The composed antigenic structure of the adenovirus hexon protein.

    PubMed

    Nász, I

    1988-01-01

    Three panels of MAbs were prepared against AV1, AV35, and BAV2 hexons, respectively. It was shown, that in all cases, antibodies are developed against the genus specific determinant of the adenovirus hexon. The other MAbs specified numerous identical or overlapping epitopes on the hexon types studied. The epitopes could be characterized as intertype-, intersubgenus-, subgenus- and type-specific ones beside the genus-specific determinant based on the RPs of the MAbs from indirect ELISA and passive HA results. The identical epitopes are present in more than one copy on the trimeric form of the hexon capsomer. The epitopes on the hexon molecule could be separated into three antigenic sites, of which one antigenic site is characterized by seven epitope clusters (antigenic site II). Monoclonal antibodies were able to precipitate different hexon types in gel diffusion tests by which the differentiation of the distinct epitopes seemed to be possible. With the help of monoclonal antibodies to AV1 hexon, 17 hours after the infection, hexons (or epitopes) were detected in the cytoplasm and in the nucleus of the infected cells showing different distribution patterns in indirect immunofluorescence assay.

  10. Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1.

    PubMed

    Nguyen, Tina T; Chang, Shih-Chung; Evnouchidou, Irini; York, Ian A; Zikos, Christos; Rock, Kenneth L; Goldberg, Alfred L; Stratikos, Efstratios; Stern, Lawrence J

    2011-05-01

    ERAP1 trims antigen precursors to fit into MHC class I proteins. To fulfill this function, ERAP1 has unique substrate preferences, trimming long peptides but sparing shorter ones. To identify the structural basis for ERAP1's unusual properties, we determined the X-ray crystal structure of human ERAP1 bound to bestatin. The structure reveals an open conformation with a large interior compartment. An extended groove originating from the enzyme's catalytic center can accommodate long peptides and has features that explain ERAP1's broad specificity for antigenic peptide precursors. Structural and biochemical analyses suggest a mechanism for ERAP1's length-dependent trimming activity, whereby binding of long rather than short substrates induces a conformational change with reorientation of a key catalytic residue toward the active site. ERAP1's unique structural elements suggest how a generic aminopeptidase structure has been adapted for the specialized function of trimming antigenic precursors.

  11. Outer domain of HIV-1 gp120: antigenic optimization, structural malleability, and crystal structure with antibody VRC-PG04.

    PubMed

    Joyce, M Gordon; Kanekiyo, Masaru; Xu, Ling; Biertümpfel, Christian; Boyington, Jeffrey C; Moquin, Stephanie; Shi, Wei; Wu, Xueling; Yang, Yongping; Yang, Zhi-Yong; Zhang, Baoshan; Zheng, Anqi; Zhou, Tongqing; Zhu, Jiang; Mascola, John R; Kwong, Peter D; Nabel, Gary J

    2013-02-01

    The outer domain of the HIV-1 gp120 envelope glycoprotein contains the epitope for broadly neutralizing antibodies directed to the CD4-binding site, many of which are able to neutralize over 90% of circulating HIV-1 isolates. While the outer domain is conformationally more stable than other portions of the HIV-1 envelope, efforts to express the outer domain as an immunogen for eliciting broadly neutralizing antibodies have not been successful, potentially because natural outer domain variants do not bind strongly to antibodies such as VRC01. In this study, we optimized the antigenic properties of the HIV-1 Env outer domain to generate OD4.2.2, from the KER2018 strain of clade A HIV-1, enabling it to bind antibodies such as VRC01 with nanomolar affinity. The crystal structure of OD4.2.2 in complex with VRC-PG04 was solved at 3.0-Å resolution and compared to known crystal structures including (i) the structure of core gp120 bound by VRC-PG04 and (ii) a circularly permutated version of the outer domain in complex with antibody PGT128. Much of the VRC-PG04 epitope was preserved in the OD4.2.2 structure, though with altered N and C termini conformations. Overall, roughly one-third of the outer domain structure appeared to be fixed in conformation, independent of alterations in termini, clade, or ligand, while other portions of the outer domain displayed substantial structural malleability. The crystal structure of OD4.2.2 with VRC-PG04 provides atomic-level details for an HIV-1 domain recognized by broadly neutralizing antibodies and insights relevant to the rational design of an immunogen that could elicit such antibodies by vaccination.

  12. O-antigens of bacteria of the genus providencia: structure, serology, genetics, and biosynthesis.

    PubMed

    Ovchinnikova, O G; Rozalski, A; Liu, B; Knirel, Y A

    2013-07-01

    The genus Providencia consists of eight species of opportunistic pathogenic enterobacteria that can cause enteric diseases and urinary tract infections. The existing combined serological classification scheme of three species, P. alcalifaciens, P. stuartii, and P. rustigianii, is based on the specificity of O-antigens (O-polysaccharides) and comprises 63 O-serogroups. Differences between serogroups are related to polymorphism at a specific genome locus, the O-antigen gene cluster, responsible for O-antigen biosynthesis. This review presents data on structures of 36 O-antigens of Providencia, many of which contain unusual monosaccharides and non-carbohydrate components. The structural data correlate with the immunospecificity of the O-antigens and enable substantiation on a molecular level of serological relationships within the genus Providencia and between strains of Providencia and bacteria of the genera Proteus, Escherichia, and Salmonella. Peculiar features of the O-antigen gene cluster organization in 10 Providencia serogroups and biosynthetic pathways of nucleotide precursors of specific monosaccharide components of the O-antigens also are discussed.

  13. Investigation of intravalence, core-valence and core-core electron correlation effects in polonium atomic structure calculations

    NASA Astrophysics Data System (ADS)

    Quinet, Pascal

    2014-09-01

    A detailed investigation of the atomic structure and radiative parameters involving the lowest states within the 6p4, 6p36d, 6p37s, 6p37p and 6p37d configurations of neutral polonium is reported in the present paper. Using different physical models based on the pseudo-relativistic Hartree-Fock approach, the influence of intravalence, core-valence and core-core electron correlation on the atomic parameters is discussed in detail. This work allowed us to fix the spectroscopic designation of some experimental level energy values and to provide for the first time a set of reliable oscillator strengths corresponding to 31 Po I spectral lines in the wavelength region from 175 to 987 nm.

  14. Interaction of the hepatitis B core antigen and the innate immune system.

    PubMed

    Lee, Byung O; Tucker, Amy; Frelin, Lars; Sallberg, Matti; Jones, Joyce; Peters, Cory; Hughes, Janice; Whitacre, David; Darsow, Bryan; Peterson, Darrell L; Milich, David R

    2009-06-01

    Previous studies demonstrated that the primary APCs for the hepatitis B core Ag (HBcAg) were B cells and not dendritic cells (DC). We now report that splenic B1a and B1b cells more efficiently present soluble HBcAg to naive CD4(+) T cells than splenic B2 cells. This was demonstrated by direct HBcAg-biotin-binding studies and by HBcAg-specific T cell activation in vitro in cultures of naive HBcAg-specific T cells and resting B cell subpopulations. The inability of DC to function as APCs for exogenous HBcAg relates to lack of uptake of HBcAg, not to processing or presentation, because HBcAg/anti-HBc immune complexes can be efficiently presented by DC. Furthermore, HBcAg-specific CD4(+) and CD8(+) T cell priming with DNA encoding HBcAg does not require B cell APCs. TLR activation, another innate immune response, was also examined. Full-length (HBcAg(183)), truncated (HBcAg(149)), and the nonparticulate HBeAg were screened for TLR stimulation via NF-kappaB activation in HEK293 cells expressing human TLRs. None of the HBc/HBeAgs activated human TLRs. Therefore, the HBc/HBeAg proteins are not ligands for human TLRs. However, the ssRNA contained within HBcAg(183) does function as a TLR-7 ligand, as demonstrated at the T and B cell levels in TLR-7 knockout mice. Bacterial, yeast, and mammalian ssRNA encapsidated within HBcAg(183) all function as TLR-7 ligands. These studies indicate that innate immune mechanisms bridge to and enhance the adaptive immune response to HBcAg and have important implications for the use of hepadnavirus core proteins as vaccine carrier platforms.

  15. Star cell type core configuration for structural sandwich materials

    DOEpatents

    Christensen, R.M.

    1995-08-01

    A new pattern for cellular core material used in sandwich type structural materials is disclosed. The new pattern involves star shaped cells intermixed with hexagonal shaped cells. The new patterned cellular core material includes star shaped cells interconnected at points thereof and having hexagonal shape cells positioned adjacent the star points. The new pattern allows more flexibility and can conform more easily to curved shapes. 3 figs.

  16. Evaluation of red blood cell and platelet antigen genotyping platforms (ID CORE XT/ID HPA XT) in routine clinical practice

    PubMed Central

    Finning, Kirstin; Bhandari, Radhika; Sellers, Fiona; Revelli, Nicoletta; Villa, Maria Antonietta; Muñiz-Díaz, Eduardo; Nogués, Núria

    2016-01-01

    Background High-throughput genotyping platforms enable simultaneous analysis of multiple polymorphisms for blood group typing. BLOODchip® ID is a genotyping platform based on Luminex® xMAP technology for simultaneous determination of 37 red blood cell (RBC) antigens (ID CORE XT) and 18 human platelet antigens (HPA) (ID HPA XT) using the BIDS XT software. Materials and methods In this international multicentre study, the performance of ID CORE XT and ID HPA XT, using the centres’ current genotyping methods as the reference for comparison, and the usability and practicality of these systems, were evaluated under working laboratory conditions. DNA was extracted from whole blood in EDTA with Qiagen methodologies. Ninety-six previously phenotyped/genotyped samples were processed per assay: 87 testing samples plus five positive controls and four negative controls. Results Results were available for 519 samples: 258 with ID CORE XT and 261 with ID HPA XT. There were three “no calls” that were either caused by human error or resolved after repeating the test. Agreement between the tests and reference methods was 99.94% for ID CORE XT (9,540/9,546 antigens determined) and 100% for ID HPA XT (all 4,698 alleles determined). There were six discrepancies in antigen results in five RBC samples, four of which (in VS, N, S and Doa) could not be investigated due to lack of sufficient sample to perform additional tests and two of which (in S and C) were resolved in favour of ID CORE XT (100% accuracy). The total hands-on time was 28–41 minutes for a batch of 16 samples. Compared with the reference platforms, ID CORE XT and ID HPA XT were considered simpler to use and had shorter processing times. Discussion ID CORE XT and ID HPA XT genotyping platforms for RBC and platelet systems were accurate and user-friendly in working laboratory settings. PMID:26674823

  17. Composite Cocured Modular Eggcrate-Core Sandwich Structure

    NASA Technical Reports Server (NTRS)

    Magurany, Charles J.

    1995-01-01

    Lightweight composite-material (e.g., graphite fiber/epoxy matrix) cocured sandwich panels with eggcratelike cores developed for use as principal components of optical benches and other structures that support precise optical instruments. Structures offer greater thermal and mechanical stability. Advantages include easier fabrication and better mechanical properties.

  18. Determining protein similarity by comparing hydrophobic core structure.

    PubMed

    Gadzała, M; Kalinowska, B; Banach, M; Konieczny, L; Roterman, I

    2017-02-01

    Formal assessment of structural similarity is - next to protein structure prediction - arguably the most important unsolved problem in proteomics. In this paper we propose a similarity criterion based on commonalities between the proteins' hydrophobic cores. The hydrophobic core emerges as a result of conformational changes through which each residue reaches its intended position in the protein body. A quantitative criterion based on this phenomenon has been proposed in the framework of the CASP challenge. The structure of the hydrophobic core - including the placement and scope of any deviations from the idealized model - may indirectly point to areas of importance from the point of view of the protein's biological function. Our analysis focuses on an arbitrarily selected target from the CASP11 challenge. The proposed measure, while compliant with CASP criteria (70-80% correlation), involves certain adjustments which acknowledge the presence of factors other than simple spatial arrangement of solids.

  19. Three dimensional inner core anisotropy, lowermost mantle structure, and inner core rotation

    NASA Astrophysics Data System (ADS)

    Sun, Xinlei

    Three-dimensional anisotropy of Earth's inner core and the lowermost mantle structures are studied from PKP waves. Using a unique data set of PKP travel times at near antipodal distances, I examine the whole inner core anisotropy and the effect from lowermost mantle heterogeneities. The results show AB-DF residuals for polar paths are consistently larger than those of equatorial paths, and are mainly from DF residuals, thus confirmed AB-DF residuals are from inner core anisotropy. Assuming a uniform cylindrical anisotropy model, the average inner core anisotropy amplitude is ˜2.5%. The equatorial PKP differential travel times, however, can be caused by the lowermost mantle structure. Compressional waves that sample the lowermost mantle west of Central America show a rapid change in travel times of up to 4 s over a distance of 300 km and a change in waveforms. The PKP differential travel times correlate remarkably well with predictions from S-wave tomography. Our modeling suggests a sharp transition in the lowermost mantle from a broad slow region to a broad fast region with a narrow zone of slowest anomaly next to the boundary beneath the Cocos and the Caribbean Plate. The structure may be the result of ponding of ancient subducted Farallon slabs situated near the edge of a thermal and chemical upwelling. Depth and longitudinal dependence of the inner core anisotropy are also investigated. I adopt a pseudo-bending ray tracing method in spherical coordinates [koketsu1998] for PKP DF rays, and use B-spline interpolation in the inversion. Our results show clearly hemispherical and depth dependence of the inner core anisotropy, and suggest a distinct inner inner core (IIC), which is about half radius of the inner core. Further examination of this issue from the corrected residuals at near antipodal distances and from the residual changes vs. distance at equatorial directions show very consistent results, indicating the distinct anisotropy in the IIC is robust. Finally

  20. A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey

    SciTech Connect

    Deng, Lu; Velikovsky, C. Alejandro; Xu, Gang; Iyer, Lakshminarayan M.; Tasumi, Satoshi; Kerzic, Melissa C.; Flajnik, Martin F.; Aravind, L.; Pancer, Zeev; Mariuzza, Roy A.

    2010-10-28

    Adaptive immunity in jawless vertebrates is mediated by leucine-rich repeat proteins called 'variable lymphocyte receptors' (VLRs). Two types of VLR (A and B) are expressed by mutually exclusive lymphocyte populations in lamprey. VLRB lymphocytes resemble the B cells of jawed vertebrates; VLRA lymphocytes are similar to T cells. We determined the structure of a high-affinity VLRA isolated from lamprey immunized with hen egg white lysozyme (HEL) in unbound and antigen-bound forms. The VLRA-HEL complex demonstrates that certain VLRAs, like {gamma}{delta} T-cell receptors (TCRs) but unlike {alpha}{beta} TCRs, can recognize antigens directly, without a requirement for processing or antigen-presenting molecules. Thus, these VLRAs feature the nanomolar affinities of antibodies, the direct recognition of unprocessed antigens of both antibodies and {gamma}{delta} TCRs, and the exclusive expression on the lymphocyte surface that is unique to {alpha}{beta} and {gamma}{delta} TCRs.

  1. Structural studies on the lipopolysaccharide core of Proteus OX strains used in Weil-Felix test: a mass spectrometric approach.

    PubMed

    Kondakova, Anna N; Vinogradov, Evgeny; Lindner, Buko; Knirel, Yuriy A; Amano, Ken-ichi

    2003-11-14

    The core region of the lipopolysaccharides of Proteus group OX bacteria, which are used as antigens in Weil-Felix test for serodiagnosis of rickettsiosis, were studied by chemical degradations in combination with ESI FTMS, including infrared multi-photon dissociation (IRMPD) MS/MS and capillary skimmer dissociation. Structural variants of the inner core region were found to be the same as in Proteus non-OX strains that have been studied earlier. The outer core region has essentially the same structure in Proteus vulgaris OX19 (serogroup O1) and OX2 (serogroup O2) and a different structure in Proteus mirabilis OXK (serogroup O3). A fragmentation due to the rupture of the linkage between GlcN or GalN and GalA was observed in IRMPD-MS/MS of core oligosaccharides and found to be useful for screening of Proteus strains to assign structures of the relatively conserved inner core region and to select for further studies strains with distinct structures of a more variable outer core region.

  2. Sensitivity of tropical cyclone intensification to inner-core structure

    NASA Astrophysics Data System (ADS)

    Ge, Xuyang; Xu, Wei; Zhou, Shunwu

    2015-10-01

    In this study, the dependence of tropical cyclone (TC) development on the inner-core structure of the parent vortex is examined using a pair of idealized numerical simulations. It is found that the radial profile of inner-core relative vorticity may have a great impact on its subsequent development. For a system with a larger inner-core relative vorticity/inertial stability, the conversion ratio of the diabatic heating to kinetic energy is greater. Furthermore, the behavior of the convective vorticity eddies is likely modulated by the system-scale circulation. For a parent vortex with a relatively higher inner-core vorticity and larger negative radial vorticity gradient, convective eddy formation and radially inward propagation is promoted through vorticity segregation. This provides a greater potential for these small-scale convective cells to self-organize into a mesoscale inner-core structure in the TC. In turn, convectively induced diabatic heating that is close to the center, along with higher inertial stability, efficiently enhances system-scale secondary circulation. This study provides a solid basis for further research into how the initial structure of a TC influences storm dynamics and thermodynamics.

  3. The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.

    PubMed

    Snyder, David A; Grullon, Jennifer; Huang, Yuanpeng J; Tejero, Roberto; Montelione, Gaetano T

    2014-02-01

    Maximizing the scientific impact of NMR-based structure determination requires robust and statistically sound methods for assessing the precision of NMR-derived structures. In particular, a method to define a core atom set for calculating superimpositions and validating structure predictions is critical to the use of NMR-derived structures as targets in the CASP competition. FindCore (Snyder and Montelione, Proteins 2005;59:673-686) is a superimposition independent method for identifying a core atom set and partitioning that set into domains. However, as FindCore optimizes superimposition by sensitively excluding not-well-defined atoms, the FindCore core may not comprise all atoms suitable for use in certain applications of NMR structures, including the CASP assessment process. Adapting the FindCore approach to assess predicted models against experimental NMR structures in CASP10 required modification of the FindCore method. This paper describes conventions and a standard protocol to calculate an "Expanded FindCore" atom set suitable for validation and application in biological and biophysical contexts. A key application of the Expanded FindCore method is to identify a core set of atoms in the experimental NMR structure for which it makes sense to validate predicted protein structure models. We demonstrate the application of this Expanded FindCore method in characterizing well-defined regions of 18 NMR-derived CASP10 target structures. The Expanded FindCore protocol defines "expanded core atom sets" that match an expert's intuition of which parts of the structure are sufficiently well defined to use in assessing CASP model predictions. We also illustrate the impact of this analysis on the CASP GDT assessment scores.

  4. A structural model for the prostate disease marker, human prostate-specific antigen.

    PubMed Central

    Villoutreix, B. O.; Getzoff, E. D.; Griffin, J. H.

    1994-01-01

    Prostate-specific antigen (PSA) provides an excellent serum marker for prostate cancer, the most frequent form of cancer in American males. PSA is a 237-residue protease based on sequence homology to kallikrein-like enzymes. To predict the 3-dimensional structure of PSA, homology modeling studies were performed based on sequence and structural alignments with tonin, pancreatic kallikrein, chymotrypsin, and trypsin. The structurally conserved regions of the 4 reference X-ray proteins provided the core structure of PSA, whereas the loop structures were modeled on the loops of tonin and kallikrein. The unique "kallikrein loop" insert, between Ser 95b and Pro 95k of kallikrein, was constructed using molecular mechanics, dynamics, and electrostatics calculations. In the resulting PSA structure, the catalytic triad, involving residues His 57, Asp 102, and Ser 195, and hydrophobic and electrostatic interactions typical of serine proteases were extremely well conserved. Similarly, the 5-disulfide bonds of kallikrein were also conserved in PSA. These results, together with the fact that no major steric clashes arose during the modeling process, provide strong evidence for the validity of the PSA model. Calculation of the electrostatic potential contours of kallikrein and PSA was carried out using the finite difference Poisson-Boltzmann method. The calculations revealed matching areas of negative potential near the catalytic triad, but differences in the positive potential surrounding the active site. The PSA glycosylation site, Asn 61, is fully accessible to the solvent and is enclosed in a positive region of the isopotential map. The bottom of the substrate specificity pocket, residue S1, is a serine (Ser 189) as in chymotrypsin, rather than aspartate (Asp 189) as in tonin, kallikrein, and trypsin. This fact, plus other features of the S1 binding-pocket region, suggest that PSA would prefer substrates with hydrophobic residues at the P1 position. The location of a

  5. Structure and Function of Latency-Associated Nuclear Antigen

    PubMed Central

    Verma, S. C.; Lan, K.

    2011-01-01

    Latency-associated nuclear antigen (LANA) encoded by open reading frame 73 (ORF73) is the major latent protein expressed in all forms of KSHV-associated malignancies. LANA is a large (222–234 kDa) nuclear protein that interacts with various cellular as well as viral proteins. LANA has been classified as an oncogenic protein as it dysregulates various cellular pathways including tumor suppressor pathways associated with pRb and p53 and can transform primary rat embryo fibroblasts in cooperation with the cellular oncogene Hras. It associates with GSK-3β, an important modulator of Wnt signaling pathway leading to the accumulation of cytoplasmic β-catenin, which upregulates Tcf/Lef regulated genes after entering into the nucleus. LANA also blocks the expression of RTA, the reactivation transcriptional activator, which is critical for the latency to lytic switch, and thus helps in maintaining viral latency. LANA tethers the viral episomal DNA to the host chromosomes by directly binding to its cognate binding sequence within the TR region of the genome through its C terminus and to the nucleosomes through the N terminus of the molecule. Tethering to the host chromosomes helps in efficient partitioning of the viral episomes in the dividing cells. Disruptions of LANA expression led to reduction in the episomal copies of the viral DNA, supporting its role in persistence of the viral DNA. The functions known so far suggest that LANA is a key player in KSHV-mediated pathogenesis. PMID:17089795

  6. Effects of core perturbations on the structure of the sun

    NASA Technical Reports Server (NTRS)

    Sweigart, A. V.

    1983-01-01

    The effects of perturbing the inner part of the solar core where the hydrogen abundance has been partially depleted by nuclear burning are investigated. Small regions are mixed within the core and the evolution of the resulting luminosity and radius perturbations is followed. The sensitivity of the solar luminosity and radius to mixing events of different sizes and at different locations in the core is determined and several relationships between the luminosity and radius perturbations are examined to see if the value of one of these perturbations can be inferred from a measurement of the other. It is found that any core perturbation which alters the hydrostatic structures will immediately affect the solar luminosity and radius. The behavior of these perturbations depends on the location of the mixing event within the core. Mixing events cannot produce the decrease in the solar radius without leading to a homogeneous evolution of the solar core and/or to a prohibitively large change in the solar luminosity.

  7. Update to Core reporting practices in structural equation modeling.

    PubMed

    Schreiber, James B

    2016-07-21

    This paper is a technical update to "Core Reporting Practices in Structural Equation Modeling."(1) As such, the content covered in this paper includes, sample size, missing data, specification and identification of models, estimation method choices, fit and residual concerns, nested, alternative, and equivalent models, and unique issues within the SEM family of techniques.

  8. Hypervelocity Impact Evaluation of Metal Foam Core Sandwich Structures

    NASA Technical Reports Server (NTRS)

    Yasensky, John; Christiansen, Eric L.

    2007-01-01

    A series of hypervelocity impact (HVI) tests were conducted by the NASA Johnson Space Center (JSC) Hypervelocity Impact Technology Facility (HITF) [1], building 267 (Houston, Texas) between January 2003 and December 2005 to test the HVI performance of metal foams, as compared to the metal honeycomb panels currently in service. The HITF testing was conducted at the NASA JSC White Sands Testing Facility (WSTF) at Las Cruces, New Mexico. Eric L. Christiansen, Ph.D., and NASA Lead for Micro-Meteoroid Orbital Debris (MMOD) Protection requested these hypervelocity impact tests as part of shielding research conducted for the JSC Center Director Discretionary Fund (CDDF) project. The structure tested is a metal foam sandwich structure; a metal foam core between two metal facesheets. Aluminum and Titanium metals were tested for foam sandwich and honeycomb sandwich structures. Aluminum honeycomb core material is currently used in Orbiter Vehicle (OV) radiator panels and in other places in space structures. It has many desirable characteristics and performs well by many measures, especially when normalized by density. Aluminum honeycomb does not perform well in Hypervelocity Impact (HVI) Testing. This is a concern, as honeycomb panels are often exposed to space environments, and take on the role of Micrometeoroid / Orbital Debris (MMOD) shielding. Therefore, information on possible replacement core materials which perform adequately in all necessary functions of the material would be useful. In this report, HVI data is gathered for these two core materials in certain configurations and compared to gain understanding of the metal foam HVI performance.

  9. The effect of erythrocyte antigen structure on requirement for T cells*

    PubMed Central

    Byrd, W.; Feldmann, Marc; Palmer, J.

    1974-01-01

    The induction in mice of a humoral immune response to intact sheep erythrocytes, both in vivo and in vitro, requires participation of thymus-derived (T) lymphocytes. In an in vitro system, spleen cells from both neonatally thymectomized and adult thymectomized irradiated bone marrow protected mice were successfully immunized, using washed sonicated sheep erythrocyte membrane fragments as antigen. This obviation of the requirement of T lymphocytes in the immune response, coupled with previous work on macrophage independence, indicates that sonicated membrane fragments were capable of directly immunizing bone marrow-derived (B) lymphocytes in vitro. These results further confirm the signal importance of antigenic structure in determining the cellular requirements for an immunological response; whereas antigens of particulate or monomeric form require the presence of both T cells and macrophages, polymeric antigens of intermediate size such as polymerized flagellin and sonicated sheep erythrocyte membranes require neither of these accessory cells. The results caution against the use of erythrocytes as models of thymus-dependent antigens. The data further suggest that reports of late antibody responses of relatively normal magnitude in thymectomized animals given larger doses of heterologous erythrocytes may have been due to direct immunization of B lymphocytes by degraded erythrocyte antigen. PMID:4138234

  10. Determination of amyloid core structure using chemical shifts.

    PubMed

    Skora, Lukasz; Zweckstetter, Markus

    2012-12-01

    Amyloid fibrils are the pathological hallmark of a large variety of neurodegenerative disorders. The structural characterization of amyloid fibrils, however, is challenging due to their non-crystalline, heterogeneous, and often dynamic nature. Thus, the structure of amyloid fibrils of many proteins is still unknown. We here show that the structure calculation program CS-Rosetta can be used to obtain insight into the core structure of amyloid fibrils. Driven by experimental solid-state NMR chemical shifts and taking into account the polymeric nature of fibrils CS-Rosetta allows modeling of the core of amyloid fibrils. Application to the Y145X stop mutant of the human prion protein reveals a left-handed β-helix.

  11. Research core drilling in the Manson impact structure, Iowa

    NASA Technical Reports Server (NTRS)

    Anderson, R. R.; Hartung, J. B.; Roddy, D. J.; Shoemaker, E. M.

    1992-01-01

    The Manson impact structure (MIS) has a diameter of 35 km and is the largest confirmed impact structure in the United States. The MIS has yielded a Ar-40/Ar-39 age of 65.7 Ma on microcline from its central peak, an age that is indistinguishable from the age of the Cretaceous-Tertiary boundary. In the summer of 1991 the Iowa Geological Survey Bureau and U.S. Geological Survey initiated a research core drilling project on the MIS. The first core was beneath 55 m of glacial drift. The core penetrated a 6-m layered sequence of shale and siltstone and 42 m of Cretaceous shale-dominated sedimentary clast breccia. Below this breccia, the core encountered two crystalline rock clast breccia units. The upper unit is 53 m thick, with a glassy matrix displaying various degrees of devitrification. The upper half of this unit is dominated by the glassy matrix, with shock-deformed mineral grains (especially quartz) the most common clast. The glassy-matrix unit grades downward into the basal unit in the core, a crystalline rock breccia with a sandy matrix, the matrix dominated by igneous and metamorphic rock fragments or disaggregated grains from those rocks. The unit is about 45 m thick, and grains display abundant shock deformation features. Preliminary interpretations suggest that the crystalline rock breccias are the transient crater floor, lifted up with the central peak. The sedimentary clast breccia probably represents a postimpact debris flow from the crater rim, and the uppermost layered unit probably represents a large block associated with the flow. The second core (M-2) was drilled near the center of the crater moat in an area where an early crater model suggested the presence of postimpact lake sediments. The core encountered 39 m of sedimentary clast breccia, similar to that in the M-1 core. Beneath the breccia, 120 m of poorly consolidated, mildly deformed, and sheared siltstone, shale, and sandstone was encountered. The basal unit in the core was another sequence

  12. Structural Studies of Lipopolysaccharide-defective Mutants from Brucella melitensis Identify a Core Oligosaccharide Critical in Virulence*

    PubMed Central

    Fontana, Carolina; Conde-Álvarez, Raquel; Ståhle, Jonas; Holst, Otto; Iriarte, Maite; Zhao, Yun; Arce-Gorvel, Vilma; Hanniffy, Seán; Gorvel, Jean-Pierre; Moriyón, Ignacio; Widmalm, Göran

    2016-01-01

    The structures of the lipooligosaccharides from Brucella melitensis mutants affected in the WbkD and ManBcore proteins have been fully characterized using NMR spectroscopy. The results revealed that disruption of wbkD gives rise to a rough lipopolysaccharide (R-LPS) with a complete core structure (β-d-Glcp-(1→4)-α-Kdop-(2→4)[β-d-GlcpN-(1→6)-β-d-GlcpN-(1→4)[β-d-GlcpN-(1→6)]-β-d-GlcpN-(1→3)-α-d-Manp-(1→5)]-α-Kdop-(2→6)-β-d-GlcpN3N4P-(1→6)-α-d-GlcpN3N1P), in addition to components lacking one of the terminal β-d-GlcpN and/or the β-d-Glcp residues (48 and 17%, respectively). These structures were identical to those of the R-LPS from B. melitensis EP, a strain simultaneously expressing both smooth and R-LPS, also studied herein. In contrast, disruption of manBcore gives rise to a deep-rough pentasaccharide core (β-d-Glcp-(1→4)-α-Kdop-(2→4)-α-Kdop-(2→6)-β-d-GlcpN3N4P-(1→6)-α-d-GlcpN3N1P) as the major component (63%), as well as a minor tetrasaccharide component lacking the terminal β-d-Glcp residue (37%). These results are in agreement with the predicted functions of the WbkD (glycosyltransferase involved in the biosynthesis of the O-antigen) and ManBcore proteins (phosphomannomutase involved in the biosynthesis of a mannosyl precursor needed for the biosynthesis of the core and O-antigen). We also report that deletion of B. melitensis wadC removes the core oligosaccharide branch not linked to the O-antigen causing an increase in overall negative charge of the remaining LPS inner section. This is in agreement with the mannosyltransferase role predicted for WadC and the lack of GlcpN residues in the defective core oligosaccharide. Despite carrying the O-antigen essential in B. melitensis virulence, the core deficiency in the wadC mutant structure resulted in a more efficient detection by innate immunity and attenuation, proving the role of the β-d-GlcpN-(1→6)-β-d-GlcpN-(1→4)[β-d-GlcpN-(1→6)]-β-d-GlcpN-(1→3)-

  13. Structural Studies of Lipopolysaccharide-defective Mutants from Brucella melitensis Identify a Core Oligosaccharide Critical in Virulence.

    PubMed

    Fontana, Carolina; Conde-Álvarez, Raquel; Ståhle, Jonas; Holst, Otto; Iriarte, Maite; Zhao, Yun; Arce-Gorvel, Vilma; Hanniffy, Seán; Gorvel, Jean-Pierre; Moriyón, Ignacio; Widmalm, Göran

    2016-04-01

    The structures of the lipooligosaccharides fromBrucella melitensismutants affected in the WbkD and ManBcoreproteins have been fully characterized using NMR spectroscopy. The results revealed that disruption ofwbkDgives rise to a rough lipopolysaccharide (R-LPS) with a complete core structure (β-d-Glcp-(1→4)-α-Kdop-(2→4)[β-d-GlcpN-(1→6)-β-d-GlcpN-(1→4)[β-d-GlcpN-(1→6)]-β-d-GlcpN-(1→3)-α-d-Manp-(1→5)]-α-Kdop-(2→6)-β-d-GlcpN3N4P-(1→6)-α-d-GlcpN3N1P), in addition to components lacking one of the terminal β-d-GlcpN and/or the β-d-Glcpresidues (48 and 17%, respectively). These structures were identical to those of the R-LPS fromB. melitensisEP, a strain simultaneously expressing both smooth and R-LPS, also studied herein. In contrast, disruption ofmanBcoregives rise to a deep-rough pentasaccharide core (β-d-Glcp-(1→4)-α-Kdop-(2→4)-α-Kdop-(2→6)-β-d-GlcpN3N4P-(1→6)-α-d-GlcpN3N1P) as the major component (63%), as well as a minor tetrasaccharide component lacking the terminal β-d-Glcpresidue (37%). These results are in agreement with the predicted functions of the WbkD (glycosyltransferase involved in the biosynthesis of the O-antigen) and ManBcoreproteins (phosphomannomutase involved in the biosynthesis of a mannosyl precursor needed for the biosynthesis of the core and O-antigen). We also report that deletion ofB. melitensis wadCremoves the core oligosaccharide branch not linked to the O-antigen causing an increase in overall negative charge of the remaining LPS inner section. This is in agreement with the mannosyltransferase role predicted for WadC and the lack of GlcpN residues in the defective core oligosaccharide. Despite carrying the O-antigen essential inB. melitensisvirulence, the core deficiency in thewadCmutant structure resulted in a more efficient detection by innate immunity and attenuation, proving the role of the β-d-GlcpN-(1→6)-β-d-GlcpN-(1→4)[β-d-GlcpN-(1→6)]-β-d-GlcpN-(1→3)-α-d-Manp-(1→5) structure

  14. A universal computational model for predicting antigenic variants of influenza A virus based on conserved antigenic structures

    PubMed Central

    Peng, Yousong; Wang, Dayan; Wang, Jianhong; Li, Kenli; Tan, Zhongyang; Shu, Yuelong; Jiang, Taijiao

    2017-01-01

    Rapid determination of the antigenicity of influenza A virus could help identify the antigenic variants in time. Currently, there is a lack of computational models for predicting antigenic variants of some common hemagglutinin (HA) subtypes of influenza A viruses. By means of sequence analysis, we demonstrate here that multiple HA subtypes of influenza A virus undergo similar mutation patterns of HA1 protein (the immunogenic part of HA). Further analysis on the antigenic variation of influenza A virus H1N1, H3N2 and H5N1 showed that the amino acid residues’ contribution to antigenic variation highly differed in these subtypes, while the regional bands, defined based on their distance to the top of HA1, played conserved roles in antigenic variation of these subtypes. Moreover, the computational models for predicting antigenic variants based on regional bands performed much better in the testing HA subtype than those did based on amino acid residues. Therefore, a universal computational model, named PREDAV-FluA, was built based on the regional bands to predict the antigenic variants for all HA subtypes of influenza A viruses. The model achieved an accuracy of 0.77 when tested with avian influenza H9N2 viruses. It may help for rapid identification of antigenic variants in influenza surveillance. PMID:28165025

  15. Functional and Structural Characterization of Francisella tularensis O-Antigen Antibodies at the Low End of Antigen Reactivity

    PubMed Central

    Lu, Zhaohua; Rynkiewicz, Michael J.; Yang, Chiou-Ying; Madico, Guillermo; Perkins, Hillary M.; Roche, Marly I.; Seaton, Barbara A.

    2014-01-01

    The O-antigen (OAg) of the Gram-negative bacterium Francisella tularensis (Ft), which is both a capsular polysaccharide and a component of lipopolysaccharide, is comprised of tetrasaccharide repeats and induces antibodies mainly against repeating internal epitopes. We previously reported on several BALB/c mouse monoclonal antibodies (MAbs) that bind to internal Ft OAg epitopes and are protective in mouse models of respiratory tularemia. We now characterize three new internal Ft OAg IgG2a MAbs, N203, N77, and N24, with 10- to 100-fold lower binding potency than previously characterized internal-OAg IgG2a MAbs, despite sharing one or more variable region germline genes with some of them. In a mouse model of respiratory tularemia with the highly virulent Ft type A strain SchuS4, the three new MAbs reduced blood bacterial burden with potencies that mirror their antigen-binding strength; the best binder of the new MAbs, N203, prolonged survival in a dose-dependent manner, but was at least 10-fold less potent than the best previously characterized IgG2a MAb, Ab52. X-ray crystallographic studies of N203 Fab showed a flexible binding site in the form of a partitioned groove, which cannot provide as many contacts to OAg as does the Ab52 binding site. These results reveal structural features of antibodies at the low end of reactivity with multi-repeat microbial carbohydrates and demonstrate that such antibodies still have substantial protective effects against infection. PMID:25171003

  16. Is iron at the Earth's core conditions hcp-structured?

    SciTech Connect

    Dubrovinsky, L; Dubrovinskaia, N; Prakapenka, V

    2012-02-07

    Iron is the main component of the Earth's core and its structure and properties are important for interpretation of geophysical observations and modeling dynamics of the core. We argue that the diffraction lines in the high temperature high pressure X-ray diffraction pattern, presented by Tateno et al., 2010 and interpreted as those of solely hot hcp-Fe, correspond indeed to the insufficiently heated part of the sample. We show that observed diffraction spots are either due to bcc-Fe or carbides.

  17. Structural, serological, and genetic characterization of the O-antigen of Providencia alcalifaciens O40.

    PubMed

    Ovchinnikova, Olga G; Liu, Bin; Guo, Dan; Kocharova, Nina A; Bialczak-Kokot, Magdalena; Shashkov, Alexander S; Feng, Lu; Rozalski, Antoni; Wang, Lei; Knirel, Yuriy A

    2012-12-01

    The O-polysaccharide chain of the lipopolysaccharide (O-antigen) on the bacterial cell surface is one of the most structurally variable cell components and serves as a basis for serotyping of Gram-negative bacteria, including human opportunistic pathogens of the genus Providencia. In this work, the O-antigen of Providencia alcalifaciens O40 was obtained by mild acid degradation of the isolated lipopolysaccharide and studied by chemical methods and high-resolution NMR spectroscopy. The following structure of the O-polysaccharide was established: →4)-β-D-Quip3NFo-(1→3)-α-D-Galp-(1→3)-β-D-GlcpA-(1→3)-β-D-GalpNAc-(1→, where GlcA stands for glucuronic acid and Qui3NFo for 3,6-dideoxy-3-formamidoglucose. The O40-antigen was found to be structurally and serologically related to the O-antigens of P. alcalifaciens O5 and Providencia stuartii O18. The O40-antigen gene cluster between cpxA and yibK was sequenced, and the gene functions were predicted in silico. In agreement with the O-polysaccharide structure established, the genes for the synthesis of dTDP-D-Qui3NFo, UDP-D-Gal, UDP-D-GlcA, and UDP-D-GalNAc as well as those encoding three glycosyltransferases, flippase (Wzx), and O-antigen polymerase (Wzy) were recognized. In addition, homologues of wza, wzb, and wzc genes, which are required for the surface expression of capsular polysaccharides, were found within the gene cluster, suggesting that the O-polysaccharide studied is a part of the capsule-related form of the lipopolysaccharide called K(LPS).

  18. Study of Toxic and Antigenic Structures of Botulinum Neurotoxin

    DTIC Science & Technology

    1986-02-04

    this NT cannot be purified by simply following the various steps required for purifying the NT from type B strain Okra . In the areas of structure and...strain Okra . Yield of toxin was very poor, not adequate to proceed through various steps of purification. The stock culture was sent to Dr. Lynr Siegel...toxin froni strain B 657 cannot be purified by simply following the various steps required for purifying the toxin from strain Okra . 2. STRUCTURE-FUNCTION

  19. Structural characterization of Mumps virus fusion protein core

    SciTech Connect

    Liu Yueyong; Xu Yanhui; Lou Zhiyong; Zhu Jieqing; Hu Xuebo; Gao, George F.; Qiu Bingsheng . E-mail: Qiubs@sun.im.ac.cn; Rao Zihe . E-mail: raozh@xtal.tsinghua.edu.cn; Tien, Po . E-mail: tienpo@sun.im.ac.cn

    2006-09-29

    The fusion proteins of enveloped viruses mediating the fusion between the viral and cellular membranes comprise two discontinuous heptad repeat (HR) domains located at the ectodomain of the enveloped glycoproteins. The crystal structure of the fusion protein core of Mumps virus (MuV) was determined at 2.2 A resolution. The complex is a six-helix bundle in which three HR1 peptides form a central highly hydrophobic coiled-coil and three HR2 peptides pack against the hydrophobic grooves on the surface of central coiled-coil in an oblique antiparallel manner. Fusion core of MuV, like those of simian virus 5 and human respiratory syncytium virus, forms typical 3-4-4-4-3 spacing. The similar charecterization in HR1 regions, as well as the existence of O-X-O motif in extended regions of HR2 helix, suggests a basic rule for the formation of the fusion core of viral fusion proteins.

  20. Effects of hepatitis B virus precore and basal core promoter mutations on the expression of viral antigens: genotype B vs C.

    PubMed

    Liu, C-J; Cheng, H-R; Chen, C-L; Chen, T-C; Tseng, T-C; Wang, Z-L; Chen, P-J; Liu, C-H; Chen, D-S; Kao, J-H

    2011-10-01

    Hepatitis B virus (HBV) genotypes/mutants are known to affect natural outcomes. The virologic differences among HBV genotype, precore and basal core promoter (BCP) mutations were investigated. HBV strains were isolated from 18 hepatitis B e antigen (HBeAg)-positive patients (nine genotype B and nine genotype C). All had precore and BCP wild-type sequences. After cloning of full-length HBV genome, the effects of viral genotype, precore and BCP mutations singly or additively on the expression of viral DNA and antigens were investigated by mutagenesis and transfection assays in Huh7 cells. Significant findings included the following: (i) expression of intracellular core protein increased when precore or BCP mutation was introduced in genotype C strains; (ii) expression of intracellular surface protein was lower in genotype C precore wild-type strain compared with genotype B; (iii) precore mutation was associated with a lower extracellular expression level of HBV DNA; (iv) secretion of hepatitis B surface antigen in genotype C was lower than that in genotype B; and (v) secretion of HBeAg in genotype B was lower than that in genotype C. No additive effect was observed by combining precore and BCP mutations. Hence, HBV genotype and precore/BCP mutations correlate with intrahepatic expression of viral antigens in vitro.

  1. New direct-acting antivirals for patients with chronic HCV infection: can we monitor treatment using an HCV core antigen assay?

    PubMed

    Alonso, R; Pérez-García, F; Ampuero, D; Reigadas, E; Bouza, E

    2017-03-01

    We evaluated the diagnostic usefulness of an HCV core antigen (HCV-Ag) assay in HCV-infected patients undergoing treatment with direct-acting antivirals. We analyzed 103 samples from 28 patients. Compared with RT-PCR, sensitivity was 96.2% and specificity was 100%. The correlation between techniques was excellent (Pearson coefficient: 0.871). HCV-Ag proved to be useful in patients with sustained viral response and in patients who experienced treatment failures.

  2. Performance comparison of new generation HCV core antigen test versus HCV RNA test in management of hepatitis C virus infection.

    PubMed

    Çetiner, Salih; Çetin Duran, Alev; Kibar, Filiz; Yaman, Akgün

    2017-03-06

    The study has evaluated the performance of HCV core antigen (Cag) test by comparing HCV RNA PCR assay which is considered the gold standard for management of HCV infection. Totally, 132 samples sent for HCV RNA (real-time PCR) test were included in the study. Anti-HCV antibody test and HCV Cag test were performed by chemiluminescent enzyme immunoassay (CMEI). Anti-HCV test was positive in all samples. HCV RNA was detected in 112/132 (84.8%) samples, and HCV Cag in 105/132 (79.5%). The most common HCV genotype was genotype 1 (86%). Considering the HCV RNA test as gold standard; the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of Cag test were found to be 93.75%, 100%, 100%, 74.07% and 94.69%, respectively, and paired test results were detected as highly concordant. A high level of correlation was seen between HCV RNA and Cag tests, however, the concordance between the two tests appeared to be disrupted at viral loads lower than 10(3)IU/mL. On the contrary, the correlation reached significance for the values higher than 10(3)IU/mL. Viral loads were in the 17-2500IU/mL range for the negative results for Cag test. Pearson's correlation coefficient revealed a considerably high correlation. The concordance between HCV RNA and Cag tests was disrupted under a viral load lower than 10(3)IU/mL. Therefore, it would be appropriate to consider cost effectiveness, advantages and limitations of the HCV RNA and Cag tests during the decision on which method to use for patient management.

  3. An Efficient Analysis Methodology for Fluted-Core Composite Structures

    NASA Technical Reports Server (NTRS)

    Oremont, Leonard; Schultz, Marc R.

    2012-01-01

    The primary loading condition in launch-vehicle barrel sections is axial compression, and it is therefore important to understand the compression behavior of any structures, structural concepts, and materials considered in launch-vehicle designs. This understanding will necessarily come from a combination of test and analysis. However, certain potentially beneficial structures and structural concepts do not lend themselves to commonly used simplified analysis methods, and therefore innovative analysis methodologies must be developed if these structures and structural concepts are to be considered. This paper discusses such an analysis technique for the fluted-core sandwich composite structural concept. The presented technique is based on commercially available finite-element codes, and uses shell elements to capture behavior that would normally require solid elements to capture the detailed mechanical response of the structure. The shell thicknesses and offsets using this analysis technique are parameterized, and the parameters are adjusted through a heuristic procedure until this model matches the mechanical behavior of a more detailed shell-and-solid model. Additionally, the detailed shell-and-solid model can be strategically placed in a larger, global shell-only model to capture important local behavior. Comparisons between shell-only models, experiments, and more detailed shell-and-solid models show excellent agreement. The discussed analysis methodology, though only discussed in the context of fluted-core composites, is widely applicable to other concepts.

  4. Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens.

    PubMed

    Liljeroos, Lassi; Malito, Enrico; Ferlenghi, Ilaria; Bottomley, Matthew James

    2015-01-01

    Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10-20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease.

  5. Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

    PubMed Central

    Liljeroos, Lassi; Malito, Enrico; Ferlenghi, Ilaria; Bottomley, Matthew James

    2015-01-01

    Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10–20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease. PMID:26526043

  6. Effect of Silicon Alloying on the Structure of Exoplanetary Cores

    NASA Astrophysics Data System (ADS)

    Wicks, J. K.; Smith, R.; Coppari, F.; Kraus, R. G.; Newman, M.; Duffy, T. S.

    2015-12-01

    The composition of cores of terrestrial planets are expected to be broadly similar to that of Earth in that they are comprised of a Fe-Ni alloy with variable amounts of light elements such as O, Si, C, S, and H. With the increasing number of discoveries of Super-Earths (rocky planets many times the mass of our own), the properties of terrestrial phases at ultrahigh pressures are required to understand and interpret the variability of large-scale exoplanet observations. The properties of the cores of these bodies are important for understanding the bulk chemistry, thermal evolution, magnetic fields, and, ultimately, habitability of a planet. Recent diamond anvil cell studies interrogating the structure of iron generally agree that Fe should be hcp at core pressures and temperatures, although other structures have been proposed. At higher pressures and with the addition of light elements, the structure is less understood. The addition of large amounts of Si, for example, stabilizes the cubic B2 structure with respect to hcp at outer core pressures. Our goal in this study is to explore the effect of Si-alloying at inner core and exoplanetary-core pressures. Dynamic compression experiments were carried out at the Omega Laser at the Laboratory for Laser Energetics, University of Rochester. High pressures were achieved by focusing laser drives onto target packages containing Fe-Si alloys. Pressures within the sample were determined by monitoring the velocity history at the sample/window interface. Quasi-monochromatic X-rays, timed with maximum compression of the Fe-alloy sample, were generated via laser irradiation of iron or germanium foils arranged in a backlighter configuration and collected on image plates lining the inner walls of a box attached to the target package. In this presentation we will report on the effect of Si-alloying on the structure and density of Fe over the pressure range 100-1000 GPa. We find that while Fe with 7 wt.% Si remains in the hcp

  7. Structure and gene cluster of the O-antigen of Escherichia coli O133.

    PubMed

    Shashkov, Alexander S; Zhang, Yuanyuan; Sun, Qiangzheng; Guo, Xi; Senchenkova, Sof'ya N; Perepelov, Andrei V; Knirel, Yuriy A

    2016-07-22

    The O-specific polysaccharide (O-antigen) of Escherichia coli O133 was obtained by mild acid hydrolysis of the lipopolysaccharide of E. coli O133. The structure of the hexasaccharide repeating unit of the polysaccharide was elucidated by (1)H and (13)C NMR spectroscopy, including a two-dimensional (1)H-(1)H ROESY experiment: Functions of genes in the O-antigen gene cluster were putatively identified by comparison with sequences in the available databases and, particularly, an encoded predicted multifunctional glycosyltransferase was assigned to three α-l-rhamnosidic linkages.

  8. Seismic structures in the Earth's inner core below Southeastern Asia

    NASA Astrophysics Data System (ADS)

    Krasnoshchekov, Dmitry; Kaazik, Petr; Ovtchinnikov, Vladimir

    2015-04-01

    Studying seismic heterogeneities in the Earth's inner core is important in terms of understanding its history and dynamics. Measurements of body waves refracted in the vicinity of the inner core boundary yield a powerful tool for studying properties and spatial structure of such heterogeneities. We present investigation of the eastern hemisphere of the solid core by means of PKP(BC)-PKP(DF) differential travel times that sample depths from 140 to 360 km below its boundary. The study includes 292 polar and 133 equatorial residuals measured over the traces that probe roughly the same volume of the inner core in both planes. Equatorial residuals show slight spatial variations in the sampled inner core volume mostly below the level of 0.5%, whereas polar residuals are up to 1.3% and exhibit higher local variations and direction dependency. On the base of these measurements we report fast changes in seismic velocity within a restricted volume of the inner core. The observations are interpreted in terms of anisotropy and checked against several anisotropy models. Few models are capable of fitting the residuals scatter, and one of such models features a dipping discontinuity that separates fully isotropic roof of the inner core from its anisotropic body. The depth of the isotropy-anisotropy transition in the model increases in southeast direction from 190 km below Southeastern Asia (off the coast of China) to 350 km beneath Australia. Another acceptable model invokes localized anisotropic heterogeneities. It is valid if 33 largest polar measurements over the rays sampling a small volume below Southeastern Asia and the rest of polar data are treated separately. This model envisages almost isotropic eastern hemisphere of the inner core at least down to the depth of 360 km below the inner core boundary and constrains the anisotropic volume only to the ranges of North latitudes from 18 to 23 degrees, East longitudes from 125 to 135 degrees and depths exceeding 170 km. The

  9. The crystal structure of iron at the inner core

    NASA Astrophysics Data System (ADS)

    Tateno, S.; Hirose, K.; Ohishi, Y.; Tatsumi, Y.

    2010-12-01

    The Earth’s solid inner core is mainly composed of iron. Thus the crystal structure of iron is of prime importance for understanding the nature of solid inner core. Despite many efforts to investigate phase relations of iron have by dynamic and static compression, and theoretical calculation, consensus on the stable phase at the inner core condition has never been achieved. While hcp-Fe can persist to core pressures at 300 K, a phase transition at elevated temperature is a possibility. Both theory and experiments proposed different forms of iron at simultaneously high P-T conditions, which include bcc, face-centered-cubic (fcc), and hcp structures. The structure of iron has never been examined experimentally at the inner core P-T conditions (>330 GPa and ≥5000 K), because such extreme conditions could only be achieved by shock-wave compression experiments. Based on static compression experiments in a laser-heated diamond-anvil cell (DAC), we determined the structure of iron up to 377 GPa and 5700 K. Iron powder and thermal insulation layers of SiO2 glass were loaded into a hole of a pre-indented rhenium gasket placed in the For experiments beyond 300 GPa, the double-beveled diamond anvils with 40-μm culets were used, and accordingly the sample size was limited to about 20 μm. Heating was performed from both sides of the sample by employing two single mode, Yb fiber lasers with output power up to 100 W each with flat-top beam shaping optics to minimize temperature gradient across the sample. Angle-dispersive x-ray diffraction measurements were conducted at BL10XU of SPring-8. Six separate sets of experiments were conducted in a wide P-T range from 135 GPa and 2690 K to 377 GPa and 5700 K. We observed crystal growth and hence the stability of hcp-Fe at these P-T conditions with no evidence for a phase transition to bcc nor fcc iron phases. The c/a axial ratio of hcp-Fe at high temperature was also studied, which has significant effect on the nature of the

  10. Detection of antibodies to hepatitis C virus (HCV) structural proteins in anti-HCV-positive sera by an enzyme-linked immunosorbent assay using synthetic peptides as antigens.

    PubMed Central

    Ishida, C; Matsumoto, K; Fukada, K; Matsushita, K; Shiraki, H; Maeda, Y

    1993-01-01

    We have defined 10 linear immunogenic regions encoded by the putative hepatitis C virus (HCV) structural proteins (core and envelope) by employing an enzyme-linked immunosorbent assay (ELISA) and by using 17 sequential synthetic peptides covering the N-terminal 330 amino acids of the structural polyproteins as antigens. These peptides correspond to amino acids 1 to 24, 21 to 44, 42 to 68, 64 to 91, and 100 to 120 of the putative core protein and amino acids 192 to 212, 223 to 238, 236 to 258, 250 to 266, and 307 to 330 of the putative envelope protein. In particular, the peptide covering amino acids 21 to 44 of the core protein was reactive with all but one (40 of 41) of the serum samples giving a positive signal in the passive hemagglutination assay (PHA) using the core and nonstructural proteins (NS 3/4) of the virus as antigens. We detected the HCV genome in 25 (61%) of 41 PHA-positive serum samples by the polymerase chain reaction (PCR) test. Of 25 PCR-positive serum samples, 17 serum samples had reactivity to the peptides derived from the envelope protein. On the other hand, only 1 of the 16 PCR-negative serum samples had reactivity to the peptides derived from the envelope protein. Interestingly, we often observed high serum alanine aminotransferase levels in PCR-positive individuals bearing antibodies to the envelope protein. PMID:7681849

  11. Structural studies of the serotype-f polysaccharide antigen from Streptococcus mutans OMZ175.

    PubMed Central

    Linzer, R; Reddy, M S; Levine, M J

    1987-01-01

    The serotype f antigen of Streptococcus mutans has been described as a rhamnose-glucose polysaccharide associated with the bacterial cell wall. In this study, the structure of serotype f polysaccharide was examined by analyses of the methylated derivatives of the antigen and the periodate-oxidized antigen. Methylated derivatives were characterized with a gas chromatograph-mass spectrometer. The polysaccharide appeared to have a backbone of alternating 1,3- and 1,2,3-linked rhamnose units. Branching occurred at the 3-position of the 1,2,3-linked rhamnose. Side chains were composed of terminal alpha-linked glucose units. A small proportion of longer side chains containing 1,2- and 1,6-linked glucose units were noted in some preparations; however, these determinants were not reactive with serotype f antisera. PMID:2824381

  12. Prediction and conformation by synthesis of two antigenic sites in human haemoglobin by extrapolation from the known antigenic structure of sperm-whale myoglobin.

    PubMed

    Kazim, A L; Atassi, M Z

    1977-10-01

    The complete antigenic structure of sperm-whale myoglobin was previously determined in our laboratory. By structural analogy with myoglobin, two regions in human haemoglobin were predicted to comprise antigenic sites. One region was on the alpha-chain [alpha-(15-23)] and the other on the beta-chain [beta-(16-23)]. These two regions were synthesized, purified and characterized, and their immunochemistry was studied. Each peptide was able specifically to bind considerable amounts of haemoglobin antibodies. In a set of homologous proteins, barring any drastic conformational or electrostatic inductive effects exerted by the substitutions, and allowing for obstruction due to subunit interaction, the determination of the antigenic structure of one protein may serve as a useful starting model for the others.

  13. Predicted primary and antigenic structure of canine corticotropin releasing hormone.

    PubMed

    Mol, J A; van Wolferen, M; Kwant, M; Meloen, R

    1994-07-01

    Although the dog has been recognized as a useful model for the study of the cerebrospinal and peripheral actions of corticotropin releasing hormone (CRH) the exact amino acid composition of canine CRH is still unknown. In the present study the structure of canine CRH was predicted from the partial sequence of the gene encoding canine CRH. The CRH gene was amplified from genomic DNA obtained from white blood cells by a polymerase chain reaction and subsequently sequenced using the dideoxy method. The likely structure of canine CRH is: SEEPPISLDLTFHLLREVLEMARAEQLAQQAHSNRKLMEII-NH2, which is identical to the structure of human, rat and equine CRH. PEPSCAN analysis of 3 different CRH antisera predicted an antiserum raised against a conjugate of human CRH and CNBr -activated thyroglobulin to be the antiserum of choice for the measurement of CRH in the dog. Preliminary data confirmed the existence of the highest cross-reactivity of a canine hypothalamus extract, known to have a high content of CRH, with antisera directed against human, rat CRH. As a result of the present study immunological tools for CRH estimations are characterized. Also, a homologous DNA probe for in situ hybridizations has become available for further investigations.

  14. The constant region affects antigen binding of antibodies to DNA by altering secondary structure.

    PubMed

    Xia, Yumin; Janda, Alena; Eryilmaz, Ertan; Casadevall, Arturo; Putterman, Chaim

    2013-11-01

    We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype-switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens.

  15. Vortex-dominated flow with viscous core structure

    NASA Technical Reports Server (NTRS)

    Liu, C. H.; Krause, E.; Ting, L.

    1985-01-01

    Recent theoretical studies of vortex-dominated flows are reviewed with special emphasis on those for which the viscous core structures play an important role. The problems to be described are: The interaction and merging of two-dimensional vortices and of curved vortex filaments, the roll-up and decay of trailing far wakes, and the initiation of vortex breakdown. The analysis utilizes finite-difference solutions of the Navier-Stokes equations complemented by asymptotic expansion techniques.

  16. Tailoring the Acoustic Properties of Truss-Core Sandwich Structure

    NASA Astrophysics Data System (ADS)

    Lee, Richard

    Undesirable cabin noise has an adverse physiological effect on passengers and crews in an aircraft. In order to reduce the noise level, a passive approach using a truss-core sandwich (TCS) panel as a sound insulator is proposed. Design guidelines and analysis methodologies were developed in order to explore the vibro-acoustic characteristics of TCS structure. Its sound isolation properties can be thereby assessed. Theoretical analyses show that the transmission-loss and sound radiation properties of a TCS structure can be represented by the root-mean-square velocity of its surface, and a beam structure analysis is sufficient to reveal many of the important aspects of TCS panel design. Using finite element analysis, a sensitivity study was performed to create design guidelines for TCS structures. Transmission-loss experiments show that the analytical and numerical analyses correctly predict the trend of TCS structure's vibro-acoustic performance.

  17. The aesthetic post and core: unifying radicular form and structure.

    PubMed

    Gluskin, Alan H; Ahmed, Irfan; Herrero, Dale B

    2002-05-01

    Use of a post system for the rehabilitation of endodontically treated teeth requires traditional planning for the function of the restoration as well as a structural and aesthetic strategy for novel technologies in ceramic and composite dentistry. Contemporary material options have greatly expanded the clinician's ability to rehabilitate the coronoradicular complex. Transilluminating posts, bondable fabrics, and high-technology ceramics create exciting possibilities in post and core design. The use of bondable materials allows the practitioner to unify the structure and morphology of root systems to provide creative solutions to challenges heretofore unmet.

  18. The "missing" typical Rhizobium leguminosarum O antigen is attached to a fatty acylated glycerol in R. leguminosarum bv. trifolii 4S, a strain that also lacks the usual tetrasaccharide "core" component.

    PubMed

    Cedergren, R A; Wang, Y; Hollingsworth, R I

    1996-09-01

    Rhizobium leguminosarum bv. trifolii 4S has a lipopolysaccharide O antigen that lacks galactose and many of the typical glycosyl components found in related strains. Here, we show that it also lacks the typical core tetrasaccharide but synthesizes an alternative glycolipid that contains galactose and the typical O-antigen glycosyl components, suggesting that in this strain, the O antigen is transferred to an alternative lipid acceptor.

  19. Stapled HIV-1 Peptides Recapitulate Antigenic Structures and Engage Broadly Neutralizing Antibodies

    PubMed Central

    Bird, Gregory H.; Irimia, Adriana; Ofek, Gilad; Kwong, Peter D.; Wilson, Ian A.; Walensky, Loren D.

    2014-01-01

    Hydrocarbon stapling can restore bioactive, α-helical structure to natural peptides, yielding research tools and prototype therapeutics to dissect and target protein interactions. Here, we explore the capacity of peptide stapling to generate high fidelity, protease-resistant mimics of antigenic structures for vaccine development. HIV-1 has been refractory to vaccine technologies thus far, although select human antibodies can broadly neutralize HIV-1 by targeting sequences of the gp41 juxtamembrane fusion apparatus. To develop candidate HIV-1 immunogens, we generated and characterized stabilized α-helices of the membrane proximal external region (SAH-MPER) of gp41. SAH-MPER peptides were remarkably protease-resistant and bound to the broadly neutralizing 4E10 and 10E8 antibodies with high affinity, recapitulating the structure of the MPER epitope when differentially engaged by the two anti-HIV Fabs. Thus, stapled peptides may provide a new opportunity to develop chemically-stabilized antigens for vaccination. PMID:25420104

  20. Stapled HIV-1 peptides recapitulate antigenic structures and engage broadly neutralizing antibodies.

    PubMed

    Bird, Gregory H; Irimia, Adriana; Ofek, Gilad; Kwong, Peter D; Wilson, Ian A; Walensky, Loren D

    2014-12-01

    Hydrocarbon stapling can restore bioactive α-helical structure to natural peptides, yielding research tools and prototype therapeutics to dissect and target protein interactions. Here we explore the capacity of peptide stapling to generate high-fidelity, protease-resistant mimics of antigenic structures for vaccine development. HIV-1 has been refractory to vaccine technologies thus far, although select human antibodies can broadly neutralize HIV-1 by targeting sequences of the gp41 juxtamembrane fusion apparatus. To develop candidate HIV-1 immunogens, we generated and characterized stabilized α-helices of the membrane-proximal external region (SAH-MPER) of gp41. SAH-MPER peptides were remarkably protease resistant and bound to the broadly neutralizing 4E10 and 10E8 antibodies with high affinity, recapitulating the structure of the MPER epitope when differentially engaged by the two anti-HIV Fabs. Thus, stapled peptides may provide a new opportunity to develop chemically stabilized antigens for vaccination.

