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Sample records for structural core antigen

  1. Antigenic potential of a highly conserved Neisseria meningitidis lipopolysaccharide inner core structure defined by chemical synthesis.

    PubMed

    Reinhardt, Anika; Yang, You; Claus, Heike; Pereira, Claney L; Cox, Andrew D; Vogel, Ulrich; Anish, Chakkumkal; Seeberger, Peter H

    2015-01-22

    Neisseria meningitidis is a leading cause of bacterial meningitis worldwide. We studied the potential of synthetic lipopolysaccharide (LPS) inner core structures as broadly protective antigens against N. meningitidis. Based on the specific reactivity of human serum antibodies to synthetic LPS cores, we selected a highly conserved LPS core tetrasaccharide as a promising antigen. This LPS inner core tetrasaccharide induced a robust IgG response in mice when formulated as an immunogenic glycoconjugate. Binding of raised mouse serum to a broad collection of N. meningitidis strains demonstrated the accessibility of the LPS core on viable bacteria. The distal trisaccharide was identified as the crucial epitope, whereas the proximal Kdo moiety was immunodominant and induced mainly nonprotective antibodies that are responsible for lack of functional protection in polyclonal serum. Our results identified key antigenic determinants of LPS core glycan and, hence, may aid the design of a broadly protective immunization against N. meningitidis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. 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).

  3. 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

  4. 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.

  5. 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

  6. The complete structure of the core of the LPS from Plesiomonas shigelloides 302-73 and the identification of its O-antigen biological repeating unit.

    PubMed

    Pieretti, Giuseppina; Carillo, Sara; Lindner, Buko; Lanzetta, Rosa; Parrilli, Michelangelo; Jimenez, Natalia; Regué, Miguel; Tomás, Juan M; Corsaro, M Michela

    2010-11-22

    Plesiomonas shigelloides is a Gram-negative opportunistic pathogen associated with gastrointestinal and extraintestinal infections, which especially invades immunocompromised patients and neonates. The lipopolysaccharides are one of the major virulence determinants in Gram-negative bacteria and are structurally composed of three different domains: the lipid A, the core oligosaccharide and the O-antigen polysaccharide. In the last few years we elucidated the structures of the O-chain and the core oligosaccharide from the P. shigelloides strain 302-73. In this paper we now report the characterization of the linkage between the core and the O-chain. The LPS obtained after PCP extraction contained a small number of O-chain repeating units. The product obtained by hydrazinolysis was analysed by FTICR-ESIMS and suggested the presence of an additional Kdo in the core oligosaccharide. Furthermore, the LPS was hydrolysed under mild acid conditions and a fraction that contained one O-chain repeating unit linked to a Kdo residue was isolated and characterized by FTICR-ESIMS and NMR spectroscopy. Moreover, after an alkaline reductive hydrolysis, a disaccharide α-Kdo-(2→6)-GlcNol was isolated and characterized. The data obtained proved the presence of an α-Kdo in the outer core and allowed the identification of the O-antigen biological repeating unit as well as its linkage with the core oligosaccharide. Copyright © 2010 Elsevier Ltd. All rights reserved.

  7. 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.

  8. 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

  9. O-antigen and Core Carbohydrate of Vibrio fischeri Lipopolysaccharide

    PubMed Central

    Post, Deborah M. B.; Yu, Liping; Krasity, Benjamin C.; Choudhury, Biswa; Mandel, Mark J.; Brennan, Caitlin A.; Ruby, Edward G.; McFall-Ngai, Margaret J.; Gibson, Bradford W.; Apicella, Michael A.

    2012-01-01

    Vibrio fischeri exists in a symbiotic relationship with the Hawaiian bobtail squid, Euprymna scolopes, where the squid provides a home for the bacteria, and the bacteria in turn provide camouflage that helps protect the squid from night-time predators. Like other Gram-negative organisms, V. fischeri expresses lipopolysaccharide (LPS) on its cell surface. The structure of the O-antigen and the core components of the LPS and their possible role in colonization of the squid have not previously been determined. In these studies, an O-antigen ligase mutant, waaL, was utilized to determine the structures of these LPS components and their roles in colonization of the squid. WaaL ligates the O-antigen to the core of the LPS; thus, LPS from waaL mutants lacks O-antigen. Our results show that the V. fischeri waaL mutant has a motility defect, is significantly delayed in colonization, and is unable to compete with the wild-type strain in co-colonization assays. Comparative analyses of the LPS from the wild-type and waaL strains showed that the V. fischeri LPS has a single O-antigen repeat composed of yersiniose, 8-epi-legionaminic acid, and N-acetylfucosamine. In addition, the LPS from the waaL strain showed that the core structure consists of l-glycero-d-manno-heptose, d-glycero-d-manno-heptose, glucose, 3-deoxy-d-manno-octulosonic acid, N-acetylgalactosamine, 8-epi-legionaminic acid, phosphate, and phosphoethanolamine. These studies indicate that the unusual V. fischeri O-antigen sugars play a role in the early phases of bacterial colonization of the squid. PMID:22247546

  10. 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.

  11. Multiple label-free detection of antigen-antibody reaction using localized surface plasmon resonance-based core-shell structured nanoparticle layer nanochip.

    PubMed

    Endo, Tatsuro; Kerman, Kagan; Nagatani, Naoki; Hiepa, Ha Minh; Kim, Do-Kyun; Yonezawa, Yuji; Nakano, Koichi; Tamiya, Eiichi

    2006-09-15

    In this research, a localized surface plasmon resonance (LSPR)-based bioanalysis method for developing multiarray optical nanochip suitable for screening bimolecular interactions is described. LSPR-based label-free monitoring enables to solve the problems of conventional methods that require large sample volumes and time-consuming labeling procedures. We developed a multiarray LSPR-based nanochip for the label-free detection of proteins. The multiarray format was constructed by a core-shell-structured nanoparticle layer, which provided 300 nanospots on the sensing surface. Antibodies were immobilized onto the nanospots using their interaction with Protein A. The concentrations of antigens were determined from the peak absorption intensity of the LSPR spectra. We demonstrated the capability of the array measurement using immunoglobulins (IgA, IgD, IgG, IgM), C-reactive protein, and fibrinogen. The detection limit of our label-free method was 100 pg/mL. Our nanochip is readily transferable to monitor the interactions of other biomolecules, such as whole cells or receptors, with a massively parallel detection capability in a highly miniaturized package. We anticipate that the direct label-free optical immunoassay of proteins reported here will revolutionize clinical diagnosis and accelerate the development of hand-held and user-friendly point-of-care devices.

  12. Hepatitis B virus core antigen: synthesis in Escherichia coli and application in diagnosis.

    PubMed Central

    Stahl, S; MacKay, P; Magazin, M; Bruce, S A; Murray, K

    1982-01-01

    Fragments of hepatitis B virus DNA cloned in plasmid pBR322 carrying the gene for the viral core antigen have been placed under the control of the lac promoter of Escherichia coli. Several of the new recombinants direct higher levels of synthesis of the antigen, but the degree of enhancement varies with the different structures of the plasmids and hence the mRNAs produced. The antigen in crude bacterial lysates is a satisfactory diagnostic reagent for antibodies to the core antigen in serum samples. Images PMID:7041126

  13. 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.

  14. ANTIGENIC STRUCTURE OF CELL SURFACES

    PubMed Central

    Aoki, Tadao; Hämmerling, Ulrich; de Harven, Etienne; Boyse, Edward A.; Old, Lloyd J.

    1969-01-01

    The representation of mouse alloantigens belonging to three systems, H-2, θ and TL, on the surface of cells from thymus, spleen, lymph nodes, and peritoneal cavity, was studied by electron microscopy with ferritin-labeled antibody. As expected from earlier serological data, TL was confined to thymocytes, θ was found on thymocytes and lymphocytes, and H-2 occurred to some extent on all cell types observed. On reticular cells, lymphocytes, plasma cells, and eosinophils, the majority of the cell surface was occupied by H-2; thymocytes had considerably less H-2, and erythrocytes and peritoneal macrophages least of all. In every instance the representation of antigen was discontinuous, the fraction of the cell surface covered being characteristic both of the antigen and of the type of cell. H-2 and θ provide a striking example of this; H-2 is present in far higher amounts on lymphocytes than on thymocytes, whereas the converse is true of θ. Within areas positive for H-2 or θ, protuberances of the surface membrane were often antigen-negative. A better definition of cell surface structure, gained from studies such as this, is necessary for further inquiry into how the cell surface is assembled, and into selective gene action in relation to cellular differentiation. PMID:5347699

  15. 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

  16. 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

  17. 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.

  18. Phage displayed HBV core antigen with immunogenic activity.

    PubMed

    Bahadir, Aylin Ozdemir; Balcioglu, Bertan Koray; Uzyol, Kamil Serkan; Hatipoglu, Ibrahim; Sogut, Ibrahim; Basalp, Aynur; Erdag, Berrin

    2011-12-01

    Hepatitis B is a major public health problem worldwide, which may lead to chronic liver diseases such as cirrhosis and hepatocellular carcinoma. The hepatitis B core antigen (HBcAg) is one of the major viral proteins, which forms the inner core of hepatitis B virus (HBV) particles. In this study, filamentous bacteriophage M13 was genetically modified to display the polypeptides of HBcAg in order to develop an alternative carrier system. HBcAg gene was inserted into the minor coat protein (pIII) gene of M13, and HBcAg was expressed on the phage surface as a whole protein. Antigenicity and immunogenicity of HBcAg were tested by immunizing BALB/c mice three times with HBcAg-displaying recombinant phages. After successful immunization, one of the mice with high antibody titer to HBcAg was selected for fusion, and four monoclonal antibodies specific for HBcAg were developed. This result showed that HBcAg-displaying recombinant bacteriophages are immunogenic and can potentially be used for the development of monoclonal antibodies.

  19. 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.

  20. Cell surface expression of hepatitis B surface and core antigens in transfected rat fibroblast cell lines.

    PubMed

    Gholson, C F; Siddiqui, A; Vierling, J M

    1990-04-01

    Hepatocellular necrosis during hepatitis B virus infection is hypothesized to result from host immune responses against either hepatitis B surface antigen or hepatitis B core antigen expressed on the surface membrane of infected hepatocytes. To study the capacity of hepatitis B deoxyribonucleic acid to induce membrane expression of either hepatitis B surface antigen or hepatitis B core antigen in vitro, we assessed transfected rat fibroblast cell lines by indirect immunofluorescence. Rat fibroblasts were transfected with plasmid vectors containing the natural promoters, native enhancer, and uninterrupted sequences of either the Pre S/S gene or core gene. Resulting cell lines produced hepatitis B surface antigen and hepatitis B core antigen/hepatitis B e antigen, respectively. Immunofluorescence microscopy or flow cytometry showed that hepatitis B surface antigen and hepatitis B core antigen were expressed in a granular pattern in the surface membrane of transfected cells. We conclude that surface membrane expression of both hepatitis B surface antigen and hepatitis B core antigen is an intrinsic consequence of expression of either the Pre S/S or core gene.