  1. Structure of the transporter associated with antigen processing trapped by herpes simplex virus.

    PubMed

    Oldham, Michael L; Grigorieff, Nikolaus; Chen, Jue

    2016-12-09

    The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved strategies to inhibit TAP so that they may go undetected by the immune system. The herpes simplex virus for example evades immune surveillance by blocking peptide transport with a small viral protein ICP47. In this study, we determined the structure of human TAP bound to ICP47 by electron cryo-microscopy (cryo-EM) to 4.0 Å. The structure shows that ICP47 traps TAP in an inactive conformation distinct from the normal transport cycle. The specificity and potency of ICP47 inhibition result from contacts between the tip of the helical hairpin and the apex of the transmembrane cavity. This work provides a clear molecular description of immune evasion by a persistent virus. It also establishes the molecular structure of TAP to facilitate mechanistic studies of the antigen presentation process.

  2. Model Building of Antibody-Antigen Complex Structures Using GBSA Scores.

    PubMed

    Shimba, Noriko; Kamiya, Narutoshi; Nakamura, Haruki

    2016-10-24

    Structure prediction of antibody-antigen complexes, which involves molecular docking to generate decoys that are ranked using a scoring function, is an important approach in the design of antibody drugs and biosensors. However, it is not easy to evaluate the stability of protein-protein complexes, using a single scoring function. Here, we developed a prediction method of antibody-antigen complex structures using the docking engine "surFit" and a scoring function (GBSA score) that combined the generalized Born (GB) energy and the hydration energy based on the solvent-accessible surface area (SA). We chose 95 antibody-antigen structural datasets for self-docking and generated many decoy structures using the surFit program. The GBSA scores were computed for all of the decoys, and the area under the curve (AUC) of the GBSA scores yielded a higher value (0.972) than the values obtained by the original surFit scores (0.873) and the ZRANK scores (0.953). To improve the accuracy of prediction, molecular dynamics (MD) simulations were performed for several decoy structures that had good GBSA scores. Consequently, average GBSA scores from MD trajectories can reduce the number of non-native decoys that have GBSA scores competitive with the near-native ones.

  3. Contrasting Population Structures of the Genes Encoding Ten Leading Vaccine-Candidate Antigens of the Human Malaria Parasite, Plasmodium falciparum

    PubMed Central

    Barry, Alyssa E.; Schultz, Lee; Buckee, Caroline O.; Reeder, John C.

    2009-01-01

    The extensive diversity of Plasmodium falciparum antigens is a major obstacle to a broadly effective malaria vaccine but population genetics has rarely been used to guide vaccine design. We have completed a meta-population genetic analysis of the genes encoding ten leading P. falciparum vaccine antigens, including the pre-erythrocytic antigens csp, trap, lsa1 and glurp; the merozoite antigens eba175, ama1, msp's 1, 3 and 4, and the gametocyte antigen pfs48/45. A total of 4553 antigen sequences were assembled from published data and we estimated the range and distribution of diversity worldwide using traditional population genetics, Bayesian clustering and network analysis. Although a large number of distinct haplotypes were identified for each antigen, they were organized into a limited number of discrete subgroups. While the non-merozoite antigens showed geographically variable levels of diversity and geographic restriction of specific subgroups, the merozoite antigens had high levels of diversity globally, and a worldwide distribution of each subgroup. This shows that the diversity of the non-merozoite antigens is organized by physical or other location-specific barriers to gene flow and that of merozoite antigens by features intrinsic to all populations, one important possibility being the immune response of the human host. We also show that current malaria vaccine formulations are based upon low prevalence haplotypes from a single subgroup and thus may represent only a small proportion of the global parasite population. This study demonstrates significant contrasts in the population structure of P. falciparum vaccine candidates that are consistent with the merozoite antigens being under stronger balancing selection than non-merozoite antigens and suggesting that unique approaches to vaccine design will be required. The results of this study also provide a realistic framework for the diversity of these antigens to be incorporated into the design of next

  4. Ion etching of human adenovirus 2: structure of the core

    SciTech Connect

    Newcomb, W.W.; Boring, J.W.; Brown, J.C.

    1984-07-01

    The surface of human adenovirus 2 was etched by irradiating intact virions with low-energy (1-keV) Ar/sup +/ ions in a Technics Hummer V sputter coater. Viral structures exposed by the etching process were shadowed and then examined in the electron microscope. Periods of etching that were sufficient to reduce the viral diameter by 20 to 30 nm revealed distinct substructural elements in the virion core. Cores were found to consist of a cluster of 12 large, uniformly sized spheres which abutted one another in the intact virion. The spheres, for which we suggest the name adenosomes, had a diameter of 23.0 +/- 2.3 nm, and they were related to each other by two-, three-, and fivefold axes of rotational symmetry. The results support the view, originally suggested by Brown et al. that the adenovirus 2 core is composed of 12 large spheres packed tightly together in such a way that each is directed toward the vertex of an icosahedron. Such a structure, constructed of 23.0-nm-diameter spheres, would have an outside diameter (vertex-to-vertex distance) of 67.0 nm and a face-to-face distance of 58.2 nm. It could be accommodated inside the icosahedral adenovirus capsid if each large sphere were located beneath a capsid vertex.

  5. FRESH INSIGHTS ON THE STRUCTURE OF THE SOLAR CORE

    SciTech Connect

    Basu, Sarbani; Chaplin, William J.; Elsworth, Yvonne; New, Roger; Serenelli, Aldo M. E-mail: w.j.chaplin@bham.ac.uk E-mail: r.new@shu.ac.uk

    2009-07-10

    We present new results on the structure of the solar core, obtained with new sets of frequencies of solar low-degree p modes obtained from the BiSON network. We find that different methods used in extracting the different sets of frequencies cause shifts in frequencies, but the shifts are not large enough to affect solar structure results. We find that the BiSON frequencies show that the solar sound speed in the core is slightly larger than that inferred from data from Michelson Doppler Imager low-degree modes, and the uncertainties on the inversion results are smaller. Density results also change by a larger amount, and we find that solar models now tend to show smaller differences in density compared to the Sun. The result is seen at all radii, a result of the fact that conservation of mass implies that density differences in one region have to cancel out density differences in others, since our models are constructed to have the same mass as the Sun. The uncertainties on the density results are much smaller too. We attribute the change in results to having more, and lower frequency, low-degree mode frequencies available. These modes provide greater sensitivity to conditions in the core.

  6. Galaxy Structure: Core Radii, and Central Mass Deficits

    NASA Astrophysics Data System (ADS)

    Graham, A. W.; Trujillo, I.; Erwin, P.

    2004-05-01

    We investigate the nuclear and global structure of elliptical galaxies, and the apparent disparity between the Nuker and Sérsic light-profile models. We show that the so-called ``power-law" galaxies in fact have Sérsic r1/n profiles over their entire observed radial range. Consequently, only three (Sérsic-profile) parameters are required to simultaneously describe both the inner (HST-resolved) and outer profiles of low-luminosity (M > -20.5 B-mag) elliptical galaxies. We also find that ``core galaxies" have Sérsic profiles with a (partially evacuated) single power-law core. We have developed a modified (5-parameter) Sérsic profile with a power-law core to model the complete radial extent of luminous galaxies with cores. In addition to quantifying the global stellar distribution in these systems, we have derived new estimates of their core radii and other central properties. Comparison of the central stellar deficits with the galaxies' black hole masses suggests that the number of (dissipationless) major mergers that have produced luminous elliptical galaxies is around 1-2, rather than 8-10, which agrees with theory and implies that the galactic merger history of the Universe is roughly an order of magnitude less violent than previous observational analyses had suggested. Support for proposal number HST-AR-09927.01-A was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555.

  7. Geochemical Comparison of Four Cores from the Manson Impact Structure

    NASA Technical Reports Server (NTRS)

    Korotev, Randy L.; Rockow, Kaylynn M.; Jolliff, Bradley L.; Haskin, Larry A.; McCarville, Peter; Crossey, Laura J.

    1996-01-01

    Concentrations of 33 elements were determined in relatively unaltered, matrix-rich samples of impact breccia at approximately 3-m-depth intervals in the M-1 core from the Manson impact structure, Iowa. In addition, 46 matrix-rich samples from visibly altered regions of the M-7, M-8, and M-10 cores were studied, along with 42 small clasts from all four cores. Major element compositions were determined for a subset of impact breccias from the M-1 core, including matrix-rich impact-melt breccia. Major- and trace-element compositions were also determined for a suite of likely target rocks. In the M-1 core, different breccia units identified from lithologic examination of cores are compositionally distinct. There is a sharp compositional discontinuity at the boundary between the Keweenawan-shale-clast breccia and the underlying unit of impact-melt breccia (IMB) for most elements, suggesting minimal physical mixing between the two units during emplacement. Samples from the 40-m-thick IMB (M-1) are all similar to each other in composition, although there are slight increases in concentration with depth for those elements that have high concentrations in the underlying fragmental-matrix suevite breccia (SB) (e.g., Na, Ca, Fe, Sc), presumably as a result of greater clast proportions at the bottom margin of the unit of impact-melt breccia. The high degree of compositional similarity we observe in the impact-melt breccias supports the interpretation that the matrix of this unit represents impact melt. That our analyses show such compositional similarity results in part from our technique for sampling these breccias: for each sample we analyzed a few small fragments (total mass: approximately 200 mg) selected to be relatively free of large clasts and visible signs of alteration instead of subsamples of powders prepared from a large mass of breccia. The mean composition of the matrix-rich part of impact-melt breccia from the M-1 core can be modeled as a mixture of approximately

  8. Core-sheath differentially biodegradable nanofiber structures for tissue engineering

    NASA Astrophysics Data System (ADS)

    Moghe, Ajit Keshav

    In recent years, it has been shown that the nanofiber structures prepared using electrospinning can serve as near ideal substrates for engineering tissues. Various biodegradable polymers of natural and synthetic origins have been used to construct the nanofiber scaffolds. The use of natural polymers is important in that they contain specific cell recognition sites that are capable of binding cells. Synthetic biodegradable polymers, on the other hand, can provide the necessary mechanical properties and their degradation rate can be controlled positively. When used alone, however, neither can provide an ideal structure for long-term development of tissues. This is because the regenerated natural polymers, although greatly biocompatible, are weak and degrade rapidly and uncontrollably, while the synthetic polymers, although mechanically more stable, are not as biocompatible. The focus of the current investigation was, therefore, to combine natural and synthetic polymers and to produce materials that have novel hybrid properties at the nano level. An optimum structure proposed was a differentially biodegradable bicomponent nanofiber with the sheath of natural and the core of synthetic polymers. Co-axial electrospinning was used to prepare the proposed core-sheath nanofibers. A major objective of the current research was to develop and optimize the technology to produce uniform bicomponent nanofibers of predictable morphologies by understanding the effects of various material and process variables such as solution concentration, solvent type, solution flow rate, and applied voltage. Two natural polymers (collagen and gelatin) and one synthetic biodegradable polymer (PCL) were used to develop the proposed structures. The factors that affected the bicomponent fiber formation were: interfacial tension between sheath and core solutions, volatility of the solvent, and applied voltage. By minimizing the interfacial tension, selecting the solvents with low vapor pressure, and

  9. Inhibitory effects of thymus-independent type 2 antigens on MHC class II-restricted antigen presentation: comparative analysis of carbohydrate structures and the antigen presenting cell.

    PubMed

    González-Fernández, M; Carrasco-Marín, E; Alvarez-Domínguez, C; Outschoorn, I M; Leyva-Cobián, F

    1997-02-25

    The role of thymus-independent type 2 (TI-2) antigens (polysaccharides) on the MHC-II-restricted processing of protein antigens was studied in vitro. In general, antigen presentation is inhibited when both peritoneal and splenic macrophages (M phi) as well as Küpffer cells (KC) are preincubated with acidic polysaccharides or branched dextrans. However, the inhibitory effect of neutral polysaccharides was minimal when KC were used as antigen presenting cells (APC). Morphological evaluation of the uptake of fluoresceinated polysaccharides clearly correlates with this selective and differential interference. Polysaccharides do not block MHC-I-restricted antigen presentation. Some chemical characteristics shared by different saccharides seem to be specially related to their potential inhibitory abilities: (i) those where two anomeric carbon atoms of two interlinked sugars and (ii) those containing several sulfate groups per disaccharide repeating unit. No polysaccharide being inhibitory in M phi abrogated antigen processing in other APC: lipopolysaccharide-activated B cells, B lymphoma cells, or dendritic cells (DC). Using radiolabeled polysaccharides it was observed that DC and B cells incorporated less radioactivity as a function of time than M phi. Morphological evaluation of these different APC incubated for extended periods of time with inhibitory concentrations of polysaccharides revealed intense cytoplasmic vacuolization in M phi but not in B cells or DC. The large majority of M phi lysosomes containing polysaccharides fail to fuse with incoming endocytic vesicles and delivery of fluid-phase tracers was reduced, suggesting that indigestible carbohydrates reduced the fusion of these loaded lysosomes with endosomes containing recently internalized tracers. It is suggested that the main causes of this antigen presentation blockade are (i) the chemical characteristics of certain carbohydrates and whether the specific enzymatic machinery for their intracellular

  10. Atypical Antigen Recognition Mode of a Shark Immunoglobulin New Antigen Receptor (IgNAR) Variable Domain Characterized by Humanization and Structural Analysis

    PubMed Central

    Kovalenko, Oleg V.; Olland, Andrea; Piché-Nicholas, Nicole; Godbole, Adarsh; King, Daniel; Svenson, Kristine; Calabro, Valerie; Müller, Mischa R.; Barelle, Caroline J.; Somers, William; Gill, Davinder S.; Mosyak, Lidia; Tchistiakova, Lioudmila

    2013-01-01

    The immunoglobulin new antigen receptors (IgNARs) are a class of Ig-like molecules of the shark immune system that exist as heavy chain-only homodimers and bind antigens by their single domain variable regions (V-NARs). Following shark immunization and/or in vitro selection, V-NARs can be generated as soluble, stable, and specific high affinity monomeric binding proteins of ∼12 kDa. We have previously isolated a V-NAR from an immunized spiny dogfish shark, named E06, that binds specifically and with high affinity to human, mouse, and rat serum albumins. Humanization of E06 was carried out by converting over 60% of non-complementarity-determining region residues to those of a human germ line Vκ1 sequence, DPK9. The resulting huE06 molecules have largely retained the specificity and affinity of antigen binding of the parental V-NAR. Crystal structures of the shark E06 and its humanized variant (huE06 v1.1) in complex with human serum albumin (HSA) were determined at 3- and 2.3-Å resolution, respectively. The huE06 v1.1 molecule retained all but one amino acid residues involved in the binding site for HSA. Structural analysis of these V-NARs has revealed an unusual variable domain-antigen interaction. E06 interacts with HSA in an atypical mode that utilizes extensive framework contacts in addition to complementarity-determining regions that has not been seen previously in V-NARs. On the basis of the structure, the roles of various elements of the molecule are described with respect to antigen binding and V-NAR stability. This information broadens the general understanding of antigen recognition and provides a framework for further design and humanization of shark IgNARs. PMID:23632026

  11. Atypical antigen recognition mode of a shark immunoglobulin new antigen receptor (IgNAR) variable domain characterized by humanization and structural analysis.

    PubMed

    Kovalenko, Oleg V; Olland, Andrea; Piché-Nicholas, Nicole; Godbole, Adarsh; King, Daniel; Svenson, Kristine; Calabro, Valerie; Müller, Mischa R; Barelle, Caroline J; Somers, William; Gill, Davinder S; Mosyak, Lidia; Tchistiakova, Lioudmila

    2013-06-14

    The immunoglobulin new antigen receptors (IgNARs) are a class of Ig-like molecules of the shark immune system that exist as heavy chain-only homodimers and bind antigens by their single domain variable regions (V-NARs). Following shark immunization and/or in vitro selection, V-NARs can be generated as soluble, stable, and specific high affinity monomeric binding proteins of ∼12 kDa. We have previously isolated a V-NAR from an immunized spiny dogfish shark, named E06, that binds specifically and with high affinity to human, mouse, and rat serum albumins. Humanization of E06 was carried out by converting over 60% of non-complementarity-determining region residues to those of a human germ line Vκ1 sequence, DPK9. The resulting huE06 molecules have largely retained the specificity and affinity of antigen binding of the parental V-NAR. Crystal structures of the shark E06 and its humanized variant (huE06 v1.1) in complex with human serum albumin (HSA) were determined at 3- and 2.3-Å resolution, respectively. The huE06 v1.1 molecule retained all but one amino acid residues involved in the binding site for HSA. Structural analysis of these V-NARs has revealed an unusual variable domain-antigen interaction. E06 interacts with HSA in an atypical mode that utilizes extensive framework contacts in addition to complementarity-determining regions that has not been seen previously in V-NARs. On the basis of the structure, the roles of various elements of the molecule are described with respect to antigen binding and V-NAR stability. This information broadens the general understanding of antigen recognition and provides a framework for further design and humanization of shark IgNARs.

  12. cDNA cloning and primary structure of a white-face hornet venom allergen, antigen 5.

    PubMed

    Fang, K S; Vitale, M; Fehlner, P; King, T P

    1988-02-01

    A major allergen of white-face hornet (Dolichovespula maculata) venom is antigen 5 (also designated Dol m V). We have determined the primary structures of two forms of this protein by cDNA and protein sequencings. These two forms with 204 and 205 amino acid residues differ in 23% of their sequences but they are antigenically similar. Both forms have sequence similarity with a pathogenesis-related protein of tobacco leaf. In a 130-residue overlap of these proteins, 35-39 residues were identical. Hornet antigen 5 cDNAs were isolated from an expression library in lambda gt11 phage using antibody probes. Several of the cDNAs were not full length, but the fusion fragments expressed were immunoreactive. These results suggest that antigenic determinants of the sequential type are distributed throughout the entire molecule of antigen 5. After subcloning, antigen 5 was also expressed in pKK233-2 plasmid.

  13. Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz

    SciTech Connect

    Bundle, D.R.; Cherwonogrodzky, J.W.; Perry, M.B.

    1987-12-29

    The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-..cap alpha..-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers of the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz /sup 1/H and 125-MHz /sup 13/C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent ..beta..-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-lined 4,6-dideoxy-4-formamido-..cap alpha..-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-..cap alpha..-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants.

  14. Ion Structure Near a Core-Shell Dielectric Nanoparticle

    NASA Astrophysics Data System (ADS)

    Ma, Manman; Gan, Zecheng; Xu, Zhenli

    2017-02-01

    A generalized image charge formulation is proposed for the Green's function of a core-shell dielectric nanoparticle for which theoretical and simulation investigations are rarely reported due to the difficulty of resolving the dielectric heterogeneity. Based on the formulation, an efficient and accurate algorithm is developed for calculating electrostatic polarization charges of mobile ions, allowing us to study related physical systems using the Monte Carlo algorithm. The computer simulations show that a fine-tuning of the shell thickness or the ion-interface correlation strength can greatly alter electric double-layer structures and capacitances, owing to the complicated interplay between dielectric boundary effects and ion-interface correlations.

  15. Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz.

    PubMed

    Bundle, D R; Cherwonogrodzky, J W; Perry, M B

    1987-12-29

    The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-alpha-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers of the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz 1H and 125-MHz 13C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent beta-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-linked 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants. Structural and serological considerations in conjuction with the sodium dodecyl sulfate banding pattern of Brucella A LPS suggest that its biosynthesis differs appreciably from that of the M antigen, which appears to be

  16. Fabrication method for cores of structural sandwich materials including star shaped core cells

    DOEpatents

    Christensen, Richard M.

    1997-01-01

    A method for fabricating structural sandwich materials having a core pattern which utilizes star and non-star shaped cells. The sheets of material are bonded together or a single folded sheet is used, and bonded or welded at specific locations, into a flat configuration, and are then mechanically pulled or expanded normal to the plane of the sheets which expand to form the cells. This method can be utilized to fabricate other geometric cell arrangements than the star/non-star shaped cells. Four sheets of material (either a pair of bonded sheets or a single folded sheet) are bonded so as to define an area therebetween, which forms the star shaped cell when expanded.

  17. Fabrication method for cores of structural sandwich materials including star shaped core cells

    DOEpatents

    Christensen, R.M.

    1997-07-15

    A method for fabricating structural sandwich materials having a core pattern which utilizes star and non-star shaped cells is disclosed. The sheets of material are bonded together or a single folded sheet is used, and bonded or welded at specific locations, into a flat configuration, and are then mechanically pulled or expanded normal to the plane of the sheets which expand to form the cells. This method can be utilized to fabricate other geometric cell arrangements than the star/non-star shaped cells. Four sheets of material (either a pair of bonded sheets or a single folded sheet) are bonded so as to define an area therebetween, which forms the star shaped cell when expanded. 3 figs.

  18. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

    PubMed Central

    DeKosky, Brandon J.; Lungu, Oana I.; Park, Daechan; Johnson, Erik L.; Charab, Wissam; Chrysostomou, Constantine; Kuroda, Daisuke; Ellington, Andrew D.; Ippolito, Gregory C.; Gray, Jeffrey J.; Georgiou, George

    2016-01-01

    Elucidating how antigen exposure and selection shape the human antibody repertoire is fundamental to our understanding of B-cell immunity. We sequenced the paired heavy- and light-chain variable regions (VH and VL, respectively) from large populations of single B cells combined with computational modeling of antibody structures to evaluate sequence and structural features of human antibody repertoires at unprecedented depth. Analysis of a dataset comprising 55,000 antibody clusters from CD19+CD20+CD27− IgM-naive B cells, >120,000 antibody clusters from CD19+CD20+CD27+ antigen–experienced B cells, and >2,000 RosettaAntibody-predicted structural models across three healthy donors led to a number of key findings: (i) VH and VL gene sequences pair in a combinatorial fashion without detectable pairing restrictions at the population level; (ii) certain VH:VL gene pairs were significantly enriched or depleted in the antigen-experienced repertoire relative to the naive repertoire; (iii) antigen selection increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-chain third complementarity-determining region (CDR-H3) antibodies in the antigen-experienced repertoire showed signs of convergent paired light-chain genetic signatures, including shared light-chain third complementarity-determining region (CDR-L3) amino acid sequences and/or Vκ,λ–Jκ,λ genes. The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease. PMID:27114511

  19. Hepatitis C Virus E2 Envelope Glycoprotein Core Structure

    SciTech Connect

    Kong, Leopold; Giang, Erick; Nieusma, Travis; Kadam, Rameshwar U.; Cogburn, Kristin E.; Hua, Yuanzi; Dai, Xiaoping; Stanfield, Robyn L.; Burton, Dennis R.; Ward, Andrew B.; Wilson, Ian A.; Law, Mansun

    2014-08-26

    Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold β sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structures differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design.

  20. Predicting the antigenic structure of the pandemic (H1N1) 2009 influenza virus hemagglutinin.

    PubMed

    Igarashi, Manabu; Ito, Kimihito; Yoshida, Reiko; Tomabechi, Daisuke; Kida, Hiroshi; Takada, Ayato

    2010-01-01

    The pandemic influenza virus (2009 H1N1) was recently introduced into the human population. The hemagglutinin (HA) gene of 2009 H1N1 is derived from "classical swine H1N1" virus, which likely shares a common ancestor with the human H1N1 virus that caused the pandemic in 1918, whose descendant viruses are still circulating in the human population with highly altered antigenicity of HA. However, information on the structural basis to compare the HA antigenicity among 2009 H1N1, the 1918 pandemic, and seasonal human H1N1 viruses has been lacking. By homology modeling of the HA structure, here we show that HAs of 2009 H1N1 and the 1918 pandemic virus share a significant number of amino acid residues in known antigenic sites, suggesting the existence of common epitopes for neutralizing antibodies cross-reactive to both HAs. It was noted that the early human H1N1 viruses isolated in the 1930s-1940s still harbored some of the original epitopes that are also found in 2009 H1N1. Interestingly, while 2009 H1N1 HA lacks the multiple N-glycosylations that have been found to be associated with an antigenic change of the human H1N1 virus during the early epidemic of this virus, 2009 H1N1 HA still retains unique three-codon motifs, some of which became N-glycosylation sites via a single nucleotide mutation in the human H1N1 virus. We thus hypothesize that the 2009 H1N1 HA antigenic sites involving the conserved amino acids will soon be targeted by antibody-mediated selection pressure in humans. Indeed, amino acid substitutions predicted here are occurring in the recent 2009 H1N1 variants. The present study suggests that antibodies elicited by natural infection with the 1918 pandemic or its early descendant viruses play a role in specific immunity against 2009 H1N1, and provides an insight into future likely antigenic changes in the evolutionary process of 2009 H1N1 in the human population.

  1. Predicting the Antigenic Structure of the Pandemic (H1N1) 2009 Influenza Virus Hemagglutinin

    PubMed Central

    Igarashi, Manabu; Ito, Kimihito; Yoshida, Reiko; Tomabechi, Daisuke; Kida, Hiroshi; Takada, Ayato

    2010-01-01

    The pandemic influenza virus (2009 H1N1) was recently introduced into the human population. The hemagglutinin (HA) gene of 2009 H1N1 is derived from “classical swine H1N1” virus, which likely shares a common ancestor with the human H1N1 virus that caused the pandemic in 1918, whose descendant viruses are still circulating in the human population with highly altered antigenicity of HA. However, information on the structural basis to compare the HA antigenicity among 2009 H1N1, the 1918 pandemic, and seasonal human H1N1 viruses has been lacking. By homology modeling of the HA structure, here we show that HAs of 2009 H1N1 and the 1918 pandemic virus share a significant number of amino acid residues in known antigenic sites, suggesting the existence of common epitopes for neutralizing antibodies cross-reactive to both HAs. It was noted that the early human H1N1 viruses isolated in the 1930s–1940s still harbored some of the original epitopes that are also found in 2009 H1N1. Interestingly, while 2009 H1N1 HA lacks the multiple N-glycosylations that have been found to be associated with an antigenic change of the human H1N1 virus during the early epidemic of this virus, 2009 H1N1 HA still retains unique three-codon motifs, some of which became N-glycosylation sites via a single nucleotide mutation in the human H1N1 virus. We thus hypothesize that the 2009 H1N1 HA antigenic sites involving the conserved amino acids will soon be targeted by antibody-mediated selection pressure in humans. Indeed, amino acid substitutions predicted here are occurring in the recent 2009 H1N1 variants. The present study suggests that antibodies elicited by natural infection with the 1918 pandemic or its early descendant viruses play a role in specific immunity against 2009 H1N1, and provides an insight into future likely antigenic changes in the evolutionary process of 2009 H1N1 in the human population. PMID:20049332

  2. Antigenic Structure of Outer Membrane Protein E of Moraxella catarrhalis and Construction and Characterization of Mutants

    PubMed Central

    Murphy, Timothy F.; Brauer, Aimee L.; Yuskiw, Norine; Hiltke, Thomas J.

    2000-01-01

    Outer membrane protein E (OMP E) is a 50-kDa protein of Moraxella catarrhalis which possesses several characteristics indicating that the protein will be an effective vaccine antigen. To study the antigenic structure of OMP E, eight monoclonal antibodies were developed and characterized. Three of the antibodies recognized epitopes which are present on the bacterial surface. Fusion peptides corresponding to overlapping regions of OMP E were constructed, and immunoblot assays were performed to localize the areas of the molecule bound by the monoclonal antibodies. These studies identified a surface-exposed epitope in the region of amino acids 80 through 180. To further study the protein, two mutants which lack OMP E were constructed. In bactericidal assays, the mutants were more readily killed by normal human serum compared to the isogenic parent strains. These results indicate that OMP E is involved in the expression of serum resistance of M. catarrhalis. PMID:11035732

  3. Binding kinetics of an antibody against HIV p24 core protein measured with real-time biomolecular interaction analysis suggest a slow conformational change in antigen p24.

    PubMed

    Glaser, R W; Hausdorf, G

    1996-01-16

    The interaction between HIV core protein p24 and the murine monoclonal antibody CB-4/1 or its Fab fragment showed unusual kinetics. Recombinant p24 was immobilised in a hydrophilic carboxymethyldextran matrix. At high concentration of CB-4/1 Fab the association of the antigen-antibody complex proceeds in two phases, while dissociation is mono-exponential. The antigen has a 'memory', i.e. shortly after dissociation of Fab-antigen complex the fast association phase is enhanced. Biphasic association was also found in solution. Experiments suggest a reversible change of binding properties in the epitope region with an overall time constant of about 100 s at room temperature. Intermediate steps with faster time constants must be involved. Slow conformational changes of p24 seem to be the most probable explanation. A simple model that provides a quantitative description of this process could not be found. Real-time analysis of antibody binding by surface plasmon resonance is a powerful method for studying such changes in the time domain of a few seconds to a few minutes.

  4. Sandwich Composite, Syntactic Foam Core Based, Application for Space Structures

    NASA Technical Reports Server (NTRS)

    Hodge, Andrew J.; Kaul, Raj K.; McMahon, William M.; Reinarts, Thomas

    2000-01-01

    The current Solid Rocket Booster (SRB) launch vehicle has several metal based components that require a Thermal Protective System (TPS) be applied to the exterior surface to ensure its structural integrity and to protect the interior hardware from aerodynamic heating. TPS materials have distinct disadvantages associated with their use. One disadvantage to the application of TPS is that it can act as a debris source to the Space Shuttle Orbiter during flight and it also adds weight to the system without directly contributing any structural strength. One of the specific areas examined under this program was to replace a metal/TPS system with polymer based composites. A polymer matrix based sandwich composite was developed which had both structural and insulative properties to meet the high aerodynamic structural and heating load survival requirements. The SRB Nose Cap was selected as a candidate for this application. The sandwich system being qualified for this application is a carbon/epoxy outer and inner skin with a high strength-low thermal conductivity syntactic foam core.

  5. Thermally induced fracture for core-veneered dental ceramic structures.

    PubMed

    Zhang, Zhongpu; Guazzato, Massimiliano; Sornsuwan, Tanapon; Scherrer, Susanne S; Rungsiyakull, Chaiy; Li, Wei; Swain, Michael V; Li, Qing

    2013-09-01

    Effective and reliable clinical uses of dental ceramics necessitate an insightful analysis of the fracture behaviour under critical conditions. To better understand failure characteristics of porcelain veneered to zirconia core ceramic structures, thermally induced cracking during the cooling phase of fabrication is studied here by using the extended finite element method (XFEM). In this study, a transient thermal analysis of cooling is conducted first to determine the temperature distributions. The time-dependent temperature field is then imported to the XFEM model for viscoelastic thermomechanical analysis, which predicts thermally induced damage and cracking at different time steps. Temperature-dependent material properties are used in both transient thermal and thermomechanical analyses. Three typical ceramic structures are considered in this paper, namely bi-layered spheres, squat cylinders and dental crowns with thickness ratios of either 1:2 or 1:1. The XFEM fracture patterns exhibit good agreement with clinical observation and the in vitro experimental results obtained from scanning electron microscopy characterization. The study reveals that fast cooling can lead to thermal fracture of these different bi-layered ceramic structures, and cooling rate (in terms of heat transfer coefficient) plays a critical role in crack initiation and propagation. By exploring different cooling rates, the heat transfer coefficient thresholds of fracture are determined for different structures, which are of clear clinical implication.

  6. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism

    PubMed Central

    Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

    2015-01-01

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOTTM). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen. PMID:26563565

  7. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.

    PubMed

    Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

    2015-11-13

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.

  8. Microfluidic immunosensor with integrated liquid core waveguides for sensitive Mie scattering detection of avian influenza antigens in a real biological matrix.

    PubMed

    Heinze, Brian C; Gamboa, Jessica R; Kim, Keesung; Song, Jae-Young; Yoon, Jeong-Yeol

    2010-11-01

    This work presents the use of integrated, liquid core, optical waveguides for measuring immunoagglutination-induced light scattering in a microfluidic device, towards rapid and sensitive detection of avian influenza (AI) viral antigens in a real biological matrix (chicken feces). Mie scattering simulations were performed and tested to optimize the scattering efficiency of the device through proper scatter angle waveguide geometry. The detection limit is demonstrated to be 1 pg mL(-1) in both clean buffer and real biological matrix. This low detection limit is made possible through on-chip diffusional mixing of AI target antigens and high acid content microparticle assay reagents, coupled with real-time monitoring of immunoagglutination-induced forward Mie scattering via high refractive index liquid core optical waveguides in close proximity (100 μm) to the sample chamber. The detection time for the assay is <2 min. This device could easily be modified to detect trace levels of any biological molecules that antibodies are available for, moving towards a robust platform for point-of-care disease diagnostics.

  9. Structure and expression of a mouse major histocompatibility antigen gene, H-2Ld.

    PubMed Central

    Evans, G A; Margulies, D H; Camerini-Otero, R D; Ozato, K; Seidman, J G

    1982-01-01

    A genomic clone encoding H-2Ld, a mouse major transplantation antigen, has been identified and the structure of the H-2Ld gene has been partially determined. We isolated 35 genomic clones from a BALB/c (H-2d) genomic library by hybridization to mouse or human probes. One of these clones encodes H-2Ld as determined by two criteria. First, the gene encodes a protein that is identical at the 76 known amino acid positions for H-2Ld. Second, when introduced into L cells by DNA-mediated gene transfer, a new H-2 antigen is expressed that is recognized by anti-H-2Ld monoclonal antibodies. The sequence of the H-2Ld protein predicted by the DNA sequences shows more than 80% homology to known H-2 antigens. H-2L-like sequences are found in mutant H-2Kb molecules, suggesting that gene conversion or reciprocal recombination may play a role in the development of H-2 polymorphism. PMID:6952248

  10. Descriptions and preliminary interpretations of cores recovered from the Manson Impact Structure (Iowa)

    NASA Technical Reports Server (NTRS)

    Anderson, R. R.; Witzke, B. J.; Hartung, J. B.; Shoemaker, E. M.; Roddy, D. J.

    1993-01-01

    A core drilling program initiated by the Iowa Geological Survey Bureau and U.S. Geological Survey in 1991 and 1992 collected 12 cores totalling over 1200 m from the Manson Impact Structure, a probable K-T boundary structure located in north-central Iowa. Cores were recovered from each of the major structural terranes, with 2 cores (M-3 and M-4) from the Terrace Terrane, 4 cores (M-2, M-2A, M-6, and M-9) from the Crater Moat, and 6 cores (M-1, M-5, M-7, M-8, M-10, and M-11) from the Central Peak. These supplemented 2 central peak cores (1-A and 2-A) drilled in 1953. The cores penetrated five major impact lithologies: (1) sedimentary clast breccia; (2) impact ejecta; (3) central peak crystallite rocks; (4) crystalline clast breccia with sandy matrix; and (5) crystallite clast breccia with a melt matrix. Descriptions and preliminary interpretations of these cores are presented.

  11. Francisella tularensis Schu S4 lipopolysaccharide core sugar and O-antigen mutants are attenuated in a mouse model of tularemia.

    PubMed

    Rasmussen, Jed A; Post, Deborah M B; Gibson, Bradford W; Lindemann, Stephen R; Apicella, Michael A; Meyerholz, David K; Jones, Bradley D

    2014-04-01

    The virulence factors mediating Francisella pathogenesis are being investigated, with an emphasis on understanding how the organism evades innate immunity mechanisms. Francisella tularensis produces a lipopolysaccharide (LPS) that is essentially inert and a polysaccharide capsule that helps the organism to evade detection by components of innate immunity. Using an F. tularensis Schu S4 mutant library, we identified strains that are disrupted for capsule and O-antigen production. These serum-sensitive strains lack both capsule production and O-antigen laddering. Analysis of the predicted protein sequences for the disrupted genes (FTT1236 and FTT1238c) revealed similarity to those for waa (rfa) biosynthetic genes in other bacteria. Mass spectrometry further revealed that these proteins are involved in LPS core sugar biosynthesis and the ligation of O antigen to the LPS core sugars. The 50% lethal dose (LD50) values of these strains are increased 100- to 1,000-fold for mice. Histopathology revealed that the immune response to the F. tularensis mutant strains was significantly different from that observed with wild-type-infected mice. The lung tissue from mutant-infected mice had widespread necrotic debris, but the spleens lacked necrosis and displayed neutrophilia. In contrast, the lungs of wild-type-infected mice had nominal necrosis, but the spleens had widespread necrosis. These data indicate that murine death caused by wild-type strains occurs by a mechanism different from that by which the mutant strains kill mice. Mice immunized with these mutant strains displayed >10-fold protective effects against virulent type A F. tularensis challenge.

  12. Francisella tularensis Schu S4 Lipopolysaccharide Core Sugar and O-Antigen Mutants Are Attenuated in a Mouse Model of Tularemia

    PubMed Central

    Rasmussen, Jed A.; Post, Deborah M. B.; Gibson, Bradford W.; Lindemann, Stephen R.; Apicella, Michael A.; Meyerholz, David K.

    2014-01-01

    The virulence factors mediating Francisella pathogenesis are being investigated, with an emphasis on understanding how the organism evades innate immunity mechanisms. Francisella tularensis produces a lipopolysaccharide (LPS) that is essentially inert and a polysaccharide capsule that helps the organism to evade detection by components of innate immunity. Using an F. tularensis Schu S4 mutant library, we identified strains that are disrupted for capsule and O-antigen production. These serum-sensitive strains lack both capsule production and O-antigen laddering. Analysis of the predicted protein sequences for the disrupted genes (FTT1236 and FTT1238c) revealed similarity to those for waa (rfa) biosynthetic genes in other bacteria. Mass spectrometry further revealed that these proteins are involved in LPS core sugar biosynthesis and the ligation of O antigen to the LPS core sugars. The 50% lethal dose (LD50) values of these strains are increased 100- to 1,000-fold for mice. Histopathology revealed that the immune response to the F. tularensis mutant strains was significantly different from that observed with wild-type-infected mice. The lung tissue from mutant-infected mice had widespread necrotic debris, but the spleens lacked necrosis and displayed neutrophilia. In contrast, the lungs of wild-type-infected mice had nominal necrosis, but the spleens had widespread necrosis. These data indicate that murine death caused by wild-type strains occurs by a mechanism different from that by which the mutant strains kill mice. Mice immunized with these mutant strains displayed >10-fold protective effects against virulent type A F. tularensis challenge. PMID:24452684

  13. Electronic structure of molecules using relativistic effective core potentials

    SciTech Connect

    Hay, P.J.

    1981-01-01

    Starting with one-component Cowan-Griffin relativistic Hartree-Fock orbitals, which successfully incorporate the mass-velocity and Darwin terms present in more complicated wavefunctions such as Dirac-Hartree-Fock, one can derive relativistic effective core potentials (RECP's) to carry out molecular calculations. These potentials implicitly include the dominant relativistic terms for molecules while allowing one to use the traditional quantum chemical techniques for studying the electronic structure of molecules. The effects of spin-orbit coupling can then be included using orbitals from such calculations using an effective 1-electron, 1-center spin-orbit operator. Applications to molecular systems involving heavy atoms, show good agreement with available spectroscopic data on molecular geometries and excitation energies.

  14. Structural, antigenic and immunogenic features of respiratory syncytial virus glycoproteins relevant for vaccine development

    PubMed Central

    Melero, José A.; Mas, Vicente; McLellan, Jason S.

    2016-01-01

    Extraordinary progress in the structure and immunobiology of the human respiratory syncytial virus glycoproteins has been accomplished during the last few years. Determination of the fusion (F) glycoprotein structure folded in either the prefusion or the postfusion conformation was an inspiring breakthrough not only to understand the structural changes associated with the membrane fusion process but additionally to appreciate the antigenic intricacies of the F molecule. Furthermore, these developments have opened new avenues for structure-based designs of promising hRSV vaccine candidates. Finally, recent advances in our knowledge of the attachment (G) glycoprotein and its interaction with cell-surface receptors have revitalized interest in this molecule as a vaccine, as well as its role in hRSV immunobiology. PMID:27692522

  15. Comparison of a newly developed automated and quantitative hepatitis C virus (HCV) core antigen test with the HCV RNA assay for clinical usefulness in confirming anti-HCV results.

    PubMed

    Kesli, Recep; Polat, Hakki; Terzi, Yuksel; Kurtoglu, Muhammet Guzel; Uyar, Yavuz

    2011-12-01

    Hepatitis C virus (HCV) is a global health care problem. Diagnosis of HCV infection is mainly based on the detection of anti-HCV antibodies as a screening test with serum samples. Recombinant immunoblot assays are used as supplemental tests and for the final detection and quantification of HCV RNA in confirmatory tests. In this study, we aimed to compare the HCV core antigen test with the HCV RNA assay for confirming anti-HCV results to determine whether the HCV core antigen test may be used as an alternative confirmatory test to the HCV RNA test and to assess the diagnostic values of the total HCV core antigen test by determining the diagnostic specificity and sensitivity rates compared with the HCV RNA test. Sera from a total of 212 treatment-naive patients were analyzed for anti-HCV and HCV core antigen both with the Abbott Architect test and with the molecular HCV RNA assay consisting of a reverse transcription-PCR method as a confirmatory test. The diagnostic sensitivity, specificity, and positive and negative predictive values of the HCV core antigen assay compared to the HCV RNA test were 96.3%, 100%, 100%, and 89.7%, respectively. The levels of HCV core antigen showed a good correlation with those from the HCV RNA quantification (r = 0.907). In conclusion, the Architect HCV antigen assay is highly specific, sensitive, reliable, easy to perform, reproducible, cost-effective, and applicable as a screening, supplemental, and preconfirmatory test for anti-HCV assays used in laboratory procedures for the diagnosis of hepatitis C virus infection.

  16. Hierarchical Velocity Structure in the Core of Abell 2597

    NASA Technical Reports Server (NTRS)

    Still, Martin; Mushotzky, Richard

    2004-01-01

    We present XMM-Newton RGS and EPIC data of the putative cooling flow cluster Abell 2597. Velocities of the low-ionization emission lines in the spectrum are blue shifted with respect to the high-ionization lines by 1320 (sup +660) (sub -210) kilometers per second, which is consistent with the difference in the two peaks of the galaxy velocity distribution and may be the signature of bulk turbulence, infall, rotation or damped oscillation in the cluster. A hierarchical velocity structure such as this could be the direct result of galaxy mergers in the cluster core, or the injection of power into the cluster gas from a central engine. The uniform X-ray morphology of the cluster, the absence of fine scale temperature structure and the random distribution of the the galaxy positions, independent of velocity, suggests that our line of sight is close to the direction of motion. These results have strong implications for cooling flow models of the cluster Abell 2597. They give impetus to those models which account for the observed temperature structure of some clusters using mergers instead of cooling flows.

  17. Population structure and minimum core genome typing of Legionella pneumophila

    PubMed Central

    Qin, Tian; Zhang, Wen; Liu, Wenbin; Zhou, Haijian; Ren, Hongyu; Shao, Zhujun; Lan, Ruiting; Xu, Jianguo

    2016-01-01

    Legionella pneumophila is an important human pathogen causing Legionnaires’ disease. In this study, whole genome sequencing (WGS) was used to study the characteristics and population structure of L. pneumophila strains. We sequenced and compared 53 isolates of L. pneumophila covering different serogroups and sequence-based typing (SBT) types (STs). We found that 1,896 single-copy orthologous genes were shared by all isolates and were defined as the minimum core genome (MCG) of L. pneumophila. A total of 323,224 single-nucleotide polymorphisms (SNPs) were identified among the 53 strains. After excluding 314,059 SNPs which were likely to be results of recombination, the remaining 9,165 SNPs were referred to as MCG SNPs. Population Structure analysis based on MCG divided the 53 L. pneumophila into nine MCG groups. The within-group distances were much smaller than the between-group distances, indicating considerable divergence between MCG groups. MCG groups were also supplied by phylogenetic analysis and may be considered as robust taxonomic units within L. pneumophila. Among the nine MCG groups, eight showed high intracellular growth ability while one showed low intracellular growth ability. Furthermore, MCG typing also showed high resolution in subtyping ST1 strains. The results obtained in this study provided significant insights into the evolution, population structure and pathogenicity of L. pneumophila. PMID:26888563

  18. Magnetic Core-Shell Morphology of Structurally Uniform Magnetite Nanoparticles

    NASA Astrophysics Data System (ADS)

    Krycka, Kathryn

    2011-03-01

    Magnetic nanoscale structures are intriguing, in part, because of the exotic properties that emerge compared with bulk. The reduction of magnetic moment per atom in magnetite with decreasing nanoparticle size, for example, has been hypothesized to originate from surface disordering to anisotropy-induced radial canting, which are difficult to distinguish using conventional magnetometry. Small-angle neutron scattering (SANS) is ideal for probing structure, both chemical and magnetic, from nm to microns across an ensemble of particles. Adding polarization analysis (PASANS) of the neutron spin orientation before and after interaction with the scattering particles allows the magnetic structure to be separated into its vector components. Application of this novel technique to 9 nm magnetite nanoparticles closed-packed into face-centered crystallites with order of a micron revealed that at nominal saturation the missing magnetic moments unexpectedly interacted to form well-ordered shells 1.0 to 1.5 nm thick canted perpendicular to their ferrimagnetic cores between 160 to 320 K. These shells additionally displayed intra-particle ``cross-talk'', selecting a common orientation over clusters of tens of nanoparticles. However, the shells disappeared when the external field was removed and interparticle magnetic interactions were negligible (300 K), confirming their magnetic origin. This work has been carried out in collaboration with Ryan Booth, Julie Borchers, Wangchun Chen, Liv Dedon, Thomas Gentile, Charles Hogg, Yumi Ijiri, Mark Laver, Sara Majetich, James Rhyne, and Shannon Watson.

  19. Serospecific antigens of Legionella pneumophila.

    PubMed Central

    Otten, S; Iyer, S; Johnson, W; Montgomery, R

    1986-01-01

    Serospecific antigens isolated by EDTA extraction from four serogroups of Legionella pneumophila were analyzed for their chemical composition, molecular heterogeneity by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and immunological properties. The antigens were shown to be lipopolysaccharides and to differ from the lipopolysaccharides of other gram-negative bacteria. The serospecific antigens contained rhamnose, mannose, glucosamine, and two unidentified sugars together with 2-keto-3-deoxyoctonate, phosphate, and fatty acids. The fatty acid composition was predominantly branched-chain acids with smaller amounts of 3-hydroxymyristic acid. The antigens contain periodate-sensitive groups; mannosyl residues were completely cleaved by periodate oxidation. Hydrolysis of the total lipopolysaccharide by acetic acid resulted in the separation of a lipid A-like material that cross-reacted with the antiserum to lipid A from Salmonella minnesota but did not comigrate with it on sodium dodecyl sulfate gels. None of the four antigens contained heptose. All of the antigen preparations showed endotoxicity when tested by the Limulus amebocyte lysate assay. The results of this study indicate that the serogroup-specific antigens of L. pneumophila are lipopolysaccharides containing an unusual lipid A and core structure and different from those of other gram-negative bacteria. Images PMID:3017918

  20. Structure of the transporter associated with antigen processing trapped by herpes simplex virus

    PubMed Central

    Oldham, Michael L; Grigorieff, Nikolaus; Chen, Jue

    2016-01-01

    The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved strategies to inhibit TAP so that they may go undetected by the immune system. The herpes simplex virus for example evades immune surveillance by blocking peptide transport with a small viral protein ICP47. In this study, we determined the structure of human TAP bound to ICP47 by electron cryo-microscopy (cryo-EM) to 4.0 Å. The structure shows that ICP47 traps TAP in an inactive conformation distinct from the normal transport cycle. The specificity and potency of ICP47 inhibition result from contacts between the tip of the helical hairpin and the apex of the transmembrane cavity. This work provides a clear molecular description of immune evasion by a persistent virus. It also establishes the molecular structure of TAP to facilitate mechanistic studies of the antigen presentation process. DOI: http://dx.doi.org/10.7554/eLife.21829.001 PMID:27935481

  1. Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP

    PubMed Central

    Nöll, Anne; Thomas, Christoph; Herbring, Valentina; Zollmann, Tina; Barth, Katja; Mehdipour, Ahmad Reza; Tomasiak, Thomas M.; Brüchert, Stefan; Joseph, Benesh; Abele, Rupert; Oliéric, Vincent; Wang, Meitian; Diederichs, Kay; Stroud, Robert M.; Pos, Klaas M.; Tampé, Robert

    2017-01-01

    ABC transporters form one of the largest protein superfamilies in all domains of life, catalyzing the movement of diverse substrates across membranes. In this key position, ABC transporters can mediate multidrug resistance in cancer therapy and their dysfunction is linked to various diseases. Here, we describe the 2.7-Å X-ray structure of heterodimeric Thermus thermophilus multidrug resistance proteins A and B (TmrAB), which not only shares structural homology with the antigen translocation complex TAP, but is also able to restore antigen processing in human TAP-deficient cells. TmrAB exhibits a broad peptide specificity and can concentrate substrates several thousandfold, using only one single active ATP-binding site. In our structure, TmrAB adopts an asymmetric inward-facing state, and we show that the C-terminal helices, arranged in a zipper-like fashion, play a crucial role in guiding the conformational changes associated with substrate transport. In conclusion, TmrAB can be regarded as a model system for asymmetric ABC exporters in general, and for TAP in particular. PMID:28069938

  2. Structural organization and polypeptide composition of the avian adenovirus core.

    PubMed Central

    Li, P; Bellett, A J; Parish, C R

    1984-01-01

    CELO virus (fowl adenovirus 1) contained three core polypeptides of molecular weights 20,000, 12,000, and 9,500. The core was similar to that of human adenoviruses, with some evidence of compact subcore domains. Micrococcal nuclease digestion of CELO virus cores produced a smear of DNA fragments of gradually decreasing size, with no nucleosome subunit or repeat pattern. Moreover, when digested cores were analyzed without protease treatment, there was again no evidence of a nucleosome substructure; neither DNA fragments nor core proteins entered a 4% polyacrylamide gel. The organization of the core is thus quite unlike that of chromatin. Restriction endonuclease analysis of the DNA from digested cores showed that the right end was on the outside of the core. We suggest that adenovirus DNA is condensed into the core by cross-linking and neutralization by the core proteins, beginning with the packaging sequence at the center of the core and ending with the right end of the DNA on the outside. Images PMID:6092686

  3. High thermal stability of core-shell structures dominated by negative interface energy.

    PubMed

    Zhu, Yong-Fu; Zhao, Ning; Jin, Bo; Zhao, Ming; Jiang, Qing

    2017-03-29

    Nanoscale core/shell structures are of interest in catalysis due to their superior catalytic properties. Here we investigated the thermal stability of the coherent core-shell structures in a thermodynamic way by considering the impact from the core with the bulk melting point Tm(∞) lower or higher than the shell. When a low-Tm(∞) core is adopted, core-shell melting induced by the melting depression of the core does not occur upon heating because of the superheating, although the melting depression of the core can be triggered ultimately by the preferential melting of the high-Tm(∞) shell for small cores. The superheating of the core is contributed by the negative solid-solid interface energy, while the depression is originated from the positive solid-liquid interface energy. Owing to the presence of the negative interface energy, moreover, the low-Tm(∞)-core structure possesses a low difference in thermal expansion between the core and the shell, high activation energy of outward atomic diffusion from the core to shell, and low heat capacity. This result is beneficial for the core-shell structure design for its application in catalysis.

  4. DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

    PubMed Central

    Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas S.; Lisby, Michael; Salanti, Ali; Fordyce, Sarah L.; Jespersen, Jakob S.; Carter, Richard; Deitsch, Kirk W.; Theander, Thor G.; Pedersen, Anders Gorm; Arnot, David E.

    2014-01-01

    Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens. PMID:24253306

  5. The structure of the cyclic enterobacterial common antigen (ECA) from Yersinia pestis.

    PubMed

    Vinogradov, E V; Knirel, Y A; Thomas-Oates, J E; Shashkov, A S; L'vov, V L

    1994-05-20

    Two antigenic acidic polysaccharides related to enterobacterial common antigen (ECA) were isolated from a vaccine strain of a pathogenic microorganism Yersinia pestis. The low molecular weight polysaccharide (LMP) is composed of equal amounts of 2-acetamido-2-deoxy-D-mannuronic acid, 4-acetamido-4,6-dideoxy-D-galactose (Fuc4NAc), and 2-amino-2-deoxy-D-glucose which is partially N- and partially 6-O-acetylated. The structure of the trisaccharide repeating unit was established by analyses of LMP and the completely N-acetylated LMP (LMP-NAc) using 1H and 13C NMR spectroscopy, including 2D COSY and 1D NOE spectroscopy. Deamination of LMP with nitrous acid gave a set of oligomers terminated with 2,5-anhydromannose and ranging from tri- to dodeca-saccharides, thus indicating a random distribution of free amino groups. FABMS analyses of LMP and LMP-NAc showed that LMP consists mainly of the cyclic tetramer of the trisaccharide repeating unit together with a small amount of the cyclic trimer and a very small amount of the cyclic pentamer and has, thus, the following structure: [formula: see text] where R is Ac or H (approximately 1:1), R' is Ac or H (approximately 1:4), and n = 4 (major), 3, 5 (minor). Small proportions of the linear trimer and the linear tetramer were also detected in the preparations. The high molecular weight polysaccharide is linear and has the same (or a very similar) repeating unit as LMP.

  6. Anti-MrkA Monoclonal Antibodies Reveal Distinct Structural and Antigenic Features of MrkA

    PubMed Central

    Wang, Qun; Chen, Yan; Cvitkovic, Romana; Pennini, Meghan E.; Chang, Chew shun; Pelletier, Mark; Bonnell, Jessica; Wu, Herren; Dall’Acqua, William F.; Stover, C. Kendall; Xiao, Xiaodong

    2017-01-01

    Antibody therapy against antibiotics resistant Klebsiella pneumoniae infections represents a promising strategy, the success of which depends critically on the ability to identify appropriate antibody targets. Using a target-agnostic strategy, we recently discovered MrkA as a potential antibody target and vaccine antigen. Interestingly, the anti-MrkA monoclonal antibodies isolated through phage display and hybridoma platforms all recognize an overlapping epitope, which opens up important questions including whether monoclonal antibodies targeting different MrkA epitopes can be generated and if they possess different protective profiles. In this study we generated four anti-MrkA antibodies targeting different epitopes through phage library panning against recombinant MrkA protein. These anti-MrkA antibodies elicited strong in vitro and in vivo protections against a multi-drug resistant Klebsiella pneumoniae strain. Furthermore, mutational and epitope analysis suggest that the two cysteine residues may play essential roles in maintaining a MrkA structure that is highly compacted and exposes limited antibody binding/neutralizing epitopes. These results suggest the need for further in-depth understandings of the structure of MrkA, the role of MrkA in the pathogenesis of Klebsiella pneumoniae and the protective mechanism adopted by anti-MrkA antibodies to fully explore the potential of MrkA as an efficient therapeutic target and vaccine antigen. PMID:28107434

  7. Seismic study of high-temperature engineering test reactor core graphite structures

    SciTech Connect

    Iyoku, T.; Inagaki, Y.; Shiozawa, S. . Oarai Research Establishment); Nishiguchi, I. )

    1992-08-01

    This paper discusses the High-Temperature Engineering Test Reactor (HTTR) a 30-MW (thermal) helium gas-cooled reactor with a core composed of prismatic graphite blocks piled on core support structures. Safety analyses have been made for the seismic design of the HTTR core using a two-dimensional seismic analysis code called SONATINA-2V, which was developed by the Japan Atomic Energy Research Institute. To evaluate the validity of the SONATINA-2V code and confirm the structural integrity of the core graphite blocks, large-scale seismic tests are conducted using a half-scale vertical section model and a full-scale seven-column model of the core graphite blocks and the core support structures. The test results are in good agreement with the analytical ones, and the validity of the analysis code is confirmed. The structural integrity of the core graphite blocks is confirmed by both analytical and test results.

  8. Evidence for a human leucocyte antigen-DM-induced structural change in human leucocyte antigen-DObeta.

    PubMed

    Deshaies, Francis; Diallo, Djibril A; Fortin, Jean-Simon; O'Rourke, Helen M; Pezeshki, Abdul Mohammad; Bellemare-Pelletier, Angélique; Raby, Nicola; Bédard, Nathalie; Brunet, Alexandre; Denzin, Lisa K; Thibodeau, Jacques

    2009-07-01

    Human leucocyte antigen (HLA)-DO is a non-classical major histocompatibility complex class II molecule which modulates the function of HLA-DM and the loading of antigenic peptides on molecules such as HLA-DR. The bulk of HLA-DO associates with HLA-DM and this interaction is critical for HLA-DO egress from the endoplasmic reticulum. HLA-DM assists the early steps of HLA-DO maturation presumably through the stabilization of the interactions between the N-terminal regions of the alpha and beta chains. To evaluate a possible role for HLA-DM in influencing the conformation of HLA-DO, we made use of a monoclonal antibody, Mags.DO5, that was raised against HLA-DO/DM complexes. Using transfected cells expressing mismatched heterodimers between HLA-DR and -DO chains, we found that the epitope for Mags.DO5 is located on the DObeta chain and that Mags.DO5 reactivity was increased upon cotransfection with HLA-DM. Our results suggest that HLA-DM influences the folding of HLA-DO in the endoplasmic reticulum. A mutant HLA-DO showing reduced capacity for endoplasmic reticulum egress was better recognized by Mags.DO5 in the presence of HLA-DM. On the other hand, an HLA-DO mutant capable of endoplasmic reticulum egress on its own was efficiently recognized by Mags.DO5, irrespective of the presence of HLA-DM. Taken together, our results suggest that HLA-DM acts as a private chaperone, directly assisting the folding of HLA-DO to promote egress from the endoplasmic reticulum.

  9. Doppler Scanning of Sediment Cores: A Useful Method for Studying Sedimentary Structures and Defining the Cutting Angle for Half Cores

    NASA Astrophysics Data System (ADS)

    Acar, Dursun; Cagatay, Namik; Biltekin, Demet; Eris, Kadir; Albut, Gulum; Ogretmen, Nazik; Arslan, Tugce; Sari, Erol

    2014-05-01

    We tested the doppler ultrasound scanning of sediment cores in PVC liners using 8 megahertz ultrasonic waves for detection of angular laminations. The method was tested with artificially prepared cores as well as marine and lake sediment cores, and proven to be a useful and fast technique for imaging and determining the vertical angularity of sedimentary structures, such as laminations and beddings. Random cutting axes provide two angularities on X and Y dimensions. In this study, the main scientific problem is 'sequential angular disconformity'. Importance of detection of these anomalies on whole cores before dividing into half cores based on determining the right cutting axes. Successful imaging was obtained from top three centimeter depth of the sediments below the PVC liner, using a linear Doppler probe. Other Doppler probes (e.g., convex probe) did not work for core scanning because of their wave-form and reflection characteristics. Longitudinal and rotational scanning with gap filler and ultrasonic wave conductive gel material for keeping energy range of wave is necessary for detecting the variation in the dip of the bedding and laminae in the cores before separation. Another angular reasoned problem is about horizontal surface and can be easily solved with adjustable position of sensor or ray source placement. Border of sampling points between two different lithology must be stay with regard to neighbour sediment angles. Vertical angularity correction is not easy and its effect on signal propagation, detection biases and effectible to mixed samples contamination during physical sampling (particle size analyzing). Determining the attitude of angled bedding before core splitting is important for further core analyses such as elemental analysis and digital X-ray radiography. After Doppler scanning, the splitting direction (i.e., vertical to bedding and lamination) can be determined. The method is cheap, quick and non- hazardous to health, unlike the x

  10. Structure and gene cluster of the O-antigen of Enterobacter cloacae G3421.

    PubMed

    Perepelov, Andrei V; Filatov, Andrei V; Wang, Min; Shashkov, Alexander S; Wang, Lei; Knirel, Yuriy A

    2016-06-02

    The O-polysaccharide was isolated by mild acid degradation of the lipopolysaccharide of Enterobacter cloacae G3421 and studied by sugar analysis along with 1D and 2D (1)H and (13)C NMR spectroscopy. In addition, partial solvolysis with anhydrous trifluoroacetic acid was applied, which cleaved selectively the α-l-rhamnopyranosidic linkages. The following structure of the branched hexasaccharide repeating unit was established. The O-polysaccharide studied shares the β-l-Rhap-(1→4)-α-l-Rhap-(1→2)-α-l-Rhap trisaccharide fragment with the O-polysaccharide of Shigella boydii type 18. The O-antigen gene cluster of E. cloacae G3421 was sequenced. Functions of genes in the cluster, including those for glycosyltransferases, were tentatively assigned by a comparison with sequences in the available databases and found to be consistent with the O-polysaccharide structure.

  11. Structure elucidation and gene cluster characterization of the O-antigen of Escherichia coli O80.

    PubMed

    Senchenkova, Sof'ya N; Guo, Xi; Filatov, Andrei V; Perepelov, Andrei V; Liu, Bin; Shashkov, Alexander S; Knirel, Yuriy A

    2016-09-02

    Mild alkaline degradation of the lipopolysaccharide of Escherichia coli O80 afforded a polysaccharide, which was studied by sugar analysis, selective cleavage of glycosidic linkages, and (1)H and (13)C NMR spectroscopy. Solvolysis of the polysaccharide with CF3CO2H cleaved the linkages of α-Fuc and β-linked GlcNAc and GalNAc residues to give two disaccharides. The following structure of the hexasaccharide repeating unit of the O-polysaccharide was established: The polysaccharide repeat also contains a minor O-acetyl group but its position was not determined. The O-antigen gene cluster of E. coli O80 between the conserved galF and gnd genes was analyzed and found to be consistent with the O-polysaccharide structure established.

  12. Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon

    SciTech Connect

    Cardona-Felix, Cesar S.; Lara-Gonzalez, Samuel; Brieba, Luis G.

    2012-02-08

    Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.

  13. Core-hole effect on XANES and electronic structure of minor actinide dioxides with fluorite structure

    NASA Astrophysics Data System (ADS)

    Suzuki, Chikashi; Nishi, Tsuyoshi; Nakada, Masami; Akabori, Mitsuo; Hirata, Masaru; Kaji, Yoshiyuki

    2012-02-01

    The authors investigated theoretically core-hole effects on X-ray absorption near-edge structures (XANES) of Np and Am LIII in neptunium dioxide (NpO2) and americium dioxide (AmO2) with CaF2-type crystal lattices using the all-electron full-potential linearized augmented plane-wave (FP-LAPW) method. The peak creation mechanism of XANES was shown by examining the electronic structures of these oxides, which indicated that core-hole screening was more marked for AmO2 than for NpO2 because of the difference in the charge transfer between these oxides. Furthermore, the results of charge density analysis suggested that the white line was assigned to the quasi-bound state composed of the localized Np d or Am d components and O components, and that the tail structure was created as a result of delocalized standing waves between the Np or Am atoms.

  14. Hepatitis B virus core antigen as a carrier for Chlamydia trachomatis MOMP multi-epitope peptide enhances protection against genital chlamydial infection.