  1. Is HCV core antigen a reliable marker of viral load? An evaluation of HCV core antigen automated immunoassay

    PubMed Central

    Hadziyannis, Emilia; Minopetrou, Martha; Georgiou, Anastasia; Spanou, Fotini; Koskinas, John

    2013-01-01

    Background Hepatitis C viral (HCV) load detection and quantification is routinely accomplished by HCV RNA measurement, an expensive but essential test, both for the diagnosis and treatment of chronic hepatitis C (CHC). HCV core antigen (Ag) testing has been suggested as an attractive alternative to molecular diagnostics. The aim of the study was to evaluate an automated chemiluminescent immunoassay (CLIA) for HCV core Ag measurement in comparison to quantitative HCV RNA determination. Methods HCV Ag was measured in 105 anti-HCV positive patients, from which 89 were HCV RNA positive with CHC and 16 HCV RNA negative after spontaneous HCV clearance. Viral load was quantified with branched DNA (bDNA, Versant, Siemens). Sera were stored at -70°C and then tested with the Architect HCV Ag test (Abbott Laboratories), a two-step CLIA assay, with high throughput and minimal handling of the specimens. Statistical analysis was performed on logarithmically transformed values. Results HCV-Ag was detectable and quantifiable in 83/89 and in grey zone in 4/89 HCV RNA positive sera. HCV-Ag was undetectable in all 16 HCV RNA negative samples. The sample with the lowest viral load that tested positive for HCV-Ag contained 1200 IU/mL HCV RNA. There was a positive correlation between HCV RNA and HCV-Ag (r=0.89). The HCV RNA/ HCV Ag ratio varied from 1.5 to 3.25. Conclusion The HCV core Ag is an easy test with comparable sensitivity (>90%) and satisfactory correlation with the HCV RNA bDNA assay. Its role in diagnostics and other clinical applications has to be determined based on cost effectiveness. PMID:24714621

  2. 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

  3. Performance of ARCHITECT HCV core antigen test with specimens from US plasma donors and injecting drug users.

    PubMed

    Mixson-Hayden, Tonya; Dawson, George J; Teshale, Eyasu; Le, Thao; Cheng, Kevin; Drobeniuc, Jan; Ward, John; Kamili, Saleem

    2015-05-01

    Hepatitis C virus (HCV) core antigen is a serological marker of current HCV infection. The aim of this study was mainly to evaluate the performance characteristics of the ARCHITECT HCV core antigen assay with specimens from US plasma donors and injecting drug users. A total of 551 serum and plasma samples with known anti-HCV and HCV RNA status were tested for HCV core antigen using the Abbott ARCHITECT HCV core antigen test. HCV core antigen was detectable in 100% of US plasma donor samples collected during the pre-seroconversion phase of infection (anti-HCV negative/HCV RNA positive). Overall sensitivity of the HCV core antigen assay was 88.9-94.3% in samples collected after seroconversion. The correlation between HCV core antigen and HCV RNA titers was 0.959. HCV core antigen testing may be reliably used to identify current HCV infection. Published by Elsevier B.V.

  4. The Structure and Function of the Rh antigen Complex

    PubMed Central

    Westhoff, Connie M.

    2007-01-01

    The Rh system is one of the most important and complex blood group systems because of the large number of antigens and the serious complications for the fetus of a woman sensitized by transfusion or pregnancy. Major advances in our understanding of the Rh system have occurred with the cloning of the genes and with functional evidence that the Rh blood group proteins belong to an ancient family of membrane proteins involved in ammonia transport. The arrangement and configuration of the genes at the RH locus promotes genetic exchange, generating new antigens. Importantly, RH genetic testing can now be applied to clinical transfusion medicine and prenatal practice. This includes testing for RHD zygosity, confirmation or resolution of D antigen status, and detection of altered RHD and RHCE genes in individuals at risk for producing antibodies to high incidence Rh antigens, particularly sickle cell disease patients. The Rh proteins form a core complex that is critical to the structure of the erythrocyte membrane, and may play a physiologically role in the sequestration of blood ammonia. The Rh family of proteins now includes non-erythroid Rh homologs present in many other tissues, and comparative genomics reveals Rh homologs in all domains of life. PMID:17198846

  5. 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

  6. Common antigenic structures of HL-A antigens

    PubMed Central

    Nakamuro, K.; Tanigaki, N.; Kreiter, V. P.; Pressman, D.

    1974-01-01

    Spent culture media of all the human cell lines tested have been found to contain the antigenic activity present on the 11,000-Dalton HL-A common portion fragment of the HL-A antigen molecule that appears to be a characteristic, invariant portion of HL-A antigen molecules. From the culture medium of one of these lines, RPMI 1788, a lymphoid cell line, the substance carrying HL-A common activity was isolated, which was shown to be identical to the HL-A common portion fragment with respect to molecular size, electrophoretic mobility, isoelectric focusing patterns, and certain antigenic characteristics. By an isolation procedure involving differential ultrafiltration, gel filtration, and column electrophoresis, 8 litres of the culture medium yielded 1.5–2.0 A280 units of the substance representing 15–20 per cent of the HL-A common antigenic activity originally present. A single protein band with a Rf of 0.47 was obtained by disc electrophoresis. The molecular size was shown to be about 11,000 Daltons by gel filtration and by sodium dodecyl sulphate—acrylamide gel electrophoresis. Upon isoelectric focusing two bands were obtained which corresponded exactly to those obtained with HL-A common portion fragment prepared from papain-solubilized HL-A antigen preparations by acid dissociation. The isoelectric point of the major band was 5.0. The reactions of this substance with rabbit antisera against human lymphoid cell membrane and against the substance were essentially identical to the reactions of HL-A common portion fragment with these same antisera. ImagesFIG. 3Fig. 4Fig. 5 PMID:4476726

  7. Hepatitis B Virus DNA in Blood Samples Positive for Antibodies to Core Antigen and Negative for Surface Antigen

    PubMed Central

    Gutiérrez, C.; León, G.; Loureiro, C. L.; Uzcátegui, N.; Liprandi, F.; Pujol, F. H.

    1999-01-01

    Anti-hepatitis B core antigen (HBcAg)-positive hepatitis B surface antigen (HBsAg)-negative plasma samples from blood donors were tested by nested PCR. DNA positivity was more significantly associated with high levels of anti-HBcAg than with low levels of anti-HBsAg antibodies. Analysis of a dilution of anti-HBcAg antibodies might result in a more rational exclusion of anti-HBcAg-positive HBsAg-negative samples, reducing the number of donations discarded and enabling more countries to incorporate anti-HBcAg testing. PMID:10473534

  8. Composite Structure with Origami Core

    DTIC Science & Technology

    2016-07-19

    AFRL-AFOSR-JP-TR-2016-0063 Composite Structure with Origami Core Zhong You THE UNIVERSITY OF OXFORD Final Report 07/19/2016 DISTRIBUTION A...ADDRESS(ES) THE UNIVERSITY OF OXFORD UNIVERSITY OFFICES OXFORD , OX1 2JD GB 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY...Institution: University of Oxford Department: Engineering Science Mailing Address: Department of Engineering Science Parks Road, Oxford , OX1 3PJ, U. K

  9. Dislocation dynamics and core structure

    NASA Astrophysics Data System (ADS)

    Lin, Karin Shu

    2000-10-01

    Understanding the dynamics of dislocations is essential to the accurate prediction of the mechanical properties of materials. In recent years, considerable progress has been made in this area through the development of large computer simulations which seek to model plastic deformation by considering the interactions of many dislocations. However, the many-body nature of the problem, as well as the limitations inherent in the elasticity theory used to describe dislocation interactions, requires that such simulations make certain simplifying assumptions. The work reported here seeks to examine some of the issues relevant to these simulations in two ways. First, the dynamics of a single dislocation are studied through the development and analysis of a mesoscopic, two-dimensional kinetic Monte Carlo simulation of dislocation motion. The stress and temperature dependence of the dislocation velocity is studied, and finite-size effects are discussed. Through a simple analogy to models of crystal growth, it is shown that the simulated dislocations exhibit kinetic roughening with scaling exponents predicted by the Kardar-Parisi-Zhang equation. Second, the structure of dislocation cores is studied at the atomic level in diamond cubic materials. These studies are necessary for understanding dislocation properties at small distances, and can provide accurate parameters for use in larger scale continuum simulations. The first study uses periodic supercells and ab initio techniques to compare two possible reconstructions of the 90° partial dislocation core in diamond. The relative energies are found to depend upon the stress field experienced by a dislocation in the periodic array. By fitting the energies to an isotropic elasticity theory expression for the dislocation core energy, values for the core radius and shear modulus of diamond are extracted and found to agree well with theoretical estimates and experimental observations. A similar analysis using empirical potentials

  10. Structural Consensus among Antibodies Defines the Antigen Binding Site

    PubMed Central

    Kunik, Vered; Peters, Bjoern; Ofran, Yanay

    2012-01-01

    The Complementarity Determining Regions (CDRs) of antibodies are assumed to account for the antigen recognition and binding and thus to contain also the antigen binding site. CDRs are typically discerned by searching for regions that are most different, in sequence or in structure, between different antibodies. Here, we show that ∼20% of the antibody residues that actually bind the antigen fall outside the CDRs. However, virtually all antigen binding residues lie in regions of structural consensus across antibodies. Furthermore, we show that these regions of structural consensus which cover the antigen binding site are identifiable from the sequence of the antibody. Analyzing the predicted contribution of antigen binding residues to the stability of the antibody-antigen complex, we show that residues that fall outside of the traditionally defined CDRs are at least as important to antigen binding as residues within the CDRs, and in some cases, they are even more important energetically. Furthermore, antigen binding residues that fall outside of the structural consensus regions but within traditionally defined CDRs show a marginal energetic contribution to antigen binding. These findings allow for systematic and comprehensive identification of antigen binding sites, which can improve the understanding of antigenic interactions and may be useful in antibody engineering and B-cell epitope identification. PMID:22383868

  11. Hepatitis C virus core antigen test in monitoring of dialysis patients.

    PubMed

    Li Cavoli, Gioacchino; Zagarrigo, Carmela; Schillaci, Onofrio; Servillo, Francesca; Tralongo, Angelo; Coglitore, Mario; Spadaro, Filippo; Scimeca, Concetta; Li Destri, Natalia; Rotolo, Ugo

    2012-01-01

    Hepatitis C virus infection is a persistent worldwide public health concern. The prevalence of HCV infection is much higher in patients on chronic haemodialysis (HD) than in the general population. HCV infection can detrimentally affect patients throughout the spectrum of chronic kidney disease. Despite the control of blood products, hepatitis C virus transmission is still being observed among patients undergoing dialysis. Detection systems for serum HCV antibodies are insensitive in the acute phase because of the long serological window. Direct detection of HCV depends on PCR test but this test is not suitable for routine screening. Recent studies have highlighted the importance of HCV core antigen detection as an alternative to PCR. Few studies exist about the efficacy of HCV core antigen test in dialysis population. We studied the utility of HCV core antigen test in routine monitoring of virological status of dialysis patients. We screened 92 patients on long-term dialysis both by PCR HCV-RNA and HCV core antigen test. The sensitivity of HCVcAg test was 90%, the specificity 100%, the positive predictive power 100%, the negative predictive power 97%, and the accuracy 97%. We think serological detection of HCV core antigen may be an alternative to NAT techniques for routine monitoring of patients on chronic dialysis.

  12. 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

  13. Structural, Mechanistic, and Antigenic Characterization of the Human Astrovirus Capsid

    PubMed Central

    York, Royce L.; Yousefi, Payam A.; Bogdanoff, Walter; Haile, Sara; Tripathi, Sarvind

    2015-01-01

    ABSTRACT Human astroviruses (HAstVs) are nonenveloped, positive-sense, single-stranded RNA viruses that are a leading cause of viral gastroenteritis. HAstV particles display T=3 icosahedral symmetry formed by 180 copies of the capsid protein (CP), which undergoes proteolytic maturation to generate infectious HAstV particles. Little is known about the molecular features that govern HAstV particle assembly, maturation, infectivity, and immunogenicity. Here we report the crystal structures of the two main structural domains of the HAstV CP: the core domain at 2.60-Å resolution and the spike domain at 0.95-Å resolution. Fitting of these structures into the previously determined 25-Å-resolution electron cryomicroscopy density maps of HAstV allowed us to characterize the molecular features on the surfaces of immature and mature T=3 HAstV particles. The highly electropositive inner surface of HAstV supports a model in which interaction of the HAstV CP core with viral RNA is a driving force in T=3 HAstV particle formation. Additionally, mapping of conserved residues onto the HAstV CP core and spike domains in the context of the immature and mature HAstV particles revealed dramatic changes to the exposure of conserved residues during virus maturation. Indeed, we show that antibodies raised against mature HAstV have reactivity to both the HAstV CP core and spike domains, revealing for the first time that the CP core domain is antigenic. Together, these data provide new molecular insights into HAstV that have practical applications for the development of vaccines and antiviral therapies. IMPORTANCE Astroviruses are a leading cause of viral diarrhea in young children, immunocompromised individuals, and the elderly. Despite the prevalence of astroviruses, little is known at the molecular level about how the astrovirus particle assembles and is converted into an infectious, mature virus. In this paper, we describe the high-resolution structures of the two main astrovirus

  14. 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. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. 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.

  16. 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

  17. 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.

  18. [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.

  19. 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.

  20. Structure-based peptide mimicry of tumor-associated antigens.

    PubMed

    Ohtaki, Akashi; Kieber-Emmons, Thomas; Murali, Ramachandran

    2013-02-01

    Two major obstacles in developing cancer vaccines are identifying unique tumor-associated antigens (TAA) and overcoming the lack of structural information about TAAs. Unlike progress with T cell-based vaccines, B cell vaccines are less well developed due to discontinuous or spatially disposed B cell epitopes. Synthetic peptides that emulate B cell epitopes are nevertheless proposed to induce immune responses to TAA. Currently, such antigen-mimicking peptides are identified using informatics approaches, by screening of random peptide libraries against an isolating antibody without any regard to structural principles and by rationale design methodologies. In our own studies we have developed various peptide mimics of TAAs based on combining the structural analysis of antibody-antigen complexes with the peptide library screening process. Understanding the structural context of antigen mimicry is key, as our studies show that mimicry depends on the structural and conformational features of the combining region of antibody-antigen surface amino acids. The ability of a mimic to contact the same set of amino acids found on a template antibody dictates whether or not it is a functional antigenic mimic capable of inducing TAA cross-reactive antibodies. Presented here is an overview of our current rationale and status of structure-based tumor antigenic mimics relevant for breast cancer TAAs.

  1. Comparison of HCV core antigen and anti-HCV with HCV RNA results.

    PubMed

    Buket, Cicioğlu Arıdoğan; Ayşe, Aynali; Selçuk, Kaya; Süleyman, Önal; Emel, Sesli Çetin

    2014-12-01

    The measurement of anti-HCV antibodies using immunological methods and the confirmation of viral nuclear acid based on molecular methods is important in diagnosis and follow-up of the HCV infection. In this study, we aimed to analyse HCV core Antigen positivity among anti-HCV antibody positive sera to determine the significance of testing of HCV core Ag for the laboratory diagnosis of HCV infection, by considering the correlation between serum HCV core Ag and HCV RNA levels. 115 patients suspected of having hepatitis C and who were positive for anti-HCV antibody were investigated using chemiluminescent and molecular methods. Anti-HCV antibody, HCV core Ag and HCV RNA levels were detected by the Vitros ECiQ immunodiagnostic system, Architect i2000 system and RT-PCR, respectively. The sensitivity, specificity, positive and negative predictive values and accuracy rate of HCV core Antigen assay were detected as 86.5%(83/96), 100%(19/19), 100%(83/83), 59.4%(19/32), 88.7%(102/115) respectively. HCV core Ag assay could be used for diagnosis of HCV infection as it is easy to perform, cost-effective, has high specificity and positive predictive value. However, it should be kept in mind that it may have lack of sensitivity and negative predictive value.

  2. 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.

  3. Antigenic variation of core, NS3, and NS5 proteins among genotypes of hepatitis C virus.

    PubMed Central

    Neville, J A; Prescott, L E; Bhattacherjee, V; Adams, N; Pike, I; Rodgers, B; El-Zayadi, A; Hamid, S; Dusheiko, G M; Saeed, A A; Haydon, G H; Simmonds, P

    1997-01-01

    Assays that detect antibody to hepatitis C virus (HCV) are used to screen blood donors and patients with hepatitis. Current enzyme-linked immunosorbent assay (ELISA)-based methods are invariably based upon antigens from expressed recombinant proteins or oligopeptides from HCV type 1. Some HCV antigens used in screening assays are coded by regions of the HCV genome that show extensive variability; therefore, HCV type 1-based assays may be less effective for the detection of antibody elicited by infection with other genotypes. In this study, we have measured antibody reactivity of sera from 110 hepatitis C patients infected with type 1b, 3a, or 4a to genotype-specific and cross-reactive epitopes present in recombinant proteins from HCV genotypes 1b (core, NS3, and NS5), 3a (NS3, NS5), and 4a (core, NS3), corresponding to those used in current third-generation screening ELISAs. By comparing the serological reactivities of sera to type-homologous and type-heterologous antigens, we detected a significant type-specific component to the reactivity to NS3 (61 to 77% of the total reactivity) and NS5 (60% of the total reactivity). Furthermore, despite the similarities in the amino acid sequences of the core antigens of type 1b and type 4a, we also found significantly greater reactivity to type-homologous antigens, with approximately 25% of reactivity being type specific. These findings are consistent with previous findings of fivefold weaker reactivity of sera from HCV type 2- and HCV type 3-infected blood donors in the currently used third-generation ELISAs and suggest that these assays are suboptimal for screening populations in which the predominant genotype is not type 1. PMID:9399495

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  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. Core-shell-structured magnetic ternary nanocubes.

    PubMed

    Wang, Lingyan; Wang, Xin; Luo, Jin; Wanjala, Bridgid N; Wang, Chongmin; Chernova, Natasha A; Engelhard, Mark H; Liu, Yao; Bae, In-Tae; Zhong, Chuan-Jian

    2010-12-22

    We report a novel core-shell-structured ternary nanocube of MnZn ferrite synthesized by controlling the reaction temperature and composition in the absence of conventionally used reducing agents. The highly monodispersed core-shell structure consists of an Fe(3)O(4) core and an MnZn Ferrite shell. The observation of a Moiré pattern indicates that the core and the shell are two highly crystalline materials with slightly different lattice constants that are rotated relative to each other by a small angle. The ternary core-shell nanocubes display magnetic properties regulated by a combination of the core-shell composition and exhibit an increased coercivity and field-cooled/zero-field-cooled characteristics drastically different from those of regular MnZn ferrite nanoparticles. The ability to engineer the spatial nanostructures of ternary magnetic nanoparticles in terms of shape and composition offers atomic-level versatility in fine-tuning the nanoscale magnetic properties.

  11. Early predictive efficacy of core antigen on antiviral outcomes in genotype 1 hepatitis C virus infected patients.

    PubMed

    Feng, Bo; Yang, Rui-Feng; Zhang, Hai-Ying; Luo, Bi-Fen; Kong, Fan-Yun; Rao, Hui-Ying; Jin, Qian; Cong, Xu; Wei, Lai

    2015-01-01

    Response-guided therapy is of limited use in developing countries because hepatitis C virus RNA detection by sensitive molecular methods is time- and labor-consuming and expensive. We evaluated early predictive efficacy of serum hepatitis C virus core antigen kinetics on sustained virologic response in patients with genotype 1 hepatitis C virus during pegylated interferon plus ribavirin treatment. For 478 patients recruited, hepatitis C virus RNAs were detected at baseline, and at weeks 4, 12, 24, 48, and 72 using Cobas TaqMan. Architect hepatitis C virus core antigen was performed at baseline, and weeks 4 and 12. Predictive values of hepatitis C virus core antigen on sustained virologic response were compared to hepatitis C virus RNA. In the first 12 weeks after treatment initiation the dynamic patterns of serum hepatitis C virus core antigen and hepatitis C virus RNA levels were similar in sustained virologic response, relapse, and null response patients groups. Although areas under the receiver operating characteristics curves of hepatitis C virus core antigen were lower than those of hepatitis C virus RNA at the same time points, modeling analysis showed that undetectable hepatitis C virus core antigen (rapid virological response based on hepatitis C virus core antigen) had similar positive predictive value on sustained virologic response to hepatitis C virus RNA at week 4 (90.4% vs 93.3%), and hepatitis C virus core antigen decrease greater than 1log10IU/mL (early virological response based on hepatitis C virus core antigen) had similar negative predictive value to hepatitis C virus RNA at week 12 (94.1% vs 95.2%). Analysis on the validation group demonstrated a positive predictive value of 97.5% in rapid virological response based on hepatitis C virus core antigen and a negative predictive value of 100% in early virological response based on hepatitis C virus core antigen. In conclusion, hepatitis C virus core antigen is comparable to hepatitis C virus RNA in

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

    PubMed

    Moriel, Danilo G; Tan, Lendl; Goh, Kelvin G K; Phan, Minh-Duy; Ipe, Deepak S; Lo, Alvin W; Peters, Kate M; Ulett, Glen C; Beatson, Scott A; Schembri, Mark A

    2016-01-01

    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. IMPORTANCEE. 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 to identify

  13. 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

  14. 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

  15. 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.

  16. 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

  17. Immunodiffusion Analysis of Yaba Poxvirus Structural and Associated Antigens 1

    PubMed Central

    Olsen, Richard G.; Yohn, David S.

    1970-01-01

    Yaba poxvirus virions were extracted and purified from Rhesus monkey tumors. A saline-soluble virion fraction (Y-xp), obtained by mechanical fractionation of purified virions with an X-press, contained seven components in acrylamide gel electrophoresis; five of these components were reactive in immunodiffusion with whole virion and Y-xp antisera produced in rabbits and monkeys. The saline-insoluble residue remaining after X-press treatment was hydrolyzed with sodium dodecyl sulfate, urea, and 2-mercaptoethanol (SUM). This fraction, Y-sum, contained five components, four of which were demonstrable by immunodiffusion. There was no evidence of antigenic relationships between Y-xp and Y-sum antigens in immunodiffusion. In acrylamide gel electrophoresis, one Y-xp and one Y-sum component had similar mobilities. Y-xp but not Y-sum antisera contained viral-neutralizing antibodies. Virus-free saline extracts of Yaba tumor prepared with Genetron (YS) were essentially devoid of virion structural antigens. They failed to induce precipitating antibodies for virion antigens, were nonreactive in immunodiffusion with virion antisera, and gave low complement-fixation titers with virion antisera. Yaba virion antigens were recovered from the Genetron tumor sediment by SUM and alkaline hydrolysis. Antisera prepared to YS extracts gave a maximum of 17 precipitin lines in immunodiffusion with YS extracts; none was identified as a virion structural antigen. Saline extracts of tumor prepared without Genetron contained immunogenic amounts of 5 virion antigens and 12 to 14 associated antigens. Animals immunized with infected cell culture extracts (virus-free) formed antibodies to six to seven virion antigens. The implications of using extracts of Yaba poxvirus-infected tissues in complement-fixation tests to measure virion antibodies were discussed. Images PMID:4317348

  18. 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.

  19. 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

  20. Core-Shell Structured Magnetic Ternary Nanocubes

    SciTech Connect

    Wang, Lingyan; Wang, Xin; Luo, Jin; Wanjala, Bridgid N.; Wang, Chong M.; Chernova, Natalya; Engelhard, Mark H.; Liu, Yao; Bae, In-Tae; Zhong, Chuan-Jian

    2010-12-01

    While transition metal-doped ferrite nanoparticles constitute an important class of soft magnetic nanomaterials with spinel structures, the ability to control the shape and composition would enable a wide range of applications in homogeneous or heterogeneous reactions such as catalysis and magnetic separation of biomolecules. This report describes novel findings of an investigation of core-shell structured MnZn ferrite nanocubes synthesized in organic solvents by manipulating the reaction temperature and capping agent composition in the absence of the conventionally-used reducing agents. The core-shell structure of the highly-monodispersed nanocubes (~20 nm) are shown to consist of an Fe3O4 core and an (Mn0.5Zn0.5)(Fe0.9, Mn1.1)O4 shell. In comparison with Fe3O4 and other binary ferrite nanoparticles, the core-shell structured nanocubes were shown to display magnetic properties regulated by a combination of the core-shell composition, leading to a higher coercivity (~350 Oe) and field-cool/zero-field-cool characteristics drastically different from many regular MnZn ferrite nanoparticles. The findings are discussed in terms of the unique core-shell composition, the understanding of which has important implication to the exploration of this class of soft magnetic nanomaterials in many potential applications such as magnetic resonance imaging, fuel cells, and batteries.

  1. 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

  2. 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

    2017-06-01

    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. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  3. Changes in the antigenic and molecular structure of. gamma. -irradiated bacterial lipopolysaccharide (LPS)

    SciTech Connect

    Csako, G.; Suba, E.A.; Tsai, C.M.; Elin, R.J.