    PubMed

    Jiang, Pengfei; Du, Wangqi; Xiong, Yirong; Lv, Yan; Feng, Juan; Zhu, Shanli; Xue, Xiangyang; Chen, Shao; Zhang, Lifang

    2015-12-22

    Chlamydia trachomatis (Ct) is the leading cause of sexually transmitted diseases worldwide. There is no safe and effective vaccine to control the spread of Ct. In development of Ct vaccine, selection of appropriate candidate antigens and an effective delivery system may be the main challenges. Multi-epitope of major outer membrane protein (MOMPm) is the most suitable candidate for a Ct vaccine, while hepatitis B virus core antigen (HBcAg) has unique advantages as vaccine delivery system. Therefore, in this study, we evaluated the immunogenicity and protective immune response of a novel candidate vaccine in a murine model of chlamydial genital infection. This candidate vaccine comprises MOMPm peptide delivered with HBcAg. Our results of Ct-specific serum IgG and secretory IgA assay, cytokine assay, and cytotoxic T-lymphocyte assay revealed that immunogenicity of the candidate vaccine was much better than that of the corresponding synthetic MOMPm peptide. Furthermore, the protective effect of the candidate vaccine was also shown much better than that of the synthetic peptide by calculating the isolation of Chlamydia from vaginal swabs and histopathological analysis. Taken together, our results indicate that HBcAg carrying Ct MOMPm could be an effective immune prophylactic for chlamydial infection.

  15. Structural basis of Lewisb antigen binding by the Helicobacter pylori adhesin BabA

    PubMed Central

    Hage, Naim; Howard, Tina; Phillips, Chris; Brassington, Claire; Overman, Ross; Debreczeni, Judit; Gellert, Paul; Stolnik, Snow; Winkler, G. Sebastiaan; Falcone, Franco H.

    2015-01-01

    Helicobacter pylori is a leading cause of peptic ulceration and gastric cancer worldwide. To achieve colonization of the stomach, this Gram-negative bacterium adheres to Lewisb (Leb) antigens in the gastric mucosa using its outer membrane protein BabA. Structural information for BabA has been elusive, and thus, its molecular mechanism for recognizing Leb antigens remains unknown. We present the crystal structure of the extracellular domain of BabA, from H. pylori strain J99, in the absence and presence of Leb at 2.0- and 2.1-Å resolutions, respectively. BabA is a predominantly α-helical molecule with a markedly kinked tertiary structure containing a single, shallow Leb binding site at its tip within a β-strand motif. No conformational change occurs in BabA upon binding of Leb, which is characterized by low affinity under acidic [KD (dissociation constant) of ~227 μM] and neutral (KD of ~252 μM) conditions. Binding is mediated by a network of hydrogen bonds between Leb Fuc1, GlcNAc3, Fuc4, and Gal5 residues and a total of eight BabA amino acids (C189, G191, N194, N206, D233, S234, S244, and T246) through both carbonyl backbone and side-chain interactions. The structural model was validated through the generation of two BabA variants containing N206A and combined D233A/S244A substitutions, which result in a reduction and complete loss of binding affinity to Leb, respectively. Knowledge of the molecular basis of Leb recognition by BabA provides a platform for the development of therapeutics targeted at inhibiting H. pylori adherence to the gastric mucosa. PMID:26601230

  16. Vaccination of ducks with a whole-cell vaccine expressing duck hepatitis B virus core antigen elicits antiviral immune responses that enable rapid resolution of de novo infection.

    PubMed

    Miller, Darren S; Halpern, Michael; Kotlarski, Ieva; Jilbert, Allison R

    2006-05-10

    As a first step in developing immuno-therapeutic vaccines for patients with chronic hepatitis B virus infection, we examined the ability of a whole-cell vaccine, expressing the duck hepatitis B virus (DHBV) core antigen (DHBcAg), to target infected cells leading to the resolution of de novo DHBV infections. Three separate experiments were performed. In each experiment, ducks were vaccinated at 7 and 14 days of age with primary duck embryonic fibroblasts (PDEF) that had been transfected 48 h earlier with plasmid DNA expressing DHBcAg with and without the addition of anti-DHBcAg (anti-DHBc) antibodies. Control ducks were injected with either 0.7% NaCl or non-transfected PDEF. The ducks were then challenged at 18 days of age by intravenous inoculation with DHBV (5 x 10(8) viral genome equivalents). Liver biopsies obtained on day 4 post-challenge demonstrated that vaccination did not prevent infection of the liver as similar numbers of infected hepatocytes were detected in all vaccinated and control ducks. However, analysis of liver tissue obtained 9 or more days post-challenge revealed that 9 out of 11 of the PDEF-DHBcAg vaccinated ducks and 8 out of 11 ducks vaccinated with PDEF-DHBcAg plus anti-DHBc antibodies had rapidly resolved the DHBV infection with clearance of infected cells. In contrast, 10 out of 11 of the control unvaccinated ducks developed chronic DHBV infection. In conclusion, vaccination of ducks with a whole-cell PDEF vaccine expressing DHBcAg elicited immune responses that induced a rapid resolution of DHBV infection. The results establish that chronic infection can be prevented via the vaccine-mediated induction of a core-antigen-specific immune response.

  17. CCD photometry of globular cluster core structure. 2: U-band profiles for 15 candidate collapsed-core clusters

    NASA Technical Reports Server (NTRS)

    Lugger, Phyllis M.; Cohn, Haldan N.; Grindlay, Jonathan E.

    1995-01-01

    We present U-band CCD surface brightness profiles for 15 of the 21 globular clusters that have been identified as having collapsed cores by Djorgovski & King (1986). Fourteen of the clusters were observed with the Cerro Tololo 4 m telescope; NGC 7078 was observed with the Canada-France-Hawaii 3.6 m telescope (CFHT). We have fitted the profiles with seeing-convolved power laws, both with and without cores, to assess the evidence for central power-law structure and to place upper limits on core radius r(sub c). We find nine of the clusters (NGC 5946, NGC 6284, NGC 6293, NGC 6325, NGC 6342, NGC 6558, NGC 6624, NGC 6681, and NGC 7078) to have unresolved cores, with upper limits r(sub c) less than or = 1.9 arcsecs. Three of the clusters (NGC 6453, NGC 6522, and NGC 7099) have marginally resolved cores, with upper limits in the range 2.7 arcsecs less than or = r(sub c) less than or = 3.4 arcsecs. The remaining three clusters (NGC 6355, NGC 6397, and NGC 6752) have resolved cores. Of the latter three clusters, NGC 6355 and NGC 6752 are consistent with single-mass King model structure. The median cluster distances are 9.2 kpc for those with unresolved cores, 7.2 kpc for those with marginally resolved cores, and 4.1 kpc for those with resolved cores. The 13 clusters that do not resemble single-mass King models have central power-law structure with surface brightness slopes in the range of d ln S/d ln r = -0.6 to -0.8. These slopes are consistent with the models of Grabhorn et al. (1992) for clusters evolving beyond core collapse. The models include a centrally concentrated population of nonluminous remnants with masses in the range 1.2-1.4 solar mass, thus providing evidence for significant neutron star populations in most of our cluster sample. This finding is consistent with the observation of centrally concentrated low-mass X-ray binary and millisecond pulsar populations in several clusters.

  18. Similarity of "core" structures in two different glycans of tyrosine-linked eubacterial S-layer glycoproteins.

    PubMed Central

    Messner, P; Christian, R; Neuninger, C; Schulz, G

    1995-01-01

    Previously, the repeating-unit structure of the S-layer glycoprotein from the eubacterium Bacillus alvei CCM 2051 has been determined to be [-->3)-beta-D-Galp-(1-->4)-[alpha-D-Glcp-(1-->6)-]-beta-D-ManpNAc- (1-->]n (E. Altman, J.-R. Brisson, P. Messner, and U. B. Sleytr, Biochem. Cell Biol. 69:72-78, 1991). Nuclear magnetic resonance spectroscopic reexamination of this glycan reveals that the O-antigen-like domain of the polysaccharide is [see text] connected with the S-layer polypeptide through the "core" structure -->3)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->3)-alpha-L-R hap-(1-->3)-beta-D-Galp-(1-->O)-Tyr. Except for the substitution in position 4 of the nonreducing rhamnose with the modified glyceric acid phosphate residue GroA-2-->OPO2-->4-beta-D-ManpNAc-(1-->, this core is identical to the core of the tyrosine-linked glycan from the S-layer glycoprotein of Thermoanaerobacter thermohydrosulfuricus L111-69 (K. Bock, J. Schuster-Kolbe, E. Altman, G. Allmaier, B. Stahl, R. Christian, U. B. Sleytr, and P. Messner, J. Biol. Chem. 269:7137-7144, 1994). PMID:7721708

  19. Using silver nanoparticle and thiol graphene quantum dots nanocomposite as a substratum to load antibody for detection of hepatitis C virus core antigen: Electrochemical oxidation of riboflavin was used as redox probe.

    PubMed

    Valipour, Akram; Roushani, Mahmoud

    2017-03-15

    In this study a facile green approach to employ silver nanoparticle (AgNPs) and thiol graphene quantum dots (GQD-SH) as the nanomaterial for ultrasensitive and selective detection of hepatitis C virus core antigen (HCV) have been investigated. AgNPs/GQD-SH was utilized as a substratum to load antibody for detection of hepatitis C virus core antigen. AgNPs have been immobilized on SH groups of GQDs via bonding formation of Ag-S and anti-HCV have been loaded on the electrode surface via the interaction between -NH2 group of antibody and AgNPs. Using the proposed nanocomposite provides a specific platform with increased surface which is capable of loading more antibodies to entrap the antigen. The decreasing of the electrochemical signal can be achieved after the specific recognition between antibodies and antigens. Riboflavin was used as a biological molecule with inherent properties, for the first time, as the redox probe in the development of HCV core antigen electrochemical immunosensor. Compared to the other redox probes, riboflavin is superior in its oxidization in negative potential range, where the number of interfering species for riboflavin is much fewer. The proposed immunosensor showed wide linear range from 0.05pgmL(-1) to 60ngmL(-1) with limit of detection of 3fgmL(-1). This novel immunosensor was used to analyze the serum sample. The immunosensor provides a convenient, low-cost and simple method for HCV core antigen detection and proposes new horizons for quantitative detection of antigen in the clinical diagnosis.

  20. Identification of antigenic domains in the non-structural protein of Muscovy duck parvovirus.

    PubMed

    Yu, Tian-Fei; Li, Ming; Yan, Bing; Shao, Shu-Li; Fan, Xing-Dong; Wang, Jia; Wang, Dan-Na

    2016-08-01

    Muscovy duck parvovirus (MDPV) infection is widespread in many Muscovy-duck-farming countries, leading to a huge economic loss. By means of overlapping peptides expressed in Escherichia coli in combination with Western blot, antigenic domains on the non-structural protein (NSP) of MDPV were identified for the first time. On the Western blot, the fragments NS(481-510), NS (501-530), NS (521-550), NS (541-570), NS (561-590), NS (581-610) and NS (601-627) were positive (the numbers in parentheses indicate the location of amino acids), and other fragments were negative. These seven fragments were also reactive in an indirect enzyme-linked immunosorbent assay (i-ELISA). We therefore conclude that a linear antigenic domain of the NSP is located at its C-terminal end (amino acid residues 481-627). These results may facilitate future investigations into the function of NSP of MDPV and the development of immunoassays for the diagnosis of MDPV infection.

  1. Crystal structure of the simian virus 40 large T-antigen origin-binding domain.

    PubMed

    Meinke, Gretchen; Bullock, Peter A; Bohm, Andrew

    2006-05-01

    The origins of replication of DNA tumor viruses have a highly conserved feature, namely, multiple binding sites for their respective initiator proteins arranged as inverted repeats. In the 1.45-angstroms crystal structure of the simian virus 40 large T-antigen (T-ag) origin-binding domain (obd) reported herein, T-ag obd monomers form a left-handed spiral with an inner channel of 30 angstroms having six monomers per turn. The inner surface of the spiral is positively charged and includes residues known to bind DNA. Residues implicated in hexamerization of full-length T-ag are located at the interface between adjacent T-ag obd monomers. These data provide a high-resolution model of the hexamer of origin-binding domains observed in electron microscopy studies and allow the obd's to be oriented relative to the hexamer of T-ag helicase domains to which they are connected.

  2. [Study of the antigenic structure of human immunoglobulin lambda-chain using monoclonal antibodies].

    PubMed

    Arsen'eva, E L; Bogacheva, G T; Solomon, A; Weiss, D; Ibragimov, A R; Rokhlin, O V

    1990-01-01

    Nine monoclonals against human Ig lambda chains were produced, 4 antibodies react with C-domain, 5--with V-domain of the lambda chain. Anti-C lambda domain antibodies recognize not less than 3 epitopes and one of them is expressed only on the isolated chain. Anti-V lambda antibodies bind both isolated lambda chain and intact IgG, IgM, IgA. Four epitopes are expressed by few lambda Bence Jones proteins of the III subgroup, the immunogen possessing the same isotype. The 4 mentioned epitopes represent private idiotypic determinants. The epitope 3E10 is characteristic of 50% Bence Jones proteins of the II and III V lambda-subgroups thus representing a common idiotypic determinant. Using anti-V lambda antibodies germ line variability of V lambda III proteins was analysed and the similarity of antigenic structure of normal and myeloma human Ig lambda chains was demonstrated.

  3. Crystal Structure of the Simian Virus 40 Large T-Antigen Origin-Binding Domain

    SciTech Connect

    Meinke,G.; Bullock, P.; Bohm, A.

    2006-01-01

    The origins of replication of DNA tumor viruses have a highly conserved feature, namely, multiple binding sites for their respective initiator proteins arranged as inverted repeats. In the 1.45- Angstroms crystal structure of the simian virus 40 large T-antigen (T-ag) origin-binding domain (obd) reported herein, T-ag obd monomers form a left-handed spiral with an inner channel of 30 Angstroms having six monomers per turn. The inner surface of the spiral is positively charged and includes residues known to bind DNA. Residues implicated in hexamerization of full-length T-ag are located at the interface between adjacent T-ag obd monomers. These data provide a high-resolution model of the hexamer of origin-binding domains observed in electron microscopy studies and allow the obd's to be oriented relative to the hexamer of T-ag helicase domains to which they are connected.

  4. Effects of messenger RNA structure and other translational control mechanisms on major histocompatibility complex-I mediated antigen presentation.

    PubMed

    Murat, Pierre; Tellam, Judy

    2015-01-01

    Effective T-cell surveillance of antigen-presenting cells is dependent on the expression of an array of antigenic peptides bound to major histocompatibility complex (MHC) class I (MHC-I) or class II (MHC-II) molecules. Pathogens co-evolving with their hosts exploit crucial translational regulatory mechanisms in order to evade host immune recognition and thereby sustain their infection. Evasion strategies that downregulate viral protein synthesis and thereby restrict antigen presentation to cytotoxic T-cells through the endogenous MHC-I pathway have been implicated in the pathogenesis of viral-associated malignancies. An understanding of the mechanisms by which messenger RNA (mRNA) structure modulates both viral mRNA translation and the antigen processing machinery to escape immune surveillance, will stimulate the development of alternative therapeutic strategies focused on RNA-directed drugs designed to enhance immune responses against infected cells. In this review, we discuss regulatory aspects of the MHC-I pathway and summarize current knowledge of the role attributed by mRNA structure and other translational regulatory mechanisms in immune evasion. In particular we highlight the impact of recently identified G-quadruplex structures within virally encoded transcripts as unique regulatory signals for translational control and antigen presentation.

  5. Time varying velocity structures in Earth's outer core: Constraints from exotic P-waves

    NASA Astrophysics Data System (ADS)

    Day, E. A.; Irving, J. C.; Deuss, A. F.; Cormier, V. F.

    2011-12-01

    The outer core is one of the most dynamic divisions of our planet. However, despite undergoing vigorous convection, the outer core is not necessarily a uniform, homogeneous layer of the Earth. Accumulation of light element enriched iron at the top of the outer core, below the core-mantle boundary, may lead to the formation of a stably stratified layer, corresponding to the E' layer as defined by Bullen. The E' layer would have different properties to the rest of the outer core and may be a source of scattering. The lowermost outer core, the F layer, may also have different physical properties than the rest of the outer core, either due to the crystallisation of iron or the release of light elements as the inner core grows. Time varying structure in the Earth's core has been observed in some previous studies, particularly using earthquake doublets. The vigorous convection in the outer core may lead to small-scale lateral variations in its velocity structure over time, due to the movement of fluids and slurry near to the core-mantle and inner core boundaries. We investigate the velocity and attenuation structure of the upper 1500 km of the outer core using high frequency PmKP seismic phases. PmKP waves travel as P-waves throughout the Earth, bouncing m-1 times on the underside of the core-mantle boundary. By analysing the relative arrival times and amplitudes of the PmKP waves and other seismic phases, and comparing these to synthetic waveforms, it is possible to constrain the velocity and attenuation characteristics of the upper 1500 km of the outer core. We correct for known mantle structure and explore the effects of core-mantle boundary topography. To investigate the scattering characteristics of the uppermost outer core and the sharpness of any stratified layers we search for precursors to PmKP phases, which are elusive. P4KP-PcP differential travel times suggest that the uppermost 1300 km of the outer core is up to 0.4% slower than PREM. There is some evidence

  6. Identifying the Core Content and Structure of a Schema for Cultural Understanding

    DTIC Science & Technology

    2009-06-01

    Technical Report 1251 Identifying the Core Content and Structure of a Schema for Cultural Understanding Joan R...333 6. AUTHOR(S): Joan Rentsch and Iona Mot (Organizational Research Group) Allison Abbe (U.S. Army Research Institute) 5e. WORK UNIT...iii Technical Report 1251 Identifying the Core Content and Structure of a Schema for Cultural Understanding Joan R. Rentsch

  7. Structure of a mutant form of proliferating cell nuclear antigen that blocks translesion DNA synthesis †

    PubMed Central

    Freudenthal, Bret D.; Ramaswamy, S.; Hingorani, Manju M.; Washington, M. Todd

    2009-01-01

    Proliferating cell nuclear antigen (PCNA) is a homotrimeric protein that functions as a sliding clamp during DNA replication. Several mutant forms of PCNA that block translesion DNA synthesis have been identified in genetic studies in yeast. One such mutant protein (encoded by the rev6-1 allele) is a glycine to serine substitution at residue 178, located at the subunit interface of PCNA. To better understand how this substitution interferes with translesion synthesis, we have determined the X-ray crystal structure of the G178S PCNA mutant protein. This substitution has little effect on the structure of the domain in which the substitution occurs. Instead, significant, local structural changes are observed in the adjacent subunit. The most notable difference between mutant and wild-type structures is in a single, extended loop (comprising amino acid residues 105-110), which we call loop J. In the mutant protein structure, loop J adopts a very different conformation in which the atoms of the protein backbone have moved by as much as 6.5 Å from their positions in the wild-type structure. To better understand the functional consequences of this structural change, we have examined the ability of this mutant protein to stimulate nucleotide incorporation by DNA polymerase eta (pol η). Steady state kinetic studies show that while wild-type PCNA stimulates incorporation by pol η opposite an abasic site, the mutant PCNA protein actually inhibits incorporation opposite this DNA lesion. These results show that the position of loop J in PCNA plays an essential role in facilitating translesion synthesis. PMID:19053247

  8. Inhibition of antigen-specific T lymphocyte activation by structurally related Ir gene-controlled polymers. II. Competitive inhibition of I-E- restricted, antigen-specific T cell responses

    PubMed Central

    1984-01-01

    Our previous studies have defined a highly specific competitive inhibition between a pair of structurally related antigens (GT and GAT) for antigen presentation by accessory cells. The present report investigates this phenomenon in a second antigenic system, which is controlled by a distinct Ir gene product. Two GL phi-specific, I-Ed- restricted, interleukin 2-producing T cell hybridomas were constructed. The antigenic fine specificity of these two hybrid clones was distinct. One hybrid reacted solely with GL phi while the second cross-reacted with GLleu and GLT. These latter two copolymers, as well as the antigen GL, were found to inhibit the GL phi response of the non-cross-reactive hybrid. The structurally related antigen G phi was not inhibitory for this clone's response. The cross-reactive GL phi hybrid could also be inhibited, but, in this case, G phi and not GL caused the inhibition. Reciprocal inhibitions could be demonstrated between these and other hybrids (e.g., GAT responsive), indicating a very high degree of specificity to the inhibition. The inhibition caused by the various copolymers was reversible by increasing the concentration of GL phi, This effect was localized to the antigen-presenting cell and not the T cell hybridoma. Functionally, this competition did not appear to be for antigen uptake or general antigen processing. These findings generalize the phenomenon of antigen competition to a second antigen system in the context of a second Ia molecule. The possible mechanisms accounting for the complex pattern of specificities in this system are discussed. PMID:6210339

  9. Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen.

    SciTech Connect

    Li, D.; Zhao, R.; Lilyestrom, W.; Gai, D.; Zhang, R.; DeCaprio, J. A.; Fanning, E.; Joachimiak, A.; Szakonyi, G.; Chen, X. S.; Univ. of Colorado Health Science Center; Dana-Farber Cancer Ins.; Vanderbilt Univ.

    2003-05-29

    The oncoprotein large tumour antigen (LTag) is encoded by the DNA tumour virus simian virus 40. LTag transforms cells and induces tumours in animals by altering the functions of tumour suppressors (including pRB and p53) and other key cellular proteins. LTag is also a molecular machine that distorts/melts the replication origin of the viral genome and unwinds duplex DNA. LTag therefore seems to be a functional homologue of the eukaryotic minichromosome maintenance (MCM) complex. Here we present the X-ray structure of a hexameric LTag with DNA helicase activity. The structure identifies the p53-binding surface and reveals the structural basis of hexamerization. The hexamer contains a long, positively charged channel with an unusually large central chamber that binds both single-stranded and double-stranded DNA. The hexamer organizes into two tiers that can potentially rotate relative to each other through connecting alpha-helices to expand/constrict the channel, producing an 'iris' effect that could be used for distorting or melting the origin and unwinding DNA at the replication fork.

  10. Molecular cloning and structural analysis of the porcine homologue to CD97 antigen.

    PubMed

    de la Lastra, José M Pérez; Shahein, Yasser E A; Garrido, Juan J; Llanes, Diego

    2003-06-20

    CD97 is a member of a novel subfamily of leukocyte proteins that are characterized by the presence of tandemly repeated extracellular epidermal growth factor (EGF)-like domains and a seven-span transmembrane region, known as EGF-TM7. We here report the cloning of cDNA encoding the pig homologue of CD97. A pig CD97 specific probe was generated by PCR amplification of pig leukocyte cDNA, using primers based on consensus regions among the known sequences of mouse and human CD97. Screening of a pig aorta smooth muscle cDNA library identified one clone containing an open reading frame (ORF) that encoded an 18 amino acid putative signal peptide, a 141 amino acid sequence consisting of three EGF domains, a mucin-like spacer region of 276 amino acid, containing a G-protein coupling motif of 52 amino acids, followed by a 250 amino acid region containing seven membrane spanning domains and a 47 amino acid cytoplasmic tail. The amino acid sequence of the clone was 75, 67 and 59% homologous to cattle, human and mouse CD97 antigen, respectively. Therefore, it was termed pig CD97. Pig CD97 antigen shares many structural features with human, cattle and mouse CD97. RT-PCR analysis of cDNA from different pig cells and tissues showed that CD97 was highly expressed in leukocytes and lymph node cells. This is the first report describing the identification of a member of the EGF-TM7 family in the pig.

  11. Rigid polyurethane foam – kenaf core composites for structural applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Kenaf (Hibiscus cannabinus L.) is a fast growing summer annual crop with numerous commercial applications (fibers, biofuels, bioremediation, paper pulp, building materials, cover crops, and livestock forages). The stalks of the kenaf plants contain two distinct fiber types, bast and core fibers. The...

  12. Coordination polymer core/shell structures: Preparation and up/down-conversion luminescence.

    PubMed

    Li, Bingmei; Xu, Hualan; Xiao, Chen; Shuai, Min; Chen, Weimin; Zhong, Shengliang

    2016-10-01

    Coordination polymer (CP) core-shell nanoparticles with Gd-based CP (GdCP) as core and Eu-based CP (EuCP) as shell have been successfully prepared. Allantoin was employed as the organic building block without the assistance of any template. The composition, size and structure of the core-shell nanospheres were well characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray (EDX), powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FT-IR), thermo-gravimetric analysis (TG). Results show that the resultant cores are uniform nanospheres with diameter of approximately 45nm, while the diameters of the core-shell nanospheres are increased to approximately 60nm. The core-shell products show enhanced luminescence efficiency than the core under 980nm laser excitation and decreased down-conversion luminescence when excited at 394nm.

  13. Direct core structuring of microstructured optical fibers using focused ion beam milling.

    PubMed

    Warren-Smith, Stephen C; André, Ricardo M; Perrella, Christopher; Dellith, Jan; Bartelt, Hartmut

    2016-01-11

    We demonstrate the use of focused ion beam milling to machine optical structures directly into the core of microstructured optical fibers. The particular fiber used was exposed-core microstructured optical fiber, which allowed direct access to the optically guiding core. Two different designs of Fabry-Perot cavity were fabricated and optically characterized. The first cavity was formed by completely removing a section of the fiber core, while the second cavity consisted of a shallow slot milled into the core, leaving the majority of the core intact. This work highlights the possibility of machining complex optical devices directly onto the core of microstructured optical fibers using focused ion beam milling for applications including environmental, chemical, and biological sensing.

  14. Crystal structure of the shrimp proliferating cell nuclear antigen: structural complementarity with WSSV DNA polymerase PIP-box.

    PubMed

    Carrasco-Miranda, Jesus S; Lopez-Zavala, Alonso A; Arvizu-Flores, Aldo A; Garcia-Orozco, Karina D; Stojanoff, Vivian; Rudiño-Piñera, Enrique; Brieba, Luis G; Sotelo-Mundo, Rogerio R

    2014-01-01

    DNA replication requires processivity factors that allow replicative DNA polymerases to extend long stretches of DNA. Some DNA viruses encode their own replicative DNA polymerase, such as the white spot syndrome virus (WSSV) that infects decapod crustaceans but still require host replication accessory factors. We have determined by X-ray diffraction the three-dimensional structure of the Pacific white leg shrimp Litopenaeus vannamei Proliferating Cell Nuclear Antigen (LvPCNA). This protein is a member of the sliding clamp family of proteins, that binds DNA replication and DNA repair proteins through a motif called PIP-box (PCNA-Interacting Protein). The crystal structure of LvPCNA was refined to a resolution of 3 Å, and allowed us to determine the trimeric protein assembly and details of the interactions between PCNA and the DNA. To address the possible interaction between LvPCNA and the viral DNA polymerase, we docked a theoretical model of a PIP-box peptide from the WSSV DNA polymerase within LvPCNA crystal structure. The theoretical model depicts a feasible model of interaction between both proteins. The crystal structure of shrimp PCNA allows us to further understand the mechanisms of DNA replication processivity factors in non-model systems.

  15. Crystal Structure of the Shrimp Proliferating Cell Nuclear Antigen: Structural Complementarity with WSSV DNA Polymerase PIP-Box

    PubMed Central

    Carrasco-Miranda, Jesus S.; Lopez-Zavala, Alonso A.; Arvizu-Flores, Aldo A.; Garcia-Orozco, Karina D.; Stojanoff, Vivian; Rudiño-Piñera, Enrique; Brieba, Luis G.; Sotelo-Mundo, Rogerio R.

    2014-01-01

    DNA replication requires processivity factors that allow replicative DNA polymerases to extend long stretches of DNA. Some DNA viruses encode their own replicative DNA polymerase, such as the white spot syndrome virus (WSSV) that infects decapod crustaceans but still require host replication accessory factors. We have determined by X-ray diffraction the three-dimensional structure of the Pacific white leg shrimp Litopenaeus vannamei Proliferating Cell Nuclear Antigen (LvPCNA). This protein is a member of the sliding clamp family of proteins, that binds DNA replication and DNA repair proteins through a motif called PIP-box (PCNA-Interacting Protein). The crystal structure of LvPCNA was refined to a resolution of 3 Å, and allowed us to determine the trimeric protein assembly and details of the interactions between PCNA and the DNA. To address the possible interaction between LvPCNA and the viral DNA polymerase, we docked a theoretical model of a PIP-box peptide from the WSSV DNA polymerase within LvPCNA crystal structure. The theoretical model depicts a feasible model of interaction between both proteins. The crystal structure of shrimp PCNA allows us to further understand the mechanisms of DNA replication processivity factors in non-model systems. PMID:24728082

  16. Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

    SciTech Connect

    Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn

    2013-11-01

    Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.

  17. The Rcs signal transduction pathway is triggered by enterobacterial common antigen structure alterations in Serratia marcescens.

    PubMed

    Castelli, María E; Véscovi, Eleonora García

    2011-01-01

    The enterobacterial common antigen (ECA) is a highly conserved exopolysaccharide in Gram-negative bacteria whose role remains largely uncharacterized. In a previous work, we have demonstrated that disrupting the integrity of the ECA biosynthetic pathway imposed severe deficiencies to the Serratia marcescens motile (swimming and swarming) capacity. In this work, we show that alterations in the ECA structure activate the Rcs phosphorelay, which results in the repression of the flagellar biogenesis regulatory cascade. In addition, a detailed analysis of wec cluster mutant strains, which provoke the disruption of the ECA biosynthesis at different levels of the pathway, suggests that the absence of the periplasmic ECA cyclic structure could constitute a potential signal detected by the RcsF-RcsCDB phosphorelay. We also identify SMA1167 as a member of the S. marcescens Rcs regulon and show that high osmolarity induces Rcs activity in this bacterium. These results provide a new perspective from which to understand the phylogenetic conservation of ECA among enterobacteria and the basis for the virulence attenuation detected in wec mutant strains in other pathogenic bacteria.

  18. Gene for the major antigenic structural protein (p100) of human herpesvirus 6.

    PubMed Central

    Neipel, F; Ellinger, K; Fleckenstein, B

    1992-01-01

    A human herpesvirus 6 (HHV-6) structural protein of 100 kDa (p100) is the polypeptide most frequently and intensively reactive in immunoblotting analyses with human sera on HHV-6-infected cells or partially purified virions. The gene for p100 was identified by screening a bacteriophage lambda library with monospecific rabbit antisera. The gene codes for a polypeptide of 870 amino acids with a calculated molecular size of 97 kDa. Its amino-terminal third is weakly homologous to the immunogenic basic matrix phosphoprotein pp150 of human cytomegalovirus. Five fragments representing more than 93% of HHV-6 p100 were prokaryotically expressed. The antigenic epitopes of p100 were preliminary mapped by immunoblotting with human sera. They are located within the carboxy-terminal part which is neither homologous nor cross-reactive to pp150 of human cytomegalovirus. Availability of the gene for the immunodominant structural protein should provide tools for studies of pathogenesis by HHV-6. Images PMID:1374813

  19. Multi-scale silica structures for improved HIV-1 Capsid (p24) antigen detection.

    PubMed

    Lin, Sophia; Hedde, Per Niklas; Venugopalan, Vasan; Gratton, Enrico; Khine, Michelle

    2016-06-20

    Silica (SiO2) micro- and nanostructures fabricated with pre-stressed thermoplastic shrink wrap film have been shown to yield far-field fluorescence signal enhancements over their planar or wrinkled counterparts. The SiO2 structures have previously been used for improved detection of fluorescently labelled proteins and DNA. In this work, we probe the mechanism responsible for the dramatic increases in fluorescence signal intensity. Optical characterization studies attribute the fluorescence signal enhancements to increased surface density and light scattering from the rough SiO2 structures. Using this information, we come up with a theoretical approximation for the enhancement factor based off the scattering effects alone. We show that increased deposition thickness of SiO2 yields improved fluorescence signal enhancements, with an optimal SiO2 thin layer achieved at 20 nm. Finally, we show that the SiO2 substrates serve as a suitable platform for disease diagnostics, and show improved limits of detection (LOD) for the human immunodeficiency virus type 1 (HIV-1) p24 antigen.

  20. Structure of an anti-Lewis X Fab fragment in complex with its Lewis X antigen.

    PubMed

    van Roon, Anne-Marie M; Pannu, Navraj S; de Vrind, Johannes P M; van der Marel, Gijs A; van Boom, Jacques H; Hokke, Cornelis H; Deelder, André M; Abrahams, Jan Pieter

    2004-07-01

    The Lewis X trisaccharide is pivotal in mediating specific cell-cell interactions. Monoclonal antibody 291-2G3-A, which was generated from mice infected with schistosomes, has been shown to recognize the Lewis X trisaccharide. Here we describe the structure of the Fab fragment of 291-2G3-A, with Lewis X, to 1.8 A resolution. The crystallographic analysis revealed that the antigen binding site is a rather shallow binding pocket, and residues from all six complementary determining regions of the antibody contact all sugar residues. The high specificity of the binding pocket does not result in high affinity; the K(D) determined by isothermal calorimetry is 11 microM. However, this affinity is in the same range as for other sugar-antibody complexes. The detailed understanding of the antibody-Lewis X interaction revealed by the crystal structure may be helpful in the design of better diagnostic tools for schistosomiasis and for studying Lewis X-mediated cell-cell interactions by antibody interference.

  1. Structure of the meningococcal vaccine antigen NadA and epitope mapping of a bactericidal antibody

    PubMed Central

    Malito, Enrico; Biancucci, Marco; Faleri, Agnese; Ferlenghi, Ilaria; Scarselli, Maria; Maruggi, Giulietta; Lo Surdo, Paola; Veggi, Daniele; Liguori, Alessia; Santini, Laura; Bertoldi, Isabella; Petracca, Roberto; Marchi, Sara; Romagnoli, Giacomo; Cartocci, Elena; Vercellino, Irene; Savino, Silvana; Spraggon, Glen; Norais, Nathalie; Pizza, Mariagrazia; Rappuoli, Rino; Masignani, Vega; Bottomley, Matthew James

    2014-01-01

    Serogroup B Neisseria meningitidis (MenB) is a major cause of severe sepsis and invasive meningococcal disease, which is associated with 5–15% mortality and devastating long-term sequelae. Neisserial adhesin A (NadA), a trimeric autotransporter adhesin (TAA) that acts in adhesion to and invasion of host epithelial cells, is one of the three antigens discovered by genome mining that are part of the MenB vaccine that recently was approved by the European Medicines Agency. Here we present the crystal structure of NadA variant 5 at 2 Å resolution and transmission electron microscopy data for NadA variant 3 that is present in the vaccine. The two variants show similar overall topology with a novel TAA fold predominantly composed of trimeric coiled-coils with three protruding wing-like structures that create an unusual N-terminal head domain. Detailed mapping of the binding site of a bactericidal antibody by hydrogen/deuterium exchange MS shows that a protective conformational epitope is located in the head of NadA. These results provide information that is important for elucidating the biological function and vaccine efficacy of NadA. PMID:25404323

  2. Genetic and Structural Characterization of the Core Region of the Lipopolysaccharide from Serratia marcescens N28b (Serovar O4)

    PubMed Central

    Coderch, Núria; Piqué, Núria; Lindner, Buko; Abitiu, Nihal; Merino, Susana; Izquierdo, Luis; Jimenez, Natalia; Tomás, Juan M.; Holst, Otto; Regué, Miguel

    2004-01-01

    The gene cluster (waa) involved in Serratia marcescens N28b core lipopolysaccharide (LPS) biosynthesis was identified, cloned, and sequenced. Complementation analysis of known waa mutants from Escherichia coli K-12, Salmonella enterica, and Klebsiella pneumoniae led to the identification of five genes coding for products involved in the biosynthesis of a shared inner core structure: [l,d-HeppIIIα(1→7)-l,d-HeppIIα(1→3)-l,d-HeppIα(1→5)-KdopI(4←2)αKdopII] (l,d-Hepp, l-glycero-d-manno-heptopyranose; Kdo, 3-deoxy-d-manno-oct-2-ulosonic acid). Complementation and/or chemical analysis of several nonpolar mutants within the S. marcescens waa gene cluster suggested that in addition, three waa genes were shared by S. marcescens and K. pneumoniae, indicating that the core region of the LPS of S. marcescens and K. pneumoniae possesses additional common features. Chemical and structural analysis of the major oligosaccharide from the core region of LPS of an O-antigen-deficient mutant of S. marcescens N28b as well as complementation analysis led to the following proposed structure: β-Glc-(1→6)-α-Glc-(1→4))-α-d-GlcN-(1→4)-α-d-GalA-[(2←1)-α-d,d-Hep-(2←1)-α-Hep]-(1→3)-α-l,d-Hep[(7←1)-α-l,d-Hep]-(1→3)-α-l,d-Hep-[(4←1)-β-d-Glc]-(1→5)-Kdo. The D configuration of the β-Glc, α-GclN, and α-GalA residues was deduced from genetic data and thus is tentative. Furthermore, other oligosaccharides were identified by ion cyclotron resonance-Fourier-transformed electrospray ionization mass spectrometry, which presumably contained in addition one residue of d-glycero-d-talo-oct-2-ulosonic acid (Ko) or of a hexuronic acid. Several ions were identified that differed from others by a mass of +80 Da, suggesting a nonstoichiometric substitution by a monophosphate residue. However, none of these molecular species could be isolated in substantial amounts and structurally analyzed. On the basis of the structure shown above and the analysis of nonpolar mutants

  3. Structure of a mushy layer at the inner core boundary

    NASA Astrophysics Data System (ADS)

    Deguen, R.; Huguet, L.; Bergman, M. I.; Labrosse, S.; Alboussiere, T.

    2015-12-01

    We present experimental results on the solidification of ammonium chloride from an aqueous solution, yielding a mushy zone, under hyper-gravity. A commercial centrifuge has been equipped with a slip-ring so that electric power, temperature and ultrasonic signals could be transmitted between the experimental setup and the laboratory. A Peltier element provides cooling at the bottom of the cell. Probes monitor the temperature along the height of the cell. Ultrasound measurements (2 to 6 MHz) is used to detect the position of the front of the mushy zone and to determine attenuation in the mush. A significant increase of solid fraction (or decrease of mushy layer thickness) and attenuation in the mush is observed as gravity is increased. Kinetic undercooling is significant in our experiments and has been included in a macroscopic mush model. The other ingredients of the model are conservation of energy and chemical species, along with heat/species transfer between the mush and the liquid phase: boundary-layer exchanges at the top of the mush and bulk convection within the mush (formation of chimneys). The outputs of the model compare well with our experiments. We have then run the model in a range of parameters suitable for the Earth's inner core, which has shown the role of bulk mush convection for the inner core and the reason why a solid fraction very close to unity should be expected. We have also run melting experiments: after crystallization of a mush, the liquid has been heated from above until the mush started to melt, while the bottom cold temperature was maintained. These melting experiments were motivated by the possible local melting at the inner core boundary that has been invoked to explain the formation of the anomalously slow F-layer at the bottom of the outer core or inner core hemispherical asymmetry. Oddly, the consequences of melting are an increase in solid fraction and a decrease in attenuation. It is hence possible that surface seismic velocity

  4. Multiple genome alignment for identifying the core structure among moderately related microbial genomes

    PubMed Central

    Uchiyama, Ikuo

    2008-01-01

    Background Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. Results The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. Conclusion The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes. PMID:18976470

  5. Modelling the structure of full-length Epstein-Barr virus nuclear antigen 1.

    PubMed

    Hussain, Mushtaq; Gatherer, Derek; Wilson, Joanna B

    2014-12-01

    Epstein-Barr virus is a clinically important human virus associated with several cancers and is the etiologic agent of infectious mononucleosis. The viral nuclear antigen-1 (EBNA1) is central to the replication and propagation of the viral genome and likely contributes to tumourigenesis. We have compared EBNA1 homologues from other primate lymphocryptoviruses and found that the central glycine/alanine repeat (GAr) domain as well as predicted cellular protein (USP7 and CK2) binding sites are present in homologues in the Old World primates, but not the marmoset, suggesting that these motifs may have co-evolved. Using the resolved structure of the C-terminal one-third of EBNA1 (homodimerization and DNA binding domain), we have gone on to develop monomeric and dimeric models in silico of the full-length protein. The C-terminal domain is predicted to be structurally highly similar between homologues, indicating conserved function. Zinc could be stably incorporated into the model, bonding with two N-terminal cysteines predicted to facilitate multimerisation. The GAr contains secondary structural elements in the models, while the protein binding regions are unstructured, irrespective of the prediction approach used and sequence origin. These intrinsically disordered regions may facilitate the diversity observed in partner interactions. We hypothesize that the structured GAr could mask the disordered regions, thereby protecting the protein from default degradation. In the dimer conformation, the C-terminal tails of each monomer wrap around a proline-rich protruding loop of the partner monomer, providing dimer stability, a feature which could be exploited in therapeutic design.

  6. Structure and genetics of the O-antigens of Escherichia coli O182-O187.

    PubMed

    Senchenkova, Sof'ya N; Guo, Xi; Naumenko, Olesya I; Shashkov, Alexander S; Perepelov, Andrei V; Liu, Bin; Knirel, Yuriy A

    2016-11-29

    O-polysaccharides (OPSs) were obtained by mild acid degradation of the lipopolysaccharides of Escherichia coli O182-O187, and their structures were established by sugar analysis, Smith degradation, and (1)H and (13)C NMR spectroscopy. In addition to the monosaccharides that occur often in E. coli OPSs (d-Glc, d-Gal, d-Man, d-GlcNAc, d-GalNAc, d-GlcA, l-Fuc, d-Rib), a number of less common components were identified as the OPS constituents, including 2-acetamido-2-deoxy-l-quinovose and 4-deoxy-4-[(S)-3-hydroxybutanoyl-l-alanyl]-d-quinovose (O186), 3-acetamido-3-deoxy-d-fucose (O187), 3-deoxy-3-[(R)-3-hydroxybutanoyl]-d-fucose (O184), and 2,3-diacetamido-2,3-dideoxy-l-rhamnose (O182). The OPS structures of E. coli O183 and O182 are identical to those of the OPS of Shigella boydii type 10 and the capsular polysaccharide of E. coli K48, respectively. The OPSs of E. coli O186 and O123 are closely related differing in the presence of a Glc residue in the former in place of a GlcNAc residue in the latter. The O-antigen gene clusters of the bacteria studied were analyzed and their contents were found to be consistent with the OPS structures. Predicted glycosyltransferases encoded in the gene clusters were tentatively assigned to glycosidic linkages based on similarities to sequences of other E. coli O-serogroups available from GenBank and taking into account the OPS structures established.

  7. Structural and spectral studies of sunspots. [umbral core modelling

    NASA Technical Reports Server (NTRS)

    Wyller, A. A.

    1974-01-01

    Observations of umbral cores, both by multicolor photometry and by narrow band photometry in the vicinity of the sodium D lines, are described, and evidence is given which supports the validity of many umbral models, each of which describes different aspects of the observed umbral cores. Theoretical studies carried on at the observatory include the following: (1) Zeeman profiles of the sodium D sub 2 line and other lines; (2) turbulent heat conduction, sound waves, and the missing flux in sunspots; (3) chromospheric heating above spots by Alfven waves; (4) magnetic convection in the sun and solar neutrinos; (5) models of starspots on flare stars; (5) starspots on the primaries of contact binary systems; and (6) implications of starspots on red dwarfs.

  8. Formation of core-shell structure in high entropy alloy coating by laser cladding

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Wu, Wanfei; He, Yizhu; Li, Mingxi; Guo, Sheng

    2016-02-01

    The formation of core-shell structure is an interesting phenomenon occurring during the solidification process, due to the liquid phase separation. The formation of core-shell structure in high-entropy alloys, a new class of advanced metallic materials, has not been reported previously, and thus constitutes an intriguing scientific question. Here, we firstly report the formation of core-shell structure in one laser cladded high-entropy alloy, where we show the nanosized-Y2O3 powder addition, serves as the catalyst for the liquid phase separation.

  9. Serum hepatitis B core-related antigen is a satisfactory surrogate marker of intrahepatic covalently closed circular DNA in chronic hepatitis B.

    PubMed

    Chen, En-Qiang; Feng, Shu; Wang, Meng-Lan; Liang, Ling-Bo; Zhou, Ling-Yun; Du, Ling-Yao; Yan, Li-Bo; Tao, Chuan-Min; Tang, Hong

    2017-12-01

    Recently, hepatitis B core-related antigen (HBcrAg) has been suggested as an additional marker of hepatitis B virus (HBV) infection. This study aimed to investigate whether serum quantitative HBcrAg (qHBcrAg) was a satisfactory surrogate marker of intrahepatic covalently closed circular DNA (cccDNA). A total of 139 patients with liver biopsy were enrolled, consisting of 59 patients in immune tolerance (IT) phase, 52 patients in immune clearance (IC) phase, 18 patients in low-replication (LR) phase, and 10 patients in reactivation phase. All patients in IC phase have received entecavir (ETV) therapy, and 32 of them undergone a second liver biopsy at 24 months. Among those patients, qHBcrAg was strongly correlated with intrahepatic cccDNA, which is superior to that of qHBsAg and HBV DNA. And similar findings were also observed in patients in IT, IC, LR and reactivation phases. Among the 32 ETV-treated patients with a second liver biopsy in IC phase, the decline of intrahepatic cccDNA was accompanied by changes in both qHBcrAg and qHBsAg. However, as compared to qHBsAg, the change of qHBcrAg was more strongly associated with intrahepatic cccDNA-decline. In summary, serum qHBcrAg should be a satisfactory surrogate of intrahepatic HBV cccDNA in CHB patients.

  10. Signal Amplification Strategy of Triple-Layered Core-Shell Au@Pd@Pt Nanoparticles for Ultrasensitive Immunoassay Detection of Squamous Cell Carcinoma Antigen.

    PubMed

    Zhang, Xiaoyue; Du, Bin; Wu, Dan; Ma, Hongmin; Zhang, Yong; Li, He; Wei, Qin

    2015-02-01

    A novel and effective nonenzymatic immunosensor for the sensitive detection of squamous cell carcinoma antigen (SCC- Ag) was described based on triple-layered core-shell Au@Pd@Pt nanoparticles (Au@Pd@Pt NPs). To prepare the immunosensor, primary anti-SCC antibodies (Ab1) were immobilized onto nanoporous gold films (NPGF) of a modified glassy carbon electrode. Au@Pd@Pt NPs that possess strong catalytic activity for the reduction of H2O2 were used as catalytic labels of secondary anti-SCC antibodies (Ab2). Because of the catalytic activities of Au@Pd@Pt NPs and the large surface area of the NPGF, high sensitivity was achieved for the detection of SCC-Ag. The prepared immunosensor showed remarkable results, such as low detection limits (0.6 pg/mL), a wide linear range (0.001-10.0 ng/mL) and high stability and selectivity in the detection of SCC-Ag. Furthermore, the prepared immunosensor exhibited promising properties, which may be useful for real serum sample tests.

  11. Graphene oxide quantum dots@silver core-shell nanocrystals as turn-on fluorescent nanoprobe for ultrasensitive detection of prostate specific antigen.

    PubMed

    Pei, Haimeng; Zhu, Shuyun; Yang, Minghui; Kong, Rongmei; Zheng, Yiqun; Qu, Fengli

    2015-12-15

    We report a fluorescent turn-on nanoprobe for ultrasensitive detection of prostate specific antigen (PSA) based on graphene oxide quantum dots@silver (GQDs@Ag) core-shell nanocrystals. The success of this work relies on the assembly of quantities of GQDs in one GQDs@Ag probe, which makes the ratio of probe to target significantly increased and thus enables the fluorescent signal enhancement. When the silver shell was removed via oxidative etching using hydrogen peroxide (H2O2), the incorporated GQDs could be readily released and the whole process caused little change to their fluorescence performance. We tested the probe for the ultrasensitive detection of PSA based on the sandwich protocol of immunosensors. In particular, magnetic beads (MBs) were employed to immobilize anti-PSA antibody (Ab1) and acted as a separable capture probe, while GQDs@Ag was used as detection probe by linking antibody (Ab2). The developed immunosensor showed a good linear relationship between the fluorescence intensity and the concentration of PSA in the range from 1 pg/mL to 20 ng/mL with a detection limit of 0.3 pg/mL. The immunosensor used for the analysis of clinical serum samples exhibited satisfactory results, which demonstrated its potential for practical diagnostic applications. This method provides a possible solution to the application of GQDs in immunosensing and could be potentially extended to other similar systems.

  12. Deletion of fusion peptide or destabilization of fusion core of HIV gp41 enhances antigenicity and immunogenicity of 4E10 epitope

    SciTech Connect

    Li Jing; Chen Xi; Jiang Shibo Chen Yinghua

    2008-11-07

    The human monoclonal antibody 4E10 against the membrane-proximal external region (MPER) of HIV-1 gp41 demonstrates broad neutralizing activity across various strains, and makes its epitope an attractive target for HIV-1 vaccine development. Although the contiguous epitope of 4E10 has been identified, attempts to re-elicit 4E10-like antibodies have failed, possibly due to the lack of proper conformation of the 4E10 epitope. Here we used pIg-tail expression system to construct a panel of eukaryotic cell-surface expression plasmids encoding the extracellular domain of gp41 with deletion of fusion peptide and/or introduction of L568P mutation that may disrupt the gp41 six-helix bundle core conformation as DNA vaccines for immunization of mice. We found that these changes resulted in significant increase of the antigenicity and immunogenicity of 4E10 epitope. This information is thus useful for rational design of vaccines targeting the HIV-1 gp41 MPER.

  13. Model for T-Antigen-Dependent Melting of the Simian Virus 40 Core Origin Based on Studies of the Interaction of the Beta-Hairpin with DNA▿

    PubMed Central

    Kumar, Anuradha; Meinke, Gretchen; Reese, Danielle K.; Moine, Stephanie; Phelan, Paul J.; Fradet-Turcotte, Amélie; Archambault, Jacques; Bohm, Andrew; Bullock, Peter A.

    2007-01-01

    The interaction of simian virus 40 (SV40) T antigen (T-ag) with the viral origin has served as a model for studies of site-specific recognition of a eukaryotic replication origin and the mechanism of DNA unwinding. These studies have revealed that a motif termed the “beta-hairpin” is necessary for assembly of T-ag on the SV40 origin. Herein it is demonstrated that residues at the tip of the “beta-hairpin” are needed to melt the origin-flanking regions and that the T-ag helicase domain selectively assembles around one of the newly generated single strands in a manner that accounts for its 3′-to-5′ helicase activity. Furthermore, T-ags mutated at the tip of the “beta-hairpin” are defective for oligomerization on duplex DNA; however, they can assemble on hybrid duplex DNA or single-stranded DNA (ssDNA) substrates provided the strand containing the 3′ extension is present. Collectively, these experiments indicate that residues at the tip of the beta-hairpin generate ssDNA in the core origin and that the ssDNA is essential for subsequent oligomerization events. PMID:17287270

  14. Novel hepatitis B virus strain from a chimpanzee of Central Africa (Pan troglodytes troglodytes) with an unusual antigenicity of the core protein.

    PubMed

    Takahashi, K; Mishiro, S; Prince, A M

    2001-01-01

    We and others have previously reported a hepatitis B virus (HBV)-like hepadnavirus strain which seemed to be indigenous to West African chimpanzees (Pan troglodytes verus). After that, we obtained an HBsAg-positive serum sample from a chimpanzee from Central Africa, named Bassi, belonging to another subspecies (P. troglodytes troglodytes). The full-genome nucleotide sequence of the hepadnavirus from Bassi showed a significant difference (9-26%) from those so far reported from primates including humans, chimpanzees and gorillas, suggesting a novel strain. More interestingly, however, the core antigen (HBcAg) deduced from Bassi's sequence showed only 78-82% similarity to known primate strains at the amino acid level, whereas the other strains shared more than 90% similarity. HBcAg expressed from Bassi HBV failed to react with monoclonal antibodies that were directed at an epitope borne by codons 135-145 of HBcAg of conventional hepadnaviruses. This could explain why Bassi was negative for anti-HBc in a routine test. Here we report the novel HBV strain presumably indigenous to P. troglodytes troglodytes in Central Africa.

  15. Changes in Serum IgA Antibody Levels against the Glycopeptidolipid Core Antigen during Antibiotic Treatment of Mycobacterium avium Complex Lung Disease.

    PubMed

    Jhun, Byung Woo; Kim, Su-Young; Park, Hye Yun; Jeon, Kyeongman; Shin, Sung Jae; Koh, Won-Jung

    2017-03-28

    We evaluated serial changes in the levels of serum immunoglobulin A (IgA) antibody to the glycopeptidolipid (GPL) core antigen during antibiotic treatment in 57 patients with M. avium complex (MAC) lung disease, at baseline (T0) and after 3 months (T3) and 6 months (T6) of treatment. The median patient age was 59 years and 37 (65%) were female. Etiologic organisms included M. avium in 32 (56%) patients and M. intracellulare in 25 (44%). Seven (12%) patients had the fibrocavitary form of the disease on computed tomography. After 12 months of treatment, 42 (74%) patients achieved favorable responses, whereas 15 (26%) patients had unfavorable responses defined as no sputum culture conversion within 12 months of treatment. The initial median serum anti-GPL IgA levels in the 57 patients was 3.50 U/mL, and measurements at T0 (median 3.50 U/mL), T3 (median 2.71 U/mL), and T6 (median 2.61 U/mL) revealed significant decreases following treatment (P < 0.001). Multivariate analysis showed that an initially elevated anti-GPL IgA level (> 3.50 U/mL) was associated with an unfavorable response (P = 0.049). Our data suggest that elevated anti-GPL IgA levels may reflect disease activity, which may help to predict treatment response in patients with MAC lung disease.

  16. [The prevalence of hepatitis C antibodies among volunteer blood donors with elevated blood transaminase and antibodies to the B virus core antigen].

    PubMed

    Gavilán Carrasco, J C; González Santos, P; Rosario Díaz, E

    1996-05-01

    The use of non-specific markers before 1989 (increased serum transaminase values and antibodies to hepatitis B core antigen) as a screening method for blood donors in an attempt to decrease the incidence of post-transfusional non-A non-B hepatitis (currently hepatitis C virus) was a matter of controversy. To determine the impact of the use of these markers on the detection of blood donors infected with hepatitis C virus, a prospective study was undertaken in Málaga (1988-1989) with 5,003 volunteer donors with two objectives: a) to know the prevalence of these non-specific markers (anti-HBc and increased serum transaminase) and antibodies to HCV (anti-C100) in our blood donor population; b) to determine whether the presence of some of these non specific markers in blood donors was associated with a higher rate of virus C infection. The prevalence of antibodies to HCV in blood donors with increased serum transaminase and/or anti-HBc was significantly higher than the prevalence found among the general blood donor population.

  17. Replication of the Adjustment Scales for Children and Adolescents Core Syndrome Factor Structure

    ERIC Educational Resources Information Center

    Canivez, Gary L.

    2004-01-01

    Independent examination and replication of the core syndrome factor structure of the Adjustment Scales for Children and Adolescents (ASCA; McDermott, Marston, & Stott, 1993) is reported. A sample of 1,020 children were randomly selected from their classroom and rated on the ASCA by their teacher. The six ASCA core syndromes produced a…

  18. Linear antigenic regions of the structural proteins of human T-cell lymphotropic virus type I detected by enzyme-linked immunosorbent assays using synthetic peptides as antigens.

    PubMed Central

    Washitani, Y; Kuroda, N; Shiraki, H; Itoyama, Y; Sato, H; Ohshima, K; Kiyokawa, H; Maeda, Y

    1992-01-01

    We synthesized 46 sequential peptides 21 to 39 amino acids long over the structural protein of human T-cell leukemia virus type I (HTLV-I; the p19 and p24 gag protein and the gp46 and p20E env proteins) and tested their reactivities against antibodies in sera from HTLV-I healthy carriers and patients diagnosed as having human T-cell leukemia-lymphoma (ATLL) and myelopathy (HAM) by using an enzyme-linked immunosorbent assay. Of the 46 synthetic peptides, 18 peptides (2 corresponding to the p19 gag protein, 2 corresponding to the p24 gag protein, 8 corresponding to the gp46 env protein, and 6 corresponding to the p20E env protein) reacted with antibodies in the sera from HTLV-I healthy carriers. In particular, the peptides comprising amino acids 100 to 119 and 119 to 130 of the gag and 175 to 199, 213 to 236, 253 to 282, and 288 to 317 of the env proteins reacted with antibodies in sera from more than 30% of HTLV-I healthy carriers. These peptides also showed high reactivities to the antibodies in the sera from patients with ATLL and HAM. The results indicate that the predominant antigenic regions of the structural protein of HTLV-I were located at the C-terminal end of the p19 gag protein and the C-terminal half of the gp46 env protein, and the corresponding peptides proved to be useful antigens in detecting antibodies in the sera from individuals infected with HTLV-I. PMID:1537894

  19. Effects of core perturbations on the structure of the sun

    SciTech Connect

    Sweigart, A.V.

    1983-10-15

    A number of numerical experiments have been carried out in order to investigate the sensivity of the solar luminosity and radius to perturbations within the radiative core. In these experiments the core was perturbed by suddenly mixing various parts of the composition profile during evolutionary sequences for the present Sun. The hydrostatic readjustment caused by these ''mixing events'' induced an immediate change in the surface luminosity and radius on both the hydrodynamic time scale (approx.15 minutes) and the thermal time scale of the superadiabatic layers (approx.1 day). The subsequent evolution of the luminosity and radius perturbations was followed for 5 x 10/sup 5/ yr after each mixing event. The time-dependent behavior of these perturbations was found to depend on where the mixing event occurred. In all cases, however, the ratio W(t) = ..delta.. log R/..delta.. log L had an initial value of 0.71 and showed only a mild time dependence during the first several thousand years. Two other relationships between the luminosity and radius perturbations are also discussed. One of these, V(t) = (d log R/dd)/(d log L/dt), has a fairly constant value of 0.3 +- 0.1. Both perturbations in the mixing-length ratio ..cap alpha.. and perturbations in the magnetic pressure within the solar convective envelope yield the same value for V/(t). During the normal unperturbed evolution of the present Sun, V(t) = 0.4. Our results show that core perturbations such as the present mixing events cannot explain the decrease in the solar radius indicated by the solar eclipse data between 1925 and 1980.

  20. Blocking anthrax lethal toxin at the protective antigen channel by using structure-inspired drug design.

    PubMed

    Karginov, Vladimir A; Nestorovich, Ekaterina M; Moayeri, Mahtab; Leppla, Stephen H; Bezrukov, Sergey M

    2005-10-18

    Bacillus anthracis secretes three polypeptides: protective antigen (PA), lethal factor (LF), and edema factor (EF), which interact at the surface of mammalian cells to form toxic complexes. LF and EF are enzymes that target substrates within the cytosol; PA provides a heptameric pore to facilitate LF and EF transport into the cytosol. Other than administration of antibiotics shortly after exposure, there is currently no approved effective treatment for inhalational anthrax. Here we demonstrate an approach to disabling the toxin: high-affinity blockage of the PA pore by a rationally designed low-molecular weight compound that prevents LF and EF entry into cells. Guided by the sevenfold symmetry and predominantly negative charge of the PA pore, we synthesized small cyclic molecules of sevenfold symmetry, beta-cyclodextrins chemically modified to add seven positive charges. By channel reconstitution and high-resolution conductance recording, we show that per-6-(3-aminopropylthio)-beta-cyclodextrin interacts strongly with the PA pore lumen, blocking PA-induced transport at subnanomolar concentrations (in 0.1 M KCl). The compound protected RAW 264.7 mouse macrophages from cytotoxicity of anthrax lethal toxin (= PA + LF). More importantly, it completely protected the highly susceptible Fischer F344 rats from lethal toxin. We anticipate that this approach will serve as the basis for a structure-directed drug discovery program to find new and effective treatments for anthrax.

  1. A novel Cryptosporidium parvum antigen, CP2, preferentially associates with membranous structures.

    PubMed

    O'Hara, Steven P; Yu, Jae-Ran; Lin, Jim Jung-Ching

    2004-03-01

    The present study addresses the cloning and characterization of a Cryptosporidium parvum antigen, CP2. Sequencing of cDNA and genomic clones revealed a novel gene capable of coding a message of 2,136 nucleotides flanked by 28 and 140 nucleotides of the 5'- and 3'-noncoding regions, respectively. The deduced amino acid sequence suggests that CP2 is a secreted and/or membrane protein. Immunofluorescence microscopy detected CP2 enrichment in sporozoites that subsequently appeared to encase type I meronts in infected HCT-8 cells. Immunogold electron microscopy revealed that CP2 consistently localized to membranous structures throughout development. In addition, progression from macrogametocyte to sporulated oocyst revealed CP2 initially at the periphery of amylopectin-like granules, in the cytoplasm and discrete vesicles, the parasitophorous vacuole, on the surface of sporozoites, and finally on the parasitophorous vacuole membrane (PVM). The observed expression pattern suggests that CP2 may be involved in the invasion process and/or PVM integrity.

  2. Measuring Core/Facesheet Bond Toughness in Honeycomb Sandwich Structures

    NASA Technical Reports Server (NTRS)

    Nettles, A. T.

    2006-01-01

    This study examines two test methods to evaluate the peel toughness of the skin to core debond of sandwich panels. The methods tested were the climbing drum (CD) peel test and the double cantilever beam (DCB) test. While the CD peel test is only intended for qualitative measurements, it is shown in this study that qualitative measurements can be performed and compare well with DCB test data. It is also shown that artificially stiffening the facesheets of a DCB specimen can cause the test to behave more like a flatwise tensile test than a peel test.

  3. AIRS-observed warm core structures of tropical cyclones over the western North Pacific

    NASA Astrophysics Data System (ADS)

    Gao, Si; Chen, Baiqing; Li, Tim; Wu, Naigeng; Deng, Wenjian

    2017-03-01

    Atmospheric Infrared Sounder (AIRS) temperature profiles during the period 2003-2013 are used to examine the warm core structures and evolution characteristics associated with the formation and development of western North Pacific (WNP) tropical cyclones (TCs). The warm core with a steady 1.5-K warming in the layer of 500-300 hPa occurs 24 h prior to tropical storm formation. Apparent eye warming extends upward to upper troposphere and downward to near surface after tropical storm formation. TC intensity shows a robust positive correlation with the warm core strength and has a weaker but still significant positive correlation with the warm core height (the weaker correlation is primarily attributed to the scattered warm core heights of weak TCs). Future 24-h intensity change of TCs has little correlation with the warm core height while it has a significant negative correlation with the warm core strength. Weak to moderate warm core at 500-200 hPa may be a necessary but not sufficient initial condition for TC rapid intensification. AIRS-observed warm core structures, in combination with other environmental factors, have the potential to improve the prediction of tropical storm formation and rapid intensification of WNP TCs.