    1986-03-01

    Ionization radiation is known to alter the biological properties of LPS. The author treated a highly purified LPS from E. coli in aqueous medium with /sup 60/Co-radiation. The changes in the antigenic and molecular structure of LPS were studied in double immunodiffusion/immunoelectrophoresis (rabbit antiserum) and sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), respectively. Untreated LPS revealed two major antigenic components and, due to varying lengths of the O-polysaccharide side chain, a series of homopolymers (SDS-PAGE). High doses of ..gamma..-radiation destroyed all antigenic reactivities and all stainable bands on SDS-PAGE. However, lower doses of radiation were selective. Disappearance of the more radiation-sensitive, electrophoretically fast-migrating antigenic component paralleled elimination of the long O-side chain containing molecules. The relatively radiation-resistant, less anodic second antigenic component cross-reacted with LPS of another E. coli strain and corresponded to LPS molecules composed of R-core and lipid A (SDS-PAGE). These findings explain the in vivo loss of antibody protection from shock before non-specific resistance with ..gamma..-irradiation of LPS.

  4. 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.

  5. 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

  6. Routine use of counter-immunoelectrophoresis test for detecting antibody to hepatitis B virus core antigen.

    PubMed Central

    Freeman, R; Hambling, M H

    1978-01-01

    Tests by counter-immunoelectrophoresis for antibody to hepatitis B core antigen (anti-HBc) were introduced into a routine testing programme for evidence of hepatitis B virus infection. Samples tested for anti-HBc were selected on the basis of the results of tests for HBsAg and clinical details. The sensitivity and specificity of the test were assessed and correlations made with the presence of HBsAg. The presence of anti-HBc was very useful in the interpretation of a doubtful positive result for HBsAg in the haemagglutination test. With very few exceptions the serum samples positive for HBsAg by routine tests also contained anti-HBc. It is concluded that the test is valuable and merits introduction into routine testing programmes. PMID:711911

  7. 3.5Å cryoEM Structure of Hepatitis B Virus Core Assembled from Full-Length Core Protein

    PubMed Central

    Yu, Xuekui; Jin, Lei; Jih, Jonathan; Shih, Chiaho; Hong Zhou, Z.

    2013-01-01

    The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM) and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149). Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90°) from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD) and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD’s accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment. PMID:24039702

  8. Hepatitis C virus core antigen assay: an alternative method for hepatitis C diagnosis.

    PubMed

    Wang, Lijuan; Lv, Hong; Zhang, Guojun

    2017-03-01

    Background The study aimed to evaluate a fully automated chemiluminescent immunoassay and compared it with a quantitative RNA assay and anti-HCV assay to verify the utility of this automated Ag assay as an alternative method for hepatitis C diagnosis. Methods A total of 229 serum samples previously tested for anti-HCV concentrations by the Architect Anti-HCV assay, were selected for HCV RNA testing by real time RT-PCR kit (Shanghai ZJ Bio-Tec Co., Ltd) and 125 specimens were tested for HCV Ag by the Architect HCV core Antigen kit. Results The log10 HCVAg and HCV RNA concentrations were highly correlated [ r = 0.834); with HCV RNA as the comparator test, HCVAg had 100% specificity, 100% positive predictive value (PPV) and 94.8% sensitivity. We found 1 pg/mL of total HCV core Ag is equivalent to approximately 6607HCV RNA international units (IU)/mL. Receiver operator characteristic curve analysis showed that the area under the curve of HCV core Ag (0.989) was greater than HCV Ab (0.871). HCV Ag concentrations and RNA-to-Ag ratio of the groups for HCV RNA concentrations ≤10(5) and >10(5 )IU/mL were both significantly different from each other ( P < 0.05). Conclusion The Architect HCV core Ag assay may be an alternative method for hepatitis C diagnosis, performed on the same analytical platform and sample as the anti-HCV assay, shortening the diagnostic window period, demonstrating good correlation with HCV RNA assay with high specificity and positive predictive value.

  9. Investigating the potential of conserved inner core oligosaccharide regions of Moraxella catarrhalis lipopolysaccharide as vaccine antigens: accessibility and functional activity of monoclonal antibodies and glycoconjugate derived sera.

    PubMed

    Cox, Andrew D; St Michael, Frank; Cairns, Chantelle M; Lacelle, Suzanne; Filion, Amy Lea; Neelamegan, Dhamodharan; Wenzel, Cory Q; Horan, Heather; Richards, James C

    2011-05-01

    We investigated the conservation and antibody accessibility of inner core epitopes of Moraxella catarrhalis lipopolysaccharide (LPS) in order to assess their potential as vaccine candidates. Two LPS mutants, a single mutant designated lgt2 and a double mutant termed lgt2/lgt4, elaborating truncated inner core structures were generated in order to preclude expression of host-like outer core structures and to create an inner core structure that was shared by all three serotypes A, B and C of M. catarrhalis. Murine monoclonal antibodies (mAbs), designated MC2-1 and MC2-10 were obtained by immunising mice with the lgt2 mutant of M. catarrhalis serotype A strain. We showed that mAb MC2-1 can bind to the core LPS of wild-type (wt) serotype A, B and C organisms and concluded that mAb MC2-1 defines an immunogenic inner core epitope of M. catarrhalis LPS. We were unsuccessful in obtaining mAbs to the lgt2/lgt4 mutant. MAb MC2-10 only recognised the lgt2 mutant and the wt serotype A strain, and exhibited a strong requirement for the terminal N-acetyl-glucosamine residue of the lgt2 mutant core oligosaccharide, suggesting that this residue was immunodominant. Subsequently, we showed that both mAbs MC2-1 and MC2-10 could facilitate bactericidal killing of the lgt2 mutant, however neither mAb could facilitate bactericidal killing of the wt serotype A strain. We then confirmed and extended the candidacy of the inner core LPS by demonstrating that it is possible to elicit functional antibodies against M. catarrhalis wt strains following immunisation of rabbits with glycoconjugates elaborating the conserved inner core LPS antigen. The present study describes three conjugation strategies that either uses amidases produced by Dictyostelium discoideum, targeting the amino functionality created by the amidase activity as the attachment point on the LPS molecule, or a strong base treatment to remove all fatty acids from the LPS, thus creating amino functionalities in the lipid A region

  10. Detection of Lewis antigen structural change by FTIR spectroscopy.

    PubMed

    Lewis, A T; Jones, K; Lewis, K E; Jones, S; Lewis, P D

    2013-02-15

    Mucins are a family of extensively glycosylated, high molecular weight glycoproteins. Secretion of mucins with altered terminal carbohydrate moieties alters the rheological and viscoelastic properties of mucus and observed glycosylation changes in respiratory diseases may vary with disease status. Structural modifications to the Lewis x antigen with sialic acid (sialyl-Lewis x) and sulphate (sulfo-Lewis x) in particular are associated with respiratory diseases and deemed potential biomarkers for disease diagnosis, severity and progression. The major aim of this study was to evaluate the ability of Fourier transform infrared spectroscopy (FTIR) to detect, via infrared (IR) spectra, the structural changes between the Lewis x antigen and sialylated and sulphated derivatives. Although FTIR only provides information on vibrations of chemical groups, we show that by comparing mono- and oligosaccharide specific IR spectra it is possible to determine the contribution of key sugar moieties to the altered Lewis x spectral pattern. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. 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

  12. 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.

  13. Thermal processing effects on peanut allergen Ara h 2 allergenicity in mice and its antigenic epitope structure.

    PubMed

    Zhang, Wenju; Zhu, Qingqing; Zhang, Tong; Cai, Qin; Chen, Qin

    2016-12-01

    Ara h 2 was purified from peanuts that were thermally treated by various processes, including boiling, glycation, frying and roasting. The allergenicity of Ara h 2 in Balb/c mice and the influence of thermal processing on the structural characteristics, and binding capacity of three core antigenic epitopes were studied. The results demonstrated that boiling, glycation and frying induced the down-regulation of the allergenicity of Ara h 2 in Balb/c mice, the collapse of its tertiary/secondary structure, and a reduction in the core epitope binding capacity; roasting showed a comparable allergenicity and the weakest inhibitory effect on core epitope binding capacity. These results indicate that thermal processing causes alteration of the protein structure and core epitopes of Ara h 2, and may affect its allergenicity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Structural Basis for Recombinatorial Permissiveness in the Generation of Anaplasma marginale Msp2 Antigenic Variants

    PubMed Central

    Silva, Marta G.; Kostyukova, Alla S.; Palmer, Guy H.

    2016-01-01

    Sequential expression of outer membrane protein antigenic variants is an evolutionarily convergent mechanism used by bacterial pathogens to escape host immune clearance and establish persistent infection. Variants must be sufficiently structurally distinct to escape existing immune effectors yet retain the core structural elements required for localization and function within the outer membrane. We examined this balance using Anaplasma marginale, which generates antigenic variants in the outer membrane protein Msp2 using gene conversion. The overwhelming majority of Msp2 variants expressed during long-term persistent infection are mosaics, derived by recombination of oligonucleotide segments from multiple alleles to form unique hypervariable regions (HVR). As a result, the mosaics are not under long-term selective pressure to encode a functional protein; consequently, we hypothesized that the Msp2 HVR is structurally permissive for mosaic expression. Using an integrated approach of predictive modeling with determination of the native Msp2 protein structure and function, we demonstrate that structured elements, most notably, β-sheets, are significantly concentrated in the highly conserved N- and C-terminal domains. In contrast, the HVR is overwhelmingly a random coil, with the structured α-helices and β-sheets being confined to the genomically defined structural tethers that separate the antigenically variable microdomains. This structure is supported by the surface exposure of the HVR microdomains and the slow diffusion-type porin function in native Msp2. Importantly, the predominance of the random coil provides plasticity for the formation of functional HVR mosaics and realization of the full potential of segmental gene conversion to dramatically expand the variant repertoire. PMID:27400719

  15. 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.

  16. The conserved core enzymatic activities and the distinct dynamics of polyomavirus large T antigens

    PubMed Central

    An, Ping; Brodsky, Jeffrey L.; Pipas, James M.

    2016-01-01

    Several human polyomaviruses including JCV, BKV and TSV are associated with diseases, particularly in immunosuppressed patients. While the large T antigen (LT) encoded by the monkey polyomavirus SV40 is well studied, and possesses intrinsic ATPase and DNA helicase activities, the LTs of the human polyomaviruses are relatively uncharacterized. In order to evaluate whether these enzymatic activities, which are required for viral DNA replication, are conserved between polyomaviruses, we performed a comparative study using the LTs from JCV, TSV and SV40. The ATPase and DNA helicase activities and the interaction with the cellular tumor suppressor p53 were assayed for the purified Zn-ATPase domains of the three LTs. We found that all Zn-ATPases were active ATPases. The Zn-ATPase domains also functioned as DNA helicases, although the measured kinetic constants differed among the three proteins. In addition, when tested against four small molecule ATPase inhibitors, the Zn-ATPase domains of TSV was more resistant than that of SV40 and JCV. Our results show that, while LTs from JCV and TSV share the core ATPase and DNA helicase activities, they possess important functional differences that might translate into their respective abilities to infect and replicate in hosts. PMID:25752954

  17. The Expression of HCG Epitope Fused to Hepatits B Virus Core Antigen.

    PubMed

    Li, Guang-Di; Wang, Bin; Chen, Zuo-Yi; Wang, Yuan; Gong, Yue-Ting

    1996-01-01

    The DNA fragments encoding HGC-beta-37-CTP was amplified by PCR and fused to the core gene of HBV at the position of amino Acid 1(N-terminal fusion, pCn-HCG), 154(C-terminal fusion, pCc-HCG), 75-83(internal fusion,pCm-HCG), and both 75-83 and 154 (pC-HCG2) respectively. The fused genes were expressed in E. coli, and the antigenicity of both HBcAg and HCG as well as the expression level were analyzed. In addition, the chimeric particular characteristics of the proteins and their immunogenicity were identified. It revealed that the fusion proteins pCm-HCG and pCc-HCG were able to form particles, and that the fusion protein pCm-HCG could induce antibody of anti-HCG of high titers in mice, suggesting that the position at 75-83 amino acid residue should be a relatively promising fusion site for HCG.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. The structure of iron in Earth's inner core.

    PubMed

    Tateno, Shigehiko; Hirose, Kei; Ohishi, Yasuo; Tatsumi, Yoshiyuki

    2010-10-15

    Earth's solid inner core is mainly composed of iron (Fe). Because the relevant ultrahigh pressure and temperature conditions are difficult to produce experimentally, the preferred crystal structure of Fe at the inner core remains uncertain. Static compression experiments showed that the hexagonal close-packed (hcp) structure of Fe is stable up to 377 gigapascals and 5700 kelvin, corresponding to inner core conditions. The observed weak temperature dependence of the c/a axial ratio suggests that hcp Fe is elastically anisotropic at core temperatures. Preferred orientation of the hcp phase may explain previously observed inner core seismic anisotropy.

  6. 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.

  7. 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.

  8. Three-dimensional structure of an antibody-antigen complex.

    PubMed Central

    Sheriff, S; Silverton, E W; Padlan, E A; Cohen, G H; Smith-Gill, S J; Finzel, B C; Davies, D R

    1987-01-01

    We have determined the three-dimensional structure of two crystal forms of an antilysozyme Fab-lysozyme complex by x-ray crystallography. The epitope on lysozyme consists of three sequentially separated subsites, including one long, nearly continuous, site from Gln-41 through Tyr-53 and one from Gly-67 through Pro-70. Antibody residues interacting with lysozyme occur in each of the six complementarity-determining regions and also include one framework residue. Arg-45 and Arg-68 form a ridge on the surface of lysozyme, which binds in a groove on the antibody surface. Otherwise the surface of interaction between the two proteins is relatively flat, although it curls at the edges. The surface of interaction is approximately 26 X 19 A. No water molecules are found in the interface. The positive charge on the two arginines is complemented by the negative charge of Glu-35 and Glu-50 from the heavy chain of the antibody. The backbone structure of the antigen, lysozyme, is mostly unperturbed, although there are some changes in the epitope region, most notably Pro-70. One side chain not in the epitope, Trp-63, undergoes a rotation of approximately 180 degrees about the C beta--C gamma bond. The Fab elbow bends in the two crystal forms differ by 7 degrees. Images PMID:2446316

  9. Should antibody to hepatitis B core antigen be tested in routine screening of donor corneas for transplant?

    PubMed

    Mattern, R M; Cavanagh, H D

    1997-03-01

    A review of the literature on transfusion-transmitted infectious diseases shows that antibody to hepatitis B core antigen (anti-HBc) is not presently viewed as helpful for hepatitis C or hepatitis non-ABC screening of blood donors. Its utility as a screen for hepatitis B or human immunodeficiency virus-1 (HIV-1) is controversial among experts. We compare relevant aspects of the screening of blood donations and the screening of cornea transplant donors to assess implications for the screening of donor corneas. We conclude that there is not sufficient evidence to warrant introducing anti-HBc as a routine screening test for cornea donors.

  10. Strong Correlation between Liver and Serum Levels of Hepatitis C Virus Core Antigen and RNA in Chronically Infected Patients

    PubMed Central

    Descamps, V.; Op de Beeck, A.; Plassart, C.; Brochot, E.; François, C.; Helle, F.; Adler, M.; Bourgeois, N.; Degré, D.; Duverlie, G.

    2012-01-01

    HCV core antigen (Ag) and HCV RNA levels were evaluated in matched liver biopsy samples and sera from 22 patients with hepatitis C infection by using the quantitative Architect HCV Ag immunoassay and a real-time RT-qPCR assay, respectively. The data showed a strong correlation between liver and serum compartments of HCV Ag levels (r = 0.80) and HCV RNA levels (r = 0.87). In summary, the serum HCV Ag and RNA levels reflect the intrahepatic values. PMID:22162563

  11. Core and periphery structures in protein interaction networks

    PubMed Central

    Luo, Feng; Li, Bo; Wan, Xiu-Feng; Scheuermann, Richard H

    2009-01-01

    Background Characterizing the structural properties of protein interaction networks will help illuminate the organizational and functional relationships among elements in biological systems. Results In this paper, we present a systematic exploration of the core/periphery structures in protein interaction networks (PINs). First, the concepts of cores and peripheries in PINs are defined. Then, computational methods are proposed to identify two types of cores, k-plex cores and star cores, from PINs. Application of these methods to a yeast protein interaction network has identified 110 k-plex cores and 109 star cores. We find that the k-plex cores consist of either "party" proteins, "date" proteins, or both. We also reveal that there are two classes of 1-peripheral proteins: "party" peripheries, which are more likely to be part of protein complex, and "connector" peripheries, which are more likely connected to different proteins or protein complexes. Our results also show that, besides connectivity, other variations in structural properties are related to the variation in biological properties. Furthermore, the negative correlation between evolutionary rate and connectivity are shown toysis. Moreover, the core/periphery structures help to reveal the existence of multiple levels of protein expression dynamics. Conclusion Our results show that both the structure and connectivity can be used to characterize topological properties in protein interaction networks, illuminating the functional organization of cellular systems. PMID:19426456

  12. 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.

  13. 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.

  14. Usefulness of a new immuno-radiometric assay to detect hepatitis C core antigen in a community-based population.

    PubMed

    Hayashi, K; Hasuike, S; Kusumoto, K; Ido, A; Uto, H; Kenji, N; Kohara, M; Stuver, S O; Tsubouchi, H

    2005-01-01

    A new immuno-radiometric assay (IRMA) to detect hepatitis C virus (HCV) core antigen (HCVcAg) has been developed. The aim of the present study was to investigate the sensitivity and specificity of this IRMA to measure HCV antigenemia, based on the detection of HCV RNA as the gold standard, and to assess the utility of the IRMA in a community-based population. Anti-HCV positive residents in a hyperendemic area of HCV infection in Japan were studied. Serum levels of HCVcAg were measured using IRMA, and the presence of HCV RNA was determined by a qualitative reverse transcription-polymerase chain reaction (RT-PCR) assay. The sensitivity and the specificity of the IRMA were 96.4 and 100%, respectively. The sensitivity of the IRMA was similar between serological HCV group I (HCV genotypes 1a and 1b) (97.6%) and group II (HCV genotypes 2a and 2b) (94.0%). There was a strong correlation between serum HCVcAg level and HCV-RNA measured by a quantitative RT-PCR (r = 0.832, P < 0.0001). There also was a very strong correlation of HCVcAg level between IRMA measurements performed on serum and those performed on plasma (r = 0.984, P < 0.0001). In conclusion, this new IRMA is useful for the detection of HCV core antigen in a community-based population.

  15. 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

  16. 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

  17. 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

  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. 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

  20. 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.

  1. 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.

  2. Process to make core-shell structured nanoparticles

    SciTech Connect

    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.

  3. 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.

  4. 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

  5. Biosynthesis and Structure of the Burkholderia cenocepacia K56-2 Lipopolysaccharide Core Oligosaccharide

    PubMed Central

    Ortega, Ximena; Silipo, Alba; Saldías, M. Soledad; Bates, Christa C.; Molinaro, Antonio; Valvano, Miguel A.

    2009-01-01

    Burkholderia cenocepacia is an opportunistic pathogen that displays a remarkably high resistance to antimicrobial peptides. We hypothesize that high resistance to antimicrobial peptides in these bacteria is because of the barrier properties of the outer membrane. Here we report the identification of genes for the biosynthesis of the core oligosaccharide (OS) moiety of the B. cenocepacia lipopolysaccharide. We constructed a panel of isogenic mutants with truncated core OS that facilitated functional gene assignments and the elucidation of the core OS structure in the prototypic strain K56-2. The core OS structure consists of three heptoses in the inner core region, 3-deoxy-d-manno-octulosonic acid, d-glycero-d-talo-octulosonic acid, and 4-amino-4-deoxy-l-arabinose linked to d-glycero-d-talo-octulosonic acid. Also, glucose is linked to heptose I, whereas heptose II carries a second glucose and a terminal heptose, which is the site of attachment of the O antigen. We established that the level of core truncation in the mutants was proportional to their increased in vitro sensitivity to polymyxin B (PmB). Binding assays using fluorescent 5-dimethylaminonaphthalene-1-sulfonyl-labeled PmB demonstrated a correlation between sensitivity and increased binding of PmB to intact cells. Also, the mutant producing a heptoseless core OS did not survive in macrophages as compared with the parental K56-2 strain. Together, our results demonstrate that a complete core OS is required for full PmB resistance in B. cenocepacia and that resistance is due, at least in part, to the ability of B. cenocepacia to prevent binding of the peptide to the bacterial cell envelope. PMID:19525227

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. [Prevalence of antibody against the hepatitis B core antigen (anti-HBc)among hospital personnel in Buenos Aires].

    PubMed

    Choc de Zanalda, B; Manterola, A C; Díaz Lestrem, M; Frider, B; Zocchi, G A; Fainboim, H; Clua, G I; Amor, E

    1990-01-01

    A group of 1,479 employees in 19 Buenos Aires hospitals were tested for antibody to hepatitis B core antigen (anti-HBc) to identify those who should be vaccinated against this infection. The average age of the subjects was 38.22 years; 70.86% of them were women and 85.5% were working in services where the risk of infection was high. The enzyme-linked immunosorbent assay (ELISA) was used, and the data were analyzed by the chi-square test. The results showed that 1,257 subjects (85.0%) did not have anti-HBc and thus were considered candidates for vaccination. The antibody was present in 222 individuals (15.0%). The prevalence of anti-HBc increased with age and with length of service, and it was greater in laboratory technicians, nurses, and those in high-risk services. These differences were statistically significant (P less than 0.01). A total of 23 carriers of hepatitis B surface antigen (AgHBs) were identified. In high-risk groups, vaccination against hepatitis B should be preceded by serological screening of susceptible individuals; the use of anti-HBc for this purpose allows carriers of AgHBs to be identified. The high prevalence of anti-HBc in laboratory technicians, nurses, and nurses' aides might justify their systematic vaccination.

  11. 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.

  12. 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.

  13. Outer Domain of HIV-1 gp120: Antigenic Optimization, Structural Malleability, and Crystal Structure with Antibody VRC-PG04

    PubMed Central

    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.

    2013-01-01

    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. PMID:23236069

  14. 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.

  15. Comparison of structural behavior of superplastically formed/diffusion-bonded sandwich structures and honeycomb core sandwich structures

    NASA Technical Reports Server (NTRS)

    Ko, W. L.

    1980-01-01

    A superplasticity formed/diffusion-bonded (SPF/DB) orthogonally corrugated core sandwich structure is discussed and its structural behavior is compared to that of a conventional honeycomb core sandwich structure. The stiffness and buckling characteristics of the two types of sandwich structures are compared under conditions of equal structural density. It is shown that under certain conditions, the SPF/DB orthogonally corrugated core sandwich structure is slightly more efficient than the optimum honeycomb core (square-cell core) sandwich structure. However, under different conditions, this effect can be reversed.

  16. 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.

  17. Disentangling structural information from core-level excitation spectra

    NASA Astrophysics Data System (ADS)

    Niskanen, Johannes; Sahle, Christoph J.; Gilmore, Keith; Uhlig, Frank; Smiatek, Jens; Föhlisch, Alexander

    2017-07-01

    Core-level spectra of liquids can be difficult to interpret due to the presence of a range of local environments. We present computational methods for investigating core-level spectra based on the idea that both local structural parameters and the x-ray spectra behave as functions of the local atomic configuration around the absorbing site. We identify correlations between structural parameters and spectral intensities in defined regions of interest, using the oxygen K-edge excitation spectrum of liquid water as a test case. Our results show that this kind of analysis can find the main structure-spectral relationships of ice, liquid water, and supercritical water.

  18. 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.

  19. 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.

  20. Structural Diversity of the Membrane Core Lipids of Extreme Halophiles.

    PubMed

    Morita, M; Yamauchi, N; Eguchi, T; Kakinuma, K

    1998-01-01

    The structural diversity of the core lipids of extreme halophiles Haloarcula japonica and Halobacterium halobium was investigated. The most significant difference is that Ha. japonica contains sn-2,3-di-O-phytanylglycerol exclusively as the core lipid, whereas Hb. halobium contains both sn-2,3-di-O-phytanylglycerol and sn-2-O-sesterterpanyl (3,7,11,15,19-pentamethyleicosanyl)-3-O-phytanylglycerol.

  1. 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.

  2. 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.

  3. Structural basis for selective cross-reactivity in a bactericidal antibody against inner core lipooligosaccharide from Neisseria meningitidis.