  4. THE STRUCTURE OF GAS-ACCRETING PROTOPLANETS AND THE CONDITION OF THE CRITICAL CORE MASS

    SciTech Connect

    Kanagawa, Kazuhiro D.; Fujimoto, Masayuki Y.

    2013-03-01

    In the core accretion model for the formation of gas giant planets, runaway gas accretion onto a core is the primary requisite, triggered when the core mass reaches a critical value. The recently revealed wide diversity of the extrasolar giant planets suggests the necessity to further the understanding of the conditions resulting in the critical core mass that initiates runaway accretion. We study the internal structure of protoplanets under hydrostatic and thermal equilibria represented in terms of a polytropic equation of state to investigate what factors determine and affect the critical core mass. We find that the protoplanets, embedded in protoplanetary disks, have the same configuration as red giants, characterized by the envelope of the centrally condensed type solution. Applying the theory of stellar structure with homology invariants, we demonstrate that there are three types of criteria for the critical core mass depending on the stiffness of polytrope and the nature of outer boundary condition. For the stiff polytropes of index N {<=} 3 with the Bondi radius as the outer boundary, the criterion governing the critical core mass occurs at the surface. For stiff polytropes with the Hill outer boundary and for soft polytropes of N > 3, this criterion acts at the bottom of gaseous envelope. Further, we elucidate the roles and effects of coexistent radiative and convective zones in the envelope of critical core mass. Based on the results, we discuss the relevance of Bondi and Hill surface conditions and explore the parameter dependences of critical core mass.

  5. The Antigenic Structure of Zika Virus and Its Relation to Other Flaviviruses: Implications for Infection and Immunoprophylaxis.

    PubMed

    Heinz, Franz X; Stiasny, Karin

    2017-03-01

    Zika virus was discovered ∼70 years ago in Uganda and maintained a low profile as a human disease agent in Africa and Asia. Only recently has it caused explosive outbreaks in previously unaffected regions, first in Oceania and then in the Americas since 2015. Of special concern is the newly identified link between congenital malformations (especially microcephaly) and Zika virus infections during pregnancy. At present, it is unclear whether Zika virus changed its pathogenicity or whether the huge number of infections allowed the recognition of a previously cryptic pathogenic property. The purpose of this review is to discuss recent data on the molecular antigenic structure of Zika virus in the context of antibody-mediated neutralization and antibody-dependent enhancement (ADE) of infection, a phenomenon that has been implicated in the development of severe disease caused by the related dengue viruses. Emphasis is given to epitopes of antibodies that potently neutralize Zika virus and also to epitopes that provide antigenic links to other important human-pathogenic flaviviruses such as dengue, yellow fever, West Nile, Japanese encephalitis, and tick-borne encephalitis viruses. The antigenic cross talk between Zika and dengue viruses appears to be of special importance, since they cocirculate in many regions of endemicity and sequential infections are likely to occur frequently. New insights into the molecular antigenic structure of Zika virus and flaviviruses in general have provided the foundation for great progress made in developing Zika virus vaccines and antibodies for passive immunization.

  6. Density-based and transport-based core-periphery structures in networks

    NASA Astrophysics Data System (ADS)

    Lee, Sang Hoon; Cucuringu, Mihai; Porter, Mason A.

    2014-03-01

    Networks often possess mesoscale structures, and studying them can yield insights into both structure and function. It is most common to study community structure, but numerous other types of mesoscale structures also exist. In this paper, we examine core-periphery structures based on both density and transport. In such structures, core network components are well-connected both among themselves and to peripheral components, which are not well-connected to anything. We examine core-periphery structures in a wide range of examples of transportation, social, and financial networks—including road networks in large urban areas, a rabbit warren, a dolphin social network, a European interbank network, and a migration network between counties in the United States. We illustrate that a recently developed transport-based notion of node coreness is very useful for characterizing transportation networks. We also generalize this notion to examine core versus peripheral edges, and we show that the resulting diagnostic is also useful for transportation networks. To examine the properties of transportation networks further, we develop a family of generative models of roadlike networks. We illustrate the effect of the dimensionality of the embedding space on transportation networks, and we demonstrate that the correlations between different measures of coreness can be very different for different types of networks.

  7. Synthesis of core-shell structured magnetic nanoparticles with a carbide shell

    NASA Astrophysics Data System (ADS)

    Hou, Shushan; Chi, Yue; Zhao, Zhankui

    2017-03-01

    Core-shell structured materials combining the functionalities of the core and shell have great application potential in many fields. In this work, by combining solvothermal, polymerization and the high temperature carbonization, we have successfully developed a facile method to generate core-shell structured nanoparticles which possess an internal magnetic nanoparticle with a carbide shell. The thickness of resorcinol formaldehyde resin as intermediate transition shell could be easily adjusted by changing the concentration of the RF precursor. The resulting nanoparticles possess well-defined structure, uniform size and high magnetization. The unique nanostructure of the magnetic core-shell structured nanoparticles could lead to many promising applications in areas ranging from drug delivery to the purifyication of sewage.

  8. Structure and electronic properties of mixed (a + c) dislocation cores in GaN

    SciTech Connect

    Horton, M. K.; Rhode, S. L.; Moram, M. A.

    2014-08-14

    Classical atomistic models and atomic-resolution scanning transmission electron microscopy studies of GaN films reveal that mixed (a + c)-type dislocations have multiple different core structures, including a dissociated structure consisting of a planar fault on one of the (12{sup ¯}10) planes terminated by two different partial dislocations. Density functional theory calculations show that all cores introduce localized states into the band gap, which affects device performance.

  9. Serum HBV core-related antigen is a good predictor for spontaneous HBeAg seroconversion in chronic hepatitis B patients.

    PubMed

    Song, Guangjun; Yang, Ruifeng; Rao, Huiying; Feng, Bo; Ma, Hui; Jin, Qian; Wei, Lai

    2017-03-01

    Early prediction of spontaneous hepatitis B virus e antigen (HBeAg) seroconversion is pivotal in the prevention of unnecessary drug prescription, corresponding financial burden, and adverse reactions. One hundred and thirteen chronic hepatitis B patients with HBeAg-positive in the immune active phase were followed up for about 1.5 years. Patients were classified into two groups: spontaneous HBeAg seroconversion group (group A, n = 18) and non-spontaneous HBeAg seroconversion group. Among the non-spontaneous HBeAg seroconversion group, 35 patients were selected as controls (group B, n = 35). At week 12, there was a significant difference in hepatitis B core-related antigen (HBcrAg) levels between the two groups (group A 4.32 ± 1.05 log10  kU/ml, and group B 5.16 ± 0.53 log10  kU/ml, P = 0.004), and this significance magnified at week 28. Only two variables, HBcrAg level and the reduction in the HBcrAg levels (ΔHBcrAg) at week 28 were enrolled, with the odds ratio of 4.19 and 0.21, respectively. The optimal cutoffs of HBcrAg levels and the ΔHBcrAg at week 28 were 4.90 and 2.00 log10  kU/ml, respectively. The positive predictive value and negative predictive value of HBcrAg levels at week 28 were 73.9% and 96.7%, respectively. The positive predictive value and negative predictive value of the ΔHBcrAg at week 28 were 76.2% and 93.8%, respectively. The measurement of HBcrAg is useful for monitoring the natural course of chronic hepatitis B virus infection. The dynamics of HBcrAg levels could accurately predict the spontaneous HBeAg seroconversion. J. Med. Virol. 89:463-468, 2017. © 2016 Wiley Periodicals, Inc.

  10. Podosomes of dendritic cells facilitate antigen sampling

    PubMed Central

    Reinieren-Beeren, Inge; Cambi, Alessandra; Figdor, Carl G.; van den Bogaart, Geert

    2014-01-01

    Summary Dendritic cells sample the environment for antigens and play an important role in establishing the link between innate and acquired immunity. Dendritic cells contain mechanosensitive adhesive structures called podosomes that consist of an actin-rich core surrounded by integrins, adaptor proteins and actin network filaments. They facilitate cell migration via localized degradation of extracellular matrix. Here we show that podosomes of human dendritic cells locate to spots of low physical resistance in the substrate (soft spots) where they can evolve into protrusive structures. Pathogen recognition receptors locate to these protrusive structures where they can trigger localized antigen uptake, processing and presentation to activate T-cells. Our data demonstrate a novel role in antigen sampling for podosomes of dendritic cells. PMID:24424029

  11. Podosomes of dendritic cells facilitate antigen sampling.

    PubMed

    Baranov, Maksim V; Ter Beest, Martin; Reinieren-Beeren, Inge; Cambi, Alessandra; Figdor, Carl G; van den Bogaart, Geert

    2014-03-01

    Dendritic cells sample the environment for antigens and play an important role in establishing the link between innate and acquired immunity. Dendritic cells contain mechanosensitive adhesive structures called podosomes that consist of an actin-rich core surrounded by integrins, adaptor proteins and actin network filaments. They facilitate cell migration via localized degradation of extracellular matrix. Here, we show that podosomes of human dendritic cells locate to spots of low physical resistance in the substrate (soft spots) where they can evolve into protrusive structures. Pathogen recognition receptors locate to these protrusive structures where they can trigger localized antigen uptake, processing and presentation to activate T-cells. Our data demonstrate a novel role in antigen sampling for the podosomes of dendritic cells.

  12. Structural Evolution of Core-Shell Gold Nanoclusters: Aun(-) (n = 42-50).

    PubMed

    Pande, Seema; Huang, Wei; Shao, Nan; Wang, Lei-Ming; Khetrapal, Navneet; Mei, Wai-Ning; Jian, Tian; Wang, Lai-Sheng; Zeng, Xiao Cheng

    2016-11-22

    Gold nanoclusters have attracted great attention in the past decade due to their remarkable size-dependent electronic, optical, and catalytic properties. However, the structures of large gold clusters are still not well-known because of the challenges in global structural searches. Here we report a joint photoelectron spectroscopy (PES) and theoretical study of the structural evolution of negatively charged core-shell gold nanoclusters (Aun(-)) for n = 42-50. Photoelectron spectra of size-selected Aun(-) clusters are well resolved with distinct spectral features, suggesting a dominating structural type. The combined PES data and density functional calculations allow us to systematically identify the global minimum or candidates of the global minima of these relatively large gold nanoclusters, which are found to possess low-symmetry structures with gradually increasing core sizes. Remarkably, the four-atom tetrahedral core, observed first in Au33(-), continues to be highly robust and is even present in clusters as large as Au42(-). Starting from Au43(-), a five-atom trigonal bipyramidal core appears and persists until Au47(-). Au48(-) possesses a six-atom core, while Au49(-) and Au50(-) feature seven- and eight-atom cores, respectively. Notably, both Au46(-) and Au47(-) contain a pyramidal Au20 motif, which is stacked with another truncated pyramid by sharing a common 10-atom triangular face. The present study sheds light on our understanding of the structural evolution of the medium-sized gold nanoclusters, the shells and core as well as how the core-shell structures may start to embrace the golden pyramid (bulk-like) fragment.

  13. Time-Dependent Inner Core Structures Examined by Repeating Earthquakes in the Southwest Pacific Subduction Zones

    NASA Astrophysics Data System (ADS)

    Yu, W. C.

    2014-12-01

    Time-dependent inner core structure is interpreted as differential rotation of the Earth's inner core. This inference is made on the basis of variations deviated from an isotropic and homogeneous inner core structure and the amount of velocity perturbations progressively evolving as a function of calendar time. Most compelling evidences for inner core rotation come from the inner core structures beneath Colombia and Venezuela, characterized by strong anisotropy and lateral variation, for the South Sandwich Islands earthquakes recorded by College (COL) and other seismic stations in Alaska. Repeating earthquakes with highly similar waveforms can minimize the potential artifacts due to inter-event separation and unknown short-scale mantle heterogeneities, and can acquire robust measurement of time shift due to temporal change of inner core structures. Moderate repeating earthquake sequences (RES) in the Tonga-Kermadec-Vanuatu in the southwest Pacific subduction zones are studied over a 20-year time window between 1990 and 2009. I select 13 RES consisting of two or three events with time separation of 2 - 14.4 years and analyze the PKiKP-PKPdf, PKPbc-PKPdf, and PKPab-PKPdf phase pairs recorded by the European, African, and central Asian stations sampling the eastern hemisphere of the inner core. I measure the double differential time of the phase pairs using waveform cross-correlation. Majority of the double differential time measurements within ±50 millisecond can largely be explained by the time shift due to inter-event distance on the order of hundreds of meters or less and null change of the PKPdf phase. These observations indicate inner core structures in the eastern hemisphere are uniform and probably insensitive to motion of the inner core.

  14. Polymeric structure and host Toll-like receptor 4 dictate immunogenicity of NY-ESO-1 antigen in vivo.

    PubMed

    Liu, Yanan; Tian, Xiaoli; Leitner, Wolfgang W; Aldridge, Michael E; Zheng, Junying; Yu, Zhiya; Restifo, Nicholas P; Weiss, Richard; Scheiblhofer, Sandra; Xie, Chong; Sun, Ren; Cheng, Genhong; Zeng, Gang

    2011-10-28

    In search of intrinsic factors that contribute to the distinctively strong immunogenicity of a non-mutated cancer/testis antigen, we found that NY-ESO-1 forms polymeric structures through disulfide bonds. NY-ESO-1 binding to immature dendritic cells was dependent on its polymeric structure and involved Toll-like receptor-4 (TLR4) on the surface of immature dendritic cells in mouse and human. Gene gun-delivered plasmid encoding the wild-type NY-ESO-1 readily induced T cell-dependent antibody (Ab) responses in wild-type C57BL/10 mice but not TLR4-knock-out C57BL/10ScNJ mice. Disrupting polymeric structures of NY-ESO-1 by cysteine-to-serine (Cys-to-Ser) substitutions lead to diminished immunogenicity and altered TLR4-dependence in the induced Ab response. To demonstrate its adjuvant effect, NY-ESO-1 was fused with a major mugwort pollen allergen Art v 1 and a tumor-associated antigen, carbonic anhydrase 9. Plasmid DNA vaccines encoding the fusion genes generated robust immune responses against otherwise non-immunogenic targets in mice. Polymeric structure and TLR4 may play important roles in rendering NY-ESO-1 immunogenic and thus serve as a potent molecular adjuvant. NY-ESO-1 thus represents the first example of a cancer/testis antigen that is a also damage-associated molecular pattern.

  15. Structure, Receptor Binding, and Antigenicity of Influenza Virus Hemagglutinins from the 1957 H2N2 Pandemic

    SciTech Connect

    Xu, Rui; McBride, Ryan; Paulson, James C.; Basler, Christopher F.; Wilson, Ian A.

    2010-03-04

    The hemagglutinin (HA) envelope protein of influenza viruses mediates essential viral functions, including receptor binding and membrane fusion, and is the major viral antigen for antibody neutralization. The 1957 H2N2 subtype (Asian flu) was one of the three great influenza pandemics of the last century and caused 1 million deaths globally from 1957 to 1968. Three crystal structures of 1957 H2 HAs have been determined at 1.60 to 1.75 {angstrom} resolutions to investigate the structural basis for their antigenicity and evolution from avian to human binding specificity that contributed to its introduction into the human population. These structures, which represent the highest resolutions yet recorded for a complete ectodomain of a glycosylated viral surface antigen, along with the results of glycan microarray binding analysis, suggest that a hydrophobicity switch at residue 226 and elongation of receptor-binding sites were both critical for avian H2 HA to acquire human receptor specificity. H2 influenza viruses continue to circulate in birds and pigs and, therefore, remain a substantial threat for transmission to humans. The H2 HA structure also reveals a highly conserved epitope that could be harnessed in the design of a broader and more universal influenza A virus vaccine.

  16. Antigenic structure of human hepatitis A virus defined by analysis of escape mutants selected against murine monoclonal antibodies.

    PubMed Central

    Ping, L H; Lemon, S M

    1992-01-01

    We examined the antigenic structure of human hepatitis A virus (HAV) by characterizing a series of 21 murine monoclonal-antibody-resistant neutralization escape mutants derived from the HM175 virus strain. The escape phenotype of each mutant was associated with reduced antibody binding in radioimmunofocus assays. Neutralization escape mutations were identified at the Asp-70 and Gln-74 residues of the capsid protein VP3, as well as at Ser-102, Val-171, Ala-176, and Lys-221 of VP1. With the exception of the Lys-221 mutants, substantial cross-resistance was evident among escape mutants tested against a panel of 22 neutralizing monoclonal antibodies, suggesting that the involved residues contribute to epitopes composing a single antigenic site. As mutations at one or more of these residues conferred resistance to 20 of 22 murine antibodies, this site appears to be immunodominant in the mouse. However, multiple mutants selected independently against any one monoclonal antibody had mutations at only one or, at the most, two amino acid residues within the capsid proteins, confirming that there are multiple epitopes within this antigenic site and suggesting that single-amino-acid residues contributing to these epitopes may play key roles in the binding of individual antibodies. A second, potentially independent antigenic site was identified by three escape mutants with different substitutions at Lys-221 of VP1. These mutants were resistant only to antibody H7C27, while H7C27 effectively neutralized all other escape mutants. These data support the existence of an immunodominant neutralization site in the antigenic structure of hepatitis A virus which involves residues of VP3 and VP1 and a second, potentially independent site involving residue 221 of VP1. PMID:1312628

  17. On the noise transmission and control for a cylindrical chamber core composite structure

    NASA Astrophysics Data System (ADS)

    Li, Deyu; Vipperman, Jeffrey S.

    2005-11-01

    The vibroacoustic properties, sound transmission behavior, and noise transmission control of a novel chamber core composite cylinder are studied. An approximate uniform shell model of the sandwich cylindrical chamber core structure is developed to aid in the calculation of the ring frequency and external critical frequency. Acoustic modal parameters are analytically and experimentally obtained. The structural modal parameters are identified from measured data. The coupling between structural and acoustic modes is investigated. The sound transmission into the cylindrical chamber core is experimentally characterized, where the stiffness-, cavity resonance-, mass-, and coincidence-controlled zones are identified. Finally, the addition of fills to the wall chambers of the chamber core is investigated as a part of passive control study, which also serves to corroborate the model development.

  18. X-ray imaging of vortex cores in confined magnetic structures

    SciTech Connect

    Fischer, P; Im, M -Y; Kasai, S; Yamada, K; Ono, T; Thiaville, A

    2011-02-11

    Cores of magnetic vortices in micron-sized NiFe disk structures, with thicknesses between 150 and 50 nm, were imaged and analyzed by high-resolution magnetic soft x-ray microscopy. A decrease of the vortex-core radius was observed from approximately 38 to 18 nm with decreasing disk thickness. By comparing with full three-dimensional micromagnetic simulations showing the well-known barrel structure, we obtained excellent agreement, taking into account instrumental broadening and a small perpendicular anisotropy. The proven magnetic spatial resolution of better than 25 nm was sufficient to identify a negative dip close to the vortex core, originating from stray fields of the core. Magnetic vortex structures can serve as test objects for evaluating sensitivity and spatial resolution of advanced magnetic microscopy techniques.

  19. Structure and genetics of the O-antigen of Enterobacter cloacae G3054 containing di-N-acetylpseudaminic acid.

    PubMed

    Perepelov, Andrei V; Wang, Min; Filatov, Andrei V; Guo, Xi; Shashkov, Alexander S; Wang, Lei; Knirel, Yuriy A

    2015-04-30

    Mild acid degradation of the lipopolysaccharide of Enterobacter cloacae G3054 resulted in the cleavage of the O-polysaccharide at the linkage of residues of 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-non-2-ulosonic acid (di-N-acetylpseudaminic acid, Pse5Ac7Ac) in the main chain. The resultant oligosaccharide and an alkali-treated lipopolysaccharide were studied by sugar analysis along with (1)H and (13)C NMR spectroscopy, and the following structure of the branched pentasaccharide O-unit of the O-polysaccharide was established: [structure: see text] The O-antigen gene cluster of E. cloacae G3054 between conserved genes galF and gnd was sequenced. Most genes necessary for the O-antigen synthesis were found in the cluster and their functions were tentatively assigned by comparison with sequences in the available databases.

  20. [Scattering properties of core-shell structure of mist wrapped dust particles].

    PubMed

    Feng, Shi-qi; Song, Wei; Wang, Yan; Miao, Xin-hui; Xu, Li-jun; Liu, Yu; Li, Cheng; Li Wen-long; Wang, Yi-ran; Cai, Hong-xing

    2014-12-01

    The authors have investigated the optical properties of core-shell structure of mist wrapped dust particles based on the method of discrete dipole approximation (DDA). The influence on the thickness of the elliptical core-shell structure were calculated which the ratio of long axis and short axis is 2:1, and the change of scattering angle for scattering characteristics. The results shows that the thickness of outer layer increase from 1.2 to 4.8 μm with the scattering and extinction coefficient of double core-shell layers particles decrease from 3.4 and 3.43 to 2.543 and 2.545, when the size of inner core isn't change. And scattering relative strength also increased obviously. The thickness of inner core increase from 0.6 to 2.4 μm with the of scattering and extinction coefficient change from 2.59 and 2.88 to 2.6 and 2.76 when thickness of outer remain constant. Effect of the thickness of visible outer layer on the scattering characteristics of double core-shell layers particles is greater, because of the interaction between scattering light and outer materials. The scattering relative intensity decrease with wavelength increased, while increased with the scale of core-shell structure increase. The results make a promotion on the study of the transportation characteristics of laser and scattering characteristics when the atmospheric aerosol and water mist interact together.

  1. A novel sandwich electrochemiluminescence immunosensor for ultrasensitive detection of carbohydrate antigen 19-9 based on immobilizing luminol on Ag@BSA core/shell microspheres.

    PubMed

    Zhang, Amin; Xiang, Hongkun; Zhang, Xin; Guo, Weiwei; Yuan, Enhui; Huang, Chusen; Jia, Nengqin

    2016-01-15

    A novel sandwich-type electrochemiluminescence immunosensor based on immobilizing luminol on Ag@BSA core/shell microspheres (Ag@BSA-luminol) for ultrasensitive detection of tumor marker carbohydrate antigen 19-9 (CA19-9) has been developed. Herein, magnetic carbon nanotubes (MAGCNTs) decorated with polyethylenimine (PEI) was used to construct the base of the immunosensor. MAGCNTs with prominent electrical conductivity and high surface area could be beneficial for promoting the electron transfer and loading plenty of primary antibodies (Ab1) via glutaraldehyde (GA). Meanwhile, the magnetic property of MAGCNTs makes it easy to be attached to the surface of magnetic glass carbon electrode (MGCE) through magnetism interaction, which provides an outstanding platform for this immunosensor. Moreover, Ag@BSA microspheres with large surface area, good stability, and excellent biocompatibility were desirable candidates for effective cross-link of CA19-9 detection antibodies (Ab2). A more interesting thing was that ELISA color reaction was used as an ultrasensitive strategy for identifying Ab2 was successfully coated on Ag@BSA with the naked eye. Additionally, we immobilized the luminol on the surface of Ag@BSA to prepare the target immunosensor. Immobilization of luminol on the surface of Ag@BSA could decrease the distance between luminophores and the electrode surface, leading to great enhancement of the ECL intensity of luminol in the present of hydrogen peroxide (H2O2). Under the optimal conditions, the intensity of the ECL immunosensor increased linearly with the logarithm of CA19-9 concentration in a wide linear range from 0.0005 to 150UmL(-1) with a detection limit of 0.0002UmL(-1) (S/N=3). All the results suggested the prepared CA19-9 immunosensor displayed high sensitivity, excellent stability and good specificity. The developed method opened a new avenue to clinical bioassay.

  2. Physical property data from the ICDP-USGS Eyreville cores A and B, Chesapeake Bay impact structure, Virginia, USA, acquired using a multisensor core logger

    USGS Publications Warehouse

    Pierce, H.A.; Murray, J.B.

    2009-01-01

    The International Continental Scientific Drilling Program (ICDP) and the U.S. Geological Survey (USGS) drilled three core holes to a composite depth of 1766 m within the moat of the Chesapeake Bay impact structure. Core recovery rates from the drilling were high (??90%), but problems with core hole collapse limited the geophysical downhole logging to natural-gamma and temperature logs. To supplement the downhole logs, ??5% of the Chesapeake Bay impact structure cores was processed through the USGS GeoTek multisensor core logger (MSCL) located in Menlo Park, California. The measured physical properties included core thickness (cm), density (g cm-3), P-wave velocity (m s-1), P-wave amplitude (%), magnetic susceptibility (cgs), and resistivity (ohm-m). Fractional porosity was a secondary calculated property. The MSCL data-sampling interval for all core sections was 1 cm longitudinally. Photos of each MSCL sampled core section were imbedded with the physical property data for direct comparison. These data have been used in seismic, geologic, thermal history, magnetic, and gravity models of the Chesapeake Bay impact structure. Each physical property curve has a unique signature when viewed over the full depth of the Chesapeake Bay impact structure core holes. Variations in the measured properties reflect differences in pre-impact target-rock lithologies and spatial variations in impact-related deformation during late-stage crater collapse and ocean resurge. ?? 2009 The Geological Society of America.

  3. Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor.

    PubMed

    Streltsov, V A; Varghese, J N; Carmichael, J A; Irving, R A; Hudson, P J; Nuttall, S D

    2004-08-24

    The Ig new antigen receptors (IgNARs) are single-domain antibodies found in the serum of sharks. Here, we report 2.2- and 2.8-A structures of the type 2 IgNAR variable domains 12Y-1 and 12Y-2. Structural features include, first, an Ig superfamily topology transitional between cell adhesion molecules, antibodies, and T cell receptors; and, second, a vestigial complementarity-determining region 2 at the "bottom" of the molecule, apparently discontinuous from the antigen-binding paratope and similar to that observed in cell adhesion molecules. Thus, we suggest that IgNARs originated as cell-surface adhesion molecules coopted to the immune repertoire and represent an evolutionary lineage independent of variable heavy chain/variable light chain type antibodies. Additionally, both 12Y-1 and 12Y-2 form unique crystallographic dimers, predominantly mediated by main-chain framework interactions, which represent a possible model for primordial cell-based interactions. Unusually, the 12Y-2 complementarity-determining region 3 also adopts an extended beta-hairpin structure, suggesting a distinct selective advantage in accessing cryptic antigenic epitopes.

  4. Structures of ribonuclease P RNAs of Vibrio core species.

    PubMed

    Maeda, T; Furushita, M; Hamamura, K; Shiba, T

    2001-05-01

    The structures of an RNA component of ribonuclease P (RNase P RNA) were examined for Vibrio parahaemolyticus, Vibrio alginolyticus, Vibrio carchariae, Vibrio natriegens, Vibrio campbellii, Vibrio proteolyticus, Vibrio pelagius and Vibrio harveyi to clearly determine their genetic differences. The RNase P RNAs ranged from 382 to 454 nucleotides (nt) in size, and were remarkably different from each other in the structure of two helices, P3 and P12. The P3 helices were comprised of tandem repeats of a palindromic sequence (24 nt), resulting in the longitudinal repetition of a stem structure. The number of repetitions ranged from four in V. harveyi, to one in both V. alginolyticus and V. proteolyticus. The genes for the RNase P RNAs of all species were located between two open reading frames, the amino acid sequences of which were similar to the hypothetical proteins located at 70.92 and 1.94 min in the Escherichia coli chromosome.

  5. Nanowire-in-microtube structured core/shell fibers via multifluidic coaxial electrospinning.

    PubMed

    Chen, Hongyan; Wang, Nü; Di, Jiancheng; Zhao, Yong; Song, Yanlin; Jiang, Lei

    2010-07-06

    A multifluidic coaxial electrospinning approach is reported here to fabricate core/shell ultrathin fibers with a novel nanowire-in-microtube structure from more optional fluid pairs than routine coaxial electrospinning. The advantage of this approach lies in the fact that it introduces an extra middle fluid between the core and shell fluids of traditional coaxial electrospinning, which can work as an effective spacer to decrease the interaction of the other two fluids. Under the protection of a proper middle fluid, more fluid pairs, even mutually miscible fluids, can be operated to generate "sandwich"-structured ultrathin fibers with a sharp boundary between the core and shell materials. It thereby largely extends the scope of optional materials. Selectively removing the middle layer of the as-prepared fibers results in an interesting nanowire-in-microtube structure. Either homogeneous or heterogeneous fibers with well-tailored sandwich structures have been successfully fabricated. This method is an important extension of traditional co-electrospinning that affords a more universal avenue to preparing core/shell fibers; moreover, the special hollow cavity structure may introduce some extra properties into the conventional core/shell structure, which may find potential applications such as optical applications, microelectronics, and others.

  6. Small Angle Neutron-Scattering Studies of the Core Structure of Intact Neurosecretory Vesicles.

    NASA Astrophysics Data System (ADS)

    Krueger, Susan Takacs

    Small angle neutron scattering (SANS) was used to study the state of the dense cores within intact neurosecretory vesicles. These vesicles transport the neurophysin proteins, along with their associated hormones, oxytocin or vasopressin, from the posterior pituitary gland to the bloodstream, where the entire vesicle contents are released. Knowledge of the vesicle core structure is important in developing an understanding of this release mechanism. Since the core constituents exist in a dense state at concentrations which cannot be reproduced (in solution) in the laboratory, a new method was developed to determine the core structure from SANS experiments performed on intact neurosecretory vesicles. These studies were complemented by biochemical assays performed to determine the role, if any, played by phospholipids in the interactions between the core constituents. H_2O/D_2 O ratio in the solvent can be adjusted, using the method of contrast variation, such that the scattering due to the vesicle membranes is minimized, thus emphasizing the scattering originating from the cores. The applicability of this method for examining the interior of biological vesicles was tested by performing an initial study on human red blood cells, which are similar in structure to other biological vesicles. Changes in intermolecular hemoglobin interactions, occurring when the ionic strength of the solvent was varied or when the cells were deoxygenated, were examined. The results agreed with those expected for dense protein solutions, indicating that the method developed was suitable for the study of hemoglobin within the cells. Similar SANS studies were then performed on intact neurosecretory vesicles. The experimental results were inconsistent with model calculations which assumed that the cores consisted of small, densely-packed particles or large, globular aggregates. Although a unique model could not be determined, the data suggest that the core constituents form long aggregates of

  7. Establishing the Structural Integrity of Core-Shell Nanoparticles against Elemental Migration using Luminescent Lanthanide Probes.

    PubMed

    Chen, Bing; Peng, Dengfeng; Chen, Xian; Qiao, Xvsheng; Fan, Xianping; Wang, Feng

    2015-10-19

    Core-shell structured nanoparticles are increasingly used to host luminescent lanthanide ions but the structural integrity of these nanoparticles still lacks sufficient understanding. Herein, we present a new approach to detect the diffusion of dopant ions in core-shell nanostructures using luminescent lanthanide probes whose emission profile and luminescence lifetime are sensitive to the chemical environment. We show that dopant ions in solution-synthesized core-shell nanoparticles are firmly confined in the designed locations. However, annealing at certain temperatures (greater than circa 350 °C) promotes diffusion of the dopant ions and leads to degradation of the integrity of the nanoparticles. These insights into core-shell nanostructures should enhance our ability to understand and use lanthanide-doped luminescent nanoparticles.

  8. Guided wave propagation in a honeycomb composite sandwich structure in presence of a high density core.

    PubMed

    Sikdar, Shirsendu; Banerjee, Sauvik

    2016-09-01

    A coordinated theoretical, numerical and experimental study is carried out in an effort to interpret the characteristics of propagating guided Lamb wave modes in presence of a high-density (HD) core region in a honeycomb composite sandwich structure (HCSS). Initially, a two-dimensional (2D) semi-analytical model based on the global matrix method is used to study the response and dispersion characteristics of the HCSS with a soft core. Due to the complex structural characteristics, the study of guided wave (GW) propagation in HCSS with HD-core region inherently poses many challenges. Therefore, a numerical simulation of GW propagation in the HCSS with and without the HD-core region is carried out, using surface-bonded piezoelectric wafer transducer (PWT) network. From the numerical results, it is observed that the presence of HD-core significantly decreases both the group velocity and the amplitude of the received GW signal. Laboratory experiments are then conducted in order to verify the theoretical and numerical results. A good agreement between the theoretical, numerical and experimental results is observed in all the cases studied. An extensive parametric study is also carried out for a range of HD-core sizes and densities in order to study the effect due to the change in size and density of the HD zone on the characteristics of propagating GW modes. It is found that the amplitudes and group velocities of the GW modes decrease with the increase in HD-core width and density.

  9. Structure and thermodynamics of core-softened models for alcohols

    SciTech Connect

    Munaò, Gianmarco; Urbic, Tomaz

    2015-06-07

    The phase behavior and the fluid structure of coarse-grain models for alcohols are studied by means of reference interaction site model (RISM) theory and Monte Carlo simulations. Specifically, we model ethanol and 1-propanol as linear rigid chains constituted by three (trimers) and four (tetramers) partially fused spheres, respectively. Thermodynamic properties of these models are examined in the RISM context, by employing closed formulæ for the calculation of free energy and pressure. Gas-liquid coexistence curves for trimers and tetramers are reported and compared with already existing data for a dimer model of methanol. Critical temperatures slightly increase with the number of CH{sub 2} groups in the chain, while critical pressures and densities decrease. Such a behavior qualitatively reproduces the trend observed in experiments on methanol, ethanol, and 1-propanol and suggests that our coarse-grain models, despite their simplicity, can reproduce the essential features of the phase behavior of such alcohols. The fluid structure of these models is investigated by computing radial distribution function g{sub ij}(r) and static structure factor S{sub ij}(k); the latter shows the presence of a low−k peak at intermediate-high packing fractions and low temperatures, suggesting the presence of aggregates for both trimers and tetramers.

  10. Structure and thermodynamics of core-softened models for alcohols.

    PubMed

    Munaò, Gianmarco; Urbic, Tomaz

    2015-06-07

    The phase behavior and the fluid structure of coarse-grain models for alcohols are studied by means of reference interaction site model (RISM) theory and Monte Carlo simulations. Specifically, we model ethanol and 1-propanol as linear rigid chains constituted by three (trimers) and four (tetramers) partially fused spheres, respectively. Thermodynamic properties of these models are examined in the RISM context, by employing closed formulæ for the calculation of free energy and pressure. Gas-liquid coexistence curves for trimers and tetramers are reported and compared with already existing data for a dimer model of methanol. Critical temperatures slightly increase with the number of CH2 groups in the chain, while critical pressures and densities decrease. Such a behavior qualitatively reproduces the trend observed in experiments on methanol, ethanol, and 1-propanol and suggests that our coarse-grain models, despite their simplicity, can reproduce the essential features of the phase behavior of such alcohols. The fluid structure of these models is investigated by computing radial distribution function gij(r) and static structure factor Sij(k); the latter shows the presence of a low-k peak at intermediate-high packing fractions and low temperatures, suggesting the presence of aggregates for both trimers and tetramers.

  11. Ising nanowires with simple core-shell structure; Their characteristic phenomena

    NASA Astrophysics Data System (ADS)

    Kaneyoshi, T.

    2016-09-01

    The phase diagrams and magnetizations of Ising nanowires with simple core-shell structure are investigated by the use of the effective field theory with correlations. A lot of characteristic behaviors observed in ferromagnetic and ferrimagnetic materials as well as novel phenomena have been obtained, although one section of the system is consisted of one spin-1/2 surface shell atom and one spin-1/2 core atom and they are coupled with a positive or a negative shell-core exchange interaction.

  12. How is kinematic structure connected to the core scale from filament scale?; Mopra mapping observations with multi-lines of dense cores in Lupus I

    NASA Astrophysics Data System (ADS)

    Kiyokane, Kazuhiro; Saito, Masao; Tachihara, Kengo; Saigo, Kazuya; van Kempen, Tim; Cortes, Paulo; Hill, Tracey; Knee, Lewis; Kurono, Yasutaka; Takahashi, Satoko; Aya, Higuchi; Nyman, Lars-Ake

    2014-06-01

    Recently, high sensitivity mappings of nearby molecular clouds in far-infrared and submillimeter wavelengths with Hershel and AzTEC/ASTE show ubiquitous existence of the filamentary structures with 0.1-pc uniform width. It is important to investigate dense core formation from large scale structure via fragmentation. We have conducted MOPRA multi-line mapping observations covered on 0.02 - 0.2 pc scales of 8 dense cores in a filamentary cloud of nearby Lupus I at 140 pc. A class 0/I protostellar core IRAS 15398-3359 is included as a sample, which has an adjacent prestellar core with the separation of 0.13pc in the west. The maps of N2H+, HNC, HC3N show well associated with each core. The velocity field of C18O shows 1.4 km/s/pc from north to south over the region containing two dense cores, which is consistent with past observation of NANTEN. In contrast to C18O results, the velocity field of HC3N shows different structures, which suggest counter rotation of two dense cores; 1.2 km/s/pc from north-west to south-east around a protostellar core and 0.8 km/s/pc from east to west around a presteller core. The filament will be fragmentized and collapsed to dense cores when the line density is over 2Cs/G (where Cs is sound speed and G is gravitational constant). If that velocity gradient was caused by such situation, it should be red-blue-red-blue across two dense cores but the observed kinematics is not consistent with this scenario, which requires that the filament structure would be extremely curved with a skew angle. Although we cannot reject the collapsing interruption, those results suggest the spin-up rotating picture separated from large-scale structure.

  13. Crystal structure to 2.45 A resolution of a monoclonal Fab specific for the Brucella A cell wall polysaccharide antigen.

    PubMed

    Rose, D R; Przybylska, M; To, R J; Kayden, C S; Oomen, R P; Vorberg, E; Young, N M; Bundle, D R

    1993-07-01

    The atomic structure of an antibody antigen-binding fragment (Fab) at 2.45 A resolution shows that polysaccharide antigen conformation and Fab structure dictated by combinatorial diversity and domain association are responsible for the fine specificity of the Brucella-specific antibody, YsT9.1. It discriminates the Brucella abortus A antigen from the nearly identical Brucella melitensis M antigen by forming a groove-type binding site, lined with tyrosine residues, that accommodates the rodlike A antigen but excludes the kinked structure of the M antigen, as envisioned by a model of the antigen built into the combining site. The variable-heavy (VH) and variable-light (VL) domains are derived from genes closely related to two used in previously solved structures, M603 and R19.9, respectively. These genes combine in YsT9.1 to form an antibody of totally different specificity. Comparison of this X-ray structure with a previously built model of the YsT9.1 combining site based on these homologies highlights the importance of VL:VH association as a determinant of specificity and suggests that small changes at the VL:VH interface, unanticipated in modeling, may cause significant modulation of binding-site properties.

  14. Noise control for a ChamberCore cylindrical structure using long T-shaped acoustic resonators

    NASA Astrophysics Data System (ADS)

    Li, Deyu; Vipperman, Jeffrey S.

    2003-10-01

    The Air Force Research Laboratory, Space Vehicles Directorate has developed a new advanced composite launch vehicle fairing (referred to as ``ChamberCore''). The ChamberCore is sandwich-type structure fabricated from multi-layered composite face sheets separated by channels that form passive acoustic chambers. These acoustic chambers have a potential to create an acoustic resonator network that can be used to attenuate noise inside the closed ChamberCore cylindrical structure. In this study, first, the feasibility of using cylindrical Helmholtz resonators to control noise in a mock-scale ChamberCore composite cylinder is investigated. The targeted frequencies for noise control are the first four acoustic cavity resonances of the ChamberCore cylinder. The optimal position of the Helmholtz resonators for controlling each targeted cavity mode is discussed, and the effects of resonator spacing on noise attenuation are also experimentally evaluated. Next, six long T-shaped acoustic resonators are designed and constructed within the acoustic chambers of the structure and investigated. Several tests are conducted to evaluate the noise control ability of the resonators in the ChamberCore cylinder. Reductions ranging from 3.2 to 6.0 dB were observed in the overall mean-square noise reduction spectrum at the targeted inner cavity resonance frequencies. [Work supported by AFRL/DV.

  15. Structure and gene cluster of the O-antigen of Escherichia coli O156 containing a pyruvic acid acetal.

    PubMed

    Duan, Zhifeng; Senchenkova, Sof'ya N; Guo, Xi; Perepelov, Andrei V; Shashkov, Alexander S; Liu, Bin; Knirel, Yuriy A

    2016-07-22

    The lipopolysaccharide of Escherichia coli O156 was degraded under mild acidic and alkaline conditions and the resulting polysaccharides were studied by sugar analysis and (1)H and (13)C NMR spectroscopy. The following structure of the pentasaccharide repeating unit of the O-polysaccharide was established: where Rpyr indicates R-configurated pyruvic acid acetal. Minor O-acetyl groups also were present and tentatively localized on the Gal residues. The gene cluster for biosynthesis of the O-antigen of E. coli O156 was analyzed and shown to be consistent with the O-polysaccharide structure.

  16. Structure of a Folding Intermediate Reveals the Interplay Between Core and Peripheral Elements in RNA Folding

    SciTech Connect

    Baird, Nathan J.; Westhof, Eric; Qin, Hong; Pan, Tao; Sosnick, Tobin R.

    2010-07-13

    Though the molecular architecture of many native RNA structures has been characterized, the structures of folding intermediates are poorly defined. Here, we present a nucleotide-level model of a highly structured equilibrium folding intermediate of the specificity domain of the Bacillus subtilis RNase P RNA, obtained using chemical and nuclease mapping, circular dichroism spectroscopy, small-angle X-ray scattering and molecular modeling. The crystal structure indicates that the 154 nucleotide specificity domain is composed of several secondary and tertiary structural modules. The structure of the intermediate contains modules composed of secondary structures and short-range tertiary interactions, implying a sequential order of tertiary structure formation during folding. The intermediate lacks the native core and several long-range interactions among peripheral regions, such as a GAAA tetraloop and its receptor. Folding to the native structure requires the local rearrangement of a T-loop in the core in concert with the formation of the GAAA tetraloop-receptor interaction. The interplay of core and peripheral structure formation rationalizes the high degree of cooperativity observed in the folding transition leading to the native structure.

  17. Controllable synthesis of a novel hedgehog-like core/shell structure

    SciTech Connect

    Wang Shumin; Tian Hongwei; Pei Yanhui; Meng Qingnan; Chen Jianli; Wang Huan; Zeng Yi; Zheng Weitao; Liu Yichun

    2012-02-15

    A novel hedgehog-like core/shell structure, consisting of a high density of vertically aligned graphene sheets and a thin graphene shell/a copper core (VGs-GS/CC), has been synthesized via a simple one-step synthesis route using radio-frequency plasma-enhanced chemical vapor deposition (RF-PECVD). Scanning and transmission electron microscopy investigations show that the morphology of this core/shell material could be controlled by deposition time. For a short deposition time, only multilayer graphene shell tightly surrounds the copper particle, while as the deposition time is relative long, graphene sheets extend from the surface of GS/CC. The GS can protect CC particles from oxidation. The growth mechanism for the obtained GS/CC and VGs-GS/CC has been revealed. Compared to VGs, VGs-GS/CC material exhibits a better electron field emission property. This investigation opens a possibility for designing a core/shell structure of different carbon-metal hybrid materials for a wide variety of practical applications. - Graphical abstract: With increasing deposition time, graphene sheets extend from the surface of GS/CC, causing the multilayer graphene encapsulated copper to be converted into vertically aligned graphene sheets-graphene shell/copper core structure. Highlights: Black-Right-Pointing-Pointer A novel hedgehog-like core/shell structure has been synthesized. Black-Right-Pointing-Pointer The structure consists of vertical graphene sheets-graphene shell and copper core. Black-Right-Pointing-Pointer The morphology of VGs-GS/CC can be controlled by choosing a proper deposition time. Black-Right-Pointing-Pointer With increasing deposition time, graphene sheets extend from the surface of GS/CC. Black-Right-Pointing-Pointer VGs-GS/CC exhibits a better electron field emission property as compared with VGs.

  18. Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization

    PubMed Central

    Kwon, Annie; Byrne, Dominic P.; Ferries, Samantha; Ruan, Zheng; Hanold, Laura E.; Katiyar, Samiksha; Kennedy, Eileen J.; Eyers, Patrick A.; Kannan, Natarajan

    2016-01-01

    Protein tyrosine kinases (PTKs) are a group of closely related enzymes that have evolutionarily diverged from serine/threonine kinases (STKs) to regulate pathways associated with multi-cellularity. Evolutionary divergence of PTKs from STKs has occurred through accumulation of mutations in the active site as well as in the commonly conserved hydrophobic core. While the functional significance of active site variations is well understood, relatively little is known about how hydrophobic core variations contribute to PTK evolutionary divergence. Here, using a combination of statistical sequence comparisons, molecular dynamics simulations, mutational analysis and in vitro thermostability and kinase assays, we investigate the structural and functional significance of key PTK-specific variations in the kinase core. We find that the nature of residues and interactions in the hydrophobic core of PTKs is strikingly different from other protein kinases, and PTK-specific variations in the core contribute to functional divergence by altering the stability and dynamics of the kinase domain. In particular, a functionally critical STK-conserved histidine that stabilizes the regulatory spine in STKs is selectively mutated to an alanine, serine or glutamate in PTKs, and this loss-of-function mutation is accommodated, in part, through compensatory PTK-specific interactions in the core. In particular, a PTK-conserved phenylalanine in the I-helix appears to structurally and functionally compensate for the loss of STK-histidine by interacting with the regulatory spine, which has far-reaching effects on enzyme activity, inhibitor sensing, and stability. We propose that hydrophobic core variations provide a selective advantage during PTK evolution by increasing the conformational flexibility, and therefore the allosteric potential of the kinase domain. Our studies also suggest that Tyrosine Kinase Like kinases such as RAF are intermediates in PTK evolutionary divergence inasmuch as they

  19. Mode I Toughness Measurements of Core/Facesheet Bonds in Honeycomb Sandwich Structures

    NASA Technical Reports Server (NTRS)

    Nettles, Alan T.; Ratcliffe, James G.

    2006-01-01

    Composite sandwich structures will be used in many future applications in aerospace, marine and offshore industries due to the fact that the strength and stiffness to mass ratios surpass any other structural type. Sandwich structure also offers advantages over traditional stiffened panels such as ease of manufacturing and repair. During the last three decades, sandwich structure has been used extensively for secondary structure in aircraft (fuselage floors, rudders and radome structure). Sandwich structure is also used as primary structure in rotorcraft, the most common example being the trailing edge of rotor blades. As with other types of composite construction, sandwich structure exhibits several types of failure mode such as facesheet wrinkling, core crushing and sandwich buckling. Facesheet/core debonding has also been observed in the marine and aerospace industry. During this failure mode, peel stresses applied to an existing facesheet/core debond or an interface low in toughness, results in the facesheet being peeled from the core material, possibly leading to a significant loss in structural integrity of the sandwich panel. In an incident during a test on a liquid hydrogen fuel tank of the X-33 prototype vehicle, the outer graphite/epoxy facesheet and honeycomb core became debonded from the inner facesheet along significant areas, leading to failure of the tank. As a consequence of the accident; significant efforts were made to characterize the toughness of the facesheet/core bond. Currently, the only standardized method available for assessing the quality of the facesheet/core interface is the climbing drum peel test (ASTM D1781). During this test a sandwich beam is removed from a panel and the lip of one of the facesheets is attached to a drum, as shown in Fig. 1. The drum is then rotated along the sandwich beam, causing the facesheet to peel from the core. This method has two major drawbacks. First, it is not possible to obtain quantitative fracture data

  20. What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties.

    PubMed Central

    Munson, M.; Balasubramanian, S.; Fleming, K. G.; Nagi, A. D.; O'Brien, R.; Sturtevant, J. M.; Regan, L.

    1996-01-01

    Here we describe how the systematic redesign of a protein's hydrophobic core alters its structure and stability. We have repacked the hydrophobic core of the four-helix-bundle protein, Rop, with altered packing patterns and various side chain shapes and sizes. Several designs reproduce the structure and native-like properties of the wild-type, while increasing the thermal stability. Other designs, either with similar sizes but different shapes, or with decreased sizes of the packing residues, destabilize the protein. Finally, overpacking the core with the larger side chains causes a loss of native-like structure. These results allow us to further define the roles of tight residue packing and the burial of hydrophobic surface area in the construction of native-like proteins. PMID:8844848

  1. Structural failure analysis of reactor vessels due to molten core debris

    SciTech Connect

    Pfeiffer, P.A.

    1993-08-01

    Maintaining structural integrity of the reactor vessel during a postulated core melt accident is an important safety consideration in the design of the vessel. This paper addresses the failure predictions of the vessel due to thermal and pressure loadings from the molten core debris depositing on the lower head of the vessel. Different loading combinations were considered based on a wet or dry cavity and pressurization of the vessel based on operating pressure or atmospheric (pipe break). The analyses considered both short term (minutes) and long term (days) failure modes. Short term failure modes include creep at elevated temperatures and plastic instabilities of the structure. Long term failure modes are caused by creep rupture that lead to plastic instability of the structure. The analyses predict the reactor vessel will remain intact after the core melt has deposited on the lower vessel head.

  2. A procedure for the automatic determination of hydrophobic cores in protein structures.

    PubMed Central

    Swindells, M. B.

    1995-01-01

    An algorithm is described for automatically detecting hydrophobic cores in proteins of known structure. Three pieces of information are considered in order to achieve this goal. These are: secondary structure, side-chain accessibility, and side-chain-side-chain contacts. Residues are considered to contribute to a core when they occur in regular secondary structure and have buried side chains that form predominantly nonpolar contacts with one another. This paper describes the algorithm's application to families of proteins with conserved topologies but low sequence similarities. The aim of this investigation is to determine the efficacy of the algorithm as well as to study the extent to which similar cores are identified within a common topology. PMID:7773181

  3. Core-satellite ZnS-Ag nanoassemblies: Synthesis, structure, and optical properties.

    PubMed

    Rohani, Parham; Sharma, Munish K; Swihart, Mark T

    2016-02-01

    We synthesized hollow core-satellite nanoassemblies comprised of hollow zinc sulfide (ZnS) shells decorated with silver nanoparticles (Ag NPs). This was achieved by solution-phase attachment of Ag NPs to hollow ZnS nanospheres (NSs) prepared by spray pyrolysis. This produces an aqueous dispersion of ZnS-Ag hybrid structures, 50-500nm in overall diameter. We characterized the nanostructures by scanning electron microscopy (SEM), transmission electron microscopy (TEM), powder X-ray diffraction (XRD), and energy dispersive X-ray spectroscopy (EDX) to elucidate the ZnS (core)-Ag (satellite) morphology and optimize conditions for producing such structures. Optical spectroscopy showed that photoluminescence of ZnS was quenched by Ag while absorbance was enhanced. This work provides a simple and general means of producing hollow core-satellite structures that could be of broad applicability.

  4. Experimental and Numerical Analysis of Composite Folded Sandwich Core Structures Under Compression

    NASA Astrophysics Data System (ADS)

    Heimbs, S.; Middendorf, P.; Kilchert, S.; Johnson, A. F.; Maier, M.

    2007-11-01

    The characterisation of the mechanical behaviour of folded core structures for advanced sandwich composites under flatwise compression load using a virtual testing approach is presented. In this context dynamic compression test simulations with the explicit solvers PAM-CRASH and LS-DYNA are compared to experimental data of two different folded core structures made of aramid paper and carbon fibre-reinforced plastic (CFRP). The focus of the investigations is the constitutive modelling of the cell wall material, the consideration of imperfections and the representation of cell wall buckling, folding or crushing phenomena. The consistency of the numerical results shows that this can be a promising and efficient approach for the determination of the effective mechanical properties and a cell geometry optimisation of folded core structures.

  5. Design and optimization of 3-mode×12-core dual-ring structured few-mode multi-core fiber

    NASA Astrophysics Data System (ADS)

    Tu, Jiajing; Long, Keping; Saitoh, Kunimasa

    2016-12-01

    We adopt dual-ring structure (DRS) for the core arrangement of 3-mode (LP01, LP11a and LP11b)×12-core few-mode multi-core fiber (FM-MCF) and then introduce the design method for this DRS-FM-MCF. After investigating the characteristics such as differential mode delay (DMD), inter-core crosstalk (XT), threshold value of bending radius (Rpk), relative core multiplicity factor (RCMF) and cable cutoff wavelength (λcc), we present an optimized scheme for this DRS-FM-MCF. For the optimized DRS-FM-MCF, | DMD | is ≤ 100 ps / km over C+L band, the maximum XT at wavelength (λ) of 1625 nm achieves -33 dB/100 km, maximum Rpk is 11.03 cm, RCMF (LP01, LP11a and LP11b) reaches 25.49 and maximum λcc is ≤ 1530 nm. Compared with one-ring structure (ORS), DRS has much more space to enlarge core pitch (Λ) so that lower XT can be achieved. Furthermore, DRS has less confinement degree on mode than square-lattice structure (SLS) if Λ and cladding diameter (Dcl) are set at similar values. It means that it is easier for DRS to make sure λcc would not be larger than the lower limit of C+L bands. In this paper, DRS is proved as a suitable core arrangement for 3-mode×12-core FM-MCF.

  6. Synthesis, structural, optical and photocatalytic properties of CdS/ZnS core/shell nanoparticles

    NASA Astrophysics Data System (ADS)

    Reddy, Ch. Venkata; Shim, Jaesool; Cho, Migyung

    2017-04-01

    CdS, ZnS and CdS/ZnS core/shell nanoparticles were successfully synthesized via two-step synthesis method. The as-prepared CdS, ZnS and CdS/ZnS core/shell nanoparticles were used to study the structural, morphological, and optical properties by PXRD, TEM, HRTEM, UV-vis spectroscopy, N2 adsorption-desorption, FT-IR, PL and Raman spectroscopy measurements. The XRD pattern confirms the crystal structure of the prepared ZnS, CdS, and CdS/ZnS core/shell nanoparticles. The crystallinity of the as-prepared samples is confirmed by PXRD, TEM and HRTEM analysis. The BET analysis showed that the CdS/ZnS core/shell nanoparticles had larger surface area and pore diameter than CdS and ZnS. The Raman and FT-IR spectra confirm the fundamental vibrational modes of CdS and ZnS respectively. Compared to pure CdS and ZnS, CdS/ZnS core/shell nanoparticles exhibited higher photocatalytic activity for the degradation of methyl orange (MO). The enhancement of photocatalytic activity in the CdS/ZnS core/shell nanoparticles is due to the interface actions between CdS and ZnS, which greatly reduces the recombination of photogenerated electrons-holes pair. The proposed mechanism for degradation of MO dye is discussed in detail.

  7. Paleomagnetic Reorientation of Structural Elements in Drill Cores: an example from Tolhuaca Geothermal Field

    NASA Astrophysics Data System (ADS)

    Perez-Flores, P.; Veloso, E. E.; Cembrano, J. M.; Sánchez, P.; Iriarte, S.; Lohmar, S.

    2013-12-01

    Reorientation of mesoscopic faults, veins and fractures recovered from drilling is critical to construct reliable structural models that can account for their architecture and deformation regime. However, oriented cores are expensive and time consuming to drill. Some techniques achieve reorientation by introducing tools into the borehole. Problems arise when boreholes are unstable or collapse. One alternative technique allowing reorientation is to obtain reliable paleomagnetic vectors to reorient each core piece after drilling. Here, we present stable and reliable remnant magnetic vectors calculated from the Tol-1 core to analyze the geometry of the fracture network and its relationship to regional tectonic. Tol-1 core is a vertical, 1073 m deep geothermal well, drilled at the Tolhuaca Geothermal Field in the Southern Volcanic Zone of the Andes by MRP Geothermal Chile Ltda (formerly GGE Chile SpA) in 2009. The core consists of basaltic/andesitic volcanic rocks with subordinate pyroclastic/volcaniclastic units, with probable Pleistocene age. Fault planes with slickenlines and mineral fiber kinematic indicators are common in the upper 700 m of the core. Calcite, quartz and calcite-quartz veins are recognized along of entire core, whereas epidote-quartz and calcite-epidote veins occur in the last 350 m, minor chlorite, anhydrite and clay-minerals are present. Orientations of structural features in the core were measured with a goniometer using the core's axis and a false north for each piece; hence, orientation data has a false strike but a real dip. To achieve total reorientation of the pieces, we collected 200 standard-size paleomagnetic specimens, ensuring that at least four of them were recovered from continuous pieces. Thermal (up to 700°C) and alternating field demagnetization (up to 90mT on steps of 2mT) methods were used to isolate a stable remnant magnetization (RM) vector, and each technique yielded similar results. RM vectors were recovered between 0 to 25

  8. Hydrogen-induced change in core structures of {110}[111] edge and {110}[111] screw dislocations in iron

    PubMed Central

    Wang, Shuai; Hashimoto, Naoyuki; Ohnuki, Somei

    2013-01-01

    Employing the empirical embedded-atom method potentials, the evolution of edge and screw dislocation core structure is calculated at different hydrogen concentrations. With hydrogen, the core energy and Peierls potential are reduced for all dislocations. A broaden-core and a quasi-split core structure are observed for edge and screw dislocation respectively. The screw dislocation and hydrogen interaction in body-centred cubic iron is found to be not mainly due to the change of elastic modulus, but the variation of dislocation core structure. PMID:24067268

  9. Structural origin for electron affinity of phenanthrene and ion cores of phenanthrene anion clusters

    NASA Astrophysics Data System (ADS)

    Lee, Sang Hak; Song, Jae Kyu; Kim, Seong Keun

    2015-04-01

    We studied anion clusters of phenanthrene using photoelectron spectra and theoretical calculations. The electron affinity of phenanthrene, which lies between those of naphthalene and anthracene, was explained by the orbital interaction model that reflected the structural differences among these molecules. The spectral feature of the photoelectron spectra indicated strong electron-vibration coupling along two symmetric vibrational modes. Since the spectral features of each ion core structure were uniquely characteristic, we could identify that the pentamer anion had coexisting monomeric and trimeric cores on the basis of the shape of the photoelectron spectra and the size-dependent evolution of the electron affinity.

  10. Damping Properties of Sandwich Truss Core Structures by Strain Energy Method

    NASA Astrophysics Data System (ADS)

    Wesolowski, M.; Rucevskis, S.; Janeliukstis, R.; Polanski, M.

    2015-11-01

    Sandwich panel structures with stiff face sheets and cellular cores are widely used to support dynamic loads. Combining face sheets made of carbon fibre reinforced plastics (CFRPs) with an aluminium pyramidal truss improves the damping performance of the structure due to viscoelastic character of CRFP composites. To predict the damping characteristics of the pyramidal truss core sandwich panel the strain energy method is adopted. The procedure for evaluating the damping of the sandwich panel was performed using commercial finite element software NASTRAN and MATLAB. Non-contact vibration tests were performed on the real sandwich panels in order to extract the modal characteristics and compare them with the numerical predictions.

  11. Synthesis and optical properties of luminescent core-shell structured silicate and phosphate nanoparticles

    NASA Astrophysics Data System (ADS)

    Dembski, Sofia; Rupp, Sabine; Milde, Moritz; Gellermann, Carsten; Dyrba, Marcel; Schweizer, Stefan; Batentschuk, Miroslaw; Osvet, Andres; Winnacker, Albrecht

    2011-05-01

    Monodisperse, luminescent core-shell structured inorganic nanoparticles were synthesized by sol-gel technology. They exhibit an amorphous SiO 2 core and a crystalline luminescent shell. Zn 2SiO 4:Mn 2+ and Ca 10(PO 4) 6OH:Eu 3+ shell materials are investigated. The influence of the doping concentration on optical and structural properties was studied. The resulting nanoparticles were characterized by X-ray diffraction analysis, transmission electron microscopy, inductively coupled plasma optical emission spectrometry, and photoluminescence spectroscopy.

  12. Electronic Structure Calculations and Adaptation Scheme in Multi-core Computing Environments

    SciTech Connect

    Seshagiri, Lakshminarasimhan; Sosonkina, Masha; Zhang, Zhao

    2009-05-20

    Multi-core processing environments have become the norm in the generic computing environment and are being considered for adding an extra dimension to the execution of any application. The T2 Niagara processor is a very unique environment where it consists of eight cores having a capability of running eight threads simultaneously in each of the cores. Applications like General Atomic and Molecular Electronic Structure (GAMESS), used for ab-initio molecular quantum chemistry calculations, can be good indicators of the performance of such machines and would be a guideline for both hardware designers and application programmers. In this paper we try to benchmark the GAMESS performance on a T2 Niagara processor for a couple of molecules. We also show the suitability of using a middleware based adaptation algorithm on GAMESS on such a multi-core environment.

  13. Enhanced expression of HIV and SIV vaccine antigens in the structural gene region of live attenuated rubella viral vectors and their incorporation into virions.

    PubMed

    Virnik, Konstantin; Ni, Yisheng; Berkower, Ira

    2013-04-19

    Despite the urgent need for an HIV vaccine, its development has been hindered by virus variability, weak immunogenicity of conserved epitopes, and limited durability of the immune response. For other viruses, difficulties with immunogenicity were overcome by developing live attenuated vaccine strains. However, there is no reliable method of attenuation for HIV, and an attenuated strain would risk reversion to wild type. We have developed rubella viral vectors, based on the live attenuated vaccine strain RA27/3, which are capable of expressing important HIV and SIV vaccine antigens. The rubella vaccine strain has demonstrated safety, immunogenicity, and long lasting protection in millions of children. Rubella vectors combine the growth and immunogenicity of live rubella vaccine with the antigenicity of HIV or SIV inserts. This is the first report showing that live attenuated rubella vectors can stably express HIV and SIV vaccine antigens at an insertion site located within the structural gene region. Unlike the Not I site described previously, the new site accommodates a broader range of vaccine antigens without interfering with essential viral functions. In addition, antigens expressed at the structural site were controlled by the strong subgenomic promoter, resulting in higher levels and longer duration of antigen expression. The inserts were expressed as part of the structural polyprotein, processed to free antigen, and incorporated into rubella virions. The rubella vaccine strain readily infects rhesus macaques, and these animals will be the model of choice for testing vector growth in vivo and immunogenicity.

  14. Structure of a Major Antigenic Site on the Respiratory Syncytial Virus Fusion Glycoprotein in Complex with Neutralizing Antibody 101F

    SciTech Connect

    McLellan, Jason S.; Chen, Man; Chang, Jung-San; Yang, Yongping; Kim, Albert; Graham, Barney S.; Kwong, Peter D.

    2010-11-19

    Respiratory syncytial virus (RSV) is a major cause of pneumonia and bronchiolitis in infants and elderly people. Currently there is no effective vaccine against RSV, but passive prophylaxis with neutralizing antibodies reduces hospitalizations. To investigate the mechanism of antibody-mediated RSV neutralization, we undertook structure-function studies of monoclonal antibody 101F, which binds a linear epitope in the RSV fusion glycoprotein. Crystal structures of the 101F antigen-binding fragment in complex with peptides from the fusion glycoprotein defined both the extent of the linear epitope and the interactions of residues that are mutated in antibody escape variants. The structure allowed for modeling of 101F in complex with trimers of the fusion glycoprotein, and the resulting models suggested that 101F may contact additional surfaces located outside the linear epitope. This hypothesis was supported by surface plasmon resonance experiments that demonstrated 101F bound the peptide epitope {approx}16,000-fold more weakly than the fusion glycoprotein. The modeling also showed no substantial clashes between 101F and the fusion glycoprotein in either the pre- or postfusion state, and cell-based assays indicated that 101F neutralization was not associated with blocking virus attachment. Collectively, these results provide a structural basis for RSV neutralization by antibodies that target a major antigenic site on the fusion glycoprotein.

  15. Relationship of D'' structure with the velocity variations near the inner-core boundary

    NASA Astrophysics Data System (ADS)

    Luo, Sheng-Nian; Ni, Sidao; Helmberger, Don

    2002-06-01

    Variations in regional differential times between PKiKP (i) and PKIKP (I) have been attributed to hemispheric P-velocity variations of about 1% in the upper 100 km of the inner core (referred to as HIC). The top of the inner core appears relatively fast beneath Asia where D'' is also fast. An alternative interpretation could be the lateral variation in P velocity at the lowermost outer core (HOC) producing the same differential times. To resolve this issue, we introduce the diffracted PKP phase near the B caustic (Bdiff) in the range of 139-145° epicenter distances, and the corresponding differential times between Bdiff and PKiKP and PKIKP as observed on broadband arrays. Due to the long-wavelength nature of Bdiff, we scaled the S-wave tomography model with k values (k ≡ dlnVs/dlnVp) to obtain large-scale P-wave velocity structure in the lower mantle as proposed by earlier studies. Waveform synthetics of Bdiff constructed with small k's predict complex waveforms not commonly observed, confirming the validity of large scaling factor k. With P-velocity in lower mantle constrained at large scale, the extra travel-time constraint imposed by Bdiff helps to resolve the HOC-HIC issue. Our preliminary results suggest k > 2 for the lowermost mantle and support HIC hypothesis. An important implication is that there appears to be a relationship of D'' velocity structures with the structures near the inner core boundary via core dynamics.

  16. ATMS- and AMSU-A-derived hurricane warm core structures using a modified retrieval algorithm

    NASA Astrophysics Data System (ADS)

    Tian, Xiaoxu; Zou, Xiaolei

    2016-11-01

    The Advanced Technology Microwave Sounder (ATMS) is a cross-track microwave radiometer. Its temperature sounding channels 5-15 can provide measurements of thermal radiation emitted from different layers of the atmosphere. In this study, a traditional Advanced Microwave Sounding Unit-A (AMSU-A) temperature retrieval algorithm is modified to remove the scan biases in the temperature retrieval and to include only those ATMS sounding channels that are correlated with the atmospheric temperatures on the pressure level of the retrieval. The warm core structures derived for Hurricane Sandy when it moved from tropics to middle latitudes are examined. It is shown that scan biases that are present in the traditional retrieval are adequately removed using the modified algorithm. In addition, temperature retrievals in the upper troposphere ( 250 hPa) obtained by using the modified algorithm have more homogeneous warm core structures and those from the traditional retrieval are affected by small-scale features from the low troposphere such as precipitation. Based on ATMS observations, Hurricane Sandy's warm core was confined to the upper troposphere during its intensifying stage and when it was located in the tropics but extended to the entire troposphere when it moved into subtropics and middle latitudes and stopped its further intensification. The modified algorithm was also applied to AMSU-A observation data to retrieve the warm core structures of Hurricane Michael. The retrieved warm core features are more realistic when compared with those from the operational Microwave Integrated Retrieval System (MIRS).

  17. The Relationship Between Atomic Structure and Strain Distribution of Misfit Dislocation Cores at Cubic Heteroepitaxial Interfaces.

    PubMed

    Wen, Cai

    2017-03-09

    The atomic reconstruction of a misfit dislocation (MD) core causes change in the strain distribution around the core. Several MD cores at the AlSb/GaAs (001) cubic zincblende interface, including a symmetrical glide set Lomer dislocation (LD), a left-displaced glide set LD, a glide set LD with an atomic step, a symmetrical shuffle set LD, and a 60° dislocation pair, were studied using simulated projected potential and aberration-corrected transmission electron microscope images. Image deconvolution was also used to restore structure images from nonoptimum-defocus images. The corresponding biaxial strain maps, ε xx (in-plane) and ε yy (out-of-plane), were obtained by geometric phase analysis using the GaAs substrate as the reference lattice. The results show that atomic structure characteristics of MD cores can be revealed by the strain maps. The strain maps should be measured from optimum-defocus images or restored structure images. Furthermore, the ε xx strain map has been found more accurate than the ε yy strain map for MD cores, and the specimen thickness should be below the critical thickness due to the influence of dynamical scattering.

  18. Proliferating cell nuclear antigen (PCNA) contributes to the high-order structure and stability of heterochromatin in Saccharomyces cerevisiae.

    PubMed

    Bi, Xin; Ren, Yue; Kath, Morgan

    2016-12-16

    Heterochromatin plays important roles in the structure, maintenance, and function of the eukaryotic genome. It is associated with special histone modifications and specialized non-histone proteins and assumes a more compact structure than euchromatin. Genes embedded in heterochromatin are generally transcriptionally silent. It was found previously that several mutations of proliferating cell nuclear antigen (PCNA), a DNA replication processivity factor, reduce transcriptional silencing at heterochromatin loci in Saccharomyces cerevisiae. However, the notion that PCNA plays a role in transcriptional silencing was recently questioned because of a potential problem concerning the silencing assays used in prior studies. To determine if PCNA is a bona fide contributor to heterochromatin-mediated transcriptional silencing, we examined the effects of PCNA mutations on heterochromatin structure. We found evidence implicating PCNA in the maintenance of the high-order structure and stability of heterochromatin, which indicates a role of DNA replication in heterochromatin maintenance.

  19. Fragmentation of massive dense cores down to ≲ 1000 AU: Relation between fragmentation and density structure

    SciTech Connect

    Palau, Aina; Girart, Josep M.; Estalella, Robert; Fuente, Asunción; Fontani, Francesco; Sánchez-Monge, Álvaro; Commerçon, Benoit; Hennebelle, Patrick; Busquet, Gemma; Bontemps, Sylvain; Zapata, Luis A.; Zhang, Qizhou; Di Francesco, James

    2014-04-10

    In order to shed light on the main physical processes controlling fragmentation of massive dense cores, we present a uniform study of the density structure of 19 massive dense cores, selected to be at similar evolutionary stages, for which their relative fragmentation level was assessed in a previous work. We inferred the density structure of the 19 cores through a simultaneous fit of the radial intensity profiles at 450 and 850 μm (or 1.2 mm in two cases) and the spectral energy distribution, assuming spherical symmetry and that the density and temperature of the cores decrease with radius following power-laws. Even though the estimated fragmentation level is strictly speaking a lower limit, its relative value is significant and several trends could be explored with our data. We find a weak (inverse) trend of fragmentation level and density power-law index, with steeper density profiles tending to show lower fragmentation, and vice versa. In addition, we find a trend of fragmentation increasing with density within a given radius, which arises from a combination of flat density profile and high central density and is consistent with Jeans fragmentation. We considered the effects of rotational-to-gravitational energy ratio, non-thermal velocity dispersion, and turbulence mode on the density structure of the cores, and found that compressive turbulence seems to yield higher central densities. Finally, a possible explanation for the origin of cores with concentrated density profiles, which are the cores showing no fragmentation, could be related with a strong magnetic field, consistent with the outcome of radiation magnetohydrodynamic simulations.

  20. The Ikaria high-temperature Metamorphic Core Complex (Cyclades, Greece): Geometry, kinematics and thermal structure

    NASA Astrophysics Data System (ADS)

    Beaudoin, Alexandre; Augier, Romain; Laurent, Valentin; Jolivet, Laurent; Lahfid, Abdeltif; Bosse, Valérie; Arbaret, Laurent; Rabillard, Aurélien; Menant, Armel

    2015-12-01

    This work attempted at clarifying the structure of Ikaria using primarily intensive geological mapping combined with structural analysis and a geothermometry approach of Raman spectrometry of carbonaceous material. Foliation over the whole island defines a structural dome cored by high-grade to partially molten rocks. Its exhumation was completed by two top-to-the-N ductile extensional shear zones, operating in the ductile and then the brittle fields, through a single extensional event coeval with progressive strain localization. The thermal structure of the dome with regard to position of ductile shear zones was retrieved using the Raman spectroscopy of carbonaceous material. Peak-metamorphic temperatures range from 390 °C in the upper parts of the structure down to 625 °C in the core of the dome in the vicinity of migmatites and S-type granite. Pioneer in situ U-Th-Pb analyses on monazite performed on the leucosome parts of these rock yielded a 15.7 ± 0.2 Ma age. Ikaria Island thus completes the series of Miocene migmatite-cored Metamorphic Core Complex in the central part of the Aegean domain where a genuine high-temperature zone can be defined as the central Aegean HT zone. There, the extreme stretching of the continental crust is associated with dominantly top-to-the-N kinematics.

  1. Seismic anisotropy in the Earth's innermost inner core: Testing structural models against mineral physics predictions

    SciTech Connect

    Romanowicz, Barbara; Cao, Aimin; Godwal, Budhiram; Wenk, Rudy; Ventosa, Sergi; Jeanloz, Raymond

    2016-01-06

    Using an updated data set of ballistic PKIKP travel time data at antipodal distances, we test different models of anisotropy in the Earth's innermost inner core (IMIC) and obtain significantly better fits for a fast axis aligned with Earth's rotation axis, rather than a quasi-equatorial direction, as proposed recently. Reviewing recent results on the single crystal structure and elasticity of iron at core conditions, we find that an hcp structure with the fast c axis parallel to Earth's rotation is more likely but a body-centered cubic structure with the [111] axis aligned in that direction results in very similar predictions for seismic anisotropy. These models are therefore not distinguishable based on current seismological data. In addition, to match the seismological observations, the inferred strength of anisotropy in the IMIC (6–7%) implies almost perfect alignment of iron crystals, an intriguing, albeit unlikely situation, especially in the presence of heterogeneity, which calls for further studies. Fast axis of anisotropy in the central part of the inner core aligned with Earth's axis of rotation Lastly, the structure of iron in the inner core is most likely hcp, not bcc Not currently possible to distinguish between hcp and bcc structures from seismic observations

  2. Seismic anisotropy in the Earth's innermost inner core: Testing structural models against mineral physics predictions

    DOE PAGES

    Romanowicz, Barbara; Cao, Aimin; Godwal, Budhiram; ...

    2016-01-06

    Using an updated data set of ballistic PKIKP travel time data at antipodal distances, we test different models of anisotropy in the Earth's innermost inner core (IMIC) and obtain significantly better fits for a fast axis aligned with Earth's rotation axis, rather than a quasi-equatorial direction, as proposed recently. Reviewing recent results on the single crystal structure and elasticity of iron at core conditions, we find that an hcp structure with the fast c axis parallel to Earth's rotation is more likely but a body-centered cubic structure with the [111] axis aligned in that direction results in very similar predictionsmore » for seismic anisotropy. These models are therefore not distinguishable based on current seismological data. In addition, to match the seismological observations, the inferred strength of anisotropy in the IMIC (6–7%) implies almost perfect alignment of iron crystals, an intriguing, albeit unlikely situation, especially in the presence of heterogeneity, which calls for further studies. Fast axis of anisotropy in the central part of the inner core aligned with Earth's axis of rotation Lastly, the structure of iron in the inner core is most likely hcp, not bcc Not currently possible to distinguish between hcp and bcc structures from seismic observations« less

  3. Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history.

    PubMed

    Fukami-Kobayashi, K; Tateno, Y; Nishikawa, K

    1999-02-12

    Periplasmic binding proteins (PBPs) serve as receptors for various water-soluble ligands in ATP-binding cassette (ABC) transport systems, and form one of the largest protein families in eubacterial and archaebacterial genomes. They are considered to be derived from a common ancestor, judging from their similarities of three-dimensional structure, their mechanism of ligand binding and the operon structure of their genes. Nevertheless, there are two types of topological arrangements of the central beta-sheets in their core structures. It follows that there must have been differentiation in the core structure, which we call "domain dislocation", in the course of evolution of the PBP family. To find a clue as to when the domain dislocation occurred, we constructed phylogenetic trees for PBPs based on their amino acid sequences and three-dimensional structures, respectively. The trees show that the proteins of each type clearly cluster together, strongly indicating that the change in the core structure occurred only once in the evolution of PBPs. We also constructed a phylogenetic tree for the ABC proteins that are encoded by the same operon of their partner PBP, and obtained the same result. Based on the phylogenetic relationship and comparison of the topological arrangements of PBPs, we obtained a reasonable genealogical chart of structural changes in the PBP family. The present analysis shows that the unidirectional change of protein evolution is clearly deduced at the level of protein three-dimensional structure rather than the level of amino acid sequence.

  4. Glycan analysis of Fonsecaea monophora from clinical and environmental origins reveals different structural profile and human antigenic response

    PubMed Central

    Burjack, Juliana R.; Santana-Filho, Arquimedes P.; Ruthes, Andrea C.; Riter, Daniel S.; Vicente, Vania A.; Alvarenga, Larissa M.; Sassaki, Guilherme L.

    2014-01-01

    Dematiaceous fungi constitute a large and heterogeneous group, characterized by having a dark pigment, the dihydroxynaftalen melanin—DHN, inside their cell walls. In nature they are found mainly as soil microbiota or decomposing organic matter, and are spread in tropical and subtropical regions. The fungus Fonsecaea monophora causes chromoblastomycosis in humans, and possesses essential mechanisms that may enhance pathogenicity, proliferation and dissemination inside the host. Glycoconjugates confer important properties to these pathogenic microorganisms. In this work, structural characterization of glycan structures present in two different strains of F. monophora MMHC82 and FE5p4, from clinical and environmental origins, respectively, was performed. Each one were grown on Minimal Medium (MM) and Czapeck-Dox (CD) medium, and the water soluble cell wall glycoconjugates and exopolysaccharides (EPS) were evaluated by NMR, methylation and principal component analysis (PCA). By combining the methylation and 2D NMR analyses, it was possible to visualize the glycosidic profiles of the complex carbohydrate mixtures. Significant differences were observed in β-D-Galf-(1→5) and (1→6) linkages, α- and β-D-Glcp-(1→3), (1→4), and (1→6) units, as well as in α-D-Manp. PCA from 1H-NMR data showed that MMHC82 from CD medium showed a higher variation in the cell wall carbohydrates, mainly related to O-2 substituted β-D-Galf (δ 106.0/5.23 and δ 105.3/5.23) units. In order to investigate the antigenic response of the glycoconjugates, these were screened against serum from chromoblastomycosis patients. The antigen which contained the cell wall of MMHC82 grown in MM had β-D-Manp units that promoted higher antigenic response. The distribution of these fungal species in nature and the knowledge of how cell wall polysaccharides and glycoconjugates structure vary, may contribute to the better understanding and the elucidation of the pathology caused by this fungus. PMID

  5. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

    PubMed Central

    Sükösd, Zsuzsanna; Andersen, Ebbe S.; Seemann, Stefan E.; Jensen, Mads Krogh; Hansen, Mathias; Gorodkin, Jan; Kjems, Jørgen

    2015-01-01

    A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus. PMID:26476446

  6. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.

    PubMed

    Sükösd, Zsuzsanna; Andersen, Ebbe S; Seemann, Stefan E; Jensen, Mads Krogh; Hansen, Mathias; Gorodkin, Jan; Kjems, Jørgen

    2015-12-02

    A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.

  7. Improved Fabrication of Ceramic Matrix Composite/Foam Core Integrated Structures

    NASA Technical Reports Server (NTRS)

    Hurwitz, Frances I.

    2009-01-01

    The use of hybridized carbon/silicon carbide (C/SiC) fabric to reinforce ceramic matrix composite face sheets and the integration of such face sheets with a foam core creates a sandwich structure capable of withstanding high-heatflux environments (150 W/cm2) in which the core provides a temperature drop of 1,000 C between the surface and the back face without cracking or delamination of the structure. The composite face sheet exhibits a bilinear response, which results from the SiC matrix not being cracked on fabrication. In addition, the structure exhibits damage tolerance under impact with projectiles, showing no penetration to the back face sheet. These attributes make the composite ideal for leading edge structures and control surfaces in aerospace vehicles, as well as for acreage thermal protection systems and in high-temperature, lightweight stiffened structures. By tailoring the coefficient of thermal expansion (CTE) of a carbon fiber containing ceramic matrix composite (CMC) face sheet to match that of a ceramic foam core, the face sheet and the core can be integrally fabricated without any delamination. Carbon and SiC are woven together in the reinforcing fabric. Integral densification of the CMC and the foam core is accomplished with chemical vapor deposition, eliminating the need for bond-line adhesive. This means there is no need to separately fabricate the core and the face sheet, or to bond the two elements together, risking edge delamination during use. Fibers of two or more types are woven together on a loom. The carbon and ceramic fibers are pulled into the same pick location during the weaving process. Tow spacing may be varied to accommodate the increased volume of the combined fiber tows while maintaining a target fiber volume fraction in the composite. Foam pore size, strut thickness, and ratio of face sheet to core thickness can be used to tailor thermal and mechanical properties. The anticipated CTE for the hybridized composite is managed by

  8. Convection Destroys the Core/Mantle Structure in Hybrid C/O/Ne White Dwarfs

    NASA Astrophysics Data System (ADS)

    Brooks, Jared; Schwab, Josiah; Bildsten, Lars; Quataert, Eliot; Paxton, Bill

    2017-01-01

    A hybrid C/O/Ne white dwarf (WD)—an unburned C/O core surrounded by an O/Ne/Na mantle—can be formed if the carbon flame is quenched in a super-AGB star or white dwarf merger remnant. We show that this segregated hybrid structure becomes unstable to rapid mixing within 2000 years of the onset of WD cooling. Carbon burning includes a weak reaction that removes electrons, resulting in a lower electron-to-baryon ratio ({Y}{{e}}) in the regions processed by carbon burning compared to the unburned C/O core, making the O/Ne mantle denser than the C/O core as the WD cools. This is unstable to efficient mixing. We use the results of {\\mathtt{MESA}} models with different size C/O cores to quantify the rate at which the cores mix with the mantle as they cool. In all cases, we find that the WDs undergo significant core/mantle mixing on timescales shorter than the time available to grow the WD to the Chandrasekhar mass (MCh) by accretion. As a result, hybrid WDs that reach MCh due to later accretion will have lower central carbon fractions than assumed thus far. We briefly discuss the implications of these results for the possibility of SNe Ia from hybrid WDs.

  9. Modeling heterogeneous polymer-grafted nanoparticle networks having biomimetic core-shell structure

    NASA Astrophysics Data System (ADS)

    Mbanga, Badel L.; Yashin, Victor V.; Holten-Andersen, Niels; Balazs, Anna C.

    Inspired by the remarkable mechanical properties of such biological structures as mussel adhesive fibers, we use 3D computational modeling to study the behavior of heterogeneous polymer-grafted nanoparticle (PGN) networks under tensile deformation. The building block of a PGN network is a nanoparticle with grafted polymer chains whose free ends' reactive groups can form both permanent and labile bonds with the end chains on the nearby particles. The tunable behavior of cross-linked PGN networks makes them excellent candidates for designing novel materials with enhanced mechanical properties. Here, we consider the PGN networks having the core-shell structures, in which the type and strength of the inter-particle bonds in the outer shell differ from those in the core. Using the computer simulations, we obtain and compare the ultimate tensile properties (strength, toughness, ductility) and the strain recovery properties for the uniform samples and various core-shell structures. We demonstrate that the core-shell structures could be designed to obtain highly resilient self-healing materials

  10. Core-shell structured TiO2@polydopamine for highly active visible-light photocatalysis.

    PubMed

    Mao, Wen-Xin; Lin, Xi-Jie; Zhang, Wei; Chi, Zi-Xiang; Lyu, Rong-Wen; Cao, An-Min; Wan, Li-Jun

    2016-06-04

    This communication reports that the TiO2@polydopamine nanocomposite with a core-shell structure could be a highly active photocatalyst working under visible light. A very thin layer of polydopamine at around 1 nm was found to be critical for the degradation of Rhodamine B.

  11. Radiographic analysis of sedimentary structures and depositional histories in Apollo 15 cores

    NASA Technical Reports Server (NTRS)

    Coch, N. K.

    1977-01-01

    Radiographs of the Apollo 15 deepdrill drive tubes were analyzed on an SDS electronic enhancer to determine sedimentary structures in the core samples. The data obtained were compared with all other Apollo mission radiographs and used to make inferences on the character of sedimentary depositional processes on the lunar surface.

  12. Simulant-material experimental investigation of flow dynamics in the CRBR Upper-Core Structure

    SciTech Connect

    Wilhelm, D.; Starkovich, V.S.; Chapyak, E.J.

    1982-09-01

    The results of a simulant-material experimental investigation of flow dynamics in the Clinch River Breeder Reactor (CRBR) Upper Core Structure are described. The methodology used to design the experimental apparatus and select test conditions is detailed. Numerous comparisons between experimental data and SIMMER-II Code calculations are presented with both advantages and limitations of the SIMMER modeling features identified.

  13. Structure and Cellular Roles of the RMI Core Complex from the Bloom Syndrome Dissolvasome

    SciTech Connect

    Hoadley, Kelly A.; Xu, Dongyi; Xue, Yutong; Satyshur, Kenneth A.; Wang, Weidong; Keck, James L.

    2010-11-11

    BLM, the protein product of the gene mutated in Bloom syndrome, is one of five human RecQ helicases. It functions to separate double Holliday junction DNA without genetic exchange as a component of the dissolvasome, which also includes topoisomerase III{alpha} and the RMI (RecQ-mediated genome instability) subcomplex (RMI1 and RMI2). We describe the crystal structure of the RMI core complex, comprising RMI2 and the C-terminal OB domain of RMI1. The overall RMI core structure strongly resembles two-thirds of the trimerization core of the eukaryotic single-stranded DNA-binding protein, Replication Protein A. Immunoprecipitation experiments with RMI2 variants confirm key interactions that stabilize the RMI core interface. Disruption of this interface leads to a dramatic increase in cellular sister chromatid exchange events similar to that seen in BLM-deficient cells. The RMI core interface is therefore crucial for BLM dissolvasome assembly and may have additional cellular roles as a docking hub for other proteins.

  14. Structural and magnetic properties of multi-core nanoparticles analysed using a generalised numerical inversion method

    PubMed Central

    Bender, P.; Bogart, L. K.; Posth, O.; Szczerba, W.; Rogers, S. E.; Castro, A.; Nilsson, L.; Zeng, L. J.; Sugunan, A.; Sommertune, J.; Fornara, A.; González-Alonso, D.; Barquín, L. Fernández; Johansson, C.

    2017-01-01

    The structural and magnetic properties of magnetic multi-core particles were determined by numerical inversion of small angle scattering and isothermal magnetisation data. The investigated particles consist of iron oxide nanoparticle cores (9 nm) embedded in poly(styrene) spheres (160 nm). A thorough physical characterisation of the particles included transmission electron microscopy, X-ray diffraction and asymmetrical flow field-flow fractionation. Their structure was ultimately disclosed by an indirect Fourier transform of static light scattering, small angle X-ray scattering and small angle neutron scattering data of the colloidal dispersion. The extracted pair distance distribution functions clearly indicated that the cores were mostly accumulated in the outer surface layers of the poly(styrene) spheres. To investigate the magnetic properties, the isothermal magnetisation curves of the multi-core particles (immobilised and dispersed in water) were analysed. The study stands out by applying the same numerical approach to extract the apparent moment distributions of the particles as for the indirect Fourier transform. It could be shown that the main peak of the apparent moment distributions correlated to the expected intrinsic moment distribution of the cores. Additional peaks were observed which signaled deviations of the isothermal magnetisation behavior from the non-interacting case, indicating weak dipolar interactions.

  15. The multifunctional wound dressing with core-shell structured fibers prepared by coaxial electrospinning

    NASA Astrophysics Data System (ADS)

    Wei, Qilin; Xu, Feiyang; Xu, Xingjian; Geng, Xue; Ye, Lin; Zhang, Aiying; Feng, Zengguo

    2016-06-01

    The non-woven wound dressing with core-shell structured fibers was prepared by coaxial electrospinning. The polycaprolactone (PCL) was electrospun as the fiber's core to provide mechanical strength whereas collagen was fabricated into the shell in order to utilize its good biocompatibility. Simultaneously, the silver nanoparticles (Ag-NPs) as anti-bacterial agent were loaded in the shell whereas the vitamin A palmitate (VA) as healing-promoting drug was encapsulated in the core. Resulting from the fiber's core-shell structure, the VA released from the core and Ag-NPs present in the shell can endow the dressing both heal-promoting and anti-bacteria ability simultaneously, which can greatly enhance the dressing's clinical therapeutic effect. The dressing can maintain high swelling ratio of 190% for 3 d indicating its potential application as wet dressing. Furthermore, the dressing's anti-bacteria ability against Staphylococcus aureus was proved by in vitro anti-bacteria test. The in vitro drug release test showed the sustainable release of VA within 72 h, while the cell attachment showed L929 cells can well attach on the dressing indicating its good biocompatibility. In conclusion, the fabricated nanofibrous dressing possesses multiple functions to benefit wound healing and shows promising potential for clinical application.

  16. One-Seeded Fruits in the Core Caryophyllales: Their Origin and Structural Diversity

    PubMed Central

    Sukhorukov, Alexander P.; Mavrodiev, Evgeny V.; Struwig, Madeleen; Nilova, Maya V.; Dzhalilova, Khalima Kh.; Balandin, Sergey A.; Erst, Andrey; Krinitsyna, Anastasiya A.

    2015-01-01

    The core Caryophyllales consist of approximately 30 families (12 000 species) distributed worldwide. Many members evolved one-seeded or conjoined fruits, but their origin and structural diversity have not been investigated. A comparative anatomical investigation of the one-seeded fruits within the core Caryophyllales was conducted. The origin of the one-seeded fruits and the evolutionary reconstructions of some carpological characters were traced using a tree based on rbcl and matK data in order to understand the ancestral characters and their changes. The one-seeded fruit type is inferred to be an ancestral character state in core Caryophyllales, with a subsequent increase in the seed number seen in all major clades. Most representatives of the ‘Earlier Diverging’ clade are distinguished in various carpological traits. The organization of the pericarp is diverse in many groups, although fruits with a dry, many-layered pericarp, consisting of sclerenchyma as outer layers and a thin-walled parenchyma below, with seeds occupying a vertical embryo position, are likely ancestral character states in the core Caryophyllales clade. Several carpological peculiarities in fruit and seed structure were discovered in obligate one-seeded Achatocarpaceae, Chenopodiaceae, Nyctaginaceae, Seguieriaceae and Sarcobataceae. The horizontal embryo evolved in only certain groups of Chenopodiaceae. The bar-thickening of endotegmen cells appears to be an additional character typical of core Caryophyllales. The syncarpy-to-lysicarpy paradigm in Caryophyllaceae needs to be reinterpreted. PMID:25710481

  17. Use of existing data for public health planning: a study of the prevalence of hepatitis B surface antigen and core antibody in Al Ain Medical District, United Arab Emirates.

    PubMed Central

    al-Owais, A.; al-Suwaidi, K.; Amiri, N.; Carter, A. O.; Hossain, M. M.; Sheek-Hussein, M. M.

    2000-01-01

    INTRODUCTION: Hepatitis B is of major public health importance. Accurate information on its occurrence, with particular reference to the prevalence of immunity and chronic infection (marked by the presence of hepatitis B core antibody and surface antigen, respectively, in serum), is essential for planning public health programmes for the control of the disease. The generation of marker prevalence data through serological surveys is costly and time-consuming. The present study in Al Ain Medical District, United Arab Emirates, investigated the possibility of obtaining sufficiently accurate marker prevalence estimates from existing data to plan public health programmes. METHODS: Two antenatal screening databases, one student serological survey database, one immunization programme database and one pre-marriage screening database containing information on marker prevalence were identified. Epidemiological data were abstracted from these databases and analysed. RESULTS: The data showed that the prevalence of hepatitis B surface antigen and the prevalence of core antibody in young citizens in 1998 were approximately 2% and 14% respectively, that any immunization campaign aimed at citizens of the United Arab Emirates should target teenagers as they had the highest risk of acquiring the disease, and that pre-immunization screening of young adults would be wasteful. However, the data did not yield information on the prevalence of hepatitis B surface antigen and core antibody in other population subgroups of public health significance. DISCUSSION: While data generated by the study are sufficient to support a hepatitis B immunization programme targeted at teenaged citizens, more accurate data, generated by a well-designed serological survey, would be essential for optimal public health planning. PMID:11143192

  18. Evaluation of monoclonal antibodies to human plasma low density lipoproteins. A requirement for lipids to maintain antigenic structure.

    PubMed

    Patton, J G; Alley, M C; Mao, S J

    1982-12-17

    Human plasma low density lipoproteins (LDL) are composed of approximately 25% apoproteins and 75% lipids (w/w). Immunochemical properties of LDL were studied using monoclonal antibodies. BALB/c mice were immunized with LDL and the spleen cells from these mice were then fused with a non-immunoglobulin secreting myeloma cell line (F0). The clones producing desirable antibodies were selected to study the antigenic properties of LDL by enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay. First, it was found that the maximal binding of 125I-labeled LDL to polyvinyl chloride microtiter dishes was not temperature dependent. The binding affinity was high with a Ka value of approximately 1.9 X 10(10) M-1 while the monoclonal antibodies possessed an affinity to LDL of 5 X 10(8) M-1 which was 2 orders less than the affinity of LDL to the dishes. The former binding, once established, was irreversible as judged by a subsequent incubation with an excess of unlabeled LDL. The latter binding could be displaced by unlabeled LDL. Therefore, the ELISA technique offered a satisfactory approach to study the interaction between LDL and monoclonal antibodies. Removal of lipids from bound LDL by organic extraction resulted in a 50% loss of immunoreactivity, suggesting that the lipids of LDL are important in maintaining the antigenic structure of LDL. Since the apoprotein of LDL also constitutes approximately 40% of the mass (w/w) of very low density lipoproteins (VLDL), the immunoreactivity of VLDL assessed by LDL-monoclonal antibodies was also carried out. Removal of triglycerides from VLDL by lipoprotein lipase resulted in a substantial loss of immunoreactivity as determined by radioimmunoassay. These findings are consistent with the concept that lipids play a role in maintaining the integrity of the antigenic structure of LDL.

  19. Structural basis for nonneutralizing antibody competition at antigenic site II of the respiratory syncytial virus fusion protein.

    PubMed

    Mousa, Jarrod J; Sauer, Marion F; Sevy, Alexander M; Finn, Jessica A; Bates, John T; Alvarado, Gabriela; King, Hannah G; Loerinc, Leah B; Fong, Rachel H; Doranz, Benjamin J; Correia, Bruno E; Kalyuzhniy, Oleksandr; Wen, Xiaolin; Jardetzky, Theodore S; Schief, William R; Ohi, Melanie D; Meiler, Jens; Crowe, James E

    2016-11-01

    Palivizumab was the first antiviral monoclonal antibody (mAb) approved for therapeutic use in humans, and remains a prophylactic treatment for infants at risk for severe disease because of respiratory syncytial virus (RSV). Palivizumab is an engineered humanized version of a murine mAb targeting antigenic site II of the RSV fusion (F) protein, a key target in vaccine development. There are limited reported naturally occurring human mAbs to site II; therefore, the structural basis for human antibody recognition of this major antigenic site is poorly understood. Here, we describe a nonneutralizing class of site II-specific mAbs that competed for binding with palivizumab to postfusion RSV F protein. We also describe two classes of site II-specific neutralizing mAbs, one of which escaped competition with nonneutralizing mAbs. An X-ray crystal structure of the neutralizing mAb 14N4 in complex with F protein showed that the binding angle at which human neutralizing mAbs interact with antigenic site II determines whether or not nonneutralizing antibodies compete with their binding. Fine-mapping studies determined that nonneutralizing mAbs that interfere with binding of neutralizing mAbs recognize site II with a pose that facilitates binding to an epitope containing F surface residues on a neighboring protomer. Neutralizing antibodies, like motavizumab and a new mAb designated 3J20 that escape interference by the inhibiting mAbs, avoid such contact by binding at an angle that is shifted away from the nonneutralizing site. Furthermore, binding to rationally and computationally designed site II helix-loop-helix epitope-scaffold vaccines distinguished neutralizing from nonneutralizing site II antibodies.

  20. Synthesis and properties MFe2O4 (M = Fe, Co) nanoparticles and core-shell structures

    NASA Astrophysics Data System (ADS)

    Yelenich, O. V.; Solopan, S. O.; Greneche, J. M.; Belous, A. G.

    2015-08-01

    Individual Fe3-xO4 and CoFe2O4 nanoparticles, as well as Fe3-xO4/CoFe2O4 core/shell structures were synthesized by the method of co-precipitation from diethylene glycol solutions. Core/shell structure were synthesized with CoFe2O4-shell thickness of 1.0, 2.5 and 3.5 nm. X-ray diffraction patterns of individual nanoparticles and core/shell are similar and indicate that all synthesized samples have a cubic spinel structure. Compares Mössbauer studies of CoFe2O4, Fe3-xO4 nanoparticles indicate superparamagnetic properties at 300 K. It was shown that individual magnetite nanoparticles are transformed into maghemite through oxidation during the synthesis procedure, wherein the smallest nanoparticles are completely oxidized while a magnetite core does occur in the case of the largest nanoparticles. The Mössbauer spectra of core/shell nanoparticles with increasing CoFe2O4-shell thickness show a gradual decrease in the relative intensity of the quadrupole doublet and significant decrease of the mean isomer shift value at both RT and 77 K indicating a decrease of the superparamagnetic relaxation phenomena. Specific loss power for the prepared ferrofluids was experimentally calculated and it was determined that under influence of ac-magnetic field magnetic fluid based on individual CoFe2O4 and Fe3-xO4 particles are characterized by very low heating temperature, when magnetic fluids based on core/shell nanoparticles demonstrate higher heating effect.

  1. Vertically aligned P(VDF-TrFE) core-shell structures on flexible pillar arrays

    PubMed Central

    Choi, Yoon-Young; Yun, Tae Gwang; Qaiser, Nadeem; Paik, Haemin; Roh, Hee Seok; Hong, Jongin; Hong, Seungbum; Han, Seung Min; No, Kwangsoo

    2015-01-01

    PVDF and P(VDF-TrFE) nano- and micro- structures have been widely used due to their potential applications in several fields, including sensors, actuators, vital sign transducers, and energy harvesters. In this study, we developed vertically aligned P(VDF-TrFE) core-shell structures using high modulus polyurethane acrylate (PUA) pillars as the support structure to maintain the structural integrity. In addition, we were able to improve the piezoelectric effect by 1.85 times from 40 ± 2 to 74 ± 2 pm/V when compared to the thin film counterpart, which contributes to the more efficient current generation under a given stress, by making an effective use of the P(VDF-TrFE) thin top layer as well as the side walls. We attribute the enhancement of piezoelectric effects to the contributions from the shell component and the strain confinement effect, which was supported by our modeling results. We envision that these organic-based P(VDF-TrFE) core-shell structures will be used widely as 3D sensors and power generators because they are optimized for current generations by utilizing all surface areas, including the side walls of core-shell structures. PMID:26040539

  2. Re-refinement of the spliceosomal U4 snRNP core-domain structure

    PubMed Central

    Li, Jade; Leung, Adelaine K.; Kondo, Yasushi; Oubridge, Chris; Nagai, Kiyoshi

    2016-01-01

    The core domain of small nuclear ribonucleoprotein (snRNP), comprised of a ring of seven paralogous proteins bound around a single-stranded RNA sequence, functions as the assembly nucleus in the maturation of U1, U2, U4 and U5 spliceosomal snRNPs. The structure of the human U4 snRNP core domain was initially solved at 3.6 Å resolution by experimental phasing using data with tetartohedral twinning. Molecular replacement from this model followed by density modification using untwinned data recently led to a structure of the minimal U1 snRNP at 3.3 Å resolution. With the latter structure providing a search model for molecular replacement, the U4 core-domain structure has now been re-refined. The U4 Sm site-sequence AAUUUUU has been shown to bind to the seven Sm proteins SmF–SmE–SmG–SmD3–SmB–SmD1–SmD2 in an identical manner as the U1 Sm-site sequence AAUUUGU, except in SmD1 where the bound U replaces G. The progression from the initial to the re-refined structure exemplifies a tortuous route to accuracy: where well diffracting crystals of complex assemblies are initially unavailable, the early model errors are rectified by exploiting preliminary interpretations in further experiments involving homologous structures. New insights are obtained from the more accurate model. PMID:26894541

  3. Vertically aligned P(VDF-TrFE) core-shell structures on flexible pillar arrays

    SciTech Connect

    Choi, Yoon-Young; Yun, Tae Gwang; Qaiser, Nadeem; Paik, Haemin; Roh, Hee Seok; Hong, Jongin; Hong, Seungbum; Han, Seung Min; No, Kwangsoo

    2015-06-04

    PVDF and P(VDF-TrFE) nano- and micro- structures are widely used due to their potential applications in several fields, including sensors, actuators, vital sign transducers, and energy harvesters. In this study, we developed vertically aligned P(VDF-TrFE) core-shell structures using high modulus polyurethane acrylate (PUA) pillars as the support structure to maintain the structural integrity. In addition, we were able to improve the piezoelectric effect by 1.85 times from 40 ± 2 to 74 ± 2 pm/V when compared to the thin film counterpart, which contributes to the more efficient current generation under a given stress, by making an effective use of the P(VDF-TrFE) thin top layer as well as the side walls. We attribute the enhancement of piezoelectric effects to the contributions from the shell component and the strain confinement effect, which was supported by our modeling results. We envision that these organic-based P(VDF-TrFE) core-shell structures will be used widely as 3D sensors and power generators because they are optimized for current generations by utilizing all surface areas, including the side walls of core-shell structures.

  4. Vertically aligned P(VDF-TrFE) core-shell structures on flexible pillar arrays

    DOE PAGES

    Choi, Yoon-Young; Yun, Tae Gwang; Qaiser, Nadeem; ...

    2015-06-04

    PVDF and P(VDF-TrFE) nano- and micro- structures are widely used due to their potential applications in several fields, including sensors, actuators, vital sign transducers, and energy harvesters. In this study, we developed vertically aligned P(VDF-TrFE) core-shell structures using high modulus polyurethane acrylate (PUA) pillars as the support structure to maintain the structural integrity. In addition, we were able to improve the piezoelectric effect by 1.85 times from 40 ± 2 to 74 ± 2 pm/V when compared to the thin film counterpart, which contributes to the more efficient current generation under a given stress, by making an effective use ofmore » the P(VDF-TrFE) thin top layer as well as the side walls. We attribute the enhancement of piezoelectric effects to the contributions from the shell component and the strain confinement effect, which was supported by our modeling results. We envision that these organic-based P(VDF-TrFE) core-shell structures will be used widely as 3D sensors and power generators because they are optimized for current generations by utilizing all surface areas, including the side walls of core-shell structures.« less

  5. Supplemental materials for the ICDP-USGS Eyreville A, B, and C core holes, Chesapeake Bay impact structure: Core-box photographs, coring-run tables, and depth-conversion files

    USGS Publications Warehouse

    Durand, C.T.; Edwards, L.E.; Malinconico, M.L.; Powars, D.S.

    2009-01-01

    During 2005-2006, the International Continental Scientific Drilling Program and the U.S. Geological Survey drilled three continuous core holes into the Chesapeake Bay impact structure to a total depth of 1766.3 m. A collection of supplemental materials that presents a record of the core recovery and measurement data for the Eyreville cores is available on CD-ROM at the end of this volume and in the GSA Data Repository. The supplemental materials on the CD-ROM include digital photographs of each core box from the three core holes, tables of the three coring-run logs, as recorded on site, and a set of depth-conversion programs. In this chapter, the contents, purposes, and basic applications of the supplemental materials are briefly described. With this information, users can quickly decide if the materials will apply to their specific research needs. ?? 2009 The Geological Society of America.

  6. Structural Basis for Near Unity Quantum Yield Core/Shell Nanostructures

    SciTech Connect

    McBride, James; Treadway, Joe; Pennycook, Stephen J; Rosenthal, Sandra

    2006-01-01

    Aberration-corrected Z-contrast scanning transmission electron microscopy of core/shell nanocrystals shows clear correlations between structure and quantum efficiency. Uniform shell coverage is obtained only for a graded CdS/ZnS shell material and is found to be critical to achieving near 100% quantum yield. The sublattice sensitivity of the images confirms that preferential growth takes place on the anion-terminated surfaces. This explains the three-dimensional "nanobullet" shape observed in the case of core/shell nanorods.

  7. Optical and mechanical properties of hollow-core fibers with cobweb cladding structure

    NASA Astrophysics Data System (ADS)

    Chen, Mingyang; Yu, Rongjin; Tian, Zhenguo; Bai, Xiangzhong

    2006-02-01

    This paper explores the possibility of realizing a hollow-core optical fiber, whose cladding is composed of cylindrical alternating layers of air and high-index material with supporting structure. The optical properties and the design criteria of the proposed fiber are evaluated by the compact two-dimensional (2D) finite-difference time-domain (FDTD) method. In particular, the influence of the number and width of supporting strips on the leakage loss of the fiber is investigated. Furthermore, the mechanical performances of the fiber are estimated by finite-element method, confirming that hollow-core fibers with a reasonable size and number of supporting strips are reliable.

  8. Structural and Optical Properties of Si-Core/SiO x -Shell Nanowires

    NASA Astrophysics Data System (ADS)

    Thuy, Nguyen Thi; Tho, Do Duc; Tu, Nguyen Cong; Vuong, Dang Duc; Chien, Nguyen Duc; Lam, Nguyen Huu

    2017-01-01

    Si-core/SiO x -shell nanowires (NWs) have been synthesized on Si(111) surfaces using the vapor-liquid-solid technique. A 2-nm-thick Au layer was deposited by electron-beam evaporation as a metal catalyst. Au nanoparticles were formed by annealing at high temperature, resulting in subsequent formation of NWs. The Si-core/SiO x -shell structure of the NWs was investigated via scanning electron microscopy, transmission electron microscopy, x-ray diffraction analysis, and Raman spectroscopy. Photoluminescence measurements demonstrated a quantum confinement effect because of the reduced diameter of the NWs.

  9. Bacterial Community Structure in the Hyperarid Core of the Atacama Desert, Chile▿

    PubMed Central

    Drees, Kevin P.; Neilson, Julia W.; Betancourt, Julio L.; Quade, Jay; Henderson, David A.; Pryor, Barry M.; Maier, Raina M.

    2006-01-01

    Soils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70°S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populations dominated by bacteria from the Gemmatimonadetes and Planctomycetes phyla. PMID:17028238

  10. Core structures of haemosiderins deposited in various organs in β-thalassaemia/haemoglobin e disease

    NASA Astrophysics Data System (ADS)

    St. Pierre, T. G.; Tran, K. C.; Webb, J.; Macey, D. J.; Pootrakul, P.; Dickson, D. P. E.

    1992-04-01

    Mössbauer spectra were recorded of tissue from β-thalassaemia/haemoglobin E spleen, liver, pancreas and heart and of crude haemosiderins (insoluble iron fractions) isolated from the organs. Iron in the crude haemosiderins from the spleen and heart remains paramagnetic below 4.2K indicating that the iron is in a non-crystalline form. Superparamagnetic behaviour of the crude haemosiderins from the pancreas and liver indicate the presence of ferrihydrite cores with some cores with a structure based on defect-goethite.

  11. Cycle 0(CY1991) NLS trade studies and analyses report. Book 1: Structures and core vehicle

    NASA Technical Reports Server (NTRS)

    1992-01-01

    This report (SR-1: Structures, Trades, and Analysis), documents the Core Tankage Trades and analyses performed in support of the National Launch System (NLS) Cycle 0 preliminary design activities. The report covers trades that were conducted on the Vehicle Assembly, Fwd Skirt, LO2 Tank, Intertank, LH2 Tank, and Aft Skirt of the NLS Core Tankage. For each trade study, a two page executive summary and the detail trade study are provided. The trade studies contain study results, recommended changes to the Cycle 0 Baselines, and suggested follow on tasks to be performed during Cycle 1.

  12. Bacterial community structure in the hyperarid core of the Atacama Desert, Chile

    USGS Publications Warehouse

    Drees, Kevin P.; Neilson, Julia W.; Betancourt, Julio L.; Quade, Jay; Henderson, David A.; Pryor, Barry M.; Maier, Raina M.

    2006-01-01

    Soils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70 degrees S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populations dominated by bacteria from the Gemmatimonadetes and Planctomycetes phyla.

  13. Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody.

    PubMed

    Favuzza, Paola; Guffart, Elena; Tamborrini, Marco; Scherer, Bianca; Dreyer, Anita M; Rufer, Arne C; Erny, Johannes; Hoernschemeyer, Joerg; Thoma, Ralf; Schmid, Georg; Gsell, Bernard; Lamelas, Araceli; Benz, Joerg; Joseph, Catherine; Matile, Hugues; Pluschke, Gerd; Rudolph, Markus G

    2017-02-14

    Invasion of erythrocytes by Plasmodial merozoites is a composite process involving the interplay of several proteins. Among them, the Plasmodium falciparum Cysteine-Rich Protective Antigen (PfCyRPA) is a crucial component of a ternary complex, including Reticulocyte binding-like Homologous protein 5 (PfRH5) and the RH5-interacting protein (PfRipr), essential for erythrocyte invasion. Here we present the crystal structure of PfCyRPA and of its complex with the antigen-binding fragment of a parasite growth inhibitory antibody. While PfCyRPA adopts a 6-bladed β-propeller structure with similarity to the classic sialidase fold, it possesses no sialidase activity, indicating that it fulfills a non-enzymatic function. Characterization of the epitope recognized by protective antibodies will facilitate design of peptidomimetics that focus vaccine responses on protective epitopes. Both in vitro and in vivo anti-PfCyRPA and anti-PfRH5 antibodies showed more potent parasite growth inhibitory activity in combination than on their own, supporting a combined delivery of PfCyRPA and PfRH5 in vaccines.

  14. Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody

    PubMed Central

    Favuzza, Paola; Guffart, Elena; Tamborrini, Marco; Scherer, Bianca; Dreyer, Anita M; Rufer, Arne C; Erny, Johannes; Hoernschemeyer, Joerg; Thoma, Ralf; Schmid, Georg; Gsell, Bernard; Lamelas, Araceli; Benz, Joerg; Joseph, Catherine; Matile, Hugues; Pluschke, Gerd; Rudolph, Markus G

    2017-01-01

    Invasion of erythrocytes by Plasmodial merozoites is a composite process involving the interplay of several proteins. Among them, the Plasmodium falciparum Cysteine-Rich Protective Antigen (PfCyRPA) is a crucial component of a ternary complex, including Reticulocyte binding-like Homologous protein 5 (PfRH5) and the RH5-interacting protein (PfRipr), essential for erythrocyte invasion. Here, we present the crystal structures of PfCyRPA and its complex with the antigen-binding fragment of a parasite growth inhibitory antibody. PfCyRPA adopts a 6-bladed β-propeller structure with similarity to the classic sialidase fold, but it has no sialidase activity and fulfills a purely non-enzymatic function. Characterization of the epitope recognized by protective antibodies may facilitate design of peptidomimetics to focus vaccine responses on protective epitopes. Both in vitro and in vivo anti-PfCyRPA and anti-PfRH5 antibodies showed more potent parasite growth inhibitory activity in combination than on their own, supporting a combined delivery of PfCyRPA and PfRH5 in vaccines. DOI: http://dx.doi.org/10.7554/eLife.20383.001 PMID:28195038

  15. Effect of trimerization motifs on quaternary structure, antigenicity, and immunogenicity of a noncleavable HIV-1 gp140 envelope glycoprotein

    SciTech Connect

    Du, Sean X.; Idiart, Rebecca J.; Mariano, Ellaine B.; Chen, Helen; Jiang Peifeng; Xu Li; Ostrow, Kristin M.; Wrin, Terri; Phung, Pham; Binley, James M.; Petropoulos, Christos J.; Ballantyne, John A.; Whalen, Robert G.

    2009-12-05

    The external domains of the HIV-1 envelope glycoprotein (gp120 and the gp41 ectodomain, collectively known as gp140) contain all known viral neutralization epitopes. Various strategies have been used to create soluble trimers of the envelope to mimic the structure of the native viral protein, including mutation of the gp120-gp41 cleavage site, introduction of disulfide bonds, and fusion to heterologous trimerization motifs. We compared the effects on quaternary structure, antigenicity, and immunogenicity of three such motifs: T4 fibritin, a GCN4 variant, and the Escherichia coli aspartate transcarbamoylase catalytic subunit. Fusion of each motif to the C-terminus of a noncleavable JRCSF gp140(-) envelope protein led to enhanced trimerization but had limited effects on the antigenic profile and CD4-binding ability of the trimers. Immunization of rabbits provided no evidence that the trimerized gp140(-) constructs induced significantly improved neutralizing antibodies to several HIV-1 pseudoviruses, compared to gp140 lacking a trimerization motif. However, modest differences in both binding specificity and neutralizing antibody responses were observed among the various immunogens.

  16. Coercivity enhancement in Ce-Fe-B based magnets by core-shell grain structuring

    NASA Astrophysics Data System (ADS)

    Ito, M.; Yano, M.; Sakuma, N.; Kishimoto, H.; Manabe, A.; Shoji, T.; Kato, A.; Dempsey, N. M.; Givord, D.; Zimanyi, G. T.

    2016-05-01

    Ce-based R2Fe14B (R= rare-earth) nano-structured permanent magnets consisting of (Ce,Nd)2Fe14B core-shell grains separated by a non-magnetic grain boundary phase, in which the relative amount of Nd to Ce is higher in the shell of the magnetic grain than in its core, were fabricated by Nd-Cu infiltration into (Ce,Nd)2Fe14B hot-deformed magnets. The coercivity values of infiltrated core-shell structured magnets are superior to those of as-hot-deformed magnets with the same overall Nd content. This is attributed to the higher value of magnetocrystalline anisotropy of the shell phase in the core-shell structured infiltrated magnets compared to the homogeneous R2Fe14B grains of the as-hot-deformed magnets, and to magnetic isolation of R2Fe14B grains by the infiltrated grain boundary phase. First order reversal curve (FORC) diagrams suggest that the higher anisotropy shell suppresses initial magnetization reversal at the edges and corners of the R2Fe14B grains.

  17. The core structure of Mars as expected to be seen by InSight's VBB seismometer

    NASA Astrophysics Data System (ADS)

    Hempel, Stefanie; Garcia, Raphael; Wieczorek, Mark; Murdoch, Naomi

    2016-04-01

    The question of the Martian core concerns our basic understanding of the planet's thermal evolution, dynamo models for the past and present, the composition of the Martian mantle, especially in regards to its iron content and prevalent phase transitions, which in turn constrain possible regimes of mantle convection. So far the (outer) core radius of Mars is uncertain to about 250 kilometers (Sohl et al., 2005), and evidence neither supports nor falsifies the existence of an inner core (Defraigne et al., 2003). We apply our extensions of the ray tracing toolbox TauP (Crotwell et al., 1999) to compute amplitude loss, ellipticity, crustal and topography corrections in combination with existing models of seismic activity on Mars (Golombek, 1992, Knapmeyer et al., 2006), crustal thickness models (Wieczorek, 2007) and structure models (e.g. Okal and Anderson, 1978, Zharkov and Gudkova, 2000, Rivoldini et al., 2011). In preparation for NASA's discovery mission InSight, we simulate the detected relative travel-time curves at a single seismic station in Elysium Planitia for several models of Martian structure, seismicity, environmental and instrumental noise. We discuss possibilities and difficulties of considering the effects of Martian ellipticity and topography up to degree 8 and 30, respectively. Furthermore, we demonstrate the effect of low velocity layers, as well as the relevance of modeling the effects of ellipticity and crustal thickness during the interpretation of seismic data acquired by InSight's SEIS instrument on Mars, especially concerning seismic phases which provide direct evidence on the core structure of Mars.

  18. Laser-assisted solid-state synthesis of carbon nanotube/silicon core/shell structures.

    PubMed

    Mahjouri-Samani, M; Zhou, Y S; Fan, L; Gao, Y; Xiong, W; More, K L; Jiang, L; Lu, Y F

    2013-06-28

    A single-step solid-state synthetic approach was developed for the synthesis of silicon-coated carbon nanotube (CNT) core/shell structures. This was achieved through laser-induced melting and evaporation of CNT-deposited Si substrates using a continuous wavelength CO2 laser. The synthesis location of the CNT/Si structures was defined by the laser-irradiated spots. The thickness of the coating was controlled by tuning the laser power and synthesis time during the coating process. This laser-based synthetic technique provides a convenient approach for solid-state, controllable, gas-free, simple and cost-effective fabrication of CNT/Si core/shell structures.

  19. Raman spectroscopic characterization of the core-rim structure in reaction bonded boron carbide ceramics

    SciTech Connect

    Jannotti, Phillip; Subhash, Ghatu; Zheng, James Q.; Halls, Virginia; Karandikar, Prashant G.; Salamone, S.; Aghajanian, Michael K.

    2015-01-26

    Raman spectroscopy was used to characterize the microstructure of reaction bonded boron carbide ceramics. Compositional and structural gradation in the silicon-doped boron carbide phase (rim), which develops around the parent boron carbide region (core) due to the reaction between silicon and boron carbide, was evaluated using changes in Raman peak position and intensity. Peak shifting and intensity variation from the core to the rim region was attributed to changes in the boron carbide crystal structure based on experimental Raman observations and ab initio calculations reported in literature. The results were consistent with compositional analysis determined by energy dispersive spectroscopy. The Raman analysis revealed the substitution of silicon atoms first into the linear 3-atom chain, and then into icosahedral units of the boron carbide structure. Thus, micro-Raman spectroscopy provided a non-destructive means of identifying the preferential positions of Si atoms in the boron carbide lattice.

  20. Seismic anisotropy in the Earth's innermost inner core: Testing structural models against mineral physics predictions

    NASA Astrophysics Data System (ADS)

    Romanowicz, Barbara; Cao, Aimin; Godwal, Budhiram; Wenk, Rudy; Ventosa, Sergi; Jeanloz, Raymond

    2016-01-01

    Using an updated data set of ballistic PKIKP travel time data at antipodal distances, we test different models of anisotropy in the Earth's innermost inner core (IMIC) and obtain significantly better fits for a fast axis aligned with Earth's rotation axis, rather than a quasi-equatorial direction, as proposed recently. Reviewing recent results on the single crystal structure and elasticity of iron at core conditions, we find that an hcp structure with the fast c axis parallel to Earth's rotation is more likely but a body-centered cubic structure with the [111] axis aligned in that direction results in very similar predictions for seismic anisotropy. These models are therefore not distinguishable based on current seismological data. In addition, to match the seismological observations, the inferred strength of anisotropy in the IMIC (6-7%) implies almost perfect alignment of iron crystals, an intriguing, albeit unlikely situation, especially in the presence of heterogeneity, which calls for further studies.

  1. Systematic mining of analog series with related core structures in multi-target activity space.

    PubMed

    Gupta-Ostermann, Disha; Hu, Ye; Bajorath, Jürgen

    2013-08-01

    We have aimed to systematically extract analog series with related core structures from multi-target activity space to explore target promiscuity of closely related analogous. Therefore, a previously introduced SAR matrix structure was adapted and further extended for large-scale data mining. These matrices organize analog series with related yet distinct core structures in a consistent manner. High-confidence compound activity data yielded more than 2,300 non-redundant matrices capturing 5,821 analog series that included 4,288 series with multi-target and 735 series with multi-family activities. Many matrices captured more than three analog series with activity against more than five targets. The matrices revealed a variety of promiscuity patterns. Compound series matrices also contain virtual compounds, which provide suggestions for compound design focusing on desired activity profiles.

  2. The structure of Fe-Ni alloy in Earth's inner core

    NASA Astrophysics Data System (ADS)

    Tateno, Shigehiko; Hirose, Kei; Komabayashi, Tetsuya; Ozawa, Haruka; Ohishi, Yasuo

    2012-06-01

    The crystal structure of Fe-10%Ni was investigated up to 340 GPa and 4700 K, corresponding to the Earth's inner core conditions by synchrotron X-ray diffraction measurements in-situ at ultrahigh pressure and temperature in a laser-heated diamond-anvil cell. The results show that hexagonal closed-packed (hcp) structure is stable throughout the experimental conditions investigated with no evidence for a phase transition to body-centered cubic (bcc) or face-centered cubic (fcc) phases. The axial c/a ratio of the hcp crystal obtained around 330 GPa has a small temperature dependence similar to the axial ratio of pure Fe. Iron alloy with less than 10% Ni crystallizes to an hcp structure with c/a ratio of ˜1.61 at inner core conditions, although the effect of small amount of light elements remains to be examined by experiments.

  3. Transforming powder mechanical properties by core/shell structure: compressible sand.

    PubMed

    Shi, Limin; Sun, Changquan Calvin

    2010-11-01

    Some active pharmaceutical ingredients possess poor mechanical properties and are not suitable for tableting. Using fine sand (silicon dioxide), we show that a core/shell structure, where a core particle (sand) is coated with a thin layer of polyvinylpyrrolidone (PVP), can profoundly improve powder compaction properties. Sand coated with 5% PVP could be compressed into intact tablets. Under a given compaction pressure, tablet tensile strength increases dramatically with the amount of coating. This is in sharp contrast to poor compaction properties of physical mixtures, where intact tablets cannot be made when PVP content is 20% or less. The profoundly improved tabletability of core/shell particles is attributed to the formation of a continuous three-dimensional bonding network in the tablet.

  4. The stability and catalytic activity of W13@Pt42 core-shell structure

    PubMed Central

    Huo, Jin-Rong; Wang, Xiao-Xu; Li, Lu; Cheng, Hai-Xia; Su, Yan-Jing; Qian, Ping

    2016-01-01

    This paper reports a study of the electronic properties, structural stability and catalytic activity of the W13@Pt42 core-shell structure using the First-principles calculations. The degree of corrosion of W13@Pt42 core-shell structure is simulated in acid solutions and through molecular absorption. The absorption energy of OH for this structure is lower than that for Pt55, which inhibits the poison effect of O containing intermediate. Furthermore we present the optimal path of oxygen reduction reaction catalyzed by W13@Pt42. Corresponding to the process of O molecular decomposition, the rate-limiting step of oxygen reduction reaction catalyzed by W13@Pt42 is 0.386 eV, which is lower than that for Pt55 of 0.5 eV. In addition by alloying with W, the core-shell structure reduces the consumption of Pt and enhances the catalytic efficiency, so W13@Pt42 has a promising perspective of industrial application. PMID:27759038

  5. The stability and catalytic activity of W13@Pt42 core-shell structure

    NASA Astrophysics Data System (ADS)

    Huo, Jin-Rong; Wang, Xiao-Xu; Li, Lu; Cheng, Hai-Xia; Su, Yan-Jing; Qian, Ping

    2016-10-01

    This paper reports a study of the electronic properties, structural stability and catalytic activity of the W13@Pt42 core-shell structure using the First-principles calculations. The degree of corrosion of W13@Pt42 core-shell structure is simulated in acid solutions and through molecular absorption. The absorption energy of OH for this structure is lower than that for Pt55, which inhibits the poison effect of O containing intermediate. Furthermore we present the optimal path of oxygen reduction reaction catalyzed by W13@Pt42. Corresponding to the process of O molecular decomposition, the rate-limiting step of oxygen reduction reaction catalyzed by W13@Pt42 is 0.386 eV, which is lower than that for Pt55 of 0.5 eV. In addition by alloying with W, the core-shell structure reduces the consumption of Pt and enhances the catalytic efficiency, so W13@Pt42 has a promising perspective of industrial application.

  6. Manson impact structure, Iowa: First geochemical results for drill core M-1

    NASA Technical Reports Server (NTRS)

    Koeberl, Christian; Anderson, Raymond R.; Hartung, Jack B.; Reimold, Wolf Uwe

    1993-01-01

    The Manson Impact Structure is a large complex impact crater centered ca. S km north of the town of Manson, Iowa. It is the largest intact impact structure recognized in the United States (35 km in diameter). Its Ar-40/Ar-39 age is indistinguishable from that of the Cretaceous-Tertiary (K-T) boundary. The Manson structure may be one element of the events at the K-T boundary. The crater is completely covered by Quaternary glacial sedimentary deposits that are normally underlain by Cretaceous clastic sediments and flat-lying carbonate sediments of Phanerozoic age, as well as Proterozoic red clastic, metamorphic, volcanic, and plutonic rock sequences. The study of a reflection seismic profile, provided by Amoco, was critical in interpreting the structure. In the 35 km diameter zone that marks the extension of the crater the normal rock sequence is disturbed due to the impact, and at the center of the structure granitic basement rocks are present that have been uplifted from about 4 km depth. Our studies consist of detailed petrological and geochemical characterization of all cores, with emphasis on a detailed description of all rock types found in the core samples and their relationship to target rocks. Geochemical data on samples from the Manson M-1 core are presented.

  7. The stability and catalytic activity of W13@Pt42 core-shell structure.

    PubMed

    Huo, Jin-Rong; Wang, Xiao-Xu; Li, Lu; Cheng, Hai-Xia; Su, Yan-Jing; Qian, Ping

    2016-10-19

    This paper reports a study of the electronic properties, structural stability and catalytic activity of the W13@Pt42 core-shell structure using the First-principles calculations. The degree of corrosion of W13@Pt42 core-shell structure is simulated in acid solutions and through molecular absorption. The absorption energy of OH for this structure is lower than that for Pt55, which inhibits the poison effect of O containing intermediate. Furthermore we present the optimal path of oxygen reduction reaction catalyzed by W13@Pt42. Corresponding to the process of O molecular decomposition, the rate-limiting step of oxygen reduction reaction catalyzed by W13@Pt42 is 0.386 eV, which is lower than that for Pt55 of 0.5 eV. In addition by alloying with W, the core-shell structure reduces the consumption of Pt and enhances the catalytic efficiency, so W13@Pt42 has a promising perspective of industrial application.

  8. THE DEPENDENCE OF PRESTELLAR CORE MASS DISTRIBUTIONS ON THE STRUCTURE OF THE PARENTAL CLOUD

    SciTech Connect

    Parravano, Antonio; Sanchez, Nestor; Alfaro, Emilio J.