    PubMed

    Parker, Matthew J; Gomery, Kathryn; Richard, Gabrielle; MacKenzie, C Roger; Cox, Andrew D; Richards, James C; Evans, Stephen V

    2014-05-01

    The structure of a antigen-binding fragment (Fab) from the bactericidal monoclonal antibody LPT3-1 specific to lipooligosaccharide (LOS) inner cores from Neisseria meningitidis has been solved in complex with an eight-sugar inner core fragment NmL3 galE lpt3 KOH to 2.69 Å resolution. The epitope is centered about an inner core N-acetylglucosamine residue unique to N. meningitidis and does not include the lipid A moiety, which is disordered in the structure, but is positioned to allow the binding of free and membrane-anchored full-length LOS. All the amino acid residues that contact antigen are of germline origin but, remarkably, two consecutive somatic mutations of serine to glycine in the heavy chain at residues 52 and 52a are positioned to deprive the antibody of advantageous interactions and so weaken binding. However, these mutations are key to allowing selective cross-reactivity with the HepII-3-PEtn inner core variant expressed by 70% of strains. Neisseria meningitidis is a leading cause of disease in the developed world and is especially dangerous to children, who lack the necessary protective antibodies. The structure of Fab LPT3-1 in complex with LOS provides insight into the antibody's selective ability to recognize multiple clinically relevant variations of the LOS inner core from N. meningitidis.

  4. Structure and composition of the adenovirus type 2 core.

    PubMed Central

    Brown, D T; Westphal, M; Burlingham, B T; Winterhoff, U; Doerfler, W

    1975-01-01

    The structure and composition of the core of adenovirus type 2 were analyzed by electron microscopy and biochemical techniques after differential degradation of the virion by heat, by pyridine, or by sarcosyl treatment. In negatively stained preparations purified sarcosyl cores reveal spherical subunits of 21.6-nm diameter in the electron microscope. It is suggested that these subunits are organized as an icosahedron which has its axes of symmetry coincident with those of the viral capsid. The subunits are connected by the viral DNA molecule. The sarcosyl cores contain the viral DNA and predominantly the arginine/alanine-rich core polypeptide VII. When sarcosyl cores are spread on a protein film, tightly coiled particles are observed which gradually unfold giving rise to a rosette-like pattern due to the uncoiling DNA molecule. Completely unfolded DNA molecules are circular. Pyridine cores consist of the viral DNA and polypeptides V and VII. In negatively stained preparations of pyridine cores the subunit arrangement apparent in the sarcosyl cores is masked by an additional shell which is probably formed by polypeptide V. In freeze-cleaved preparations of the adenovirion two fracture planes can be recognized. One fracture plane probably passes between the outer capsid of the virion and polypeptide V exposing a subviral particle which corresponds to the pyridine core. The second fracture plane observed could be located between polypeptide V and the polypeptide VII-DNA complex, thus uncovering a subviral structure which corresponds to the sarcosyl core. In the sarcosyl core polypeptide VII is tightly bound to the viral DNA which is susceptible to digestion with DNase. The restriction endonuclease EcoRI cleaves the viral DNA in the sarcosyl cores into the six specific fragments. These fragments can be resolved on polyacrylamide-agarose gels provided the sarcosyl cores are treated with pronase after incubation with the restriction endonuclease. When pronase digestion

  5. Flexural Behavior of Aluminum Honeycomb Core Sandwich Structure

    NASA Astrophysics Data System (ADS)

    Matta, Vidyasagar; Kumar, J. Suresh; Venkataraviteja, Duddu; Reddy, Guggulla Bharath Kumar

    2017-05-01

    This project is concerned with the fabrication and flexural testing of aluminium honey comb sandwich structure which is a special case of composite materials that is fabricated by attaching two thin but stiff skins to a light weight but thick core. The core material is normally low density material but its high thickness provide the sandwich composite with high bonding stiffness. Honeycomb core are classified into two types based on the materials and structures. Hexagonal shape has a unique properties i.e has more bonding strength and less formation time based on the cell size and sheet thickness. Sandwich structure exhibit different properties such as high load bearing capacity at low weight and has excellent thermal insulation. By considering the above properties it has tendency to minimize the structural problem. So honey comb sandwich structure is choosed. The core structure has a different applications such as aircraft, ship interiors, construction industries. As there is no proper research on strength characteristics of sandwich structure. So, we use light weight material to desire the strength. There are different parameters involved in this structure i.e cell size, sheet thickness and core height. In this project we considered 3 level of comparison among the 3 different parameters cell size of 4, 6 and 8 mm, sheet thickness of 0.3, 0.5 and 0.7 mm, and core height of 20,25 and 30 mm. In order to reduce the number of experiment we use taguchi design of experiment, and we select the L8 orthogonal array is the best array for this type of situation, which clearly identifies the parameters by independent of material weight to support this we add the minitab software, to identify the main effective plots and regression equation which involves the individual response and corresponding parameters. Aluminium material is used for the fabrication of Honeycomb sandwich structure among the various grades of aluminium we consider the AL6061 which is light weight material

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. Near-core structure of a propagating optical vortex.

    PubMed

    Lochab, Priyanka; Senthilkumaran, P; Khare, Kedar

    2016-12-01

    We study the propagation of a charge-1 vortex beam using the angular spectrum method. While vortex beams are commonly assumed to have a helical wavefront, it is well known that the phase of the vortex in the near-core region varies arbitrarily quickly. In order to explain the wavefront behavior in the near-core region, ideas such as evanescent fields or superoscillatory functions have been used before. Our study using the angular spectrum method can inherently take into account the propagating as well as evanescent spatial frequencies and is able to provide the detailed wavefront structure as the vortex wavefront evolves. We report that the vortex wavefront shows a significant phase dip in the near-core region for all propagation distances, and the phase contour lines in this region are seen to spiral around the core. While the radial extent of this phase dip is seen to expand on propagation, the magnitude of the dip remains constant. Both propagating as well as evanescent components are seen to contribute to this phase dip, which we attribute to the presence of the radial component in the propagation vector near the core. The angular spectrum method as used here can be a valuable tool for probing the near-core structure of optical vortices.

  11. Plant-expressed Hepatitis B core antigen virus-like particles: Characterization and investigation of their stability in simulated and pig gastro-intestinal fluids.

    PubMed

    Berardi, Alberto; Lomonossoff, George P; Evans, David J; Barker, Susan A

    2017-04-30

    Virus-like particles (VLPs) are potential oral vaccine candidates, as their highly compact structure may allow them to withstand the harsh conditions of the gastro-intestinal (GI) environment. Hepatitis B core antigen (HBcAg) is an immunogenic protein that assembles into 30 or 34nm diameter VLPs. Here, the stabilities of both the HBcAg polypeptide itself and the three-dimensional structure of the VLPs upon exposure to in vitro and ex vivo simulated gastric and intestinal fluids were investigated. Plant-expressed HBcAg VLPs were efficiently purified by sucrose density gradient and characterized. The purified VLPs did not show major chemical or physical instability upon exposure to the low pH conditions typically found in the stomach; however, they completely agglomerated upon acidification and subsequent pH neutralization. The HBcAg polypeptide was highly digested upon exposure to pepsin in simulated gastric fluids. HBcAg appeared more stable in both simulated and ex vivo intestinal fluids, where despite a partial digestion of the HBcAg polypeptide, the VLPs maintained their most immunogenic epitopes and their particulate conformation. These results suggest that HBcAg VLPs are likely to be unstable in gastric fluids, yet if the gastric instability could be bypassed, they could maintain their particulate structure and immunogenicity in intestinal fluids. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Magnetization processes in core/shell exchange-spring structures.

    SciTech Connect

    Jiang, J. S.

    2015-03-27

    The magnetization reversal processes in cylindrical and spherical soft core/hard shell exchange-spring structures are investigated via the analytical nucleation theory, and are verified with numerical micromagnetic simulations. At small core sizes, the nucleation of magnetic reversal proceeds via the modified bulging mode, where the transverse component of the magnetization is only semi-coherent in direction and the nucleation field contains a contribution from self-demagnetization. For large core sizes, the modified curling mode, where the magnetization configuration is vortex-like, is favored at nucleation. The preference for the modified curling mode is beneficial in that the fluxclosure allows cylindrical and spherical core/shell exchange-spring elements to be densely packed into bulk permanent magnets without affecting the nucleation field, thereby offering the potential for high energy product.

  13. 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.

  14. 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.

  15. Identification of core-periphery structure in networks

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao; Martin, Travis; Newman, M. E. J.

    2015-03-01

    Many networks can be usefully decomposed into a dense core plus an outlying, loosely connected periphery. Here we propose an algorithm for performing such a decomposition on empirical network data using methods of statistical inference. Our method fits a generative model of core-periphery structure to observed data using a combination of an expectation-maximization algorithm for calculating the parameters of the model and a belief propagation algorithm for calculating the decomposition itself. We find the method to be efficient, scaling easily to networks with a million or more nodes, and we test it on a range of networks, including real-world examples as well as computer-generated benchmarks, for which it successfully identifies known core-periphery structure with low error rate. We also demonstrate that the method is immune to the detectability transition observed in the related community detection problem, which prevents the detection of community structure when that structure is too weak. There is no such transition for core-periphery structure, which is detectable, albeit with some statistical error, no matter how weak it is.

  16. 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.

  17. 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.

  18. Regional Variations of the Inner Core Attenuation Structure

    NASA Astrophysics Data System (ADS)

    Sun, X.; Qin, J.

    2016-12-01

    Three-dimensional velocity structure of the inner core has raised great challenge to the inner core formation and evolution mechanisms. Besides velocity, attenuation is also studied to help answering these questions. However, because of the waveform quality and limited earthquake-station distribution in high latitudes, attenuation studies are even harder. Previous inner core attenuation results showthat the shallow part of the inner core attenuation may have hemispherical differences and may change with depths, but the study areas are very limited, and conflictresults still exist. In this study, we systematically collect seismic data from global, regional and temporary seismic networks from year 1990 to 2014, in distance range of 146-156 degree. To ensure the quality of the data, we only chose earthquakes with magnitudesgreater than 5.5 and depths deeper than 50 km. After carefully checked the coverage of the good data, we finally select three regions (Australia, Africa and central Pacific) where PKP phases are generally good in both polar and equatorial directions to study inner core structure. During the data processing, we also compared different methods, such as spectral amplitude ratio of BC and DF, attenuation inversion from observed and synthetic data, to obtain the more reliable results. Our results show that the inner core velocity underneath Australia has no anisotropy, while Africa and central Pacific region have obvious anisotropy; Meanwhile, the average velocity is 0.5% faster underneath Australia, and 0.3% slower underneath Africa and central Pacific than AK135. For inner core attenuation structure, we have the following results: 1) Underneath Australia, Q value remain almost constant, ranging between 300-400, and show no anisotropy; 2) Underneath Africa and central Pacific, Q value change with depth, and show obvious anisotropy structure. Finally, we find that the velocity and attenuation in all three areas have good correlation, with fast velocity

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. Core Promoter Structure in the Oomycete Phytophthora infestans

    PubMed Central

    McLeod, Adele; Smart, Christine D.; Fry, William E.