    2012-08-01

    The mass distribution of prestellar cores is obtained for clouds with arbitrary internal mass distributions using a selection criterion based on the thermal and turbulent Jeans mass and applied hierarchically from small to large scales. We have checked this methodology by comparing our results for a log-normal density probability distribution function with the theoretical core mass function (CMF) derived by Hennebelle and Chabrier, namely a power law at large scales and a log-normal cutoff at low scales, but our method can be applied to any mass distributions representing a star-forming cloud. This methodology enables us to connect the parental cloud structure with the mass distribution of the cores and their spatial distribution, providing an efficient tool for investigating the physical properties of the molecular clouds that give rise to the prestellar core distributions observed. Simulated fractional Brownian motion (fBm) clouds with the Hurst exponent close to the value H = 1/3 give the best agreement with the theoretical CMF derived by Hennebelle and Chabrier and Chabrier's system initial mass function. Likewise, the spatial distribution of the cores derived from our methodology shows a surface density of companions compatible with those observed in Trapezium and Ophiucus star-forming regions. This method also allows us to analyze the properties of the mass distribution of cores for different realizations. We found that the variations in the number of cores formed in different realizations of fBm clouds (with the same Hurst exponent) are much larger than the expected root N statistical fluctuations, increasing with H.

  9. A novel virus-like particle based on hepatitis B core antigen and substrate-binding domain of bacterial molecular chaperone DnaK.

    PubMed

    Wang, Xue Jun; Gu, Kai; Xiong, Qi Yan; Shen, Liang; Cao, Rong Yue; Li, Ming Hui; Li, Tai Ming; Wu, Jie; Liu, Jing Jing

    2009-12-09

    Hepatitis B virus core (HBc) protein has been proved to be an attractive carrier for foreign epitopes, and can display green fluorescent protein (GFP) on its surface. The structure of substrate-binding domain of DnaK [DnaK (394-504 aa), DnaK SBD] is similar to GFP, we therefore reasoned that DnaK SBD might also be tolerated. Electron microscopic observations suggested that the chimeric proteins containing the truncated HBc (HBcDelta) and DnaK SBD could self-assemble into virus-like particle (VLP). Then the accessibility of DnaK SBD and the adjuvanticity of VLP HBcDelta-SBD were demonstrated by two recombinant peptide vaccines against gonadotropin-releasing hormone (GnRH), GhM and GhMNR. The latter carries in addition the peptide motif NRLLLTG which is known to bind to DnaK and DnaK SBD. The combination of VLP HBcDelta-SBD and GhMNR elicited stronger humoral responses and caused further testicular atrophy than the combinations of VLP HBcDelta and GhMNR or VLP HBcDelta-SBD and GhM in Balb/c mice. These findings indicate VLP HBcDelta-SBD might serve as an excellent carrier for GhMNR and some other peptide vaccines.

  10. Core lipid structure is a major determinant of the oxidative resistance of low density lipoprotein.

    PubMed Central

    Schuster, B; Prassl, R; Nigon, F; Chapman, M J; Laggner, P

    1995-01-01

    The influence of thermally induced changes in the lipid core structure on the oxidative resistance of discrete, homogeneous low density lipoprotein (LDL) subspecies (d, 1.0297-1.0327 and 1.0327-1.0358 g/ml) has been evaluated. The thermotropic transition of the LDL lipid core at temperatures between 15 degrees C and 37 degrees C, determined by differential scanning calorimetry, exerted significant effects on the kinetics of copper-mediated LDL oxidation expressed in terms of intrinsic antioxidant efficiency (lag time) and diene production rate. Thus, the temperature coefficients of oxidative resistance and maximum oxidation rate showed break points at the core transition temperature. Temperature-induced changes in copper binding were excluded as the molecular basis of such effects, as the saturation of LDL with copper was identical below and above the core transition. At temperatures below the transition, the elevation in lag time indicated a greater resistance to oxidation, reflecting a higher degree of antioxidant protection. This effect can be explained by higher motional constraints and local antioxidant concentrations, the latter resulting from the freezing out of antioxidants from crystalline domains of cholesteryl esters and triglycerides. Below the transition temperature, the conjugated diene production rate was decreased, a finding that correlated positively with the average size of the cooperative units of neutral lipids estimated from the calorimetric transition width. The reduced accessibility and structural hindrance in the cluster organization of the core lipids therefore inhibits peroxidation. Our findings provide evidence for a distinct effect of the dynamic state of the core lipids on the oxidative susceptibility of LDL and are therefore relevant to the atherogenicity of these cholesterol-rich particles. PMID:7708675

  11. Detectability of temporal changes in fine structures near the inner core boundary beneath the eastern hemisphere

    NASA Astrophysics Data System (ADS)

    Yu, Wen-che

    2016-04-01

    The inner core boundary (ICB), where melting and solidification of the core occur, plays a crucial role in the dynamics of the Earth's interior. To probe temporal changes near the ICB beneath the eastern hemisphere, I analyze differential times of PKiKP (dt(PKiKP)), double differential times of PKiKP-PKPdf, and PKiKP coda waves from repeating earthquakes in the Southwest Pacific subduction zones. Most PKiKP differential times are within ±30 ms, comparable to inherent travel time uncertainties due to inter-event separations, and suggest no systematic changes as a function of calendar time. Double differential times measured between PKiKP codas and PKiKP main phases show promising temporal changes, with absolute values of time shifts of >50 ms for some observations. However, there are discrepancies among results from different seismographs in the same calendar time window. Negligible changes in PKiKP times, combined with changes in PKiKP coda wave times on 5 year timescales, favor a smooth inner core boundary with fine-scale structures present in the upper inner core. Differential times of PKiKP can be interpreted in the context of either melting based on translational convection, or growth based on thermochemical mantle-inner core coupling. Small dt(PKiKP) values with inherent uncertainties do not have sufficient resolution to distinguish the resultant longitudinal (melting) and latitudinal (growth) dependencies predicted on the basis of the two models on 5 year timescales.

  12. Hurricane Sandy warm-core structure observed from advanced Technology Microwave Sounder

    NASA Astrophysics Data System (ADS)

    Zhu, Tong; Weng, Fuzhong

    2013-06-01

    The warm-core structures of Hurricane Sandy and other nine tropical cyclones (TCs) are studied using the temperatures retrieved from Advanced Technology Microwave Sounder (ATMS). A new algorithm is developed for the retrieval of atmospheric temperature profiles from the ATMS radiances. Since ATMS observation has a higher spatial resolution and better coverage than its predecessor, Advanced Microwave Sounding Unit-A, the retrieved temperature field explicitly resolves TC warm core throughout troposphere and depicts the cold temperature anomalies in the eyewall and spiral rainbands. Unlike a typical TC, the height of maximum warm core of Hurricane Sandy is very low, but the storm size is quite large. Based on the analysis of 10 TCs in 2012, close correlations are found between ATMS-derived warm core and the TC maximum sustained wind (MSW) or minimum sea level pressure (MSLP). The estimation errors of MSW and MSLP from ATMS-retrieved warm core are 13.5 mph and 13.1 hPa, respectively.

  13. Effect of Eshelby twist on core structure of screw dislocations in molybdenum: atomic structure and electron microscope image simulations

    NASA Astrophysics Data System (ADS)

    Gröger, R.; Dudeck, K. J.; Nellist, P. D.; Vitek, V.; Hirsch, P. B.; Cockayne, D. J. H.

    2011-06-01

    This paper addresses the question as to whether the core structure of screw dislocations in Mo in the bulk can be obtained from high-resolution electron microscopy (HREM) images of such dislocations viewed end-on in a thin foil. Atomistic simulations of the core structure of screw dislocations in elastically anisotropic Mo were carried out using bond order potentials. These simulations take account automatically of the effects of the surface relaxation displacements (anisotropic Eshelby twist). They show that the differential displacements of the atoms at the surface are different with components perpendicular to the Burgers vector about five times larger than those in the middle of the foil, the latter being characteristic of the bulk. Nye tensor plots show that the surface relaxation stresses strongly affect the incompatible distortions. HREM simulations of the computed structure reflect the displacements at the exit surface, modified by interband scattering and the microscope transfer function. Nye tensor plots obtained from the HREM images show that interband scattering also affects the incompatible distortions. It is concluded that it would be very difficult to obtain information on the core structure of screw dislocations in the bulk Mo from HREM images, even under ideal experimental conditions, and that quantitative comparisons between experimental and simulated images from assumed model structures would be essential.

  14. Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody

    PubMed Central

    Vulliez-Le Normand, B.; Saul, F. A.; Phalipon, A.; Bélot, F.; Guerreiro, C.; Mulard, L. A.; Bentley, G. A.

    2008-01-01

    The anti-LPS IgG mAb F22-4, raised against Shigella flexneri serotype 2a bacteria, protects against homologous, but not heterologous, challenge in an experimental animal model. We report the crystal structures of complexes formed between Fab F22-4 and two synthetic oligosaccharides, a decasaccharide and a pentadecasaccharide that were previously shown to be both immunogenic and antigenic mimics of the S. flexneri serotype 2a O-antigen. F22-4 binds to an epitope contained within two consecutive 2a serotype pentasaccharide repeat units (RU). Six sugar residues from a contiguous nine-residue segment make direct contacts with the antibody, including the nonreducing rhamnose and both branching glucosyl residues from the two RUs. The glucosyl residue, whose position of attachment to the tetrasaccharide backbone of the RU defines the serotype 2a O-antigen, is critical for recognition by F22-4. Although the complete decasaccharide is visible in the electron density maps, the last four pentadecasaccharide residues from the reducing end, which do not contact the antibody, could not be traced. Although considerable mobility in the free oligosaccharides can thus be expected, the conformational similarity between the individual RUs, both within and between the two complexes, suggests that short-range transient ordering to a helical conformation might occur in solution. Although the observed epitope includes the terminal nonreducing residue, binding to internal epitopes within the polysaccharide chain is not precluded. Our results have implications for vaccine development because they suggest that a minimum of two RUs of synthetic serotype 2a oligosaccharide is required for optimal mimicry of O-Ag epitopes. PMID:18621718

  15. Unique epitopes recognized by monoclonal antibodies against HP-PRRSV: deep understanding of antigenic structure and virus-antibody interaction.

    PubMed

    Wang, Qian; Peng, Jinmei; Sun, Yan; Chen, Jiazeng; An, Tongqing; Leng, Chaoliang; Li, Lin; Zhao, Hongyuan; Guo, Xin; Ge, Xinna; Yang, Hanchun; Tian, Zhijun

    2014-01-01

    Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) is a member of the genus Arterivirus within the family Arteriviridae. N and GP3 proteins are the immunodominance regions of the PRRSV viral proteins. To identify the B-cell linear antigenic epitopes within HP-PRRSV N and GP3 proteins, two monoclonal antibodies (mAbs) against N and GP3 proteins were generated and characterized, designated as 3D7 and 1F10 respectively. The mAb 3D7 recognized only HuN4-F112 not the corresponding virulent strain (HuN4-F5). It also recognized two other commercial vaccines (JXA1-R and TJM-F92), but not two other HP-PRRSV strains (HNZJJ-F1 and HLJMZ-F2). The B-cell epitope recognized by the mAb 3D7 was localized to N protein amino acids 7-33. Western blot showed that the only difference amino acid between HuN4-F112-N and HuN4-F5-N did not change the mAb 3D7 recognization to N protein. The epitope targeted by the mAb 1F10 was mapped by truncated proteins. We found a new epitope (68-76aa) can be recognized by the mAb. However, the epitope could not be recognized by the positive sera, suggesting the epitope could not induce antibody in pigs. These results should extend our understanding of the antigenic structure of the N protein and antigen-antibody reactions of the GP3 protein in different species.

  16. Three-Dimensional Structure and Biophysical Characterization of Staphylococcus aureus Cell Surface Antigen-Manganese Transporter MntC

    SciTech Connect

    Gribenko, Alexey; Mosyak, Lidia; Ghosh, Sharmistha; Parris, Kevin; Svenson, Kristine; Moran, Justin; Chu, Ling; Li, Sheng; Liu, Tong; Woods, Jr., Virgil L.; Jansen, Kathrin U.; Green, Bruce A.; Anderson, Annaliesa S.; Matsuka, Yury V.

    2013-08-23

    MntC is a metal-binding protein component of the Mn2 +-specific mntABC transporter from the pathogen Staphylococcus aureus. The protein is expressed during the early stages of infection and was proven to be effective at reducing both S. aureus and Staphylococcus epidermidis infections in a murine animal model when used as a vaccine antigen. MntC is currently being tested in human clinical trials as a component of a multiantigen vaccine for the prevention of S. aureus infections. To better understand the biological function of MntC, we are providing structural and biophysical characterization of the protein in this work. The three-dimensional structure of the protein was solved by X-ray crystallography at 2.2 Å resolution and suggests two potential metal binding modes, which may lead to reversible as well as irreversible metal binding. Precise Mn2 +-binding affinity of the protein was determined from the isothermal titration calorimetry experiments using a competition approach. Differential scanning calorimetry experiments confirmed that divalent metals can indeed bind to MntC reversibly as well as irreversibly. Finally, Mn2 +-induced structural and dynamics changes have been characterized using spectroscopic methods and deuterium–hydrogen exchange mass spectroscopy. Results of the experiments show that these changes are minimal and are largely restricted to the structural elements involved in metal coordination. Therefore, it is unlikely that antibody binding to this antigen will be affected by the occupancy of the metal-binding site by Mn2 +.

  17. Crystallographic structure of the human leukocyte antigen DRA, DRB3*0101: models of a directional alloimmune response and autoimmunity.

    PubMed

    Parry, Christian S; Gorski, Jack; Stern, Lawrence J

    2007-08-10

    We describe structural studies of the human leukocyte antigen DR52a, HLA-DRA/DRB3*0101, in complex with an N-terminal human platelet integrin alphaII(B)betaIII glycoprotein peptide which contains a Leu/Pro dimorphism. The 33:Leu dimorphism is the epitope for the T cell directed response in neonatal alloimmune thrombocytopenia and post-transfusion purpura in individuals with the alphaII(B)betaIII 33:Pro allele, and defines the unidirectional alloimmune response. This condition is always associated with DR52a. The crystallographic structure has been refined to 2.25 A. There are two alphabeta heterodimers to the asymmetric unit in space group P4(1)2(1)2. The molecule is characterized by two prominent hydrophobic pockets at either end of the peptide binding cleft and a deep, narrower and highly charged P4 opening underneath the beta 1 chain. Further, the peptide in the second molecule displays a sharp upward turn after pocket P9. The structure reveals the role of pockets and the distinctive basic P4 pocket, shared by DR52a and DR3, in selecting their respective binding peptide repertoire. We observe an interesting switch in a residue from the canonically assigned pocket 6 seen in prior class II structures to pocket 4. This occludes the P6 pocket helping to explain the distinctive "1-4-9" peptide binding motif. A beta57 Asp-->Val substitution abrogates the salt-bridge to alpha76 Arg and along with a hydrophobic beta37 is important in shaping the P9 pocket. DRB3*0101 and DRB1*0301 belong to an ancestral haplotype and are associated with many autoimmune diseases linked to antigen presentation, but whereas DR3 is susceptible to type 1 diabetes DR52a is not. This dichotomy is explored for clues to the disease.

  18. Crystallographic Structure of the Human Leukocyte Antigen DRA, DRB3*0101: Models of a Directional Alloimmune Respone and Autoimmunity

    SciTech Connect

    Parry,C.; Gorski, J.; Stern, L.

    2007-01-01

    We describe structural studies of the human leukocyte antigen DR52a, HLA-DRA/DRB3*0101, in complex with an N-terminal human platelet integrin {alpha}II{sub B}{beta}III glycoprotein peptide which contains a Leu/Pro dimorphism. The 33:Leu dimorphism is the epitope for the T cell directed response in neonatal alloimmune thrombocytopenia and post-transfusion purpura in individuals with the {alpha}II{sub B}{beta}III 33:Pro allele, and defines the unidirectional alloimmune response. This condition is always associated with DR52a. The crystallographic structure has been refined to 2.25 {angstrom}. There are two {alpha}{beta} heterodimers to the asymmetric unit in space group P4{sub 1}2{sub 1}2. The molecule is characterized by two prominent hydrophobic pockets at either end of the peptide binding cleft and a deep, narrower and highly charged P4 opening underneath the beta 1 chain. Further, the peptide in the second molecule displays a sharp upward turn after pocket P9. The structure reveals the role of pockets and the distinctive basic P4 pocket, shared by DR52a and DR3, in selecting their respective binding peptide repertoire. We observe an interesting switch in a residue from the canonically assigned pocket 6 seen in prior class II structures to pocket 4. This occludes the P6 pocket helping to explain the distinctive '1-4-9' peptide binding motif. A {beta}57 Asp {yields} Val substitution abrogates the salt-bridge to {alpha}76 Arg and along with a hydrophobic {beta}37 is important in shaping the P9 pocket. DRB3*0101 and DRB1*0301 belong to an ancestral haplotype and are associated with many autoimmune diseases linked to antigen presentation, but whereas DR3 is susceptible to type 1 diabetes DR52a is not. This dichotomy is explored for clues to the disease.

  19. Structure and cross-reactivity of the O-antigen of Providencia stuartii O18 containing 3-acetamido-3,6-dideoxy-D-glucose.

    PubMed

    Kocharova, Nina A; Błaszczyk, Aleksandra; Zatonsky, George V; Torzewska, Agnieszka; Bystrova, Olga V; Shashkov, Alexander S; Knirel, Yuriy A; Rozalski, Antoni

    2004-01-22

    The O-polysaccharide (O-antigen) of Providencia stuartii O18 was obtained by mild acid degradation of the lipopolysaccharide and studied by chemical methods and NMR spectroscopy, including 2D 1H,1H COSY, TOCSY, NOESY and 1H,13C HSQC experiments. The following structure of the tetrasaccharide repeating unit of the polysaccharide was established: [structure: see text] where Qui3NAc is 3-acetamido-3,6-dideoxyglucose. Anti-P. stuartii O18 serum cross-reacted with the O-antigen of Proteus genomospecies 4, which could be accounted for the marked structural similarities of the main chain.

  20. Importin β Can Bind Hepatitis B Virus Core Protein and Empty Core-Like Particles and Induce Structural Changes

    PubMed Central

    Pierson, Elizabeth E.; Keifer, David Z.; Delaleau, Mildred; Gallucci, Lara; Cazenave, Christian; Kann, Michael; Jarrold, Martin F.; Zlotnick, Adam

    2016-01-01

    Hepatitis B virus (HBV) capsids are found in many forms: immature single-stranded RNA-filled cores, single-stranded DNA-filled replication intermediates, mature cores with relaxed circular double-stranded DNA, and empty capsids. A capsid, the protein shell of the core, is a complex of 240 copies of core protein. Mature cores are transported to the nucleus by a complex that includes both importin α and importin β (Impα and Impβ), which bind to the core protein’s C-terminal domains (CTDs). Here we have investigated the interactions of HBV core protein with importins in vitro. Strikingly, empty capsids and free core protein can bind Impβ without Impα. Cryo-EM image reconstructions show that the CTDs, which are located inside the capsid, can extrude through the capsid to be bound by Impβ. Impβ density localized on the capsid exterior near the quasi-sixfold vertices, suggested a maximum of 30 Impβ per capsid. However, examination of complexes using single molecule charge-detection mass spectrometry indicate that some complexes include over 90 Impβ molecules. Cryo-EM of capsids incubated with excess Impβ shows a population of damaged particles and a population of “dark” particles with internal density, suggesting that Impβ is effectively swallowed by the capsids, which implies that the capsids transiently open and close and can be destabilized by Impβ. Though the in vitro complexes with great excess of Impβ are not biological, these results have implications for trafficking of empty capsids and free core protein; activities that affect the basis of chronic HBV infection. PMID:27518410

  1. A facile route to synthesize core/shell structured carbon/magnetic nanoparticles hybrid and their magnetic properties

    SciTech Connect

    Qi, Xiaosi; Xu, Jianle; Zhong, Wei; Du, Youwei

    2015-07-15

    Graphical abstract: Controllable synthesis of core/shell structured carbon/magnetic nanoparticles hybrid and their tunable magnetic properties. - Highlights: • The paper reports a simple route for core/shell structured carbon/magnetic nanoparticles hybrid. • By controlling the temperature, Fe{sub 3}O{sub 4}@CNCs, Fe@HCNTs and Fe@LCNTs were produced selectively. • The magnetic properties of the obtained core/shell structured hybrid could be tuned effectively. - Abstract: By controlling the pyrolysis temperature, core/shell structured Fe{sub 3}O{sub 4}/carbon nanocages, Fe/helical carbon nanotubes and Fe/low helicity of carbon nanotubes could be synthesized selectively over Fe{sub 2}O{sub 3} nanotubes generated by a hydrothermal method. The transmission electron microscopic and scanning electron microscopic investigations revealed that the efficiency of generating core/shell structured hybrid was high, exceeding 90%. Because of the magnetic nanoparticles tightly wrapped in graphitic layers, the obtained core/shell structured hybrids showed high stability and good magnetic properties. And the magnetic properties of the obtained core/shell structured hybrid could be tuned by the decomposition temperature and time. Therefore, a simple, inexpensive and environment-benign route was proposed to produce magnetism-tunable core/shell structured hybrid in large quantities.

  2. Structural and magnetic properties of core-shell Au/Fe3O4 nanoparticles

    NASA Astrophysics Data System (ADS)

    León Félix, L.; Coaquira, J. A. H.; Martínez, M. A. R.; Goya, G. F.; Mantilla, J.; Sousa, M. H.; Valladares, L. De Los Santos; Barnes, C. H. W.; Morais, P. C.

    2017-02-01

    We present a systematic study of core-shell Au/Fe3O4 nanoparticles produced by thermal decomposition under mild conditions. The morphology and crystal structure of the nanoparticles revealed the presence of Au core of d = (6.9 ± 1.0) nm surrounded by Fe3O4 shell with a thickness of ~3.5 nm, epitaxially grown onto the Au core surface. The Au/Fe3O4 core-shell structure was demonstrated by high angle annular dark field scanning transmission electron microscopy analysis. The magnetite shell grown on top of the Au nanoparticle displayed a thermal blocking state at temperatures below TB = 59 K and a relaxed state well above TB. Remarkably, an exchange bias effect was observed when cooling down the samples below room temperature under an external magnetic field. Moreover, the exchange bias field (HEX) started to appear at T~40 K and its value increased by decreasing the temperature. This effect has been assigned to the interaction of spins located in the magnetically disordered regions (in the inner and outer surface of the Fe3O4 shell) and spins located in the ordered region of the Fe3O4 shell.

  3. Structural and magnetic properties of core-shell Au/Fe3O4 nanoparticles

    PubMed Central

    León Félix, L.; Coaquira, J. A. H.; Martínez, M. A. R.; Goya, G. F.; Mantilla, J.; Sousa, M. H.; Valladares, L. de los Santos; Barnes, C. H. W.; Morais, P. C.

    2017-01-01

    We present a systematic study of core-shell Au/Fe3O4 nanoparticles produced by thermal decomposition under mild conditions. The morphology and crystal structure of the nanoparticles revealed the presence of Au core of d = (6.9 ± 1.0) nm surrounded by Fe3O4 shell with a thickness of ~3.5 nm, epitaxially grown onto the Au core surface. The Au/Fe3O4 core-shell structure was demonstrated by high angle annular dark field scanning transmission electron microscopy analysis. The magnetite shell grown on top of the Au nanoparticle displayed a thermal blocking state at temperatures below TB = 59 K and a relaxed state well above TB. Remarkably, an exchange bias effect was observed when cooling down the samples below room temperature under an external magnetic field. Moreover, the exchange bias field (HEX) started to appear at T~40 K and its value increased by decreasing the temperature. This effect has been assigned to the interaction of spins located in the magnetically disordered regions (in the inner and outer surface of the Fe3O4 shell) and spins located in the ordered region of the Fe3O4 shell. PMID:28165012

  4. Structural evaluation of a mimicry-recognizing paratope: plasticity in antigen-antibody interactions manifests in molecular mimicry.

    PubMed

    Tapryal, Suman; Gaur, Vineet; Kaur, Kanwal J; Salunke, Dinakar M

    2013-07-01

    Molecular mimicry manifests antagonistically with respect to the specificity of immune recognition. However, it often occurs because different Ags share surface topologies in terms of shape or chemical nature. It also occurs when a flexible paratope accommodates dissimilar Ags by adjusting structural features according to the antigenic epitopes or differential positioning in the Ag combining site. Toward deciphering the structural basis of molecular mimicry, mAb 2D10 was isolated from a maturing immune response elicited against methyl α-d-mannopyranoside and also bound equivalently to a dodecapeptide. The physicochemical evidence of this carbohydrate-peptide mimicry in the case of mAb 2D10 had been established earlier. These studies had strongly suggested direct involvement of a flexible paratope in the observed mimicry. Surprisingly, comparison of the Ag-free structure of single-chain variable fragment 2D10 with those bound to sugar and peptide Ags revealed a conformationally invariant state of the Ab while binding to chemically and structurally disparate Ags. This equivalent binding of the two dissimilar Ags was through mutually independent interactions, demonstrating functional equivalence in the absence of structural correlation. Thus, existence of a multispecific, mature Ab in the secondary immune response was evident, as was the plasticity in the interactions while accommodating topologically diverse Ags. Although our data highlight the structural basis of receptor multispecificity, they also illustrate mechanisms adopted by the immune system to neutralize the escape mutants generated during pathogenic insult.

  5. Structural Performance of a Compressively Loaded Foam-Core Hat-Stiffened Textile Composite Panel

    NASA Technical Reports Server (NTRS)

    Ambur, Damodar R.; Dexter, Benson H.

    1996-01-01

    A structurally efficient hat-stiffened panel concept that utilizes a structural foam as a stiffener core material has been designed and developed for aircraft primary structural applications. This stiffener concept is fabricated from textile composite material forms with a resin transfer molding process. This foam-filled hat-stiffener concept is structurally more efficient than most other prismatically stiffened panel configurations in a load range that is typical for both fuselage and wing structures. The panel design is based on woven/stitched and braided graphite-fiber textile preforms, an epoxy resin system, and Rohacell foam core. The structural response of this panel design was evaluated for its buckling and postbuckling behavior with and without low-speed impact damage. The results from single-stiffener and multi-stiffener specimen tests suggest that this structural concept responds to loading as anticipated and has excellent damage tolerance characteristics compared to a similar panel design made from preimpregnated graphite-epoxy tape material.

  6. Efficient Design and Analysis of Lightweight Reinforced Core Sandwich and PRSEUS Structures

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.; Yarrington, Phillip W.; Lucking, Ryan C.; Collier, Craig S.; Ainsworth, James J.; Toubia, Elias A.

    2012-01-01

    Design, analysis, and sizing methods for two novel structural panel concepts have been developed and incorporated into the HyperSizer Structural Sizing Software. Reinforced Core Sandwich (RCS) panels consist of a foam core with reinforcing composite webs connecting composite facesheets. Boeing s Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) panels use a pultruded unidirectional composite rod to provide axial stiffness along with integrated transverse frames and stitching. Both of these structural concepts are ovencured and have shown great promise applications in lightweight structures, but have suffered from the lack of efficient sizing capabilities similar to those that exist for honeycomb sandwich, foam sandwich, hat stiffened, and other, more traditional concepts. Now, with accurate design methods for RCS and PRSEUS panels available in HyperSizer, these concepts can be traded and used in designs as is done with the more traditional structural concepts. The methods developed to enable sizing of RCS and PRSEUS are outlined, as are results showing the validity and utility of the methods. Applications include several large NASA heavy lift launch vehicle structures.

  7. Switching of the core structures of glycosphingolipids from globo- and lacto- to ganglio-series upon human embryonic stem cell differentiation.

    PubMed

    Liang, Yuh-Jin; Kuo, Huan-Hsien; Lin, Chi-Hung; Chen, Yen-Ying; Yang, Bei-Chia; Cheng, Yuan-Yuan; Yu, Alice L; Khoo, Kay-Hooi; Yu, John

    2010-12-28

    A systematic survey of expression profiles of glycosphingolipids (GSLs) in two hESC lines and their differentiated embryoid body (EB) outgrowth with three germ layers was carried out using immunofluorescence, flow cytometry, and MALDI-MS and MS/MS analyses. In addition to the well-known hESC-specific markers stage-specific embryonic antigen 3 (SSEA-3) and SSEA-4, we identified several globosides and lacto-series GSLs, previously unrevealed in hESCs, including Gb(4)Cer, Lc(4)Cer, fucosyl Lc(4)Cer, Globo H, and disialyl Gb(5)Cer. During hESC differentiation into EBs, MS analysis revealed a clear-cut switch in the core structures of GSLs from globo- and lacto- to ganglio-series, which was not as evident by immunostaining with antibodies against SSEA-3 and SSEA-4, owing to their cross-reactivities with various glycosphingolipids. Such a switch was attributable to altered expression of key glycosyltransferases (GTs) in the biosynthetic pathways by the up-regulation of ganglio-series-related GTs with simultaneous down-regulation of globo- and lacto-series-related GTs. Thus, these results provide insights into the unique stage-specific transition and mechanism for alterations of GSL core structures during hESC differentiation. In addition, unique glycan structures uncovered by MS analyses may serve as surface markers for further delineation of hESCs and help identify of their functional roles not only in hESCs but also in cancers.

  8. Switching of the core structures of glycosphingolipids from globo- and lacto- to ganglio-series upon human embryonic stem cell differentiation

    PubMed Central

    Liang, Yuh-Jin; Kuo, Huan-Hsien; Chen, Yen-Ying; Yang, Bei-Chia; Cheng, Yuan-Yuan; Yu, Alice L.; Khoo, Kay-Hooi; Yu, John

    2010-01-01

    A systematic survey of expression profiles of glycosphingolipids (GSLs) in two hESC lines and their differentiated embryoid body (EB) outgrowth with three germ layers was carried out using immunofluorescence, flow cytometry, and MALDI-MS and MS/MS analyses. In addition to the well-known hESC-specific markers stage-specific embryonic antigen 3 (SSEA-3) and SSEA-4, we identified several globosides and lacto-series GSLs, previously unrevealed in hESCs, including Gb4Cer, Lc4Cer, fucosyl Lc4Cer, Globo H, and disialyl Gb5Cer. During hESC differentiation into EBs, MS analysis revealed a clear-cut switch in the core structures of GSLs from globo- and lacto- to ganglio-series, which was not as evident by immunostaining with antibodies against SSEA-3 and SSEA-4, owing to their cross-reactivities with various glycosphingolipids. Such a switch was attributable to altered expression of key glycosyltransferases (GTs) in the biosynthetic pathways by the up-regulation of ganglio-series–related GTs with simultaneous down-regulation of globo- and lacto-series–related GTs. Thus, these results provide insights into the unique stage-specific transition and mechanism for alterations of GSL core structures during hESC differentiation. In addition, unique glycan structures uncovered by MS analyses may serve as surface markers for further delineation of hESCs and help identify of their functional roles not only in hESCs but also in cancers. PMID:21149694

  9. Hypervelocity Impact Performance of Open Cell Foam Core Sandwich Panel Structures

    NASA Technical Reports Server (NTRS)

    Ryan, Shannon; Christiansen, Eric; Lear, Dana

    2009-01-01

    Metallic foams are a relatively new class of materials with low density and novel physical, mechanical, thermal, electrical and acoustic properties. Although incompletely characterized, they offer comparable mechanical performance to traditional spacecraft structural materials (i.e. honeycomb sandwich panels) without detrimental through-thickness channeling cells. There are two competing types of metallic foams: open cell and closed cell. Open cell foams are considered the more promising technology due to their lower weight and higher degree of homogeneity. Leading micrometeoroid and orbital debris shields (MMOD) incorporate thin plates separated by a void space (i.e. Whipple shield). Inclusion of intermediate fabric layers, or multiple bumper plates have led to significant performance enhancements, yet these shields require additional non-ballistic mass for installation (fasteners, supports, etc.) that can consume up to 35% of the total shield weight [1]. Structural panels, such as open cell foam core sandwich panels, that are also capable of providing sufficient MMOD protection, represent a significant potential for increased efficiency in hypervelocity impact shielding from a systems perspective through a reduction in required non-ballistic mass. In this paper, the results of an extensive impact test program on aluminum foam core sandwich panels are reported. The effect of pore density, and core thickness on shielding performance have been evaluated over impact velocities ranging from 2.2 - 9.3 km/s at various angles. A number of additional tests on alternate sandwich panel configurations of comparable-weight have also been performed, including aluminum honeycomb sandwich panels (see Figure 1), Nomex honeycomb core sandwich panels, and 3D aluminum honeycomb sandwich panels. A total of 70 hypervelocity impact tests are reported, from which an empirical ballistic limit equation (BLE) has been derived. The BLE is in the standard form suitable for implementation in

  10. Design and optimization of 32-core rod/trench assisted square-lattice structured single-mode multi-core fiber.

    PubMed

    Xie, Xueqin; Tu, Jiajing; Zhou, Xian; Long, Keping; Saitoh, Kunimasa

    2017-03-06

    We propose and design a kind of heterogeneous rod-assisted and trench-assisted multi-core fiber (Hetero-RA-TA-MCF) with 32 cores arranged in square-lattice structure (SLS), and then we introduce the design method for Hetero-RA-TA-MCF. Simulation results show that the Hetero-RA-TA-32-Core-Fiber achieves average effective area (Aeff) of about 74 μm2, low crosstalk (XT) of about -31 dB/100km, threshold value of bending radius (Rpk) of 7.0 cm, relative core multiplicity factor (RCMF) of 8.74, and cable cutoff wavelength (λcc) of less than 1.53 μm.

  11. Structure of RCC1 chromatin factor bound to the nucleosome core particle

    SciTech Connect

    Makde, Ravindra D.; England, Joseph R.; Yennawar, Hemant P.; Tan, Song

    2010-11-11

    The small GTPase Ran enzyme regulates critical eukaryotic cellular functions including nuclear transport and mitosis through the creation of a RanGTP gradient around the chromosomes. This concentration gradient is created by the chromatin-bound RCC1 (regulator of chromosome condensation) protein, which recruits Ran to nucleosomes and activates Ran's nucleotide exchange activity. Although RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. Here we determine the crystal structure of a complex of Drosophila RCC1 and the nucleosome core particle at 2.9 {angstrom} resolution, providing an atomic view of how a chromatin protein interacts with the histone and DNA components of the nucleosome. Our structure also suggests that the Widom 601 DNA positioning sequence present in the nucleosomes forms a 145-base-pair nucleosome core particle, not the expected canonical 147-base-pair particle.

  12. Crystal Structure of the Protease-Resistant Core Domain of Yersinia Pestis Virulence Factor Yopr

    SciTech Connect

    Schubot,F.; Cherry, S.; Austin, B.; Tropea, J.; Waugh, D.

    2005-01-01

    Yersinia pestis, the causative agent of the plague, employs a type III secretion system (T3SS) to secrete and translocate virulence factors into the cytoplasm of mammalian host cells. One of the secreted virulence factors is YopR. Little is known about the function of YopR other than that it is secreted into the extracellular milieu during the early stages of infection and that it contributes to virulence. Hoping to gain some insight into the function of YopR, we determined the crystal structure of its protease-resistant core domain, which consists of residues 38--149 out of 165 amino acids. The core domain is composed of five {alpha}-helices that display unexpected structural similarity with one domain of YopN, a central regulator of type III secretion in Y. pestis. This finding raises the possibility that YopR may play a role in the regulation of type III secretion.

  13. Cometary cores with multiple structure from the oort cloud and the general scheme of origin of unusually active comets

    SciTech Connect

    Davydov, V.D.

    1986-03-01

    A newly conceived scheme is constructed which synthesizes consistent solutions to several principal problems concerning multiple-core comets: a power mechanism, a place and epoch of formation of the multiple core structure, the qualitative differences between current structure and younger structure, the origin of two types of cometary orbits, and a trigger mechanism for recent ignition of cometary activity of a multiple core. This scheme uses a new explanation of the ejection of dust (including icy dust) from various cometary cores as evidence that the material of multiple-core comets may be collisionally ablated at the expense of the comet-centered orbital energy of a multitude of massive boulders (see Kosm. Issled., No. 6 (1984)). Natural mechanisms are shown which preserve this important feature of multiple cores. The concept consists of the following elements: evolution of a system of satellites of the core toward a colli sionless structure; preservation of internal kinetic energy in the collisionless system over astro nomically lengthy time scales; tidal initiation of a collisional mechanism with the first revolution of the ancient multiple core in the zone of visibility. It is possible that such revoltions correspond to the existence of especially active comets in nearly parabolic orbits. Multiple structure in the core of active short-period comets might be descended from a nearly parabolic comet (if the theory holds on perturbational multistage transformation of near-parabolic orbits into contemporary short-period orbits).

  14. Physical Properties of Suevite Section of the Eyreville Core, Chesapeake Bay Impact Structure

    NASA Astrophysics Data System (ADS)

    Elbra, T.; Pesonen, L. J.

    2007-12-01

    Chesapeake is a 35 Ma old shallow marine, complex impact structure with a diameter of ca. 85 km. The structure has previously been mapped with shallow drillings. Recently, the deep drilling into inner crater zone near Cape Charles was carried out in order to provide constraints on cratering processes in multi-layered marine targets. The Eyreville-1 core includes three holes with total depth of 1766m (Gohn et al. 2006). We are analyzing the fragments of the Eyreville core including post-impact, impact and basement units of the structure. The sampling interval was chosen dense enough to allow high-resolution petrophysical, paleomagnetic and rock magnetic data to be extracted from the core. Hereby we report the preliminary petrophysical and rock-magnetic data from suevite section of Eyreville core B. Results obtained so far show large variations in magnetic susceptibility data of suevite section. Polymict lithic breccias and cataclasites in lower part of the section are characterized by low magnetic susceptibility (below 0.0003 SI). The upper part, however, consists of more magnetic (susceptibility up to 0.006 SI) suevites. The rock- magnetic measurements (including thermal behavior of magnetic susceptibility and magnetic hysteresis) show the presence of magnetites in lower part of the section. Upper part shows additionally a distinct change in the slope of the susceptibility curve also near 350C, which may indicate the presence of pyrrhotites or maghemites. More extensive studies will be applied in near future in order to clarify the magnetomineralogy and will be presented. References: G. S. Gohn, C. Koeberl, K. G. Miller, W. U. Reimold, C. S. Cockell, J. W. Horton, W. E. Sanford, M. A. Voytek, 2006. Chesapeake Bay Impact Structure Drilled. EOS, vol 87. nr 35

  15. Gap state related blue light emitting boron-carbon core shell structures

    NASA Astrophysics Data System (ADS)

    Singh, Paviter; Kaur, Manpreet; Singh, Bikramjeet; Kaur, Gurpreet; Singh, Kulwinder; Kumar, Manjeet; Bala, Rajni; Thakur, Anup; Kumar, Akshay

    2016-05-01

    Boron- carbon core shell structures have been synthesized by solvo-thermal synthesis route. The synthesized material is highly pure. X-ray diffraction analysis confirms the reduction of reactants in to boron and carbon. Scanning Electron Microscopy (SEM) analysis showed that the shell is uniform with average thickness of 340 nm. Photo luminescence studies showed that the material is blue light emitting with CIE color coordinates: x=0.16085, y=0.07554.

  16. Structure of Protein Phosphatase 2A Core Enzyme Bound to Tumor-Inducing Toxins

    SciTech Connect

    Xing,Y.; Xu, Y.; Chen, Y.; Jeffrey, P.; Chao, Y.; Lin, Z.; Li, Z.; Strack, S.; Stock, J.; Shi, Y.

    2006-01-01

    The serine/threonine phosphatase protein phosphatase 2A (PP2A) plays an essential role in many aspects of cellular functions and has been shown to be an important tumor suppressor. The core enzyme of PP2A comprises a 65 kDa scaffolding subunit and a 36 kDa catalytic subunit. Here we report the crystal structures of the PP2A core enzyme bound to two of its inhibitors, the tumor-inducing agents okadaic acid and microcystin-LR, at 2.6 and 2.8 {angstrom} resolution, respectively. The catalytic subunit recognizes one end of the elongated scaffolding subunit by interacting with the conserved ridges of HEAT repeats 11-15. Formation of the core enzyme forces the scaffolding subunit to undergo pronounced structural rearrangement. The scaffolding subunit exhibits considerable conformational flexibility, which is proposed to play an essential role in PP2A function. These structures, together with biochemical analyses, reveal significant insights into PP2A function and serve as a framework for deciphering the diverse roles of PP2A in cellular physiology.

  17. On the mineral core of ferritin-like proteins: structural and magnetic characterization.

    PubMed

    García-Prieto, A; Alonso, J; Muñoz, D; Marcano, L; Abad Díaz de Cerio, A; Fernández de Luis, R; Orue, I; Mathon, O; Muela, A; Fdez-Gubieda, M L

    2016-01-14

    It is generally accepted that the mineral core synthesized by ferritin-like proteins consists of a ferric oxy-hydroxide mineral similar to ferrihydrite in the case of horse spleen ferritin (HoSF) and an oxy-hydroxide-phosphate phase in plant and prokaryotic ferritins. The structure reflects a dynamic process of deposition and dissolution, influenced by different biological, chemical and physical variables. In this work we shed light on this matter by combining a structural (High Resolution Transmission Electron Microscopy (HRTEM) and Fe K-edge X-ray Absorption Spectroscopy (XAS)) and a magnetic study of the mineral core biomineralized by horse spleen ferritin (HoSF) and three prokaryotic ferritin-like proteins: bacterial ferritin (FtnA) and bacterioferritin (Bfr) from Escherichia coli and archaeal ferritin (PfFtn) from Pyrococcus furiosus. The prokaryotic ferritin-like proteins have been studied under native conditions and inside the cells for the sake of preserving their natural attributes. They share with HoSF a nanocrystalline structure rather than an amorphous one as has been frequently reported. However, the presence of phosphorus changes drastically the short-range order and magnetic response of the prokaryotic cores with respect to HoSF. The superparamagnetism observed in HoSF is absent in the prokaryotic proteins, which show a pure atomic-like paramagnetic behaviour attributed to phosphorus breaking the Fe-Fe exchange interaction.

  18. Insert Design and Manufacturing for Foam-Core Composite Sandwich Structures

    NASA Astrophysics Data System (ADS)

    Lares, Alan

    Sandwich structures have been used in the aerospace industry for many years. The high strength to weight ratios that are possible with sandwich constructions makes them desirable for airframe applications. While sandwich structures are effective at handling distributed loads such as aerodynamic forces, they are prone to damage from concentrated loads at joints or due to impact. This is due to the relatively thin face-sheets and soft core materials typically found in sandwich structures. Carleton University's Uninhabited Aerial Vehicle (UAV) Project Team has designed and manufactured a UAV (GeoSury II Prototype) which features an all composite sandwich structure fuselage structure. The purpose of the aircraft is to conduct geomagnetic surveys. The GeoSury II Prototype serves as the test bed for many areas of research in advancing UAV technologies. Those areas of research include: low cost composite materials manufacturing, geomagnetic data acquisition, obstacle detection, autonomous operations and magnetic signature control. In this thesis work a methodology for designing and manufacturing inserts for foam-core sandwich structures was developed. The results of this research work enables a designer wishing to design a foam-core sandwich airframe structure, a means of quickly manufacturing optimized inserts for the safe introduction of discrete loads into the airframe. The previous GeoSury II Prototype insert designs (v.1 & v.2) were performance tested to establish a benchmark with which to compare future insert designs. Several designs and materials were considered for the new v.3 inserts. A plug and sleeve design was selected, due to its ability to effectively transfer the required loads to the sandwich structure. The insert material was chosen to be epoxy, reinforced with chopped carbon fibre. This material was chosen for its combination of strength, low mass and also compatibility with the face-sheet material. The v.3 insert assembly is 60% lighter than the

  19. Simulation Based Optimization of Complex Monolithic Composite Structures Using Cellular Core Technology

    NASA Astrophysics Data System (ADS)

    Hickmott, Curtis W.

    Cellular core tooling is a new technology which has the capability to manufacture complex integrated monolithic composite structures. This novel tooling method utilizes thermoplastic cellular cores as inner tooling. The semi-rigid nature of the cellular cores makes them convenient for lay-up, and under autoclave temperature and pressure they soften and expand providing uniform compaction on all surfaces including internal features such as ribs and spar tubes. This process has the capability of developing fully optimized aerospace structures by reducing or eliminating assembly using fasteners or bonded joints. The technology is studied in the context of evaluating its capabilities, advantages, and limitations in developing high quality structures. The complex nature of these parts has led to development of a model using the Finite Element Analysis (FEA) software Abaqus and the plug-in COMPRO Common Component Architecture (CCA) provided by Convergent Manufacturing Technologies. This model utilizes a "virtual autoclave" technique to simulate temperature profiles, resin flow paths, and ultimately deformation from residual stress. A model has been developed simulating the temperature profile during curing of composite parts made with the cellular core technology. While modeling of composites has been performed in the past, this project will look to take this existing knowledge and apply it to this new manufacturing method capable of building more complex parts and develop a model designed specifically for building large, complex components with a high degree of accuracy. The model development has been carried out in conjunction with experimental validation. A double box beam structure was chosen for analysis to determine the effects of the technology on internal ribs and joints. Double box beams were manufactured and sectioned into T-joints for characterization. Mechanical behavior of T-joints was performed using the T-joint pull-off test and compared to traditional

  20. Size and structure of antigen-antibody complexes. Electron microscopy and light scattering studies.

    PubMed Central

    Murphy, R M; Slayter, H; Schurtenberger, P; Chamberlin, R A; Colton, C K; Yarmush, M L

    1988-01-01

    Size parameters of model antigen-antibody (Ag-Ab) complexes formed by the interaction of bovine serum albumin (BSA) and pairs of monoclonal anti-BSA antibodies (mAb) were evaluated by quasielastic light scattering, classical light scattering, and electron microscopy (EM). Mean values for the hydrodynamic radius, radius of gyration, and molecular weight were determined by light scattering. Detailed information regarding the molecular weight distribution and the presence of cycles or open chains was obtained with EM. Average molecular weights were calculated from the EM data, and the Porod-Kratky wormlike chain theory was used to model the conformational behavior of the Ag-mAb complexes. Ag-mAb complexes prepared from three different mAb pairs displayed significantly different properties as assessed by each of the techniques employed. Observations and size parameter calculations from EM photomicrographs were consistent with the results from light scattering. The differences observed between the mab pairs would not have been predicted by idealized thermodynamic models. These results suggest that the geometric constraints imposed by the individual epitope environment and/or the relative epitope location are important in determining the average size of complexes and the ratio of linear to cyclic complexes. Images FIGURE 3 FIGURE 3 FIGURE 5 FIGURE 7 PMID:3416033

  1. Structural and antigenic identification of the ORF12 protein (alpha TIF) of equine herpesvirus 1.

    PubMed

    Lewis, J B; Thompson, Y G; Feng, X; Holden, V R; O'Callaghan, D; Caughman, G B

    1997-04-14

    The equine herpesvirus 1 (EHV-1) homolog of the herpes simplex virus type 1 (HSV-1) tegument phosphoprotein, alpha TIF (Vmw65; VP16), was identified previously as the product of open reading frame 12 (ORF12) and shown to transactivate immediate early (IE) gene promoters. However, a specific virion protein corresponding to the ORF12 product has not been identified definitively. In the present study the ORF12 protein, designated ETIF, was identified as a 60-kDa virion component on the basis of protein fingerprint analyses in which the limited proteolysis profiles of the major 60-kDa in vitro transcription/ translation product of an ORF12 expression vector (pT7-12) were compared to those of purified virion proteins of similar size. ETIF was localized to the viral tegument in Western blot assays of EHV-1 virions and subvirion fractions using polyclonal antiserum and monoclonal antibodies generated against a glutathione-S-transferase-ETIF fusion protein. Northern and Western blot analyses of EHV-1-infected cell lysates prepared under various metabolic blocks indicated that ORF12 is expressed as a late gene, and cross reaction of polyclonal anti-GST-ETIF with a 63.5-kDa HSV-1 protein species suggested that ETIF and HSV-1 alpha TIF are antigenically related. Last, DNA band shift assays used to assess ETIF-specific complex formation indicated that ETIF participates in an infected cell protein complex with the EHV-1 IE promoter TAATGARAT motif.

  2. Evidence implicating Ku antigen as a structural factor in RNA polymerase II-mediated transcription.

    PubMed

    Bertinato, Jesse; Tomlinson, Julianna J; Schild-Poulter, Caroline; Haché, Robert J G

    2003-01-02

    Ku antigen is an abundant nuclear protein with multiple functions that depend mainly on Ku's prolific and highly verstatile interactions with DNA. We have shown previously that the direct binding of Ku in vitro to negative regulatory element 1 (NRE1), a transcriptional regulatory element in the long terminal repeat of mouse mammary tumour virus, correlates with the regulation of viral transcription by Ku. In this study, we have sought to explore the interaction of Ku with NRE1 in vivo in yeast one-hybrid experiments. Unexpectedly, we observed that human Ku70 carrying a transcriptional activation domain from the yeast Gal4 protein induced transcription of yeast reporter genes pleiotrophically, independent of NRE1, promoter, reporter gene and chromosomal location. Ku80 with the same activation domain had no effect on transcription when expressed alone, but reconstituted activation when co-expressed with native human Ku70. The requirements for transcriptional activation by Ku-Gal4 activation domain proteins correlated with previous descriptions of the requirements for DNA sequence-independent DNA binding by Ku, but were distinct from determinants for DNA-end binding by a truncated Ku heterodimer determined recently by crystallography. These results suggest a preferential targeting of Ku to transcriptionally active chromatin that indicate a possible function for Ku within the RNA polymerase II holoenzyme.

  3. Hydrogen peroxide inactivation of influenza virus preserves antigenic structure and immunogenicity.

    PubMed

    Dembinski, Jennifer L; Hungnes, Olav; Hauge, Anna Germundsson; Kristoffersen, Anne-Cathrine; Haneberg, Bjørn; Mjaaland, Siri

    2014-10-01

    The use of live virus in the laboratory requires additional precautions, such as personnel training and special equipment, in order to limit the transmission risk. This is a requirement which not all laboratories can fulfill. In this study, a viral inactivation method is introduced using hydrogen peroxide (H2O2), which maintains antigenicity. Three strains of influenza viruses were inactivated and the ex vivo cellular and humoral immune responses were further analyzed, by comparing them to live viruses, in ELISpot, Multiplex and ELISA assays. In all assays, the H2O2 inactivated viruses displayed comparable responses to the live viruses, suggesting that the inactivated viruses still elicited immunogenic responses even though inactivation was confirmed by lack of viral replication in MDCK cells. Taken together, this study demonstrates that influenza viruses inactivated with H2O2 retain immunogenicity and are able to both detect humoral and elicit cellular immune responses in vitro, which could reduce the need to handle live viruses in the laboratory.

  4. [Somatic antigens of the Brucella genus. The structure of the O-specific polysaccharide chain of Brucella melitensis lipopolysaccharide].

    PubMed

    L'vov, V L; Malikov, V E; Shashkov, A S; Dranovskaia, E A; Dmitriev, B A

    1985-07-01

    The phenol-phase soluble antigenic lipopolysaccharide was isolated from Brucella melitensis, strain 565, by the routine phenol/water procedure followed by chromatography on Sepharose 4B. After mild acid hydrolysis and chromatography on Sephadex G-50, the lipopolysaccharide yielded a linear O-specific polysaccharide built up from 1,2-linked 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl units. The structure of the polysaccharide was deduced mainly from the nuclear magnetic resonance and methylation analyses. The phenol-soluble lipopolysaccharide, isolated from commercial vaccine strain B. abortus 19-BA, on mild hydrolysis afforded material, 13C and 1H-NMR spectra of which were identical to those of the O-specific polysaccharide from B. melitensis 565.

  5. Structure-Dependent Photophysics of First-Generation; Phenyl-Cored Thiophene Dendrimers

    SciTech Connect

    Mitchell, W. J.; Ferguson, A. J.; Kose, M. E.; Rupert, B. L.; Ginley, D. S.; Rumbles, G.; Shaheen, S. E.; Kopidakis, N.

    2009-01-01

    We have prepared two series of first-generation thiophene-bridge dendrimers, with either three (3G1) or four (4G1) arms attached to a phenyl core, to elucidate their structure-property relationships. Optical properties were investigated with a combination of steady-state and time-resolved spectroscopic techniques. Steady-state spectroscopic data for the 3-arm dendrimers suggests that the exciton is delocalized over the {alpha}-conjugated thiophene segment and the phenyl core, but that the meta-linking of the dendrons prevents their electronic communication. In contrast, conjugation through the core to dendrons in the ortho and para positions is permitted in the 4-arm dendrimers, although the data suggest that the conjugation length does not extend over the full length of the {alpha}-conjugated sections of two coupled dendrons. This observation is due to steric interactions between neighboring arms, which forces the arms to twist and bend out of the plane of the phenyl core, and is particularly prevalent in disrupting the conjugation through the ortho positions. As expected, our results show that an increase in the bridge length results in an increase in the conjugation length for both dendrimers, and a subsequent red-shift of the absorption and emission. In addition, an increase in the dendron length results in an increase in the photoluminescence quantum yield and lifetime, suggesting that the ground and excited-state geometries are very similar and that the electronic transition is coupled to fewer vibrational modes.

  6. Contamination assessment in microbiological sampling of the Eyreville core, Chesapeake Bay impact structure

    USGS Publications Warehouse

    Gronstal, A.L.; Voytek, M.A.; Kirshtein, J.D.; Von der, Heyde; Lowit, M.D.; Cockell, C.S.

    2009-01-01

    Knowledge of the deep subsurface biosphere is limited due to difficulties in recovering materials. Deep drilling projects provide access to the subsurface; however, contamination introduced during drilling poses a major obstacle in obtaining clean samples. To monitor contamination during the 2005 International Continental Scientific Drilling Program (ICDP)-U.S. Geological Survey (USGS) deep drilling of the Chesapeake Bay impact structure, four methods were utilized. Fluorescent microspheres were used to mimic the ability of contaminant cells to enter samples through fractures in the core material during retrieval. Drilling mud was infused with a chemical tracer (Halon 1211) in order to monitor penetration of mud into cores. Pore water from samples was examined using excitation-emission matrix (EEM) fl uorescence spectroscopy to characterize dissolved organic carbon (DOC) present at various depths. DOC signatures at depth were compared to signatures from drilling mud in order to identify potential contamination. Finally, microbial contaminants present in drilling mud were identified through 16S ribosomal deoxyribonucleic acid (rDNA) clone libraries and compared to species cultured from core samples. Together, these methods allowed us to categorize the recovered core samples according to the likelihood of contamination. Twenty-two of the 47 subcores that were retrieved were free of contamination by all the methods used and were subsequently used for microbiological culture and culture-independent analysis. Our approach provides a comprehensive assessment of both particulate and dissolved contaminants that could be applied to any environment with low biomass. ?? 2009 The Geological Society of America.

  7. Strain-induced structural defects and their effects on the electrochemical performances of silicon core/germanium shell nanowire heterostructures.

    PubMed

    Lin, Yung-Chen; Kim, Dongheun; Li, Zhen; Nguyen, Binh-Minh; Li, Nan; Zhang, Shixiong; Yoo, Jinkyoung

    2017-01-19

    We report on strain-induced structural defect formation in core Si nanowires of a Si/Ge core/shell nanowire heterostructure and the influence of the structural defects on the electrochemical performances in lithium-ion battery anodes based on Si/Ge core/shell nanowire heterostructures. The induced structural defects consisting of stacking faults and dislocations in the core Si nanowire were observed for the first time. The generation of stacking faults in the Si/Ge core/shell nanowire heterostructure is observed to prefer settling in either only the Ge shell region or in both the Ge shell and Si core regions and is associated with the increase of the shell volume fraction. The relaxation of the misfit strain in the [112] oriented core/shell nanowire heterostructure leads to subsequent gliding of Shockley partial dislocations, preferentially forming the twins. The observation of crossover of defect formation is of great importance for understanding heteroepitaxy in radial heterostructures at the nanoscale and for building three dimensional heterostructures for the various applications. Furthermore, the effect of the defect formation on the nanomaterial's functionality is investigated using electrochemical performance tests. The Si/Ge core/shell nanowire heterostructures enhance the gravimetric capacity of lithium ion battery anodes under fast charging/discharging rates compared to Si nanowires. However, the induced structural defects hamper lithiation of the Si/Ge core/shell nanowire heterostructure.

  8. Strain-induced structural defects and their effects on the electrochemical performances of silicon core/germanium shell nanowire heterostructures

    DOE PAGES

    Lin, Yung-Chen; Kim, Dongheun; Li, Zhen; ...

    2016-12-14

    Here we report on strain-induced structural defect formation in core Si nanowire of Si/Ge core/shell nanowire heterostructure and influences of the structural defects on the electrochemical performances in lithium-ion battery anodes based on Si/Ge core/shell nanowire heterostructures. The induced structural defects consisting of stacking faults and dislocations in the core Si nanowire were observed for the first time. The generation of stacking faults in Si/Ge core/shell nanowire heterostructure is observed to prefer settling in either only Ge shell region or in both Ge shell and Si core regions and is associated with the increase of the shell volume fraction. Themore » relax of misfit strain in [112] oriented core/shell nanowire heterostructure leads to subsequent gliding of Shockley partial dislocations, preferentially forming the twins. The observation of cross-over defect formation is of great importance for the understanding of heteroepitaxy in radial heterostructures at nanoscale and building the three dimensional heterostructures for the various applications. In addition, the effect of the defect formation on nanomaterial’s functionality is investigated by electrochemical performance test. The Si/Ge core/shell nanowire heterostructures enhance the gravimetric capacity of lithium ion battery anodes under fast charging/discharging rates compared to Si nanowires. However, the induced structural defects hamper lithiation of the Si/Ge core/shell nanowire heterostructure.« less

  9. Strain-induced structural defects and their effects on the electrochemical performances of silicon core/germanium shell nanowire heterostructures

    SciTech Connect

    Lin, Yung-Chen; Kim, Dongheun; Li, Zhen; Nguyen, Binh-Minh; Li, Nan; Zhang, Shixiong; Yoo, Jinkyoung

    2016-12-14

    Here we report on strain-induced structural defect formation in core Si nanowire of Si/Ge core/shell nanowire heterostructure and influences of the structural defects on the electrochemical performances in lithium-ion battery anodes based on Si/Ge core/shell nanowire heterostructures. The induced structural defects consisting of stacking faults and dislocations in the core Si nanowire were observed for the first time. The generation of stacking faults in Si/Ge core/shell nanowire heterostructure is observed to prefer settling in either only Ge shell region or in both Ge shell and Si core regions and is associated with the increase of the shell volume fraction. The relax of misfit strain in [112] oriented core/shell nanowire heterostructure leads to subsequent gliding of Shockley partial dislocations, preferentially forming the twins. The observation of cross-over defect formation is of great importance for the understanding of heteroepitaxy in radial heterostructures at nanoscale and building the three dimensional heterostructures for the various applications. In addition, the effect of the defect formation on nanomaterial’s functionality is investigated by electrochemical performance test. The Si/Ge core/shell nanowire heterostructures enhance the gravimetric capacity of lithium ion battery anodes under fast charging/discharging rates compared to Si nanowires. However, the induced structural defects hamper lithiation of the Si/Ge core/shell nanowire heterostructure.

  10. Synthesis and characterisation of core-shell structures for orthopaedic surgery.

    PubMed

    Rusen, Edina; Zaharia, Cătălin; Zecheru, Teodora; Mărculescu, Bogdan; Filmon, Robert; Chappard, Daniel; Bădulescu, Roxana; Cincu, Corneliu

    2007-01-01

    This paperwork deals with the obtaining and characterisation of new acrylic cements for bone surgery. The final mixture of cement contains derivatives of methacryloyloxyethyl phosphate, methacrylic acid or 2-acrylamido-2-methyl-1-propane sulphonic acid. The idea of using these monomers is sustained by their ability to form ionic bonds with barium, which is responsible for X-ray reflection and by the biocompatibility of these structures. The strategy consists in the obtaining of core-shell structures through heterogeneous polymerisation, which are used for final cement's manufacture. The orthopaedic cements were characterised by SEM, EDX, compression resistance and cytotoxicity assays.

  11. Structural Insights into the Protease-like Antigen Plasmodium falciparum SERA5 and Its Noncanonical Active-Site Serine

    SciTech Connect

    Hodder, Anthony N.; Malby, Robyn L.; Clarke, Oliver B.; Fairlie, W. Douglas; Colman, Peter M.; Crabb, Brendan S.; Smith, Brian J.

    2009-08-28

    The sera genes of the malaria-causing parasite Plasmodium encode a family of unique proteins that are maximally expressed at the time of egress of parasites from infected red blood cells. These multi-domain proteins are unique, containing a central papain-like cysteine-protease fragment enclosed between the disulfide-linked N- and C-terminal domains. However, the central fragment of several members of this family, including serine repeat antigen 5 (SERA5), contains a serine (S596) in place of the active-site cysteine. Here we report the crystal structure of the central protease-like domain of Plasmodium falciparum SERA5, revealing a number of anomalies in addition to the putative nucleophilic serine: (1) the structure of the putative active site is not conducive to binding substrate in the canonical cysteine-protease manner; (2) the side chain of D594 restricts access of substrate to the putative active site; and (3) the S{sub 2} specificity pocket is occupied by the side chain of Y735, reducing this site to a small depression on the protein surface. Attempts to determine the structure in complex with known inhibitors were not successful. Thus, despite having revealed its structure, the function of the catalytic domain of SERA5 remains an enigma.