    2004-01-01

    We have investigated the core promoter structure of the oomycete Phytophthora infestans. The transcriptional start sites (TSS) of three previously characterized P. infestans genes, Piexo1, Piexo3, and Piendo1, were determined by primer extension analyses. The TSS regions were homologous to a previously identified 16-nucleotide (nt) core sequence that overlaps the TSS in most oomycete genes. The core promoter regions of Piexo1 and Piendo1 were investigated by using a transient protoplast expression assay and the reporter gene β-glucuronidase. Mutational analyses of the promoters of Piexo1 and Piendo1 showed that there is a putative core promoter element encompassing the TSS (−2 to + 5) that has high sequence and functional homology to a known core promoter element present in other eukaryotes, the initiator element (Inr). Downstream and flanking the Inr is a highly conserved oomycete promoter region (+7 to + 15), hereafter referred to as FPR (flanking promoter region), which is also important for promoter function. The importance of the 19-nt core promoter region (Inr and FPR) in Piexo1 and Piendo1 was further investigated through electrophoretic mobility shift assays (EMSA). The EMSA studies showed that (i) both core promoters were able to specifically bind a protein or protein complex in a P. infestans whole-cell protein extract and (ii) the same mutations that reduced binding of the EMSA complex also reduced β-glucuronidase (GUS) levels in transient expression assays. The consistency of results obtained using two different assays (GUS transient assays [in vivo] and EMSA studies [in vitro]) supports a convergence of inference about the relative importance of specific nucleotides within the 19-nt core promoter region. PMID:14871940

  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. 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

  7. Hepatitis C virus core antigen in the management of patients treated with new direct-acting antivirals.

    PubMed

    Arboledas, Juan Carlos Alados; Guerrero, Inmaculada Pavón; Rodríguez, María José Blanco; Martos, Eva Torres; Pérez, Ana Belén; León, Cristina Cepero; Sierra Sánchez, Jesus F; Prieto, María Dolores López; Porcuna, Natalia Chueca; Mochón, María Dolores Ocete; Macías, Juan; de la Iglesia Salgado, Alberto; Granger, Javier Rodríguez; Fernández, Marcial Delgado; Lozano, Inmaculada Guerrero; Ramírez, Elena Reigadas; Rivero, Antonio; Del Carmen Lozano Domínguez, María; Viciana, Isabel; Montemayor, Juan Carlos Galán; García, Federico García

    2017-09-01

    We evaluated the utility of Architect core antigen assay® Abbott Diagnostics (HCVAg) for monitoring patients with HCV infection and compared to HCV-RNA quantification (Cobas Ampliprep TaqMan-Roche Diagnostics). Samples from 262 patients were studied. Mean baseline HCV RNA and HCVAg levels were similar for responders (6.2 log IU/mL and 3.4 log fmol/L) and non-responders (6.1 log IU/mL and 3.2 log fmol/L), respectively. Only 10 patients failed to achieve SVR12 and all were detected by both assays. To evaluate HCVAg quantification as a tool for the detection of failure to DAAs, we performed a retrospective study of 132 non-responder patients. Mean HCV RNA and HCVAg levels at the time of detection of therapeutic failure were 5.88±0.97 log IU/mL and 3.19±0.79 log fmol/L, respectively. HCVAg (>3 fmol/L) was detected in 130/132 patients (98.5%). HCVAg assay was useful for patient selection and for evaluating virological response to DAAs in the real world. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. The Expanded FindCore Method for Identification of a Core Atom Set for Assessment of Protein Structure Prediction

    PubMed Central

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

    2014-01-01

    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 (D.A. Snyder and G.T. 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. PMID:24327305

  9. 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.

  10. 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

  11. 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

  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. Dislocation core structures in (0001) InGaN

    SciTech Connect

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

    2016-03-14

    Threading dislocation core structures in c-plane GaN and In{sub x}Ga{sub 1−x}N (0.057 ≤ x ≤ 0.20) films were investigated by aberration-corrected scanning transmission electron microscopy. a-type dislocations are unaffected by alloying with indium and have a 5/7-atom ring core structure in both GaN and In{sub x}Ga{sub 1−x}N. In contrast, the dissociation lengths of (a + c)-type dislocations are reduced, and new 7/4/9-atom ring and 7/4/8/5-atom ring core structures were observed for the dissociated (a + c)-type dislocations in In{sub x}Ga{sub 1−x}N, which is associated with the segregation of indium near (a + c)-type and c-type dislocation cores in In{sub x}Ga{sub 1−x}N, consistent with predictions from atomistic Monte Carlo simulations.

  14. Evaluation of clinical usefulness of second-generation HCV core antigen assay: comparison with COBAS AMPLICOR HCV MONITOR assay version 2.0.

    PubMed

    Yokosuka, Osamu; Kawai, Shigenobu; Suzuki, Yoichi; Fukai, Kenichi; Imazeki, Fumio; Kanda, Tatsuo; Tada, Motohisa; Mikata, Rintarou; Hata, Akira; Saisho, Hiromitsu

    2005-12-01

    Hepatitis C virus (HCV) is an important etiologic agent for chronic liver diseases. The aim of this study was to evaluate the clinical usefulness of second-generation HCV core antigen assay by comparing the results of the assay with those of the COBAS AMPLICOR HCV MONITOR version 2.0 (COBAS v2.0). HCV core antigen was detectable by this assay in 142/149 (95.3%) of serotype 1 (3821+/-322 fmol/l; mean+/-SD), in 56/58 (96.6%) of serotype 2 (2589+/-449 fmol/l), and in 6/6 (100%) of serotypes 1+2 (1240+/-548 fmol/l). The HCV core antigen levels measured by this assay correlated well with the HCV RNA levels by COBAS v2.0 (r=0.848, P<0.0001). In relation to the outcome of interferon monotherapy, the pretreatment HCV core antigen levels of sustained and non-sustained virological responders were 659+/-189 and 4904+/-376 fmol/l in serotype 1, 1993+/-740 and 3145+/-519 fmol/l in serotype 2. The cutoff values with the best accuracy for HCV core Ag levels to discriminate between sustained and non-sustained virological response were 699 fmol/l for serotype 1 and 292 fmol/l for serotype 2, respectively, by receiver operating characteristic curve analysis. This new assay was considered to be useful in evaluating the HCV levels in patients with chronic hepatitis C.

  15. Insights from 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; Haslam, Stuart M; Dell, Anne; Stubbs, Keith A; Marshall, Barry J; Benghezal, Mohammed

    2017-04-25

    H. pylori is a Gram-negative extracellular bacterium, first discovered by the Australian physicians Barry Marshall and Robin Warren in 1982, that colonises the human stomach mucosa. It is the leading cause of peptic ulcer and commonly infects humans worldwide with prevalence as high as 90% in some countries. H. pylori infection usually results in asymptomatic chronic gastritis, however 10-15% of cases develop duodenal or gastric ulcers and 1-3% develop stomach cancer. Infection is generally acquired during childhood and persists for life in the absence of antibiotic treatment. H. pylori has had a long period of co-evolution with humans, going back to human migration out of Africa. This prolonged relationship is likely to have shaped the overall host-pathogen interactions and repertoire of virulence strategies which H. pylori employs to establish robust colonisation, escape immune responses and persist in the gastric niche. In this regard, H. pylori lipopolysaccharide (LPS) is a key surface determinant in establishing colonisation and persistence via host mimicry and resistance to cationic antimicrobial peptides. Thus, elucidation of the H. pylori LPS structure and corresponding biosynthetic pathway represents an important step towards better understanding of H. pylori pathogenesis and the development of novel therapeutic interventions.

  16. 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.

  17. Structural characterization of plant-derived hepatitis B surface antigen employed in oral immunization studies.

    PubMed

    Smith, Mark L; Richter, Lizabeth; Arntzen, Charles J; Shuler, Michael L; Mason, Hugh S

    2003-09-08

    Several subunit vaccine antigens have been successfully expressed in plants and recently the hepatitis B surface antigen (HBsAg), expressed in potatoes, was shown to be orally immunogenic in animal studies. However, to date, a detailed analysis of the plant-derived antigen is lacking. Herein, we comprehensively characterize the structure and post-translational processing of HBsAg from potato tuber and two plant cell suspension cultures. The HBsAg was found to accumulate intracellularly as tubular structures, with a complex size distribution, differing substantially from the virus-like particle (VLP) preparations of the current commercial vaccines. Extensive disulfide-bond cross-linking, which is important for immunogenicity, was evident and 21-37% of total HBsAg protein displayed epitopes which correlate with vaccine potency. The significance of these results with regard to the production of cost-effective orally delivered vaccines is discussed.

  18. 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

  19. 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

  20. 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

  1. Structural Analysis and Biosynthesis Gene Cluster of an Antigenic Glycopeptidolipid from Mycobacterium intracellulare▿ †

    PubMed Central

    Fujiwara, Nagatoshi; Nakata, Noboru; Naka, Takashi; Yano, Ikuya; Doe, Matsumi; Chatterjee, Delphi; McNeil, Michael; Brennan, Patrick J.; Kobayashi, Kazuo; Makino, Masahiko; Matsumoto, Sohkichi; Ogura, Hisashi; Maeda, Shinji

    2008-01-01

    Mycobacterium avium-Mycobacterium intracellulare complex (MAC) is the most common isolate of nontuberculous mycobacteria and causes pulmonary and extrapulmonary diseases. MAC species can be grouped into 31 serotypes by the epitopic oligosaccharide structure of the species-specific glycopeptidolipid (GPL) antigen. The GPL consists of a serotype-common fatty acyl peptide core with 3,4-di-O-methyl-rhamnose at the terminal alaninol and a 6-deoxy-talose at the allo-threonine and serotype-specific oligosaccharides extending from the 6-deoxy-talose. Although the complete structures of 15 serotype-specific GPLs have been defined, the serotype 16-specific GPL structure has not yet been elucidated. In this study, the chemical structure of the serotype 16 GPL derived from M. intracellulare was determined by using chromatography, mass spectrometry, and nuclear magnetic resonance analyses. The result indicates that the terminal carbohydrate epitope of the oligosaccharide is a novel N-acyl-dideoxy-hexose. By the combined linkage analysis, the oligosaccharide structure of serotype 16 GPL was determined to be 3-2′-methyl-3′-hydroxy-4′-methoxy-pentanoyl-amido-3,6-dideoxy-β-hexose-(1→3)-4-O-methyl-α-l-rhamnose-(1→3)-α-l-rhamnose-(1→3)-α-l-rhamnose-(1→2)-6-deoxy-α-l-talose. Next, the 22.9-kb serotype 16-specific gene cluster involved in the glycosylation of oligosaccharide was isolated and sequenced. The cluster contained 17 open reading frames (ORFs). Based on the similarity of the deduced amino acid sequences, it was assumed that the ORF functions include encoding three glycosyltransferases, an acyltransferase, an aminotransferase, and a methyltransferase. An M. avium serotype 1 strain was transformed with cosmid clone no. 253 containing gtfB-drrC of M. intracellulare serotype 16, and the transformant produced serotype 16 GPL. Together, the ORFs of this serotype 16-specific gene cluster are responsible for the biosynthesis of serotype 16 GPL. PMID:18326570

  2. 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).

  3. Antibody to hepatitis B core antigen levels in the natural history of chronic hepatitis B: a prospective observational study.

    PubMed

    Jia, Wei; Song, Liu-Wei; Fang, Yu-Qing; Wu, Xiao-Feng; Liu, Dan-Yang; Xu, Chun; Wang, Xiao-Mei; Wang, Wen; Lv, Dong-Xia; Li, Jun; Deng, Yong-Qiong; Wang, Yan; Huo, Na; Yu, Min; Xi, Hong-Li; Liu, Dan; Zhou, Yi-Xing; Wang, Gui-Qiang; Xia, Ning-Shao; Zhang, Ming-Xiang

    2014-12-01

    Previous studies have revealed antibody to hepatitis B core antigen (anti-HBc) levels as a predictor of treatment response in hepatitis B early antigen (HBeAg)-positive chronic hepatitis B (CHB) patients in both interferon and nucleos(t)ide analog therapy cohorts. However, there is no information about anti-HBc levels in the natural history of CHB. This study aimed to define anti-HBc levels of different phases in the natural history of CHB. Two hundred eleven treatment-naive CHB patients were included in the study. They were classified into 4 phases: immune tolerance (IT) phase (n = 39), immune clearance (IC) phase (n = 48), low or no-replicative (LR) phase (n = 55), and HBeAg-negative hepatitis (ENH, n = 69). Fifty patients who were HBsAg negative and anti-HBc positive were also recruited as past HBV infection (PBI) control group. Anti-HBc levels were measured by a newly developed double-sandwich immunoassay. Correlation of anti-HBc levels with alanine aminotransferase (ALT) and other HBV-related markers within each phase was performed. Serum anti-HBc levels were statistically significant between patients in different phases of CHB (P < 0.001). The median anti-HBc levels were: IT (3.17 log 10 IU/mL), IC (4.39 log 10 IU/mL), LR (3.29 log 10 IU/mL), ENH (4.12 log 10 IU/mL), and PBI (0.61 log 10 IU/mL). There existed a strong correlation in IC (r = 0.489, P < 0.001), a poor correlation in ENH (r = 0.275, P = 0.042), and no correlation in patients with ALT reached 5 times upper limit of normal (r = 0.120, P = 0.616). Anti-HBc levels show significant differences during the natural course of CHB. These results may provide some potentially useful insights into hepatitis B pathogenesis and immune activation against hepatitis B virus.

  4. 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.