  12. Discovery of protein complexes with core-attachment structures from Tandem Affinity Purification (TAP) data.

    PubMed

    Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong; Ng, See-Kiong; Wong, Limsoon

    2012-09-01

    Many cellular functions involve protein complexes that are formed by multiple interacting proteins. Tandem Affinity Purification (TAP) is a popular experimental method for detecting such multi-protein interactions. However, current computational methods that predict protein complexes from TAP data require converting the co-complex relationships in TAP data into binary interactions. The resulting pairwise protein-protein interaction (PPI) network is then mined for densely connected regions that are identified as putative protein complexes. Converting the TAP data into PPI data not only introduces errors but also loses useful information about the underlying multi-protein relationships that can be exploited to detect the internal organization (i.e., core-attachment structures) of protein complexes. In this article, we propose a method called CACHET that detects protein complexes with Core-AttaCHment structures directly from bipartitETAP data. CACHET models the TAP data as a bipartite graph in which the two vertex sets are the baits and the preys, respectively. The edges between the two vertex sets represent bait-prey relationships. CACHET first focuses on detecting high-quality protein-complex cores from the bipartite graph. To minimize the effects of false positive interactions, the bait-prey relationships are indexed with reliability scores. Only non-redundant, reliable bicliques computed from the TAP bipartite graph are regarded as protein-complex cores. CACHET constructs protein complexes by including attachment proteins into the cores. We applied CACHET on large-scale TAP datasets and found that CACHET outperformed existing methods in terms of prediction accuracy (i.e., F-measure and functional homogeneity of predicted complexes). In addition, the protein complexes predicted by CACHET are equipped with core-attachment structures that provide useful biological insights into the inherent functional organization of protein complexes. Our supplementary material can

  13. Direct observation of Σ7 domain boundary core structure in magnetic skyrmion lattice

    PubMed Central

    Matsumoto, Takao; So, Yeong-Gi; Kohno, Yuji; Sawada, Hidetaka; Ikuhara, Yuichi; Shibata, Naoya

    2016-01-01

    Skyrmions are topologically protected nanoscale magnetic spin entities in helical magnets. They behave like particles and tend to form hexagonal close-packed lattices, like atoms, as their stable structure. Domain boundaries in skyrmion lattices are considered to be important as they affect the dynamic properties of magnetic skyrmions. However, little is known about the fine structure of such skyrmion domain boundaries. We use differential phase contrast scanning transmission electron microscopy to directly visualize skyrmion domain boundaries in FeGe1−xSix induced by the influence of an “edge” of a crystal grain. Similar to hexagonal close-packed atomic lattices, we find the formation of skyrmion “Σ7” domain boundary, whose orientation relationship is predicted by the coincidence site lattice theory to be geometrically stable. On the contrary, the skyrmion domain boundary core structure shows a very different structure relaxation mode. Individual skyrmions can flexibly change their size and shape to accommodate local coordination changes and free volumes formed at the domain boundary cores. Although atomic rearrangement is a common structural relaxation mode in crystalline grain boundaries, skyrmions show very unique and thus different responses to such local lattice disorders. PMID:26933690

  14. Crystal Structure of the Heterotrimer Core of Saccharomyces cerevisiae AMPK Homologue SNF1

    SciTech Connect

    Amodeo,G.; Rudolph, M.; Tong, L.

    2007-01-01

    AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis in mammals and is an attractive target for drug discovery against diabetes, obesity and other diseases. The AMPK homologue in Saccharomyces cerevisiae, known as SNF1, is essential for responses to glucose starvation as well as for other cellular processes, although SNF1 seems to be activated by a ligand other than AMP. Here we report the crystal structure at 2.6 resolution of the heterotrimer core of SNF1. The ligand-binding site in the {gamma}-subunit (Snf4) has clear structural differences from that of the Schizosaccharomyces pombe enzyme, although our crystallographic data indicate that AMP can also bind to Snf4. The glycogen-binding domain in the {beta}-subunit (Sip2) interacts with Snf4 in the heterotrimer but should still be able to bind carbohydrates. Our structure is supported by a large body of biochemical and genetic data on this complex. Most significantly, the structure reveals that part of the regulatory sequence in the {alpha}-subunit (Snf1) is sequestered by Snf4, demonstrating a direct interaction between the {alpha}- and {gamma}-subunits and indicating that our structure may represent the heterotrimer core of SNF1 in its activated state.

  15. Structure and antigenicity analysis of the IgG gene for Nyctereutes procyonoides

    PubMed Central

    Zhao, Cui; Guo, Shuyuan; Pang, Xiaoru; Song, Daozhen; Fu, Shijun

    2015-01-01

    Objective Nyctereutes procyonoides immunoglobulin G (IgG) gene is partially cloned. Material and methods In order to obtain a certain length (966bp) of Nyctereutes procyonoides immunoglobulin G (IgG), two pairs of primers are designed according to the conserved nucleotide sequence of canine (GenBank:AF354265, AF354265, AF354266, AF354267) and mink (GenBank: L07789). Using Bioinformatics technology and Western-blot to analyze antigenicity of Nyctereutes procyonoides IgG-B gene. Results The homology for nucleotide sequence of IgG between Nyctereutes procyonoides and canine (IgG A, IgG B, IgG C, IgG D), mink, Homo sapiens, Oryctolagus cuniculus, Mus musculus, Anas platyrhynchos and gallus were respectively (88.1%, 93.6%, 85.4%, 87.2%), 83.7%, 74.8%, 71.8%, 69.2%, 51.6%, 48.4%. It can be seen that there was high homology of aminoacid sequence between IgG of Nyctereutes procyonoides and IgG (A, B, C, D) of canine. And the serum antibody of Nyctereutes procyonoides had obviously cross-reaction with HRP conjugated rabbit anti-dog IgG, compared with those of canine, oryctolagus cuniculus, mus musculus, mink, gallus. Conclusions We successfully got Nyctereutes procyonoides immuneglobulin G (IgG) gene (Gen- Bank: KM010191). There is the closest ties of consanguinity of IgG exist between Nyctereutes procyonoides and canine among the mammal through the genetic evolution. The detection and treament of canine distemper can be used on Nyctereutes procyonoides. PMID:26648768

  16. Modeling of dislocation core structures in Mg7Si2O8(OH)6 phase A

    NASA Astrophysics Data System (ADS)

    Gouriet, K.; Cordier, P.; Carrez, P.; Mussi, A.; Caracas, R.

    2013-12-01

    Dense hydrous magnesium silicates (DHMS), such as Phase A [Mg7Si2O8(OH)6] play an important role in the transport of water within the upper mantle. The importance of these hydrous phases is not restricted to water storage. Indeed, at greater depths, the knowledge of the rheological properties of hydrous phases is also important for a best understanding of the dynamics of subduction. Recently, Mussi et al. [1] have performed an experimental study of the deformation mechanisms of phase A at 400°C and 700°C at 11 GPa. The authors have observed dislocation activity in basal, prismatic and pyramidal planes, with dissociation of dislocations in the basal and pyramidal planes. To complement this study, we modeled dislocation core structures in this mineral. In this study, we focus on the core structures of dislocations with 1/3[2-1-10] and 1/3[01-10] Burgers vectors. We have first investigated the structural and elastic properties of phase A at high pressure based on first-principles calculations. To understand how the structure of phase A can be sheared, the generalized stacking fault energies (or γ-surfaces) are calculated for the basal and prismatic planes. We found stable stacking fault in the basal plane at 1/3[01-10], suggesting possible dislocation dissociation in this plane. The core structures of screw dislocations have been calculated using the Peierls-Nabarro-Galerkin method involving γ-surfaces as an input. These calculations confirm the dissociation of dislocations with 1/3[2-1-10]Burgers vector in the basal plane. [1] A. Mussi, P. Cordier, D. J. Frost, Europeen Journal of Mineralogy 24 pp. 429-438 (2012)

  17. Structures of MART-126/27-35Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition

    SciTech Connect

    Borbulevych, Oleg Y; Insaidoo, Francis K; Baxter, Tiffany K; Powell, Jr., Daniel J.; Johnson, Laura A; Restifo, Nicholas P; Baker, Brian M

    2008-09-17

    Small structural changes in peptides presented by major histocompatibility complex (MHC) molecules often result in large changes in immunogenicity, supporting the notion that T cell receptors are exquisitely sensitive to antigen structure. Yet there are striking examples of TCR recognition of structurally dissimilar ligands. The resulting unpredictability of how T cells will respond to different or modified antigens impacts both our understanding of the physical bases for TCR specificity as well as efforts to engineer peptides for immunomodulation. In cancer immunotherapy, epitopes and variants derived from the MART-1/Melan-A protein are widely used as clinical vaccines. Two overlapping epitopes spanning amino acid residues 26 through 35 are of particular interest: numerous clinical studies have been performed using variants of the MART-1 26-35 decamer, although only the 27-35 nonamer has been found on the surface of targeted melanoma cells. Here, we show that the 26-35 and 27-35 peptides adopt strikingly different conformations when bound to HLA-A2. Nevertheless, clonally distinct MART-1{sub 26/27-35}-reactive T cells show broad cross-reactivity towards these ligands. Simultaneously, however, many of the cross-reactive T cells remain unable to recognize anchor-modified variants with very subtle structural differences. These dichotomous observations challenge our thinking about how structural information on unligated peptide/MHC complexes should be best used when addressing questions of TCR specificity. Our findings also indicate that caution is warranted in the design of immunotherapeutics based on the MART-1 26/27-35 epitopes, as neither cross-reactivity nor selectivity is predictable based on the analysis of the structures alone.

  18. Core-shell structured PEO-chitosan nanofibers by coaxial electrospinning.

    PubMed

    Pakravan, Mehdi; Heuzey, Marie-Claude; Ajji, Abdellah

    2012-02-13

    Core-shell structured PEO-chitosan nanofibers have been produced using a coaxial electrospinning setup. PEO and chitosan solutions, both in an aqueous acetic acid solvent, were used as the inner (core) and outer (shell) layer, respectively. Uniform-sized defect-free nanofibers of 150-190 nm diameter were produced. In addition, hollow nanofibers could be obtained subsequent to PEO washing of the membranes. The core-shell nanostructure and existence of chitosan on the shell layer were confirmed by TEM images obtained before and after washing the PEO content with water. The presence of chitosan on the surface of the composite nanofibers was further supported by XPS studies. The chitosan and PEO compositions in the nanofibrous mats were determined by TGA analysis, which were similar to their ratio in the feed solutions. The local compositional homogeneity of the membranes and the efficiency of the washing step to remove PEO were also verified by FTIR. In addition, DSC and XRD were used to characterize the crystalline structure and morphology of the co-electrospun nonwoven mats. The prepared coaxial nanofibers (hollow and solid) have several potential applications due to the presence of chitosan on their outer surfaces.

  19. Controllable synthesis and characterization of novel copper-carbon core-shell structured nanoparticles

    SciTech Connect

    Zhai, Jing; Tao, Xia; Pu, Yuan; Zeng, Xiao-Fei; Chen, Jian-Feng

    2011-06-15

    Highlights: {yields} We reported a facile, green and cheap hydrothermal method to obtain novel copper-carbon core-shell nanoparticles. {yields} The as-formed particles with controllable size and morphology are antioxidant. {yields} The particles with organic-group-loaded surfaces and protective shells are expected to be applied in fields of medicine, electronics, sensors and lubricant. -- Abstract: A facile hydrothermal method was developed for preparing copper-carbon core-shell structured particles through a reaction at 160 {sup o}C in which glucose, copper sulfate pentahydrate and cetyltrimethylammonium bromide were used as starting materials. The original copper-carbon core-shell structured particles obtained were sized of 100-250 nm. The thickness of carbonaceous shells was controlled ranging from 25 to 100 nm by adjusting the hydrothermal duration time and the concentrations of glucose in the process. Products were characterized with transmission electron microscopy, X-ray diffraction, energy dispersive spectroscopy, Fourier transform infrared spectroscopy. Since no toxic materials were involved in the preparation, particles with stable carbonaceous framework and reactive surface also showed promising applications in medicine, electronics, sensors, lubricant, etc.

  20. Shell-anchor-core structures for enhanced stability and catalytic oxygen reduction activity

    NASA Astrophysics Data System (ADS)

    Ramirez-Caballero, Gustavo E.; Hirunsit, Pussana; Balbuena, Perla B.

    2010-10-01

    Density functional theory is used to evaluate activity and stability properties of shell-anchor-core structures. The structures consist of a Pt surface monolayer and a composite core having an anchor bilayer where C atoms in the interstitial sites lock 3d metals in their locations, thus avoiding their surface segregation and posterior dissolution. The modified subsurface geometry induces less strain on the top surface, thus exerting a favorable effect on the surface catalytic activity where the adsorption strength of the oxygenated species becomes more moderate: weaker than on pure Pt(111) but stronger than on a Pt monolayer having a 3d metal subsurface. Here we analyze the effect of changing the nature of the 3d metal in the subsurface anchor bilayer, and we also test the use of a Pd monolayer instead of Pt on the surface. It is found that a subsurface constituted by two layers with an approximate composition of M2C (M=Fe, Ni, and Co) provides a barrier for the migration of subsurface core metal atoms to the surface. Consequently, an enhanced resistance against dissolution in parallel to improved oxygen reduction activity is expected, as given by the values of adsorption energies of reaction intermediates, delayed onset of water oxidation, and/or low coverage of oxygenated species at surface oxidation potentials.

  1. Identification and Structural Characterization of the N-terminal Amyloid Core of Orb2 isoform A

    PubMed Central

    Cervantes, Silvia A.; Bajakian, Thalia H.; Soria, Maria A.; Falk, Alexander S.; Service, Rachel J.; Langen, Ralf; Siemer, Ansgar B.

    2016-01-01

    Orb2 is a functional amyloid that plays a key role in Drosophila long-term memory formation. Orb2 has two isoforms that differ in their N-termini. The N-terminus of the A isoform (Orb2A) that precedes its Q-rich prion-like domain has been shown to be important for Orb2 aggregation and long-term memory. However, besides the fact that it forms fibrillar aggregates, structural information of Orb2 is largely absent. To understand the importance of the N-terminus of Orb2A and its relation to the fibril core, we recorded solid-state NMR and EPR data on fibrils formed by the first 88 residues of Orb2A (Orb2A88). These data show that the N-terminus of Orb2A not only promotes the formation of fibrils, but also forms the fibril core of Orb2A88. This fibril core has an in-register parallel β-sheet structure and does not include the Q-rich, prion-like domain of Orb2. The Q-rich domain is part of the unstructured region, which becomes increasingly dynamic towards the C-terminus. PMID:27922050

  2. Potassium dependent rescue of a myopathy with core-like structures in mouse.

    PubMed

    Hanson, M Gartz; Wilde, Jonathan J; Moreno, Rosa L; Minic, Angela D; Niswander, Lee

    2015-01-07

    Myopathies decrease muscle functionality. Mutations in ryanodine receptor 1 (RyR1) are often associated with myopathies with microscopic core-like structures in the muscle fiber. In this study, we identify a mouse RyR1 model in which heterozygous animals display clinical and pathological hallmarks of myopathy with core-like structures. The RyR1 mutation decreases sensitivity to activated calcium release and myoplasmic calcium levels, subsequently affecting mitochondrial calcium and ATP production. Mutant muscle shows a persistent potassium leak and disrupted expression of regulators of potassium homeostasis. Inhibition of KATP channels or increasing interstitial potassium by diet or FDA-approved drugs can reverse the muscle weakness, fatigue-like physiology and pathology. We identify regulators of potassium homeostasis as biomarkers of disease that may reveal therapeutic targets in human patients with myopathy of central core disease (CCD). Altogether, our results suggest that amelioration of potassium leaks through potassium homeostasis mechanisms may minimize muscle damage of myopathies due to certain RyR1 mutations.

  3. The 2.5 Å Structure of CD1c in Complex with a Mycobacterial Lipid Reveals an Open Groove Ideally Suited for Diverse Antigen Presentation

    SciTech Connect

    Scharf, Louise; Li, Nan-Sheng; Hawk, Andrew J.; Garzón, Diana; Zhang, Tejia; Fox, Lisa M.; Kazen, Allison R.; Shah, Sneha; Haddadian, Esmael J.; Gumperz, Jenny E.; Saghatelian, Alan; Faraldo-Gómez, José D.; Meredith, Stephen C.; Piccirilli, Joseph A.; Adams, Erin J.

    2011-08-24

    CD1 molecules function to present lipid-based antigens to T cells. Here we present the crystal structure of CD1c at 2.5 {angstrom} resolution, in complex with the pathogenic Mycobacterium tuberculosis antigen mannosyl-{beta}1-phosphomycoketide (MPM). CD1c accommodated MPM's methylated alkyl chain exclusively in the A pocket, aided by a unique exit portal underneath the {alpha}1 helix. Most striking was an open F pocket architecture lacking the closed cavity structure of other CD1 molecules, reminiscent of peptide binding grooves of classical major histocompatibility complex molecules. This feature, combined with tryptophan-fluorescence quenching during loading of a dodecameric lipopeptide antigen, provides a compelling model by which both the lipid and peptide moieties of the lipopeptide are involved in CD1c presentation of lipopeptides.

  4. Hydrophobic core/hydrophilic shell structured mesoporous silica nanospheres: enhanced adsorption of organic compounds from water.

    PubMed

    Li, Shuru; Jiao, Xuan; Yang, Hengquan

    2013-01-29

    Inspired by the structure features of micelle, we attempt to synthesize a novel functionalized mesoporous silica nanosphere consisting of a hydrophobic core and a hydrophilic shell. The obtained solid materials were structurally confirmed by N(2) sorption, X-ray diffraction (XRD), and transmission electron microscopy (TEM). Their compositions were characterized by Fourier transfer infrared spectroscopy (FT-IR), solid state NMR, X-ray photoelectron spectroscopy (XPS), and elemental analysis. Its fundamental properties such as dispersibility in water or organic phase, wettability, and adsorption ability toward hydrophobic organics in water were investigated. It was revealed that these important properties could be facilely adjusted through varying structure and composition. In particular, these materials showed much better adsorption ability toward hydrophobic organic molecules in water than conventional monofunctionalized mesoporous materials, owing to possessing the hydrophobic/hydrophilic domain-segregated and hierarchically functionalized mesoporous structures. The intriguing properties would make mesoporous materials more accessible to many important applications, especially in aqueous systems.

  5. Open structure ZnO/CdSe core/shell nanoneedle arrays for solar cells

    PubMed Central

    2012-01-01

    Open structure ZnO/CdSe core/shell nanoneedle arrays were prepared on a conducting glass (SnO2:F) substrate by solution deposition and electrochemical techniques. A uniform CdSe shell layer with a grain size of approximately several tens of nanometers was formed on the surface of ZnO nanoneedle cores after annealing at 400°C for 1.5 h. Fabricated solar cells based on these nanostructures exhibited a high short-circuit current density of about 10.5 mA/cm2 and an overall power conversion efficiency of 1.07% with solar illumination of 100 mW/cm2. Incident photo-to-current conversion efficiencies higher than 75% were also obtained. PMID:22995031

  6. A novel approach to preparing magnetic protein microspheres with core-shell structure

    NASA Astrophysics Data System (ADS)

    Jiang, Wei; Sun, Zhendong; Li, Fengsheng; Chen, Kai; Liu, Tianyu; Liu, Jialing; Zhou, Tianle; Guo, Rui

    2011-03-01

    Magnetic protein microspheres with core-shell structure were prepared through a novel approach based on the sonochemical method and the emulsion solvent evaporation method. The microspheres are composed of the oleic acid and undecylenic acid modified Fe 3O 4 cores and coated with globular bovine serum albumin (BSA). Under an optimized condition, up to 57.8 wt% of approximately 10 nm superparamagnetic Fe 3O 4 nanoparticles could be uniformly encapsulated into the BSA microspheres with the diameter of approximately 160 nm and the high saturation magnetization of 38.5 emu/g, besides of the abundant functional groups. The possible formation mechanism of magnetic microspheres was discussed in detail.

  7. Open structure ZnO/CdSe core/shell nanoneedle arrays for solar cells.

    PubMed

    Chen, Yanxue; Wei, Lin; Zhang, Guanghua; Jiao, Jun

    2012-09-20

    Open structure ZnO/CdSe core/shell nanoneedle arrays were prepared on a conducting glass (SnO2:F) substrate by solution deposition and electrochemical techniques. A uniform CdSe shell layer with a grain size of approximately several tens of nanometers was formed on the surface of ZnO nanoneedle cores after annealing at 400°C for 1.5 h. Fabricated solar cells based on these nanostructures exhibited a high short-circuit current density of about 10.5 mA/cm2 and an overall power conversion efficiency of 1.07% with solar illumination of 100 mW/cm2. Incident photo-to-current conversion efficiencies higher than 75% were also obtained.

  8. Linear structures in the core of the Coma cluster of galaxies.

    PubMed

    Sanders, J S; Fabian, A C; Churazov, E; Schekochihin, A A; Simionescu, A; Walker, S A; Werner, N

    2013-09-20

    The hot x-ray-emitting plasma in galaxy clusters is predicted to have turbulent motion, which can contribute around 10% of the cluster's central energy density. We report deep Chandra X-ray Observatory observations of the Coma cluster core, showing the presence of quasi-linear high-density arms spanning 150 kiloparsecs, consisting of low-entropy material that was probably stripped from merging subclusters. Two appear to be connected with a subgroup of galaxies at a 650-kiloparsec radius that is merging into the cluster, implying coherence over several hundred million years. Such a long lifetime implies that strong isotropic turbulence and conduction are suppressed in the core, despite the unrelaxed state of the cluster. Magnetic fields are presumably responsible. The structures seen in Coma present insight into the past billion years of subcluster merger activity.

  9. Size-dependent structural evolution of the biomineralized iron-core nanoparticles in ferritins

    NASA Astrophysics Data System (ADS)

    Lee, Eunsook; Kim, D. H.; Hwang, Jihoon; Lee, Kiho; Yoon, Sungwon; Suh, B. J.; Hyun Kim, Kyung; Kim, J.-Y.; Jang, Z. H.; Kim, Bongjae; Min, B. I.; Kang, J.-S.

    2013-04-01

    The structural identity of the biomineralized iron core nanoparticles in Helicobacter pylori ferritins (Hpf's) has been determined by employing soft x-ray absorption spectroscopy and soft x-ray magnetic circular dichroism. Valence states of Fe ions are nearly trivalent in all Hpf's, indicating that the amount of magnetite (Fe3O4) is negligible. With increasing filling of Fe ions, the local configurations of Fe3+ ions change from the mixture of the tetrahedral and octahedral symmetries to the octahedral symmetry. These results demonstrate that the biomineralization of the ferritin core changes from maghemite-like (γ-Fe2O3) formation to hematite-like (α-Fe2O3) formation with increasing Fe content.

  10. Sizing Single Cantilever Beam Specimens for Characterizing Facesheet/Core Peel Debonding in Sandwich Structure

    NASA Technical Reports Server (NTRS)

    Ratcliffe, James G.

    2010-01-01

    This paper details part of an effort focused on the development of a standardized facesheet/core peel debonding test procedure. The purpose of the test is to characterize facesheet/core peel in sandwich structure, accomplished through the measurement of the critical strain energy release rate associated with the debonding process. The specific test method selected for the standardized test procedure utilizes a single cantilever beam (SCB) specimen configuration. The objective of the current work is to develop a method for establishing SCB specimen dimensions. This is achieved by imposing specific limitations on specimen dimensions, with the objectives of promoting a linear elastic specimen response, and simplifying the data reduction method required for computing the critical strain energy release rate associated with debonding. The sizing method is also designed to be suitable for incorporation into a standardized test protocol. Preliminary application of the resulting sizing method yields practical specimen dimensions.

  11. Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA.

    PubMed

    Bochkareva, Elena; Martynowski, Dariusz; Seitova, Almagoul; Bochkarev, Alexey

    2006-12-13

    The large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we determined the crystal structures of the T-ag origin-binding domain (OBD) in apo form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA palindrome comprising all four GAGGC binding sites for OBD. The T-ag OBDs were shown to interact with the DNA through a loop comprising Ser147-Thr155 (A1 loop), a combination of a DNA-binding helix and loop (His203-Asn210), and Asn227. The A1 loop traveled back-and-forth along the major groove and accounted for most of the sequence-determining contacts with the DNA. Unexpectedly, in both T-ag-DNA structures, the T-ag OBDs bound DNA independently and did not make direct protein-protein contacts. The T-ag OBD was also captured bound to a non-consensus site ATGGC even in the presence of its canonical site GAGGC. Our observations taken together with the known biochemical and structural features of the T-ag-origin interaction suggest a model for origin unwinding.

  12. Structural characterization of the N-glycans of a recombinant hepatitis B surface antigen derived from yeast

    SciTech Connect

    Ip, C.C.Y.; Miller, W.J.; Kubek, D.J. ); Strang, A.M.; van Halbeek, H. ); Piesecki, S.J.; Alhadeff, J.A. )

    1992-01-14

    The N-glycans of purified recombinant middle surface protein (preS2+S) from hepatitis B virus, a candidate vaccine antigen expressed in a mnn9 mutant strain of Saccharomyces cerevisiae, have been characterized structurally. The glycans were released by N-glycanase treatment, isolated by size-exclusion chromatography on Sephadex G-50 and Bio-Gel P-4 columns, and analyzed by 500-MHz {sup 1}H NMR spectroscopy and fast atom bombardment mass spectrometry. The mixture of oligosaccharides was fractionated by HPLC, the major subfractions were isolated, and their carbohydrate compositions were determined by high-pH anion-exchange chromatography with pulsed amperometric detection. The combined results suggest that high-mannose oligosaccharides account for all the N-glycans released from preS2+S: structures include Man{sub 7}GlcNAc{sub 2}, Man{sub 8}GlcNAc{sub 2} isomers in the ratios of 3:6:1. Approximately 80% of the oligosaccharides contain the C2, C6-branched trimannosyl structural element typical of yeast high-mannose oligosaccharides but not usually found in high-mannose oligosaccharides in animal glycoproteins.

  13. [Effect of silver/zinc selenide core-shell structure spheres on the infrared absorption properties of sodium nitrate].

    PubMed

    Guo, Qiang; Li, Chun; Jia, Zhi-Jun; Yuan, Guang

    2013-10-01

    Silver/zinc selenide (Ag/ZnSe) core-shell structure spheres were made through the method of silver mirror reaction on zinc selenide micro spheres. Surface morphology of the spheres was depicted by scanning electron microscopy, X-ray diffraction and Fourier infrared absorption spectrum. This paper studies the effect of Ag/ZnSe core-shell structure spheres on the infrared absorption properties of sodium nitrate solution. The results show that, the anti-symmetric vibration absorption peaks of nitrate are blue-shifted, and the intensity are improved obviously by the effect of core-shell structure spheres.

  14. Crystal Structure of TDP-Fucosamine Acetyl Transferase (WECD) from Escherichia Coli, an Enzyme Required for Enterobacterial Common Antigen Synthesis

    SciTech Connect

    Hung,M.; Rangarajan, E.; Munger, C.; Nadeau, G.; Sulea, T.; Matte, A.

    2006-01-01

    Enterobacterial common antigen (ECA) is a polysaccharide found on the outer membrane of virtually all gram-negative enteric bacteria and consists of three sugars, N-acetyl-D-glucosamine, N-acetyl-D-mannosaminuronic acid, and 4-acetamido-4,6-dideoxy-D-galactose, organized into trisaccharide repeating units having the sequence {yields}(3)-{alpha}-D-Fuc4NAc-(1{yields}4)-{beta}-D-ManNAcA-(1{yields}4)-{alpha}-D-GlcNAc-(1{yields}). While the precise function of ECA is unknown, it has been linked to the resistance of Shiga-toxin-producing Escherichia coli (STEC) O157:H7 to organic acids and the resistance of Salmonella enterica to bile salts. The final step in the synthesis of 4-acetamido-4,6-dideoxy-D-galactose, the acetyl-coenzyme A (CoA)-dependent acetylation of the 4-amino group, is carried out by TDP-fucosamine acetyltransferase (WecD). We have determined the crystal structure of WecD in apo form at a 1.95-Angstroms resolution and bound to acetyl-CoA at a 1.66-Angstroms resolution. WecD is a dimeric enzyme, with each monomer adopting the GNAT N-acetyltransferase fold, common to a number of enzymes involved in acetylation of histones, aminoglycoside antibiotics, serotonin, and sugars. The crystal structure of WecD, however, represents the first structure of a GNAT family member that acts on nucleotide sugars. Based on this cocrystal structure, we have used flexible docking to generate a WecD-bound model of the acetyl-CoA-TDP-fucosamine tetrahedral intermediate, representing the structure during acetyl transfer. Our structural data show that WecD does not possess a residue that directly functions as a catalytic base, although Tyr208 is well positioned to function as a general acid by protonating the thiolate anion of coenzyme A.

  15. Chagas disease: a homology model for the three-dimensional structure of the Trypanosoma cruzi ribosomal P0 antigenic protein.

    PubMed

    Gomez Barroso, Juan Arturo; Aguilar, Carlos Fernando

    2014-09-01

    Ribosomal P proteins form a "stalk" complex in the large subunit of the ribosomes. In Trypanosoma cruzi, the etiological agent of Chagas disease, the complex is formed by five P protein members: TcP0, TcP1α, TcP1β, TcP2α and TcP2β. The TcP0 protein has 34 kDa, and TcP1 and TcP2 proteins have 10 kDa. The structure of T. cruzi P0 and the stalk complex TcP0-TcP1α-TcP1β-TcP2α-TcP2β have not been solved to date. In this work, we constructed a three-dimensional molecular model for TcP0 using homology modeling as implemented in the MODELLER 9v12 software. The model was constructed using different templates: the X-ray structures of the protein P0 from Pirococcus horikoshii, a segment from the Danio renio Ca(+2)/K(+) channel and the C-terminal peptide (C13) from T. cruzi ribosomal P2 protein; the Cryo-EM structure of Triticum aestivum P0 protein and the NMR structure of Homo sapiens P1 ribosomal protein. TcP0 has a 200-residue-long N-terminal, which is an α/β globular stable domain, and a flexible C-terminal, 120-residue-long domain. The molecular surface electrostatic potential and hydrophobic surface were calculated. The surface properties are important for the C-terminal's antigenic properties. They are also responsible for P0-specific binding to RNA26S and the binding to the P1-P2 proteins. We explored and identified protein interactions that may be involved in conformational stability. The structure proposed in this work represents a first structural report for the TcP0 protein.

  16. Structural optical correlated properties of SnO2/Al2O3 core@ shell heterostructure

    NASA Astrophysics Data System (ADS)

    Heiba, Zein K.; Imam, N. G.; Bakr Mohamed, Mohamed

    2016-07-01

    Nano size polycrystalline samples of the core@shell heterostructure of SnO2 @ xAl2O3 (x = 0, 25, 50, 75 wt.%) were synthesized by sol-gel technique. The resulting samples were characterized with fourier transform infrared spectroscopy (FT-IR), photoluminescence (PL) and X-ray powder diffraction (XRD). The XRD patterns manifest diffraction peaks of SnO2 as main phase with weak peaks corresponding to Al2O3 phase. The formation of core@ shell structure is confirmed by TEM images and Rietveld quantitative phase analysis which revealed that small part of Al2O3 is incorporated into the SnO2 lattice while the main part (shell) remains as a separate phase segregated on the grain boundary surface of SnO2 (core). It is found that the grain size of the mixed oxides SnO2 @ xAl2O3 is below 10 nm while for pure SnO2 it is over 41 nm, indicating that alumina can effectively prevent SnO2 from further growing up in the process of calcination. This is confirmed by the large increase in the specific surface area for mixed oxide samples. The PL emission showed great dependence on the structure properties analyzed by XRD and FTIR. The PL results recommend Al2O3@SnO2 core@shell heterostructure to be a promising short-wavelength luminescent optoelectronic devices for blue, UV, and laser light-emitting diodes.

  17. The Dependence of ITCZ Structure on Model Resolution and Dynamical Core in Aquaplanet Simulations

    SciTech Connect

    Landu, Kiranmayi; Leung, Lai-Yung R.; Hagos, Samson M.; Vinoj, V.; Rauscher, Sara; Ringler, Todd; Taylor, Mark

    2014-03-15

    Aqua-planet simulations using the Community Atmosphere Model version 4 (CAM4) with the Model for Prediction Across Scales Atmosphere (MPAS-A) and Higher Order Method Modeling Environment (HOMME) dynamical cores and zonally symmetric sea surface temperature (SST) structure are studied to understand the dependence of the inter-tropical convergence zone (ITCZ) structure on resolution and dynamical core. While all resolutions in HOMME and the low-resolution MPAS-A simulations give a single equatorial peak in zonal mean precipitation, the high-resolution MPAS-A simulations give a double ITCZ with precipitation peaking around 2° to 3° on either side of the equator. This study reveals that the structure of ITCZ is dependent on the feedbacks among convection and large-scale circulation and surface heat fluxes. We show that, by increasing convective available potential energy (CAPE) off the equator, the simulations with higher wind induced surface heat fluxes result in double ITCZ structure. This in turn leads to stronger convection and positive feedback with the large-scale circulation. We further show that the dominance of anti-symmetric waves in a model is not enough to cause double ITCZ, and the lateral extent of equatorial waves does not play an important role in determining the width of the ITCZ but rather the latter may influence the former.

  18. Hypervelocity Impact Performance of Open Cell Foam Core Sandwich Panel Structures

    NASA Technical Reports Server (NTRS)

    Ryan, S.; Ordonez, E.; Christiansen, E. L.; Lear, D. M.

    2010-01-01

    Open cell metallic foam core sandwich panel structures are of interest for application in spacecraft micrometeoroid and orbital debris shields due to their novel form and advantageous structural and thermal performance. Repeated shocking as a result of secondary impacts upon individual foam ligaments during the penetration process acts to raise the thermal state of impacting projectiles ; resulting in fragmentation, melting, and vaporization at lower velocities than with traditional shielding configurations (e.g. Whipple shield). In order to characterize the protective capability of these structures, an extensive experimental campaign was performed by the Johnson Space Center Hypervelocity Impact Technology Facility, the results of which are reported in this paper. Although not capable of competing against the protection levels achievable with leading heavy shields in use on modern high-risk vehicles (i.e. International Space Station modules), metallic foam core sandwich panels are shown to provide a substantial improvement over comparable structural panels and traditional low weight shielding alternatives such as honeycomb sandwich panels and metallic Whipple shields. A ballistic limit equation, generalized in terms of panel geometry, is derived and presented in a form suitable for application in risk assessment codes.

  19. Structural Analysis of a Highly Glycosylated and Unliganded gp120-Based Antigen Using Mass Spectrometry

    SciTech Connect

    L Wang; Y Qin; S Ilchenko; J Bohon; W Shi; M Cho; K Takamoto; M Chance

    2011-12-31

    Structural characterization of the HIV-1 envelope protein gp120 is very important for providing an understanding of the protein's immunogenicity and its binding to cell receptors. So far, the crystallographic structure of gp120 with an intact V3 loop (in the absence of a CD4 coreceptor or antibody) has not been determined. The third variable region (V3) of the gp120 is immunodominant and contains glycosylation signatures that are essential for coreceptor binding and entry of the virus into T-cells. In this study, we characterized the structure of the outer domain of gp120 with an intact V3 loop (gp120-OD8) purified from Drosophila S2 cells utilizing mass spectrometry-based approaches. We mapped the glycosylation sites and calculated the glycosylation occupancy of gp120-OD8; 11 sites from 15 glycosylation motifs were determined as having high-mannose or hybrid glycosylation structures. The specific glycan moieties of nine glycosylation sites from eight unique glycopeptides were determined by a combination of ECD and CID MS approaches. Hydroxyl radical-mediated protein footprinting coupled with mass spectrometry analysis was employed to provide detailed information about protein structure of gp120-OD8 by directly identifying accessible and hydroxyl radical-reactive side chain residues. Comparison of gp120-OD8 experimental footprinting data with a homology model derived from the ligated CD4-gp120-OD8 crystal structure revealed a flexible V3 loop structure in which the V3 tip may provide contacts with the rest of the protein while residues in the V3 base remain solvent accessible. In addition, the data illustrate interactions between specific sugar moieties and amino acid side chains potentially important to the gp120-OD8 structure.

  20. Structural analysis of a highly glycosylated and unliganded gp120-based antigen using mass spectrometry†

    PubMed Central

    Wang, Liwen; Qin, Yali; Ilchenko, Serguei; Bohon, Jen; Shi, Wuxian; Cho, Michael W.; Takamoto, Keiji; Chance, Mark R.

    2010-01-01

    Structural characterization of the HIV envelope protein gp120 is very important to provide an understanding of the protein's immunogenicity and it's binding to cell receptors. So far, crystallographic structure determination of gp120 with an intact V3 loop (in the absence of CD4 co-receptor or antibody) has not been achieved. The third variable region (V3) of the gp120 is immunodominant and contains glycosylation signatures that are essential for co-receptor binding and viral entry to T-cells. In this study, we characterized the structure of the outer domain of gp120 with an intact V3 loop (gp120-OD8) purified from Drosophila S2 cells utilizing mass spectrometry-based approaches. We mapped the glycosylation sites and calculated glycosylation occupancy of gp120-OD8; eleven sites from fifteen glycosylation motifs were determined as having high mannose or hybrid glycosylation structures. The specific glycan moieties of nine glycosylation sites from eight unique glycopeptides were determined by a combination of ECD and CID MS approaches. Hydroxyl radical-mediated protein footprinting coupled with mass spectrometry analysis was employed to provide detailed information on protein structure of gp120-OD8 by directly identifying accessible and hydroxyl radical-reactive side chain residues. Comparison of gp120-OD8 experimental footprinting data with a homology model derived from the ligated CD4/ gp120-OD8 crystal structure revealed a flexible V3 loop structure where the V3 tip may provide contacts with the rest of the protein while residues in the V3 base remain solvent accessible. In addition, the data illustrate interactions between specific sugar moieties and amino acid side chains potentially important to the gp120-OD8 structure. PMID:20825246

  1. The structure, morphology, and the metal-enhanced fluorescence of nano-Ag/ZnO core-shell structure

    NASA Astrophysics Data System (ADS)

    Zhao, Yue; Ding, Yanli; Peng, Xiang; Zhou, Mingtao; Liang, Xiaoyan; Min, Jiahua; Wang, Linjun; Shi, Weimin

    2015-06-01

    Nano-polyc rystalline silver (Ag) particles with the diameter of 60 nm were synthesized by the reducing agent sodium citrate. An amorphous zinc oxide (ZnO) shell layer was then coated on the surface of silver particles using wet chemical method. The Ag/ZnO core-shell structure was characterized by scanning electron microscope, transmission electron microscopy, ultraviolet-visible spectroscopy and fluorescence (FL) measurement. The results showed that nano-Ag/ZnO core-shell particles with an average diameter of ~100 nm were prepared successfully, and the FL intensity of Rhodamine 6G (R6G) mixed with Ag/ZnO nanoparticle was 53 % greater than that of the same amount of R6G without any nanoparticles, which may be related to the effect of surface plasmon resonance.

  2. Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core.

    PubMed

    Montemayor, Eric J; Didychuk, Allison L; Liao, Honghong; Hu, Panzhou; Brow, David A; Butcher, Samuel E

    2017-01-01

    U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al. (2014), Nature Struct. Mol. Biol. 21, 544-551]. The structure revealed a novel topology containing interlocked rings of protein and RNA that was not predicted by prior biochemical and genetic data. Here, the crystal structure of the U6 snRNP core with a wild-type ISL is reported. This complex crystallized in a new space group, apparently owing in part to the presence of an intramolecular cross-link in RRM1 that was not observed in the previously reported U6-A62G structure. The structure exhibits the same protein-RNA interface and maintains the unique interlocked topology. However, the orientation of the wild-type ISL is altered relative to the A62G mutant structure, suggesting inherent structural dynamics that may facilitate its pairing with U4. Consistent with their similar architectures in the crystalline state, the wild-type and A62G variants of U6 exhibit similar Prp24-binding affinities and electrophoretic mobilities when analyzed by gel-shift assay.

  3. Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core

    SciTech Connect

    Stahley,M.; Adams, P.; Wang, J.; Strobel, S.

    2007-01-01

    Metal ions play key roles in the folding and function for many structured RNAs, including group I introns. We determined the X-ray crystal structure of the Azoarcus bacterial group I intron in complex with its 5' and 3' exons. In addition to 222 nucleotides of RNA, the model includes 18 Mg2+ and K+ ions. Five of the metals bind within 12 Angstroms of the scissile phosphate and coordinate the majority of the oxygen atoms biochemically implicated in conserved metal-RNA interactions. The metals are buried deep within the structure and form a multiple metal ion core that is critical to group I intron structure and function. Eight metal ions bind in other conserved regions of the intron structure, and the remaining five interact with peripheral structural elements. Each of the 18 metals mediates tertiary interactions, facilitates local bends in the sugar-phosphate backbone or binds in the major groove of helices. The group I intron has a rich history of biochemical efforts aimed to identify RNA-metal ion interactions. The structural data are correlated to the biochemical results to further understand the role of metal ions in group I intron structure and function.

  4. Antibody and antigen contact residues define epitope and paratope size and structure.

    PubMed

    Stave, James W; Lindpaintner, Klaus

    2013-08-01

    A total of 111 Ag-Ab x-ray crystal structures of large protein Ag epitopes and paratopes were analyzed to inform the process of eliciting or selecting functional and therapeutic Abs. These analyses illustrate that Ab contact residues (CR) are distributed in three prominent CR regions (CRR) on L and H chains that overlap but do not coincide with Ab CDR. The number of Ag and Ab CRs per structure are overlapping and centered around 18 and 19, respectively. The CR span (CRS), a novel measure introduced in this article, is defined as the minimum contiguous amino acid sequence containing all CRs of an Ag or Ab and represents the size of a complete structural epitope or paratope, inclusive of CR and the minimum set of supporting residues required for proper conformation. The most frequent size of epitope CRS is 50-79 aa, which is similar in size to L (60-69) and H chain (70-79) CRS. The size distribution of epitope CRS analyzed in this study ranges from ~20 to 400 aa, similar to the distribution of independent protein domain sizes reported in the literature. Together, the number of CRs and the size of the CRS demonstrate that, on average, complete structural epitopes and paratopes are equal in size to each other and similar in size to intact protein domains. Thus, independent protein domains inclusive of biologically relevant sites represent the fundamental structural unit bound by, and useful for eliciting or selecting, functional and therapeutic Abs.

  5. Effect of Hydrophobic Core Topology and Composition on the Structure and Kinetics of Star Polymers: A Molecular Dynamics Study.

    PubMed

    Carr, Amber C; Felberg, Lisa E; Piunova, Victoria A; Rice, Julia E; Head-Gordon, Teresa; Swope, William C

    2017-04-06

    We present a molecular dynamics study of the effect of core chemistry on star polymer structural and kinetic properties. This work serves to validate the choice of a model adamantane core used in previous simulations to represent larger star polymeric systems in an aqueous environment, as well as to explore how the choice of size and core chemistry using a dendrimer or nanogel core may affect these polymeric nanoparticle systems, particularly with respect to thermosensitivity and solvation properties that are relevant for applications in drug loading and delivery.

  6. On the mineral core of ferritin-like proteins: structural and magnetic characterization

    NASA Astrophysics Data System (ADS)

    García-Prieto, A.; Alonso, J.; Muñoz, D.; Marcano, L.; Abad Díaz de Cerio, A.; Fernández de Luis, R.; Orue, I.; Mathon, O.; Muela, A.; Fdez-Gubieda, M. L.

    2015-12-01

    It is generally accepted that the mineral core synthesized by ferritin-like proteins consists of a ferric oxy-hydroxide mineral similar to ferrihydrite in the case of horse spleen ferritin (HoSF) and an oxy-hydroxide-phosphate phase in plant and prokaryotic ferritins. The structure reflects a dynamic process of deposition and dissolution, influenced by different biological, chemical and physical variables. In this work we shed light on this matter by combining a structural (High Resolution Transmission Electron Microscopy (HRTEM) and Fe K-edge X-ray Absorption Spectroscopy (XAS)) and a magnetic study of the mineral core biomineralized by horse spleen ferritin (HoSF) and three prokaryotic ferritin-like proteins: bacterial ferritin (FtnA) and bacterioferritin (Bfr) from Escherichia coli and archaeal ferritin (PfFtn) from Pyrococcus furiosus. The prokaryotic ferritin-like proteins have been studied under native conditions and inside the cells for the sake of preserving their natural attributes. They share with HoSF a nanocrystalline structure rather than an amorphous one as has been frequently reported. However, the presence of phosphorus changes drastically the short-range order and magnetic response of the prokaryotic cores with respect to HoSF. The superparamagnetism observed in HoSF is absent in the prokaryotic proteins, which show a pure atomic-like paramagnetic behaviour attributed to phosphorus breaking the Fe-Fe exchange interaction.It is generally accepted that the mineral core synthesized by ferritin-like proteins consists of a ferric oxy-hydroxide mineral similar to ferrihydrite in the case of horse spleen ferritin (HoSF) and an oxy-hydroxide-phosphate phase in plant and prokaryotic ferritins. The structure reflects a dynamic process of deposition and dissolution, influenced by different biological, chemical and physical variables. In this work we shed light on this matter by combining a structural (High Resolution Transmission Electron Microscopy (HRTEM

  7. Immune recognition of protein antigens

    SciTech Connect

    Laver, W.G.; Air, G.M.

    1985-01-01

    This book contains 33 papers. Some of the titles are: Antigenic Structure of Influenze Virus Hemagglutinin; Germ-line and Somatic Diversity in the Antibody Response to the Influenza Virus A/PR/8/34 Hemagglutinin; Recognition of Cloned Influenza A Virus Gene Products by Cytotoxic T Lymphocytes; Antigenic Structure of the Influenza Virus N2 Neuraminidase; and The Molecular and Genetic Basis of Antigenic Variation in Gonococcal Pillin.

  8. Structure of human plasma low-density lipoproteins: molecular organization of the central core.

    PubMed Central

    Atkinson, D; Deckelbaum, R J; Small, D M; Shipley, G G

    1977-01-01

    Human plasma low density lipoprotein (LDL) exhibits a thermal transition over the temperature range 20-40 degrees. This transition is associated with a structural change within the lipoprotein particle and is reflected in the small-angle x-ray scattering profiles from LDL. The scattering profile of the quasispherical LDL particle at 10 degrees shows a relatively intense maximum at 1/36 A-1 which is absent from the scattering of LDL at 45 degrees. Theoretical calculations, using model electron density distributions, have been carried out to describe the packing of arrangement of the cholesterol esters, based on perturbations of the molecular packing of crystalline cholesteryl myristate, adequately reproduces the high relative intensity of the x-ray scattering maximum at 1/36 A-1. The perturbations of the packing in the crystal structure of cholesteryl myristate involve "melting" of the hydrocarbon chains of the esters together with translations of pairs of molecules parallel to the molecular long axis. The interaction of opposing steroid moieties, with C18 and C19 angular methyl groups interlocked, exhibited in the crystal structure is retained in the perturbed arrangement. At 45 degrees, thermally induced disorder of this arrangement averages the electron density of the central core. The x-ray scattering profiles of particles with a homogeneous electron density in the core region do not show a high relative intensity of the subsidiary maxima in the 1/36 A-1 region, in agreement with experimental observation. The results of these calculations support the concept that the thermal transition observed for LDL is due to a smectic leads to disordered transition of the cholesterol esters in the core of the LDL particle. PMID:191827

  9. Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation.

    PubMed

    Fujii, Yoshifumi; Wakamori, Masatoshi; Umehara, Takashi; Yokoyama, Shigeyuki

    2016-06-01

    Cytosine methylation, predominantly of the CpG sequence in vertebrates, is one of the major epigenetic modifications crucially involved in the control of gene expression. Due to the difficulty of reconstituting site-specifically methylated nucleosomal DNA at crystallization quality, most structural analyses of CpG methylation have been performed using chemically synthesized oligonucleotides, There has been just one recent study of nucleosome core particles (NCPs) reconstituted with nonpalindromic human satellite 2-derived DNAs. Through the preparation of a 146-bp palindromic α-satellite-based nucleosomal DNA containing four CpG dinucleotide sequences and its enzymatic methylation and restriction, we reconstituted a 'symmetric' human CpG-methylated nucleosome core particle (NCP). We solved the crystal structures of the CpG-methylated and unmodified NCPs at 2.6 and 3.0 Å resolution, respectively. We observed the electron densities of two methyl groups, among the eight 5-methylcytosines introduced in the CpG-fully methylated NCP. There were no obvious structural differences between the CpG-methylated 'symmetric NCP' and the unmodified NCP. The preparation of a crystallization-grade CpG-methylated NCP provides a platform for the analysis of CpG-methyl reader and eraser proteins.

  10. Structural and Magnetic Response in Bimetallic Core/Shell Magnetic Nanoparticles

    PubMed Central

    Nairan, Adeela; Khan, Usman; Iqbal, Munawar; Khan, Maaz; Javed, Khalid; Riaz, Saira; Naseem, Shahzad; Han, Xiufeng

    2016-01-01

    Bimagnetic monodisperse CoFe2O4/Fe3O4 core/shell nanoparticles have been prepared by solution evaporation route. To demonstrate preferential coating of iron oxide onto the surface of ferrite nanoparticles X-ray diffraction (XRD), High resolution transmission electron microscope (HR-TEM) and Raman spectroscopy have been performed. XRD analysis using Rietveld refinement technique confirms single phase nanoparticles with average seed size of about 18 nm and thickness of shell is 3 nm, which corroborates with transmission electron microscopy (TEM) analysis. Low temperature magnetic hysteresis loops showed interesting behavior. We have observed large coercivity 15.8 kOe at T = 5 K, whereas maximum saturation magnetization (125 emu/g) is attained at T = 100 K for CoFe2O4/Fe3O4 core/shell nanoparticles. Saturation magnetization decreases due to structural distortions at the surface of shell below 100 K. Zero field cooled (ZFC) and Field cooled (FC) plots show that synthesized nanoparticles are ferromagnetic till room temperature and it has been noticed that core/shell sample possess high blocking temperature than Cobalt Ferrite. Results indicate that presence of iron oxide shell significantly increases magnetic parameters as compared to the simple cobalt ferrite. PMID:28335200

  11. Petrophysical and paleomagnetic data of drill cores from the Bosumtwi impact structure, Ghana

    NASA Astrophysics Data System (ADS)

    Elbra, T.; Kontny, A.; Pesonen, L. J.; Schleifer, N.; Schell, C.

    Physical properties from rocks of the Bosumtwi impact structure, Ghana, Central Africa, are essential to understand the formation of the relatively young (1.07 Ma) and small (10.5 km) impact crater and to improve its geophysical modeling. Results of our petrophysical studies of deep drill cores LB-07A and LB-08A reveal distinct lithological patterns but no depth dependence. The most conspicuous difference between impactites and target lithologies are the lower bulk densities and significantly higher porosities of the suevite and lithic breccia units compared to meta-graywacke and metapelites of target lithologies. Magnetic susceptibility shows mostly paramagnetic values (200-500 × 10-6 SI) throughout the core, with an exception of a few metasediment samples, and correlates positively with natural remanent magnetization (NRM) and Q values. These data indicate that magnetic parameters are related to inhomogeneously distributed ferrimagnetic pyrrhotite. The paleomagnetic data reveals that the characteristic direction of NRM has shallow normal (in a few cases shallow reversed) polarity, which is in agreement with the Lower Jaramillo N-polarity chron direction, and is carried by ferrimagnetic pyrrhotite. However, our study has not revealed the expected high magnetization body required from previous magnetic modeling. Furthermore, the LB-07A and LB08-A drill cores did not show the predicted high content of melt in the rocks, requiring a new interpretation model for magnetic data.

  12. Structure-Based Drug Discovery Accelerated by Many-Core Devices.

    PubMed

    Feinstein, Wei; Brylinski, Michal

    2016-01-01

    Computer-aided design is one of the critical components of modern drug discovery. Drug development is routinely streamlined using computational approaches to improve hit identification and lead selection, enhance bioavailability, and reduce toxicity. A mounting body of genomic knowledge accumulated during the last decade or so presents great opportunities for pharmaceutical research. However, new challenges also arose because processing this large volume of data demands unprecedented computing resources. On the other hand, the state-of-the-art heterogeneous systems deliver petaflops of peak performance to accelerate scientific discovery. In this communication, we review modern parallel accelerator architectures, mainly focusing on Intel Xeon Phi many-core devices. Xeon Phi is a relatively new platform that features tens of computing cores with hundreds of threads offering massively parallel capabilities for a broad range of application. We also discuss common parallel programming frameworks targeted to this accelerator, including OpenMP, OpenCL, MPI and HPX. Recent advances in code development for many-core devices are described to demonstrate the advantages of heterogeneous implementations over the traditional, serial computing. Finally, we highlight selected algorithms, eFindSite, a ligand binding site predictor, a force field for bio-molecular simulations, and BUDE, a structure-based virtual screening engine, to demonstrate how modern drug discovery is accelerated by heterogeneous systems equipped with parallel computing devices.

  13. Proliferating cell nuclear antigen structure and interactions: too many partners for one dancer?

    PubMed

    De Biasio, Alfredo; Blanco, Francisco J

    2013-01-01

    PCNA is the DNA sliding clamp found in eukaryotes and archaebacteria. Sliding clamps were first described as processivity factors in DNA replication. They consist of multimeric, toroidal-shaped structures with pseudo-sixfold symmetry that encircle the DNA duplex and tether the replicative polymerases to the genomic template. Later, it was found that PCNA serves as a docking platform where other proteins dock to carry out different DNA metabolic processes. The structure of the bacterial clamp bound to a short primed DNA shows a tilted duplex in the central channel, which is lined by α-helices with net positive charges. Many of the proteins reported to interact with PCNA do so via the PCNA Interaction Protein sequence (PIP-box). The structures of several proteins and peptides bound to PCNA show a common binding mode, but it is still unknown how the many different partners compete for binding and exert their enzymatic and regulatory functions. Furthermore, the literature contains many reports on proteins that directly bind to PCNA as detected by different methods, but only few of the putative complexes have been examined in detail by quantitative analytical techniques or high-resolution structural methods. Some of the reported interactions are not observed in solution using the pure proteins, indicating that the direct interaction is nonexistent or very weak and is likely mediated by other factors. We review here the current knowledge on PCNA interactions from a structural point of view, with a focus on human proteins and highlighting the questions that remain to be answered.

  14. The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping

    PubMed Central

    Heras, Begoña; Totsika, Makrina; Peters, Kate M.; Paxman, Jason J.; Gee, Christine L.; Jarrott, Russell J.; Perugini, Matthew A.; Whitten, Andrew E.; Schembri, Mark A.

    2014-01-01

    Aggregation and biofilm formation are critical mechanisms for bacterial resistance to host immune factors and antibiotics. Autotransporter (AT) proteins, which represent the largest group of outer-membrane and secreted proteins in Gram-negative bacteria, contribute significantly to these phenotypes. Despite their abundance and role in bacterial pathogenesis, most AT proteins have not been structurally characterized, and there is a paucity of detailed information with regard to their mode of action. Here we report the structure–function relationships of Antigen 43 (Ag43a), a prototypic self-associating AT protein from uropathogenic Escherichia coli. The functional domain of Ag43a displays a twisted L-shaped β-helical structure firmly stabilized by a 3D hydrogen-bonded scaffold. Notably, the distinctive Ag43a L shape facilitates self-association and cell aggregation. Combining all our data, we define a molecular “Velcro-like” mechanism of AT-mediated bacterial clumping, which can be tailored to fit different bacterial lifestyles such as the formation of biofilms. PMID:24335802

  15. Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment

    SciTech Connect

    Morgunova, Ekaterina; Gray, Fiona C.; MacNeill, Stuart A.; Ladenstein, Rudolf

    2009-10-01

    The crystal structure of PCNA from the halophilic archaeon H. volcanii reveals specific features of the charge distribution on the protein surface that reflect adaptation to a high-salt environment and suggests a different type of interaction with DNA in halophilic PCNAs. The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from the halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The structure was determined by molecular replacement and refined at 3.5 Å resolution to a final R factor of 23.7% (R{sub free} = 25%). PCNA from H. volcanii was found to be homotrimeric and to resemble other homotrimeric PCNA clamps but with several differences that appear to be associated with adaptation of the protein to the high intracellular salt concentrations found in H. volcanii cells.

  16. Brake performance of core-shell structured carbonyl iron/silica based magnetorheological suspension

    NASA Astrophysics Data System (ADS)

    Nguyen, Phuong-Bac; Do, Xuan-Phu; Jeon, Juncheol; Choi, Seung-Bok; Liu, Ying Dan; Choi, Hyoung Jin

    2014-10-01

    Chemically stable core-shell structured magnetic particles were synthesized by coating soft-magnetic carbonyl iron (CI) microspheres with silica through a sol-gel reaction, and applied as magnetorheological (MR) materials for a specially designed small-sized MR brake. The dynamic yield stress of the MR suspension containing the synthesized particles was also measured using a rotational rheometer under an applied magnetic field. The performance characteristics of the MR brake, including field dependent torque, hysteresis, time and torque tracking control responses were examined. The results showed that with the exception of the settling time, the other response times were faster than those of the pristine CI based MR fluid.

  17. Core size determination and structural characterization of intravenous iron complexes by cryogenic transmission electron microscopy.

    PubMed

    Wu, Yong; Petrochenko, Peter; Chen, Lynn; Wong, Sook Yee; Absar, Mohammad; Choi, Stephanie; Zheng, Jiwen

    2016-05-30

    Understanding physicochemical properties of intravenous (IV) iron drug products is essential to ensure the manufacturing process is consistent and streamlined. The history of physicochemical characterization of IV iron complex formulations stretches over several decades, with disparities in iron core size and particle morphology as the major source of debate. One of the main reasons for this controversy is room temperature sample preparation artifacts, which affect accurate determination of size, shape and agglomeration/aggregation of nanoscale iron particles. The present study is first to report the ultra-fine iron core structures of four IV iron complex formulations, sodium ferric gluconate, iron sucrose, low molecular weight iron dextran and ferumoxytol, using a cryogenic transmission electron microscopy (cryo-TEM) preservation technique, as opposed to the conventional room temperature (RT-TEM) technique. Our results show that room temperature preparation causes nanoparticle aggregation and deformation, while cryo-TEM preserves IV iron colloidal suspension in their native frozen-hydrated and undiluted state. In contrast to the current consensus in literature, all four IV iron colloids exhibit a similar morphology of their iron oxide cores with a spherical shape, narrow size distribution and an average size of 2nm. Moreover, out of the four tested formulations, ferumoxytol exhibits a cluster-like community of several iron carbohydrate particles which likely accounts for its large hydrodynamic size of 25nm, measured with dynamic light scattering. Our findings outline a suitable method for identifying colloidal nanoparticle core size in the native state, which is increasingly important for manufacturing and design control of complex drug formulations, such as IV iron drug products.

  18. Babesia divergens and Neospora caninum apical membrane antigen 1 structures reveal selectivity and plasticity in apicomplexan parasite host cell invasion

    PubMed Central

    Tonkin, Michelle L; Crawford, Joanna; Lebrun, Maryse L; Boulanger, Martin J

    2013-01-01

    Host cell invasion by the obligate intracellular apicomplexan parasites, including Plasmodium (malaria) and Toxoplasma (toxoplasmosis), requires a step-wise mechanism unique among known host–pathogen interactions. A key step is the formation of the moving junction (MJ) complex, a circumferential constriction between the apical tip of the parasite and the host cell membrane that traverses in a posterior direction to enclose the parasite in a protective vacuole essential for intracellular survival. The leading model of MJ assembly proposes that Rhoptry Neck Protein 2 (RON2) is secreted into the host cell and integrated into the membrane where it serves as the receptor for apical membrane antigen 1 (AMA1) on the parasite surface. We have previously demonstrated that the AMA1-RON2 interaction is an effective target for inhibiting apicomplexan invasion. To better understand the AMA1-dependant molecular recognition events that promote invasion, including the significant AMA1-RON2 interaction, we present the structural characterization of AMA1 from the apicomplexan parasites Babesia divergens (BdAMA1) and Neospora caninum (NcAMA1) by X-ray crystallography. These studies offer intriguing structural insight into the RON2-binding surface groove in the AMA1 apical domain, which shows clear evidence for receptor–ligand co-evolution, and the hyper variability of the membrane proximal domain, which in Plasmodium is responsible for direct binding to erythrocytes. By incorporating the structural analysis of BdAMA1 and NcAMA1 with existing AMA1 structures and complexes we were able to define conserved pockets in the AMA1 apical groove that could be targeted for the design of broadly reactive therapeutics. PMID:23169033

  19. Structural prerequisites for intersubtype B and D antigenicity of the third variable envelope region (V3) of human immunodeficiency virus type 1.

    PubMed

    Lawoko, A; Johansson, B; Ljunggren, J; Fries, A; Fredriksson, R; Georgievska, L; Malmvall, B; Pipkorn, R; Fenyö, E M; Blomberg, J

    2000-07-01

    To elucidate the structural requirements for intersubtype antigenicity of human immunodeficiency virus type 1 (HIV-1) third variable envelope region (V3), synthetic peptides were used in enzyme immunoassays (EIAs) with serum samples from persons with proven or probable subtype B and D infections. Mathematical analyses of results from EIAs with singly substituted V3 peptides revealed important residues determining overall N-terminal V3 peptide antigenicity. This information was used to design V3 immunogens, rabbit antiserum to which were tested in EIA and for in vitro neutralization of molecular clones of HIV-1(MN) and HIV-1(MAL). Intersubtype-reactive epitopes were distributed toward the N-terminal half of the V3 loop. Lysine at position 310, arginine at position 311, and isoleucine at position 314, all derived from the MN primary sequence, were major determinants of intersubtype V3 antigenicity. Combinations of residues that enhanced antigenicity often contained lysine at position 310. Threonine at position 308 was common in the least advantageous combinations. V3 immunogens modified to achieve optimal antigenicity induced antiserum with augmented cross-neutralization of virus from MAL and MN molecular clones, suggesting one approach to subunit vaccine development.

  20. Influence of shape, size and internal structure on magnetic properties of core-edge nanodots with perpendicular anisotropy

    SciTech Connect

    Milińska, E. Wawro, A.

    2014-11-21

    The properties of perpendicularly magnetized isolated nanodots different in shape, size, and internal structure are simulated by micromagnetic calculations. Investigated dots are magnetically uniform, or they are composed of a core and an edge characterized by different anisotropy—stronger or weaker than that of the core. Based on calculated hysteresis loops, we discuss in details the magnetization reversal processes, stability of magnetic structures, and spin configurations in the dots.

  1. The Chicxulub impact structure: What does the Yaxcopoil-1 drill core reveal?

    NASA Astrophysics Data System (ADS)

    Elbra, T.

    2013-05-01

    The Chicxulub impact structure, one of the largest impact structures on Earth, was formed 65 Ma by hypervelocity impact which led to the large mass-extinction at K-Pg boundary. This well preserved but buried structure has undergone numerous drillings and studies aimed to understand the formation mechanism, structure and age of the crater. The Yaxcopoil-1 (Yax-1) drill core, located in the southern sector of the Chicxulub crater, in the outer part of an annular trough, 62 km from the crater center, was drilled by ICDP in 2001-2002. Petrophysical, rock- and paleomagnetic studies of Yax-1 (Elbra and Pesonen, 2011) showed that physical properties characterize the various lithological units. Dependence on mineral composition rather than fabric was observed in pre-impact lithologies contrarily to the post-impact and impact rocks where the physical properties were dominated by porosity and reflected, in case of impactites, the impact formation mechanism with its numerous features resulting from melting, brecciation and fracturing. Furthermore, while the pre- and post-impact lithologies in Yax-1 are mostly dia- or paramagnetic, the impactite units indicated enhanced magnetizations and the presence of ferromagnetic, probably hydrothermally deposited magnetite and pyrrhotite. The sharp contrast of the impactites to the target and to post-impact lithologies allowed establishing the contact (especially the K-Pg boundary) between. The anisotropy, shape and orientation of the magnetic fraction illustrated the fabric randomization and showed the influence of impact-related redeposition and hydrothermal activity. The paleomagnetic data suggested that the Chicxulub impact occurred during the reverse polarity geomagnetic chron 29R, which is in agreement with the isotopic dates of the Chicxulub impact as well as with expected K-Pg boundary polarity. Reference Elbra, T. and Pesonen, L.J., 2011. Physical properties of the Yaxcopoil-1 deep drill core, Chicxulub impact structure, Mexico

  2. Optical and Structural Characterization of Confined and Strained Core/Multi-Shell Semiconducting Nanowires

    NASA Astrophysics Data System (ADS)

    Fickenscher, Melodie

    This work uses a broad range of optical spectroscopies and electron microscopy to characterize the structure and electronic states of nanowires. We place an emphasis on understanding how to alter the electronic properties using strain and quantum confinement. We seek to develop a comprehensive understanding of NW properties through comparisons with model predictions. In addition, we adapt optical techniques traditionally used with larger structures to obtain a sub-micron measurement of nanowire diffusion and mobility. First, we extend our optical techniques by spatially resolving the diffusion of excitons along the long axis of a nanowire using a solid immersion lens (SIL). By sampling the time decays as a function of distance along the nanowire, we can measure the diffusion of excitons directly. The extracted diffusion constants for defect free single crystal GaAs measured between 45--100 cm2/s with resultant mobilities of 52,000--116,000 cm 2/eV s. In contrast, a mixed phase InP nanowire shows a much shorter spatial diffusion limited by defect states with measured diffusion constants of 22 cm2/s and mobilities of 29,000 cm2/eV s. Turning our focus to novel NW morphologies in Chapter 3--5, we first study the strain effects from a series of a lattice mismatched (3.6%) GaAs/GaP core shell NWs. Strain on a semiconductor creates deformations in the lattice of the material which in turn effect the electronic states and possibly the material quality. We compare our PL energies with theoretical predictions and find that our measurements are lower than predicted. We next exploit correlations between PL emission and TO2 phonon emission to predict the hydrostatic and sheer strains in cases when the light hole emission is not visible and/or TO1 phonon cannot be resolved. In chapter 4, we investigate the material quality issues with these strained nanowires and find that the presence of dislocations results in non-radiative recombination centers which causes the electron

  3. Electronic and magnetic structures of magnetic vortex core in an Fe quantum dot

    NASA Astrophysics Data System (ADS)

    Nakamura, Kohji; Ito, Tomonori; Freeman, A. J.

    2003-03-01

    Interest in the magnetism of nano-scale structures have increased in both basic and applied science. In ferromagnetic quantum dot structures, curling magnetic structures are known to form, and the magnetization close to the center of the dot may assume a perpendicular orientation. Although many experimental and theoretical investigations have been performed, little is so far known about the electronic and magnetic structures on an atomic scale. Here, we determine the magnetic vortex core structure, modeled by a rod geometry with 29 Fe atoms, from the first-principles FLAPW method(Wimmer, Krakauer, Weinert and Freeman, PRB 24, 864(1981)) including noncollinear magnetism with no shape approximation of the magnetization density.(Nakamura, Freeman, Wang, Zhong, and Fernandez-de-Castro, PRB 65, 12402(2002)) The self-consistent LSDA calculations demonstrate that a swirling magnetic structure is stabilized, in which the spin directions close to the center turn up along the perpendicular orientation with respect to the swirling plane. We find that a swirling intra-atomic noncollinear magnetism is observed near the center, in which the moments continuously orient in circular directions on a smaller length scale inside the atoms and induce orbital moments along the perpendicular direction.

  4. Structure and cross-reactivity of the O-antigen of Proteus vulgaris O8.

    PubMed

    Perepelov, A V; Babicka, D; Shashkov, A S; Arbatsky, N P; Senchenkova, S N; Rozalski, A; Knirel, Y A

    1999-05-31

    A high-molecular-mass O-specific polysaccharide was obtained by mild acid degradation of Proteus vulgaris O8 lipopolysaccharide followed by gel permeation chromatography. Studies of the polysaccharide by sugar and methylation analyses and 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, NOESY, and H-detected 1H, 13C heteronuclear multiple-quantum coherence (HMQC) experiments, demonstrated the presence of a tetrasaccharide repeating unit having the following structure: [sequence: see text] The role of an epitope associated with the alpha-L-FucpNAc-(1-->3)-D-GlcpNAc disaccharide in serological cross-reactivity of P. vulgaris O8 is discussed.

  5. Structures of a pan-specific antagonist antibody complexed to different isoforms of TGFβ reveal structural plasticity of antibody-antigen interactions.

    PubMed

    Moulin, Aaron; Mathieu, Magali; Lawrence, Catherine; Bigelow, Russell; Levine, Mark; Hamel, Christine; Marquette, Jean-Piere; Le Parc, Josiane; Loux, Christophe; Ferrari, Paul; Capdevila, Cecile; Dumas, Jacques; Dumas, Bruno; Rak, Alexey; Bird, Julie; Qiu, Huawei; Pan, Clark Q; Edmunds, Tim; Wei, Ronnie R

    2014-12-01

    Various important biological pathways are modulated by TGFβ isoforms; as such they are potential targets for therapeutic intervention. Fresolimumab, also known as GC1008, is a pan-TGFβ neutralizing antibody that has been tested clinically for several indications including an ongoing trial for focal segmental glomerulosclerosis. The structure of the antigen-binding fragment of fresolimumab (GC1008 Fab) in complex with TGFβ3 has been reported previously, but the structural capacity of fresolimumab to accommodate tight interactions with TGFβ1 and TGFβ2 was insufficiently understood. We report the crystal structure of the single-chain variable fragment of fresolimumab (GC1008 scFv) in complex with target TGFβ1 to a resolution of 3.00 Å and the crystal structure of GC1008 Fab in complex with TGFβ2 to 2.83 Å. The structures provide further insight into the details of TGFβ recognition by fresolimumab, give a clear indication of the determinants of fresolimumab pan-specificity and provide potential starting points for the development of isoform-specific antibodies using a fresolimumab scaffold.

  6. Structures of a pan-specific antagonist antibody complexed to different isoforms of TGFβ reveal structural plasticity of antibody–antigen interactions

    PubMed Central

    Moulin, Aaron; Mathieu, Magali; Lawrence, Catherine; Bigelow, Russell; Levine, Mark; Hamel, Christine; Marquette, Jean-Piere; Le Parc, Josiane; Loux, Christophe; Ferrari, Paul; Capdevila, Cecile; Dumas, Jacques; Dumas, Bruno; Rak, Alexey; Bird, Julie; Qiu, Huawei; Pan, Clark Q; Edmunds, Tim; Wei, Ronnie R

    2014-01-01

    Various important biological pathways are modulated by TGFβ isoforms; as such they are potential targets for therapeutic intervention. Fresolimumab, also known as GC1008, is a pan-TGFβ neutralizing antibody that has been tested clinically for several indications including an ongoing trial for focal segmental glomerulosclerosis. The structure of the antigen-binding fragment of fresolimumab (GC1008 Fab) in complex with TGFβ3 has been reported previously, but the structural capacity of fresolimumab to accommodate tight interactions with TGFβ1 and TGFβ2 was insufficiently understood. We report the crystal structure of the single-chain variable fragment of fresolimumab (GC1008 scFv) in complex with target TGFβ1 to a resolution of 3.00 Å and the crystal structure of GC1008 Fab in complex with TGFβ2 to 2.83 Å. The structures provide further insight into the details of TGFβ recognition by fresolimumab, give a clear indication of the determinants of fresolimumab pan-specificity and provide potential starting points for the development of isoform-specific antibodies using a fresolimumab scaffold. 4KV5; 4KXZ PMID:25209176

  7. Screw dislocations in complex, low symmetry oxides: core structures, energetics, and impact on crystal growth.

    PubMed

    Shahsavari, Rouzbeh; Chen, Lu

    2015-02-04

    Determining the atomic structure and the influence of defects on properties of low symmetry oxides have long been an engineering pursuit. Here, we focus on five thermodynamically reversible monoclinic and orthorhombic polymorphs of dicalcium silicates (Ca2SiO3)-a key cement constituent-as a model system and use atomistic simulations to unravel the interplay between the screw dislocation core energies, nonplanar core structures, and Peierls stresses along different crystallographic planes. Among different polymorphs, we found that the α polymorphs (α-C2S) has the largest Peierls stress, corresponding to the most brittle polymorph, which make it attractive for grinding processes. Interestingly, our analyses indicate that this polymorphs has the lowest dislocation core energy, making it ideal for reactivity and crystal growth. Generally, we identified the following order in terms of grinding efficiency based on screw dislocation analysis, α-C2S > αH-C2S > αL-C2S > β-C2S > γ-C2S, and the following order in term of reactivity, α -C2S > αL-C2S > γ-C2S > αH-C2S > β-C2S. This information, combined with other deformation-based mechanisms, such as twinning and edge dislocation, can provide crucial insights and guiding hypotheses for experimentalists to tune the cement grinding mechanisms and reactivity processes for an overall optimum solution with regard to both energy consumption and performance. Our findings significantly broaden the spectrum of strategies for leveraging both crystallographic directions and crystal symmetry to concurrently modulate mechanics and crystal growth processes within an identical chemical composition.

  8. Genetic Structure and Selection of a Core Collection for Long Term Conservation of Avocado in Mexico

    PubMed Central

    Guzmán, Luis F.; Machida-Hirano, Ryoko; Borrayo, Ernesto; Cortés-Cruz, Moisés; Espíndola-Barquera, María del Carmen; Heredia García, Elena

    2017-01-01

    Mexico, as the center of origin of avocado (Persea americama Mill.), harbors a wide genetic diversity of this species, whose identification may provide the grounds to not only understand its unique population structure and domestication history, but also inform the efforts aimed at its conservation. Although molecular characterization of cultivated avocado germplasm has been studied by several research groups, this had not been the case in Mexico. In order to elucidate the genetic structure of avocado in Mexico and the sustainable use of its genetic resources, 318 avocado accessions conserved in the germplasm collection in the National Avocado Genebank were analyzed using 28 markers [9 expressed sequence tag-Simple Sequence Repeats (SSRs) and 19 genomic SSRs]. Deviation from Hardy Weinberg Equilibrium and high inter-locus linkage disequilibrium were observed especially in drymifolia, and guatemalensis. Total averages of the observed and expected heterozygosity were 0.59 and 0.75, respectively. Although clear genetic differentiation was not observed among 3 botanical races: americana, drymifolia, and guatemalensis, the analyzed Mexican population can be classified into two groups that correspond to two different ecological regions. We developed a core-collection by K-means clustering method. The selected 36 individuals as core-collection successfully represented more than 80% of total alleles and showed heterozygosity values equal to or higher than those of the original collection, despite its constituting slightly more than 10% of the latter. Accessions selected as members of the core collection have now become candidates to be introduced in cryopreservation implying a minimum loss of genetic diversity and a back-up for existing field collections of such important genetic resources. PMID:28286510

  9. Characterization of recombinant foot-and-mouth disease virus pentamer-like structures expressed by baculovirus and their use as diagnostic antigens in a blocking ELISA.

    PubMed

    Oem, Jae-Ku; Park, Jong-Hyeon; Lee, Kwang-Nyeong; Kim, Yong-Joo; Kye, Soo-Jeong; Park, Jee-Yong; Song, Hee-Jong

    2007-05-16

    Non-infectious recombinant pentamer-like structures of the foot-and-mouth disease virus (FMDV) were expressed by baculovirus, and the antigenicity and immunogenicity of the proteins were analyzed in a blocking ELISA for the detection of FMDV antibodies. The recombinant pentamer-like structures were produced in insect (Sf9) cells that were inoculated with recombinant baculoviruses that expressed, simultaneously, the genes for the P1 and 3C proteins of FMDV from individual promoters. The FMDV pentamer-like structures were processed by viral 3C protease, as shown in Western blots, and were antigenic, as revealed by their reactivities in an indirect ELISA. Analysis by CsCl gradient centrifugation showed that the pentamer-like structures were similar to authentic pentameric subunits from FMDV in terms of sedimentation velocity. Furthermore, the pentamer-like structures induced high levels of FMDV-specific antibodies in mice following immunization. Observations made under the electron microscope revealed that the pentamer-like structures expressed by insect cells self-assembled to form pentameric subunits of 7-8 nm in diameter, which resemble the authentic FMDV (23+/-2 nm in diameter). The results indicate that these pentamer-like structures are as antigenic and immunogenic as authentic FMDV, although the former are smaller in size. Based on these results, a blocking ELISA was developed using the recombinant pentamer-like structure. The ELISA showed specificity of 99.5% and sensitivity of 98.5% when tested with FMDV antibody-negative and -positive sera, respectively. This blocking ELISA is highly specific and offers many advantages over the current ELISAs that use inactivated FMDV antigen. This is the first report of the production and diagnostic application of recombinant pentameric subunits of FMDV.

  10. Conserved structure of amphibian T-cell antigen receptor beta chain.

    PubMed Central

    Fellah, J S; Kerfourn, F; Guillet, F; Charlemagne, J

    1993-01-01

    All jawed vertebrates possess well-differentiated thymuses and elicit T-cell-like cell-mediated responses; however, no surface T-cell receptor (TCR) molecules or TCR genes have been identified in ectothermic vertebrate species. Here we describe cDNA clones from an amphibian species, Ambystoma mexicanum (the Mexican axolotl), that have sequences highly homologous to the avian and mammalian TCR beta chains. The cloned amphibian beta chain variable region (V beta) shares most of the structural characteristics with the more evolved vertebrate V beta and presents approximately 56% amino acid identities with the murine V beta 14 and human V beta 18 families. The two different cloned axolotl beta chain joining regions (J beta) were found to have conserved all the invariant mammalian J beta residues, and in addition, the presence of a conserved glycine at the V beta-J beta junction suggests the existence of diversity elements. The extracellular domains of the two axolotl beta chain constant region isotypes C beta 1 and C beta 2 show an impressively high degree of identity, thus suggesting that a very efficient mechanism of gene correction has been in operation to preserve this structure at least from the early tetrapod evolution. The transmembrane axolotl C beta domains have been less well conserved when compared to the mammalian C beta but they do maintain the lysine residue that is thought to be involved in the charged interaction between the TCR alpha beta heterodimer and the CD3 complex. Images Fig. 1 PMID:8341702

  11. Interface effect of magnetic properties in Ni nanoparticles with a hcp core and fcc shell structure.

    PubMed

    Choo, Seongmin; Lee, Kyujoon; Jo, Younghun; Yoon, Seon-Mi; Choi, Jae-Young; Kim, Jea-Young; Park, Jea-Hoon; Lee, Kyung-Jin; Lee, Jong-Heun; Jung, Myung-Hwa

    2011-07-01

    We have fabricated hexagonal close-packed (hcp) Ni nanoparticles covered by a face-centered cubic (fcc) Ni surface layer by polyol method. The magnetic properties have been investigated as a function of temperature and applied magnetic field. The magnetic behavior reveals that the system should be divided magnetically into three distinct phases with different origins. The fcc Ni phase on the shell contributes to the superparamagnetism through a wide temperature range up to 360 K. The hcp Ni phase at the core is associated with antiferromagnetic nature below 12 K. These observations are in good agreement with the X-ray absorption spectroscopy and magnetic circular dichroism measurements. In our particular case, the unique hcp core and fcc shell structure gives rise to an additional anomaly at 20 K in the zero-field-cooled magnetization curve. Its position is barely affected by the magnetic field but its structure disappears above 30 kOe, showing a metamagnetic transition in the magnetization versus magnetic field curve. This new phase originates from the magnetic exchange at the interface between the hcp and fcc Ni sublattices.

  12. Impact of structure and functionality of core polyol in highly functional biobased epoxy resins.

    PubMed

    Pan, Xiao; Webster, Dean C

    2011-09-01

    Highly functional biobased epoxy resins were prepared using dipentaerythritol (DPE), tripentaerythritol (TPE), and sucrose as core polyols that were substituted with epoxidized soybean oil fatty acids, and the impact of structure and functionality of the core polyol on the properties of the macromolecular resins and their epoxy-anhydride thermosets was explored. The chemical structures, functional groups, molecular weights, and compositions of epoxies were characterized using nuclear magnetic resonance (NMR) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy, gel permeation chromatography (GPC), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI MS). The epoxies were also studied for their bulk viscosity, intrinsic viscosity, and density. Crosslinked with dodecenyl succinic anhydride (DDSA), epoxy-anhydride thermosets were evaluated using differential scanning calorimetry (DSC), dynamic mechanical analysis (DMA), tensile tests, and tests of coating properties. Epoxidized soybean oil (ESO) was used as a control. Overall, the sucrose-based thermosets exhibited the highest moduli, having the most rigid and ductile performance while maintaining the highest biobased content. DPE/TPE-based thermosets showed modestly better thermosetting performance than the control ESO thermoset.

  13. Rich club analysis in the Alzheimer's disease connectome reveals a relatively undisturbed structural core network.

    PubMed

    Daianu, Madelaine; Jahanshad, Neda; Nir, Talia M; Jack, Clifford R; Weiner, Michael W; Bernstein, Matt A; Thompson, Paul M

    2015-08-01

    Diffusion imaging can assess the white matter connections within the brain, revealing how neural pathways break down in Alzheimer's disease (AD). We analyzed 3-Tesla whole-brain diffusion-weighted images from 202 participants scanned by the Alzheimer's Disease Neuroimaging Initiative-50 healthy controls, 110 with mild cognitive impairment (MCI) and 42 AD patients. From whole-brain tractography, we reconstructed structural brain connectivity networks to map connections between cortical regions. We tested whether AD disrupts the "rich club" - a network property where high-degree network nodes are more interconnected than expected by chance. We calculated the rich club properties at a range of degree thresholds, as well as other network topology measures including global degree, clustering coefficient, path length, and efficiency. Network disruptions predominated in the low-degree regions of the connectome in patients, relative to controls. The other metrics also showed alterations, suggesting a distinctive pattern of disruption in AD, less pronounced in MCI, targeting global brain connectivity, and focusing on more remotely connected nodes rather than the central core of the network. AD involves severely reduced structural connectivity; our step-wise rich club coefficients analyze points to disruptions predominantly in the peripheral network components; other modalities of data are needed to know if this indicates impaired communication among non rich club regions. The highly connected core was relatively preserved, offering new evidence on the neural basis of progressive risk for cognitive decline.

  14. Mutagenicity in a Molecule: Identification of Core Structural Features of Mutagenicity Using a Scaffold Analysis

    PubMed Central

    Hsu, Kuo-Hsiang; Su, Bo-Han; Tu, Yi-Shu; Lin, Olivia A.; Tseng, Yufeng J.

    2016-01-01

    With advances in the development and application of Ames mutagenicity in silico prediction tools, the International Conference on Harmonisation (ICH) has amended its M7 guideline to reflect the use of such prediction models for the detection of mutagenic activity in early drug safety evaluation processes. Since current Ames mutagenicity prediction tools only focus on functional group alerts or side chain modifications of an analog series, these tools are unable to identify mutagenicity derived from core structures or specific scaffolds of a compound. In this study, a large collection of 6512 compounds are used to perform scaffold tree analysis. By relating different scaffolds on constructed scaffold trees with Ames mutagenicity, four major and one minor novel mutagenic groups of scaffold are identified. The recognized mutagenic groups of scaffold can serve as a guide for medicinal chemists to prevent the development of potentially mutagenic therapeutic agents in early drug design or development phases, by modifying the core structures of mutagenic compounds to form non-mutagenic compounds. In addition, five series of substructures are provided as recommendations, for direct modification of potentially mutagenic scaffolds to decrease associated mutagenic activities. PMID:26863515

  15. Radioimmunoassays of hidden viral antigens

    SciTech Connect

    Neurath, A.R.; Strick, N.; Baker, L.; Krugman, S.

    1982-07-01

    Antigens corresponding to infectious agents may be present in biological specimens only in a cryptic form bound to antibodies and, thus, may elude detection. We describe a solid-phase technique for separation of antigens from antibodies. Immune complexes are precipitated from serum by polyethylene glycol, dissociated with NaSCN, and adsorbed onto nitrocellulose or polystyrene supports. Antigens remain topographically separated from antibodies after removal of NaSCN and can be detected with radiolabeled antibodies. Genomes from viruses immobilized on nitrocellulose can be identified by nucleic acid hybridization. Nanogram quantities of sequestered hepatitis B surface and core antigens and picogram amounts of hepatitis B virus DNA were detected. Antibody-bound adenovirus, herpesvirus, and measles virus antigens were discerned by the procedure.

  16. Radioimmunoassays of hidden viral antigens.

    PubMed Central

    Neurath, A R; Strick, N; Baker, L; Krugman, S

    1982-01-01

    Antigens corresponding to infectious agents may be present in biological specimens only in a cryptic form bound to antibodies and, thus, may elude detection. We describe a solid phase technique for separation of antigens from antibodies. Immune complexes are precipitated from serum by polyethylene glycol, dissociated with NaSCN, and adsorbed onto nitrocellulose or polystyrene supports. Antigens remain topographically separated from antibodies after removal of NaSCN and can be detected with radiolabeled antibodies. Genomes from viruses immobilized on nitrocellulose can be identified by nucleic acid hybridization. Nanogram quantities of sequestered hepatitis B surface and core antigens and picogram amounts of hepatitis B virus DNA were detected. Antibody-bond adenovirus, herpesvirus, and measles virus antigens were discerned by the procedure. Images PMID:6956871

  17. Structural Basis for Antigen Recognition by Transglutaminase 2-specific Autoantibodies in Celiac Disease*

    PubMed Central

    Chen, Xi; Hnida, Kathrin; Graewert, Melissa Ann; Andersen, Jan Terje; Iversen, Rasmus; Tuukkanen, Anne; Svergun, Dmitri; Sollid, Ludvig M.

    2015-01-01

    Antibodies to the autoantigen transglutaminase 2 (TG2) are a hallmark of celiac disease. We have studied the interaction between TG2 and an anti-TG2 antibody (679-14-E06) derived from a single gut IgA plasma cell of a celiac disease patient. The antibody recognizes one of four identified epitopes targeted by antibodies of plasma cells of the disease lesion. The binding interface was identified by small angle x-ray scattering, ab initio and rigid body modeling using the known crystal structure of TG2 and the crystal structure of the antibody Fab fragment, which was solved at 2.4 Å resolution. The result was confirmed by testing binding of the antibody to TG2 mutants by ELISA and surface plasmon resonance. TG2 residues Arg-116 and His-134 were identified to be critical for binding of 679-14-E06 as well as other epitope 1 antibodies. In contrast, antibodies directed toward the two other main epitopes (epitopes 2 and 3) were not affected by these mutations. Molecular dynamics simulations suggest interactions of 679-14-E06 with the N-terminal domain of TG2 via the CDR2 and CDR3 loops of the heavy chain and the CDR2 loop of the light chain. In addition there were contacts of the framework 3 region of the heavy chain with the catalytic domain of TG2. The results provide an explanation for the biased usage of certain heavy and light chain gene segments by epitope 1-specific antibodies in celiac disease. PMID:26160175

  18. Dynamic structural evolution of supported palladium-ceria core-shell catalysts revealed by in situ electron microscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Shuyi; Chen, Chen; Cargnello, Matteo; Fornasiero, Paolo; Gorte, Raymond J.; Graham, George W.; Pan, Xiaoqing

    2015-07-01

    The exceptional activity for methane combustion of modular palladium-ceria core-shell subunits on silicon-functionalized alumina that was recently reported has created renewed interest in the potential of core-shell structures as catalysts. Here we report on our use of advanced ex situ and in situ electron microscopy with atomic resolution to show that the modular palladium-ceria core-shell subunits undergo structural evolution over a wide temperature range. In situ observations performed in an atmospheric gas cell within this temperature range provide real-time evidence that the palladium and ceria nanoparticle constituents of the palladium-ceria core-shell participate in a dynamical process that leads to the formation of an unanticipated structure comprised of an intimate mixture of palladium, cerium, silicon and oxygen, with very high dispersion. This finding may open new perspectives about the origin of the activity of this catalyst.

  19. Dynamic structural evolution of supported palladium-ceria core-shell catalysts revealed by in situ electron microscopy.

    PubMed

    Zhang, Shuyi; Chen, Chen; Cargnello, Matteo; Fornasiero, Paolo; Gorte, Raymond J; Graham, George W; Pan, Xiaoqing

    2015-07-10

    The exceptional activity for methane combustion of modular palladium-ceria core-shell subunits on silicon-functionalized alumina that was recently reported has created renewed interest in the potential of core-shell structures as catalysts. Here we report on our use of advanced ex situ and in situ electron microscopy with atomic resolution to show that the modular palladium-ceria core-shell subunits undergo structural evolution over a wide temperature range. In situ observations performed in an atmospheric gas cell within this temperature range provide real-time evidence that the palladium and ceria nanoparticle constituents of the palladium-ceria core-shell participate in a dynamical process that leads to the formation of an unanticipated structure comprised of an intimate mixture of palladium, cerium, silicon and oxygen, with very high dispersion. This finding may open new perspectives about the origin of the activity of this catalyst.

  20. Isostructural solid-solid phase transition in monolayers of soft core-shell particles at fluid interfaces: structure and mechanics.

    PubMed

    Rey, Marcel; Fernández-Rodríguez, Miguel Ángel; Steinacher, Mathias; Scheidegger, Laura; Geisel, Karen; Richtering, Walter; Squires, Todd M; Isa, Lucio

    2016-04-21

    We have studied the complete two-dimensional phase diagram of a core-shell microgel-laden fluid interface by synchronizing its compression with the deposition of the interfacial monolayer. Applying a new protocol, different positions on the substrate correspond to different values of the monolayer surface pressure and specific area. Analyzing the microstructure of the deposited monolayers, we discovered an isostructural solid-solid phase transition between two crystalline phases with the same hexagonal symmetry, but with two different lattice constants. The two phases corresponded to shell-shell and core-core inter-particle contacts, respectively; with increasing surface pressure the former mechanically failed enabling the particle cores to come into contact. In the phase-transition region, clusters of particles in core-core contacts nucleate, melting the surrounding shell-shell crystal, until the whole monolayer moves into the second phase. We furthermore measured the interfacial rheology of the monolayers as a function of the surface pressure using an interfacial microdisk rheometer. The interfaces always showed a strong elastic response, with a dip in the shear elastic modulus in correspondence with the melting of the shell-shell phase, followed by a steep increase upon the formation of a percolating network of the core-core contacts. These results demonstrate that the core-shell nature of the particles leads to a rich mechanical and structural behavior that can be externally tuned by compressing the interface, indicating new routes for applications, e.g. in surface patterning or emulsion stabilization.

  1. Fabrication of continuous highly ordered mesoporous silica nanofibre with core/sheath structure and its application as catalyst carrier

    NASA Astrophysics Data System (ADS)

    Wang, Haiyan; Wu, Dayong; Li, Dongzhou; Niu, Zhongwei; Chen, Yuzhe; Tang, Daihua; Wu, Min; Cao, Jianhua; Huang, Yong

    2011-09-01

    A core/sheath structured mesoporous silica nanofibre was prepared by coaxial electrospinning combined with the solvent evaporation induced surfactant assembly process. The characterization has given convincing evidence for the continuous highly ordered mesoporous structures, and its catalyst application was tested.A core/sheath structured mesoporous silica nanofibre was prepared by coaxial electrospinning combined with the solvent evaporation induced surfactant assembly process. The characterization has given convincing evidence for the continuous highly ordered mesoporous structures, and its catalyst application was tested. Electronic supplementary information (ESI) available: Synthesis of highly ordered mesoporous silica nanofibres and immobilized catalysts, characterization, and photosensitized oxidation. See DOI: 10.1039/c1nr10547g

  2. Optimal design at inner core of the shaped pyramidal truss structure

    SciTech Connect

    Lee, Sung-Uk; Yang, Dong-Yol

    2013-12-16

    Sandwich material is a type of composite material with lightweight, high strength, good dynamic properties and high bending stiffness-to-weight ratio. This can be found well such structures in the nature (for example, internal structure of bones, plants, etc.). New trend which prefers eco-friendly products and energy efficiency is emerging in industries recently. Demand for materials with high strength and light weight is also increasing. In line with these trends, researches about manufacturing methods of sandwich material have been actively conducted. In this study, a sandwich structure named as “Shaped Pyramidal Truss Structure” is proposed to improve mechanical strength and to apply a manufacturing process suitable for massive production. The new sandwich structure was designed to enhance compressive strength by changing the cross-sectional shape at the central portion of the core. As the next step, optimization of the shape was required. Optimization technique used here was the SZGA(Successive Zooming Genetic Algorithm), which is one of GA(Genetic Algorithm) methods gradually reducing the area of design variable. The objective function was defined as moment of inertia of the cross-sectional shape of the strut. The control points of cubic Bezier curve, which was assumed to be the shape of the cross section, were used as design variables. By using FEM simulation, it was found that the structure exhibited superior mechanical properties compared to the simple design of the prior art.

  3. Retention of structure, antigenicity, and biological function of pneumococcal surface protein A (PspA) released from polyanhydride nanoparticles

    PubMed Central

    Haughney, Shannon L.; Petersen, Latrisha K.; Schoofs, Amy D.; Ramer-Tait, Amanda E.; King, Janice; Briles, David; Wannemuehler, Michael J.; Narasimhan, Balaji

    2013-01-01

    Pneumococcal surface protein A (PspA) is a choline-binding protein which is a virulence factor found on the surface of all Streptococcus pneumoniae strains. Vaccination with PspA has been shown to be protective against a lethal challenge with S. pneumoniae, making it a promising immunogen for use in vaccines. Herein, the design of a PspA-based subunit vaccine using polyanhydride nanoparticles as a delivery platform is described. Nanoparticles based on sebacic acid (SA), 1,6-bis-(p-carboxyphenoxy)hexane (CPH) and 1,8-bis-(p-carboxyphenoxy)-3,6-dioxaoctane (CPTEG), specifically 50:50 CPTEG:CPH and 20:80 CPH:SA, were used to encapsulate and release PspA. The protein released from the nanoparticle formulations retained its primary and secondary structure as well as its antigenicity. The released PspA was also biologically functional based on its ability to bind to apolactoferrin and prevent its bactericidal activity towards Escherichia coli. When the PspA nanoparticle formulations were administered subcutaneously to mice, the animals elicited a high titer and high avidity anti-PspA antibody response. Together, these studies provide a framework for the rational design of a vaccine against S. pneumoniae based on polyanhydride nanoparticles. PMID:23774257

  4. Structure of a TCR with High Affinity for Self-antigen Reveals Basis for Escape from Negative Selection

    SciTech Connect

    Y Yin; Y Li; M Kerzic; R Martin; R Mariuzza

    2011-12-31

    The failure to eliminate self-reactive T cells during negative selection is a prerequisite for autoimmunity. To escape deletion, autoreactive T-cell receptors (TCRs) may form unstable complexes with self-peptide-MHC by adopting suboptimal binding topologies compared with anti-microbial TCRs. Alternatively, escape can occur by weak binding between self-peptides and MHC. We determined the structure of a human autoimmune TCR (MS2-3C8) bound to a self-peptide from myelin basic protein (MBP) and the multiple sclerosis-associated MHC molecule HLA-DR4. MBP is loosely accommodated in the HLA-DR4-binding groove, accounting for its low affinity. Conversely, MS2-3C8 binds MBP-DR4 as tightly as the most avid anti-microbial TCRs. MS2-3C8 engages self-antigen via a docking mode that resembles the optimal topology of anti-foreign TCRs, but is distinct from that of other autoreactive TCRs. Combined with a unique CDR3 conformation, this docking mode compensates for the weak binding of MBP to HLA-DR4 by maximizing interactions between MS2-3C8 and MBP. Thus, the MS2-3C8-MBP-DR4 complex reveals the basis for an alternative strategy whereby autoreactive T cells escape negative selection, yet retain the ability to initiate autoimmunity.

  5. Crystal structural basis for Rv0315, an immunostimulatory antigen and inactive beta-1,3-glucanase of Mycobacterium tuberculosis

    PubMed Central

    Dong, Wanyu; Huang, Junhua; Li, Yanan; Tan, Yubei; Shen, Zhou; Song, Yunfeng; Wang, Dang; Xiao, Shaobo; Chen, Huanchun; Fu, Zhen F.; Peng, Guiqing

    2015-01-01

    Mycobacterium tuberculosis (Mtb) remains a leading cause of morbidity and mortality worldwide, as two billion people are latently infected with Mtb. To address Mtb drug resistance and the limitations of current vaccines, the characteristics of candidate Mtb vaccines need to be explored. Here, we report the three-dimensional structure of Rv0315 at 1.70 Å resolution, a novel immunostimulatory antigen of Mtb, and demonstrate that Rv0315 is an inactive β-1,3-glucanase of the glycoside hydrolase 16 (GH16) family. Our study further elaborates the molecular basis for the lack of glucan recognition by Rv0315. Rv0315 has a large open groove, and this particular topology cannot bind oligosaccharide chains in solution, thus explaining the lack of detectable hydrolytic activity towards its substrate. Additionally, we identified Glu-176, a conserved catalytic residue in GH16 endo-β-1,3-glucanases, as essential for Rv0315 to induce immunological responses. These results indicate that Rv0315 likely diverged from a broad-specificity ancestral GH16 glucanase, and this inactive member of the GH16 family offers new insights into the GH16 glucanase. Together, our findings suggest that an inactive β-1,3-glucanase in Mtb drives T-helper 1 (Th1) immune responses, which may help develop more effective vaccines against Mtb infection. PMID:26469317

  6. Core/shell structured magnetic nanoparticles synthesized by inert gas condensation

    NASA Astrophysics Data System (ADS)

    Ceylan, Abdullah

    In this work, it is our goal to investigate the structural and magnetic properties of core/shell magnetic nanoparticles synthesized by inert gas condensation technique. For that purpose, Fe/FeO, Fe/FeO/PMMA, Ni/NiO/CoO, and NiFe 2O4 have been chosen to study exchange bias phenomenon that is observed in these systems. Two sets (small and large) of Fe/FeO nanoparticles with different particle sizes, (6.0/1.5nm and 9.0/3.0nm) have been prepared and the magnetic properties in terms of temperature dependencies of exchange bias field (H EB, horizontal shift of the hysteresis loops) and magnetic viscosity were investigated. Small particles have shown superparamagnetic behavior above Blocking Temperature, TB and exhibited 1574+/-25Oe exchange bias whereas the large particles had 277+/-25Oe. It has been observed that HEB is inversely proportional with the particle size and exponentially decreases and vanishes as the temperature increases up to TB. Along with the horizontal shift, vertical shift of the hysteresis loops due to pinned interface spins has also been realized. Dispersion of 14nm Fe/FeO particles in a non-magnetic polymer PMMA in order to study interparticle interactions has revealed that the magnetic response is in general nonmonotonic as a function of particle concentration in the polymer. The nonmonotonic behavior is linked to the competition between the exchange and dipolar interactions one of which being dominant above/below a threshold concentration. In order to synthesize core/shell nanoparticles composed of different metal and metal oxides rather than metal and its native oxide forming the core/shell, two techniques, resistive evaporation and laser ablation, have been combined in our inert gas condensation system. Condensation of evaporated Ni and laser ablated CoO allowed us to prepare core/shell particles. Structural analyses have revealed that Ni/CoO nanoparticles with a thin (˜1nm) NiO intermediate layer in the form of Ni/NiO/CoO can only be formed

  7. Epitope structure of the Bordetella pertussis protein P.69 pertactin, a major vaccine component and protective antigen.

    PubMed

    Hijnen, Marcel; Mooi, Frits R; van Gageldonk, Pieter G M; Hoogerhout, Peter; King, Audrey J; Berbers, Guy A M

    2004-07-01

    Bordetella pertussis is reemerging in several countries with a traditionally high vaccine uptake. An analysis of clinical isolates revealed antigenic divergence between vaccine strains and circulating strains with respect to P.69 pertactin. Polymorphisms in P.69 pertactin are mainly limited to regions comprised of amino acid repeats, designated region 1 and region 2. Region 1 flanks the RGD motif, which is involved in adherence. Although antibodies against P.69 pertactin are implicated in protective immunity, little is known about the structure and location of its epitopes. Here we describe the identification by pepscan analysis of the locations of mainly linear epitopes recognized by human sera and mouse monoclonal antibodies (MAbs). A total of 24 epitopes were identified, and of these only 2 were recognized by both MAbs and human antibodies in serum. A number of immunodominant epitopes were identified which were recognized by 78 to 93% of the human sera tested. Blocking experiments indicated the presence of high-avidity human antibodies against conformational epitopes. Human antibodies against linear epitopes had much lower avidities, as they were unable to block MAbs. Pepscan analyses revealed several MAbs which bound to both region 1 and region 2. The two regions are separated by 289 amino acids in the primary structure, and we discuss the possibility that they form a single conformational epitope. Thus, both repeat regions may serve to deflect the immune response targeted to the functional domain of P.69 pertactin. This may explain why the variation in P.69 pertactin is so effective, despite the fact that it is limited to only two small segments of the molecule.

  8. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

    PubMed Central

    Schöne, Stefanie; Jurk, Marcel; Helabad, Mahdi Bagherpoor; Dror, Iris; Lebars, Isabelle; Kieffer, Bruno; Imhof, Petra; Rohs, Remo; Vingron, Martin; Thomas-Chollier, Morgane; Meijsing, Sebastiaan H.

    2016-01-01

    The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes. PMID:27581526

  9. Structure of evolving Accretion Discs and their Implications to the Formation of Planetary Cores

    NASA Astrophysics Data System (ADS)

    Bitsch, Bertram; Morbidelli, A.; Crida, A.; Lega, E.

    2013-10-01

    Two features in a protoplanetary disc can have profound effects on planet formation. The first feature is "pressure bumps", i.e. local maxima in the gas surface density distribution that can arise e.g. at the inner edge of the dead zone. Pressure bumps stop the inward migration of small bodies undergoing gas drag (Brauer et al., 2008), promote the onset of the streaming instability (Johansen and Youdin, 2007), help the accretion of planetary embryos by the pebble-accretion process (Lambrechts and Johansen, 2012) and stop inward type-I migration by the planet-trap mechanism (Masset et al., 2006). The second feature is "scale height bumps", that originate from opacity transitions. The regions of the disc that are shadowed, where H/r decreases with r, allow planetary cores to migrate outwards due to entropy gradient effects (Paardekooper and Mellema (2006), Baruteau and Masset (2008)), until they reach the local minimum of the H/r profile (Bitsch et al. 2013). Thus, it is important to model the existence and the location of these structures in realistic protoplanetary discs. The structure of the disc is dependent on the mass-flux (accretion rate) through the disc, which determines the evolution of the density profile. This mass-flux changes in time, as the whole disc gets accreted onto the central star. We will show using 2D hydrodynamical models how the change of the accretion rate affects the disc structure and how this will change the sweet-spots for saving planetary cores from too rapid inward migration. We will focus here on "scale height bumps" in the disc that will change the alpha-viscosity and consequently the gas surface density (as the mass-flux is constant through the disc). Therefore the formation of pressure bumps is possible, whose prominence and effects on migration will be investigated in detail. This will give important indications of where and when in the disc the cores of giant planets and thus giant planets can form.

  10. Core level excitations—A fingerprint of structural and electronic properties of epitaxial silicene

    SciTech Connect

    Friedlein, R. Fleurence, A.; Aoyagi, K.; Yamada-Takamura, Y.; Jong, M. P. de; Van Bui, H.; Wiggers, F. B.; Yoshimoto, S.; Koitaya, T.; Shimizu, S.; Noritake, H.; Mukai, K.; Yoshinobu, J.

    2014-05-14

    From the analysis of high-resolution Si 2p photoelectron and near-edge x-ray absorption fine structure (NEXAFS) spectra, we show that core level excitations of epitaxial silicene on ZrB{sub 2}(0001) thin films are characteristically different from those of sp{sup 3}-hybridized silicon. In particular, it is revealed that the lower Si 2p binding energies and the low onset in the NEXAFS spectra as well as the occurrence of satellite features in the core level spectra are attributed to the screening by low-energy valence electrons and interband transitions between π bands, respectively. The analysis of observed Si 2p intensities related to chemically distinct Si atoms indicates the presence of at least one previously unidentified component. The presence of this component suggests that the observation of stress-related stripe domains in scanning tunnelling microscopy images is intrinsically linked to the relaxation of Si atoms away from energetically unfavourable positions.

  11. Sizing Single Cantilever Beam Specimens for Characterizing Facesheet/Core Peel Debonding in Sandwich Structure

    NASA Technical Reports Server (NTRS)

    Ratcliffe, James G.

    2010-01-01

    This technical publication details part of an effort focused on the development of a standardized facesheet/core peel debonding test procedure. The purpose of the test is to characterize facesheet/core peel in sandwich structure, accomplished through the measurement of the critical strain energy release rate associated with the debonding process. Following an examination of previously developed tests and a recent evaluation of a selection of these methods, a single cantilever beam (SCB) specimen was identified as being a promising candidate for establishing such a standardized test procedure. The objective of the work described here was to begin development of a protocol for conducting a SCB test that will render the procedure suitable for standardization. To this end, a sizing methodology was developed to ensure appropriate SCB specimen dimensions are selected for a given sandwich system. Application of this method to actual sandwich systems yielded SCB specimen dimensions that would be practical for use. This study resulted in the development of a practical SCB specimen sizing method, which should be well-suited for incorporation into a standardized testing protocol.

  12. Alloy Cu₃Pt nanoframes through the structure evolution in Cu-Pt nanoparticles with a core-shell construction.

    PubMed

    Han, Lin; Liu, Hui; Cui, Penglei; Peng, Zhijian; Zhang, Suojiang; Yang, Jun

    2014-09-18

    Noble metal nanoparticles with hollow interiors and customizable shell compositions have immense potential for catalysis. Herein, we present an unique structure transformation phenomenon for the fabrication of alloy Cu₃Pt nanoframes with polyhedral morphology. This strategy starts with the preparation of polyhedral Cu-Pt nanoparticles with a core-shell construction upon the anisotropic growth of Pt on multiply twinned Cu seed particles, which are subsequently transformed into alloy Cu₃Pt nanoframes due to the Kirkendall effect between the Cu core and Pt shell. The as-prepared alloy Cu₃Pt nanoframes possess the rhombic dodecahedral morphology of their core-shell parents after the structural evolution. In particular, the resulting alloy Cu₃Pt nanoframes are more effective for oxygen reduction reaction but ineffective for methanol oxidation reaction in comparison with their original Cu-Pt core-shell precursors.

  13. Dye-sensitized solar cells based on organic dual-channel anchorable dyes with well-defined core bridge structures.

    PubMed

    Seo, Kang Deuk; You, Ban Seok; Choi, In Taek; Ju, Myung Jong; You, Mi; Kang, Hong Seok; Kim, Hwan Kyu

    2013-11-01

    In stereo, where available: A new approach towards dye-sensitized solar cells is based on dianchoring structural motifs with two donors, two acceptors, and a core bridge donor as a spacer. Their high molar absorption coefficients result in favorable light-harvesting efficiencies for DSSCs based on these dyes. A high conversion efficiency of 4.90 % is achieved when using dye DC4, containing a core bridge carbazole unit, with a multifunctional coadsorbent.

  14. Using Powder Cored Tubular Wire Technology to Enhance Electron Beam Freeform Fabricated Structures

    NASA Technical Reports Server (NTRS)

    Gonzales, Devon; Liu, Stephen; Domack, Marcia; Hafley, Robert

    2016-01-01

    Electron Beam Freeform Fabrication (EBF3) is an additive manufacturing technique, developed at NASA Langley Research Center, capable of fabricating large scale aerospace parts. Advantages of using EBF3 as opposed to conventional manufacturing methods include, decreased design-to-product time, decreased wasted material, and the ability to adapt controls to produce geometrically complex parts with properties comparable to wrought products. However, to fully exploit the potential of the EBF3 process development of materials tailored for the process is required. Powder cored tubular wire (PCTW) technology was used to modify Ti-6Al-4V and Al 6061 feedstock to enhance alloy content, refine grain size, and create a metal matrix composite in the as-solidified structures, respectively.

  15. Crystal structure of Deinococcus radiodurans RecQ helicase catalytic core domain: the interdomain flexibility.

    PubMed

    Chen, Sheng-Chia; Huang, Chi-Hung; Yang, Chia Shin; Way, Tzong-Der; Chang, Ming-Chung; Chen, Yeh

    2014-01-01

    RecQ DNA helicases are key enzymes in the maintenance of genome integrity, and they have functions in DNA replication, recombination, and repair. In contrast to most RecQs, RecQ from Deinococcus radiodurans (DrRecQ) possesses an unusual domain architecture that is crucial for its remarkable ability to repair DNA. Here, we determined the crystal structures of the DrRecQ helicase catalytic core and its ADP-bound form, revealing interdomain flexibility in its first RecA-like and winged-helix (WH) domains. Additionally, the WH domain of DrRecQ is positioned in a different orientation from that of the E. coli RecQ (EcRecQ). These results suggest that the orientation of the protein during DNA-binding is significantly different when comparing DrRecQ and EcRecQ.

  16. Modeling two-dimensional structure at the core-mantle boundary

    NASA Astrophysics Data System (ADS)

    Helmberger, D. V.; Garnero, E. J.; Ding, X.

    1996-06-01

    Recent studies of SKS waveform modeling emphasize the strong variation of seismic properties at the core-mantle boundary (CMB) and the need for two-dimensional and three-dimensional waveform modeling capabilities. In particular, the bifurcation of SKS into SP dKS and SKP dS near 110° shows strong regional variations. The first of these phases has a P wave diffraction along the bottom of the mantle near the source, while the latter phase occurs at the receiver end. Generalized ray theory proves effective in generating theoretical seismograms in this type of problem because each of these diffractions is associated with a particular transmission coefficient: Tsp which transmits shear waves into primary waves when crossing the CMB and Tsp which transmits the primary waves back into shear waves at the receiver end. Each region can then be isolated and have its separate fine structure, sharp or gradational. Two classes of boundaries are explored: the CMB as a simple, sharp interface and the CMB with a very low velocity transition layer (10% slower than reference models). The two diffractions produced by these structures have diagnostic arrival times and wave shapes and when combined with the geometric SKS produce distinct waveform characteristics not easily generated by other means. Since the ray paths associated with these three phases are virtually identical in the mantle and only differ along a short sample of CMB and in the one-dimensional fluid core, we can isolate the small localized CMB region sampled. Thus the waveform character of the extended SKS in the range of 105° to 120° becomes an excellent CMB probe which we demonstrate on a small sample of observations from the Fiji-Tonga region as recorded in North America.

  17. Emergence of cluster structures and collectivity within a no-core shell-model framework

    NASA Astrophysics Data System (ADS)

    Launey, K. D.; Dreyfuss, A. C.; Draayer, J. P.; Dytrych, T.; Baker, R.

    2014-12-01

    An innovative symmetry-guided concept, which capitalizes on partial as well as exact symmetries that underpin the structure of nuclei, is discussed. Within this framework, ab initio applications of the theory to light nuclei reveal the origin of collective modes and the emergence a simple orderly pattern from first principles. This provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small fraction of the complete shell-model space, which, in turn, can be used to explore ultra-large model spaces for a description of alpha-cluster and highly deformed structures together with the associated rotations. We find that by using only a fraction of the model space extended far beyond current no-core shell-model limits and a long-range interaction that respects the symmetries in play, the outcome reproduces characteristic features of the low-lying 0+ states in 12 C (including the elusive Hoyle state and its 2+ excitation) and agrees with ab initio results in smaller spaces. This is achieved by selecting those particle configurations and components of the interaction found to be foremost responsible for the primary physics governing clustering phenomena and large spatial deformation in the ground-state and Hoyle-state rotational bands of 12 C. For these states, we offer a novel perspective emerging out of no-core shell-model considerations, including a discussion of associated nuclear deformation, matter radii, and density distribution. The framework we find is also extensible to negative-parity states (e.g., the 3-1 state in 12C) and beyond, namely, to the low-lying 0+ states of 8Be as well as the ground-state rotational band of Ne, Mg, and Si isotopes. The findings inform key features of the nuclear interaction and point to a new insight into the formation of highly-organized simple patterns in nuclear dynamics.

  18. Structure of the protein core of the glypican Dally-like and localization of a region important for hedgehog signaling

    SciTech Connect

    Kim, Min-Sung; Saunders, Adam M.; Hamaoka, Brent Y.; Beachy, Philip A.; Leahy, Daniel J.

    2011-09-20

    Glypicans are heparan sulfate proteoglycans that modulate the signaling of multiple growth factors active during animal development, and loss of glypican function is associated with widespread developmental abnormalities. Glypicans consist of a conserved, approximately 45-kDa N-terminal protein core region followed by a stalk region that is tethered to the cell membrane by a glycosyl-phosphatidylinositol anchor. The stalk regions are predicted to be random coil but contain a variable number of attachment sites for heparan sulfate chains. Both the N-terminal protein core and the heparan sulfate attachments are important for glypican function. We report here the 2.4-{angstrom} crystal structure of the N-terminal protein core region of the Drosophila glypican Dally-like (Dlp). This structure reveals an elongated, {alpha}-helical fold for glypican core regions that does not appear homologous to any known structure. The Dlp core protein is required for normal responsiveness to Hedgehog (Hh) signals, and we identify a localized region on the Dlp surface important for mediating its function in Hh signaling. Purified Dlp protein core does not, however, interact appreciably with either Hh or an Hh:Ihog complex.

  19. Site-specific carbon deposition for hierarchically ordered core/shell-structured graphitic carbon with remarkable electrochemical performance.

    PubMed

    Lv, Yingying; Wu, Zhangxiong; Qian, Xufang; Fang, Yin; Feng, Dan; Xia, Yongyao; Tu, Bo; Zhao, Dongyuan

    2013-10-01

    A fascinating core-shell-structured graphitic carbon material composed of ordered microporous core and uniform mesoporous shell is fabricated for the first time through a site-specific chemical vapor deposition process by using a nanozeolite@mesostructured silica composite molecular sieve as the template. The mesostructure-directing agent cetyltrimethylammonium bromide in the shell of the template can be either burned off or carbonized so that it is successfully utilized as a pore switch to turn the shell of the template "on" or "off" to allow selective carbon deposition. The preferred carbon deposition process can be performed only in the inner microporous zeolite cores or just within the outer mesoporous shells, resulting in a zeolite-like ordered microporous carbon or a hollow mesoporous carbon. Full carbon deposition in the template leads to the new core-shell-structured microporous@mesoporous carbon with a nanographene-constructed framework for fast electron transport, a microporous nanocore with large surface area for high-capacity storage of lithium ions, a mesoporous shell with highly opened mesopores as a transport layer for lithium ions and electron channels to access inner cores. The ordered micropores are protected by the mesoporous shell, avoiding pore blockage as the formation of solid electrolyte interphase layers. Such a unique core-shell-structured microporous@mesoporous carbon material represents a newly established lithium ion storage model, demonstrating high reversible energy storage, excellent rate capability, and long cyclic stability.

  20. Synthesis, structural characterization and magnetic properties of Fe/Pt core-shell nanoparticles

    SciTech Connect

    Pisane, K. L.; Singh, Sobhit; Seehra, M. S.

    2015-05-07

    Structural and magnetic properties of Fe/Pt core-shell nanostructure prepared by a sequential reduction process are reported. Transmission electron microscopy shows nearly spherical particles fitting a lognormal size distribution with D{sub o} = 3.0 nm and distribution width λ{sub D} = 0.31. In x-ray diffraction, Bragg lines only from the Pt shell are clearly identified with line-widths yielding crystallite size = 3.1 nm. Measurements of magnetization M vs. T (2 K–350 K) in magnetic fields up to 90 kOe show a blocking temperature T{sub B} = 13 K below which hysteresis loops are observed with coercivity H{sub C} increasing with decreasing T reaching H{sub C} = 750 Oe at 2 K. Temperature dependence of the ac susceptibilities at frequencies f{sub m} = 10 Hz–5 kHz is measured to determine the change in T{sub B} with f{sub m} using the Vogel-Fulcher law. This analysis shows the presence of significant interparticle interaction, the Neel-Brown relaxation frequency f{sub o} = 5.3 × 10{sup 10 }Hz and anisotropy constant K{sub a} = 3.6 × 10{sup 6 }ergs/cm{sup 3}. A fit of the M vs. H data up to H = 90 kOe for T > T{sub B} to the modified Langevin function taking particle size distribution into account yields magnetic moment per particle consistent with the proposed core-shell structure; Fe core of 2.2 nm diameter and Pt shell of 0.4 nm thickness.

  1. The metal core structures in the recombinant Escherichia coli transcriptional factor SoxR.

    PubMed

    Lo, Feng-Chun; Lee, Jyh-Fu; Liaw, Wen-Feng; Hsu, I-Jui; Tsai, Yi-Fang; Chan, Sunney I; Yu, Steve S-F

    2012-02-27

    X-ray absorption, circular dichroism, and EPR spectroscopy were employed to investigate the metal-core structures in the Escherichia coli transcriptional factor SoxR under reduced, oxidized, and nitrosylated conditions. The spectroscopic data revealed that the coordination environments of the metal active centers varied only very slightly between the reduced and oxidized states, similar to most other proteins containing iron-sulfur clusters. Upon nitrosylation of oxidized SoxR, however, we observed a low-temperature EPR spectrum characteristic of a protein dinitrosyl iron complex (DNIC), with an intensity corresponding to about two DNICs per iron sulfur cluster in the protein, according to spin quantification relative to a low-molecular-weight DNIC standard. In addition, there was no evidence for dichroic spectral features in the responsive region of the nitrosyl iron complexes, as well as for Fe-Fe back-scattering in the fitting of the Fe extended X-ray absorption fine structure (EXAFS) spectrum. Instead the Fe EXAFS spectrum of the nitrosylated SoxR core exhibited the same first- and second-shell coordination environments characteristic of modeled small molecular DNICs, indicating that each of the [2 Fe-2 S] cores in the homodimeric SoxR was dissociated into two individual DNICs. Similar nitrosylation of the reduced mixed-valence SoxR for 1 min led to degradation of the iron-sulfur clusters to give several iron species, including one with EPR signals characteristic of a reduced Roussin's red ester (rRRE), a diamagnetic species, presumably Roussin's red ester (RRE), and a small amount of DNIC. We also undertook in vivo time-course studies of E. coli cells containing recombinant SoxR after rapid purging of the cells with exogenous NO gas. Rapid freeze-quenched EPR experiments demonstrated rapid formation of the SoxR rRRE species, followed by fast breakup of this precursor intermediate to form the stable protein-bound DNIC species. Accordingly, under nitrosative

  2. Structural stability of alloyed and core-shell Cu-Pt bimetallic nanoparticles

    NASA Astrophysics Data System (ADS)

    Peng, Hongcheng; Qi, Weihong; Ji, Wenhai; Li, Siqi; He, Jieting

    2017-03-01

    Combining the bond-energy model and Debye theory, we generalized the Gibbs free energy model for Cu-Pt nanoparticles (NPs) by introducing a shape factor considering the shape effect. We studied the structural stability of the Cu-Pt NPs and plotted the corresponding composition-, shape- and size-dependent phase diagrams. It is shown that the Cu-Pt NPs can form alloyed structure in a large size range. But when the particle size continues to decrease, the NPs will form the core-shell structure due to surface segregation. Meanwhile, the composition segregation could make the atoms of less-content element to gather in the surface. The predictions from the present calculated phase diagrams are consistent with a series of experimental results in literatures. To further prove the efficiency of the phase diagrams, we synthesized the alloyed Cu-Pt NPs of 4-15 nm by a co-reduction method, which is in agreement with the predictions from the phase diagrams.

  3. Detection of antibodies to hepatitis B core antigen using the Abbott ARCHITECT anti-HBc assay: analysis of borderline reactive sera.

    PubMed

    Ollier, Laurence; Laffont, Catherine; Kechkekian, Aurore; Doglio, Alain; Giordanengo, Valérie

    2008-12-01

    Routine use of the automated chemiluminescent microparticle immunoassay Abbott ARCHITECT anti-HBc for diagnosis of hepatitis B is limited in case of borderline reactive sera with low signal close to the cut-off index. In order to determine the significance of anti-HBc detection when borderline reactivity occurs using the ARCHITECT anti-HBc assay, a comparative study was designed. 3540 serum samples collected over a 2-month period in the hospital of Nice were examined for markers of HBV infection (HBsAg, anti-HBs and anti-HBc). One hundred seven samples with sufficient volume and with borderline reactivity by the ARCHITECT assay were tested by two other anti-HBc assays, a microparticle enzyme immunoassay (MEIA, AxSYM Core, Abbott Laboratories, IL, USA) and an enzyme linked fluorescent assay (ELFA, VIDAS Anti-HBc Total II, bioMérieux, Lyon, France). Only 46 samples were confirmed by the AxSYM and the VIDAS assays. Additional serological information linked to patient history showed that the remaining samples (61) were false positives (11), had low titer of anti-HBc antibodies (13), or were inconclusive (37). This comparative study highlighted the existence of a grey zone around the cut-off index. Confirmative results through a different immunoassay are needed to confirm the diagnosis of HBV on borderline reactive sera using the ARCHITECT anti-HBc assay.

  4. Crystal Structure of Plasmodium knowlesi Apical Membrane Antigen 1 and Its Complex with an Invasion-Inhibitory Monoclonal Antibody

    PubMed Central

    van der Eijk, Marjolein; Thomas, Alan W.; Singh, Balbir; Kocken, Clemens H. M.

    2015-01-01

    The malaria parasite Plasmodium knowlesi, previously associated only with infection of macaques, is now known to infect humans as well and has become a significant public health problem in Southeast Asia. This species should therefore be targeted in vaccine and therapeutic strategies against human malaria. Apical Membrane Antigen 1 (AMA1), which plays a role in Plasmodium merozoite invasion of the erythrocyte, is currently being pursued in human vaccine trials against P. falciparum. Recent vaccine trials in macaques using the P. knowlesi orthologue PkAMA1 have shown that it protects against infection by this parasite species and thus should be developed for human vaccination as well. Here, we present the crystal structure of Domains 1 and 2 of the PkAMA1 ectodomain, and of its complex with the invasion-inhibitory monoclonal antibody R31C2. The Domain 2 (D2) loop, which is displaced upon binding the Rhoptry Neck Protein 2 (RON2) receptor, makes significant contacts with the antibody. R31C2 inhibits binding of the Rhoptry Neck Protein 2 (RON2) receptor by steric blocking of the hydrophobic groove and by preventing the displacement of the D2 loop which is essential for exposing the complete binding site on AMA1. R31C2 recognizes a non-polymorphic epitope and should thus be cross-strain reactive. PkAMA1 is much less polymorphic than the P. falciparum and P. vivax orthologues. Unlike these two latter species, there are no polymorphic sites close to the RON2-binding site of PkAMA1, suggesting that P. knowlesi has not developed a mechanism of immune escape from the host’s humoral response to AMA1. PMID:25886591

  5. Detection of the Elite Structure in a Virtual Multiplex Social System by Means of a Generalised K-Core

    PubMed Central

    Corominas-Murtra, Bernat; Fuchs, Benedikt; Thurner, Stefan

    2014-01-01

    Elites are subgroups of individuals within a society that have the ability and means to influence, lead, govern, and shape societies. Members of elites are often well connected individuals, which enables them to impose their influence to many and to quickly gather, process, and spread information. Here we argue that elites are not only composed of highly connected individuals, but also of intermediaries connecting hubs to form a cohesive and structured elite-subgroup at the core of a social network. For this purpose we present a generalization of the -core algorithm that allows to identify a social core that is composed of well-connected hubs together with their ‘connectors’. We show the validity of the idea in the framework of a virtual world defined by a massive multiplayer online game, on which we have complete information of various social networks. Exploiting this multiplex structure, we find that the hubs of the generalised -core identify those individuals that are high social performers in terms of a series of indicators that are available in the game. In addition, using a combined strategy which involves the generalised -core and the recently introduced -core, the elites of the different ’nations’ present in the game are perfectly identified as modules of the generalised -core. Interesting sudden shifts in the composition of the elite cores are observed at deep levels. We show that elite detection with the traditional -core is not possible in a reliable way. The proposed method might be useful in a series of more general applications, such as community detection. PMID:25541957

  6. Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex.

    PubMed

    Xu, Jianqing; Tack, Drew; Hughes, Randall A; Ellington, Andrew D; Gray, Jeffrey J

    2014-02-01

    Engineering antibodies to utilize non-canonical amino acids (NCAA) should greatly expand the utility of an already important biological reagent. In particular, introducing crosslinking reagents into antibody complementarity determining regions (CDRs) should provide a means to covalently crosslink residues at the antibody-antigen interface. Unfortunately, finding the optimum position for crosslinking two proteins is often a matter of iterative guessing, even when the interface is known in atomic detail. Computer-aided antibody design can potentially greatly restrict the number of variants that must be explored in order to identify successful crosslinking sites. We have therefore used Rosetta to guide the introduction of an oxidizable crosslinking NCAA, l-3,4-dihydroxyphenylalanine (l-DOPA), into the CDRs of the anti-protective antigen scFv antibody M18, and have measured crosslinking to its cognate antigen, domain 4 of the anthrax protective antigen. Computed crosslinking distance, solvent accessibility, and interface energetics were three factors considered that could impact the efficiency of l-DOPA-mediated crosslinking. In the end, 10 variants were synthesized, and crosslinking efficiencies were generally 10% or higher, with the best variant crosslinking to 52% of the available antigen. The results suggest that computational analysis can be used in a pipeline for engineering crosslinking antibodies. The rules learned from l-DOPA crosslinking of antibodies may also be generalizable to the formation of other crosslinked interfaces and complexes.

  7. Synthesis and in vitro transfection efficiency of spermine-based cationic lipids with different central core structures and lipophilic tails.

    PubMed

    Niyomtham, Nattisa; Apiratikul, Nuttapon; Suksen, Kanoknetr; Opanasopit, Praneet; Yingyongnarongkul, Boon-Ek

    2015-02-01

    Twelve spermine-based cationic lipids with four different central core structures (di(oxyethyl)amino, di(oxyethyl)amino carboxy, 3-amino-1,2-dioxypropyl and 2-amino-1,3-dioxypropyl) and three hydrophobic tails (lauric acid, myristic acid and palmitic acid) were synthesized. The liposomes containing lipids and DOPE showed moderate to good in vitro DNA delivery into HeLa cells. GFP expression experiments revealed that liposomes composed of lipids with 3-amino-1,2-dioxypropyl as a central core structure exhibited highest transfection efficiency under serum-free condition. Whereas,