  5. 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

  6. Structural coloring in large scale core-shell nanowires.

    PubMed

    Khudiyev, Tural; Ozgur, Erol; Yaman, Mecit; Bayindir, Mehmet

    2011-11-09

    We demonstrated two complementary size-dependent structural coloring mechanisms, interference and scattering, in indefinitely long core-shell nanowire arrays. The unusual nanostructures are comprised of an amorphous semiconducting core and a polymer shell layer with disparate refractive indices but with similar thermomechanical properties. Core-shell nanowires are mass produced from a macroscopic semiconductor rod by using a new top-to-bottom fabrication approach based on thermal size reduction. Nanostructures with diameters from 30 to 200 nm result in coloration that spans the whole visible spectrum via resonant Mie scattering. Nanoshell coloration based on thin film interference is proposed as a structural coloration mechanism which becomes dominant for nanowires having 700-1200 nm diameter. Controlled color generation in any part of visible and infrared spectral regions can be achieved by the simple scaling down procedure. Spectral color generation in mass-produced uniform core-shell nanowire arrays paves the way for applications such as spectral authentication at nanoscale, light-scattering ingredients in paints and cosmetics, large-area devices, and infrared shielding.

  7. Sequence and structure conservation in a protein core.

    PubMed

    Rodionov, M A; Blundell, T L

    1998-11-15

    In order to study structural aspects of sequence conservation in families of homologous proteins, we have analyzed structurally aligned sequences of 585 proteins grouped into 128 homologous families. The conservation of a residue in a family is defined as the average residue similarity in a given position of aligned sequences. The residue similarities were expressed in the form of log-odd substitution tables that take into account the environments of amino acids in three-dimensional structures. The protein core is defined as those residues that have less then 7% solvent accessibility. The density of a protein core is described in terms of atom packing, which is investigated as a criterion for residue substitution and conservation. Although there is no significant correlation between sequence conservation and average atom packing around nonpolar residues such as leucine, valine and isoleucine, a significant correlation is observed for polar residues in the protein core. This may be explained by the hydrogen bonds in which polar residues are involved; the better their protection from water access the more stable should be the structure in that position.

  8. Structural flexibility at a major conserved antibody target on hepatitis C virus E2 antigen

    PubMed Central

    Kong, Leopold; Lee, David E.; Kadam, Rameshwar U.; Liu, Tong; Giang, Erick; Nieusma, Travis; Garces, Fernando; Tzarum, Netanel; Woods, Virgil L.; Ward, Andrew B.; Li, Sheng; Wilson, Ian A.; Law, Mansun

    2016-01-01

    Hepatitis C virus (HCV) is a major cause of liver disease, affecting over 2% of the world’s population. The HCV envelope glycoproteins E1 and E2 mediate viral entry, with E2 being the main target of neutralizing antibody responses. Structural investigations of E2 have produced templates for vaccine design, including the conserved CD81 receptor-binding site (CD81bs) that is a key target of broadly neutralizing antibodies (bNAbs). Unfortunately, immunization with recombinant E2 and E1E2 rarely elicits sufficient levels of bNAbs for protection. To understand the challenges for eliciting bNAb responses against the CD81bs, we investigated the E2 CD81bs by electron microscopy (EM), hydrogen–deuterium exchange (HDX), molecular dynamics (MD), and calorimetry. By EM, we observed that HCV1, a bNAb recognizing the N-terminal region of the CD81bs, bound a soluble E2 core construct from multiple angles of approach, suggesting components of the CD81bs are flexible. HDX of multiple E2 constructs consistently indicated the entire CD81bs was flexible relative to the rest of the E2 protein, which was further confirmed by MD simulations. However, E2 has a high melting temperature of 84.8 °C, which is more akin to proteins from thermophilic organisms. Thus, recombinant E2 is a highly stable protein overall, but with an exceptionally flexible CD81bs. Such flexibility may promote induction of nonneutralizing antibodies over bNAbs to E2 CD81bs, underscoring the necessity of rigidifying this antigenic region as a target for rational vaccine design. PMID:27791120

  9. 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

  10. 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

  11. 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

  12. 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.

  13. Adjuvanted pandemic influenza vaccine: variation of emulsion components affects stability, antigen structure, and vaccine efficacy.

    PubMed

    Fox, Christopher B; Barnes V, Lucien; Evers, Tara; Chesko, James D; Vedvick, Thomas S; Coler, Rhea N; Reed, Steven G; Baldwin, Susan L

    2013-09-01

    Adjuvant formulations are critical components of modern vaccines based on recombinant proteins, which are often poorly immunogenic without additional immune stimulants. Oil-in-water emulsions comprise an advanced class of vaccine adjuvants that are components of approved seasonal and pandemic influenza vaccines. However, few reports have been published that systematically evaluate the in vitro stability and in vivo adjuvant effects of different emulsion components. To evaluate distinct classes of surfactants, oils, and excipients, for their effects on emulsion particle size stability, antigen structural interactions, and in vivo activity when formulated with a recombinant H5N1 antigen. Emulsions were manufactured by high pressure homogenization and characterized alone or in the presence of vaccine antigen by dynamic light scattering, zeta potential, viscosity, pH, hemolytic activity, electron microscopy, fluorescence spectroscopy, and SDS-PAGE. In vivo vaccine activity in the murine model was characterized by measuring antibody titers, antibody-secreting plasma cells, hemagglutination inhibition titers, and cytokine production. We demonstrate that surfactant class and presence of additional excipients are not critical for biological activity, whereas oil structure is crucial. Moreover, we report that simplified two-component emulsions appear more stable by particle size than more complex formulations.Finally, differences in antigen structural interactions with the various emulsions do not appear to correlate with in vivo activity. Oil-in-water emulsions can significantly enhance antibody and cellular immune responses to a pandemic influenza antigen. The dramatic differences in adjuvant activity between squalene-based emulsion and medium chain triglyceride-based emulsion are due principally to the biological activity of the oil composition rather than physical interactions of the antigen with the emulsion. © 2012 John Wiley & Sons Ltd.

  14. 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.

  15. 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.

  16. 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.

  17. 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

    2017-06-01

    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. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. 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.

  19. 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.

  20. Structural materials for breeder reactor cores and coolant circuits

    SciTech Connect

    Diercks, D.R.

    1984-02-01

    The structural components of principal interest in LMFBR cores and cooling circuits include the reactor vessel, primary and secondary piping, intermediate heat exchanger (IHX), and steam generator. Load-bearing components inside the vessel, among these the fuel cladding and duct, are also included. The operating conditions present in a fast-breeder nuclear reactor impose a number of requirements on the mechanical, physical, and neutronic properties of the materials used to construct these components.

  1. 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.

  2. 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

  3. Structure of the Inner Core-Outer Core Boundary Inferred From PKPBC Diffracted Waves

    NASA Astrophysics Data System (ADS)

    Zou, Z.; Koper, K. D.

    2004-12-01

    Examining the structure of the inner core-outer core boundary (ICB) is important for understanding the evolution and dynamics of the Earth's core. Seismic waves that diffract past the C cusp (PKPCdiff) preferentially sample the ICB and so contain important clues about this region. Just as Pdiff has been studied to infer core-mantle boundary structure, we expect that analysis of PKPCdiff will reveal ICB structure. However, there have been few systematic studies of PKPCdiff. We examined all of the IRIS temporary networks for which data are currently available and found three that provide enough high-quality PKPCdiff data for array processing techniques to be used effectively: INDEPTH-II, INDEPTH-III, and BANJO. We apply the cross-correlation and adaptive stacking techniques to the broadband waveforms to extract the differential travel times of PKPCdiff across the arrays, and use a weighted least-squares technique to invert theses times for the three-dimensional PKPCdiff slowness vector. We generate standard errors for the ray parameter and backazimuth using a bootstrap-type resampling algorithm. The earthquakes we analyze at the three networks sample different regions of ICB. For the earthquakes recorded at INDEPTH-II and INDEPTH-III arrays, PKPCdiff phases sample the ICB beneath north Africa and southwest Europe, and for the earthquakes at BANJO, they sample the ICB beneath Antarctica and west North America. We find PKPCdiff ray parameters vary from 1.79 ± 0.11 to 1.95 ± 0.05 s/deg beneath north Africa and southwest Europe,from 1.60 ± 0.08 to 1.74 ± 0.07 beneath Antarctica and have values around 1.82 ± 0.09 beneath west North America. In order to lessen the effect of shallow structure on the travel times, we also invert the differential travel times (PKPCdiff}-PKP{DF) for differential slowness vectors. We find less variation in them, however the differences appear to be significant. Therefore, our initial results support the idea of modest lateral heterogeneity

  4. Structural characterization of core-bradavidin in complex with biotin

    PubMed Central

    Agrawal, Nitin; Määttä, Juha A. E.; Kulomaa, Markku S.; Hytönen, Vesa P.; Johnson, Mark S.; Airenne, Tomi T.

    2017-01-01

    Bradavidin is a tetrameric biotin-binding protein similar to chicken avidin and bacterial streptavidin, and was originally cloned from the nitrogen-fixing bacteria Bradyrhizobium diazoefficiens. We have previously reported the crystal structure of the full-length, wild-type (wt) bradavidin with 138 amino acids, where the C-terminal residues Gly129-Lys138 (“Brad-tag”) act as an intrinsic ligand (i.e. Gly129-Lys138 bind into the biotin-binding site of an adjacent subunit within the same tetramer) and has potential as an affinity tag for biotechnological purposes. Here, the X-ray structure of core-bradavidin lacking the C-terminal residues Gly114-Lys138, and hence missing the Brad-tag, was crystallized in complex with biotin at 1.60 Å resolution [PDB:4BBO]. We also report a homology model of rhodavidin, an avidin-like protein from Rhodopseudomonas palustris, and of an avidin-like protein from Bradyrhizobium sp. Ai1a-2, both of which have the Brad-tag sequence at their C-terminus. Moreover, core-bradavidin V1, an engineered variant of the original core-bradavidin, was also expressed at high levels in E. coli, as well as a double mutant (Cys39Ala and Cys69Ala) of core-bradavidin (CC mutant). Our data help us to further engineer the core-bradavidin–Brad-tag pair for biotechnological assays and chemical biology applications, and provide deeper insight into the biotin-binding mode of bradavidin. PMID:28426764

  5. Structural characterization of core-bradavidin in complex with biotin.

    PubMed

    Agrawal, Nitin; Määttä, Juha A E; Kulomaa, Markku S; Hytönen, Vesa P; Johnson, Mark S; Airenne, Tomi T

    2017-01-01

    Bradavidin is a tetrameric biotin-binding protein similar to chicken avidin and bacterial streptavidin, and was originally cloned from the nitrogen-fixing bacteria Bradyrhizobium diazoefficiens. We have previously reported the crystal structure of the full-length, wild-type (wt) bradavidin with 138 amino acids, where the C-terminal residues Gly129-Lys138 ("Brad-tag") act as an intrinsic ligand (i.e. Gly129-Lys138 bind into the biotin-binding site of an adjacent subunit within the same tetramer) and has potential as an affinity tag for biotechnological purposes. Here, the X-ray structure of core-bradavidin lacking the C-terminal residues Gly114-Lys138, and hence missing the Brad-tag, was crystallized in complex with biotin at 1.60 Å resolution [PDB:4BBO]. We also report a homology model of rhodavidin, an avidin-like protein from Rhodopseudomonas palustris, and of an avidin-like protein from Bradyrhizobium sp. Ai1a-2, both of which have the Brad-tag sequence at their C-terminus. Moreover, core-bradavidin V1, an engineered variant of the original core-bradavidin, was also expressed at high levels in E. coli, as well as a double mutant (Cys39Ala and Cys69Ala) of core-bradavidin (CC mutant). Our data help us to further engineer the core-bradavidin-Brad-tag pair for biotechnological assays and chemical biology applications, and provide deeper insight into the biotin-binding mode of bradavidin.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Coimmunization with IL-15 plasmid enhances the longevity of CD8 T cells induced by DNA encoding hepatitis B virus core antigen

    PubMed Central

    Zhang, Wei; Dong, Sheng-Fu; Sun, Shu-Hui; Wang, Yuan; Li, Guang-Di; Qu, Di

    2006-01-01

    AIM: To test the feasibility of delivering a plasmid encoding IL-15 as a DNA vaccine adjuvant for improving the immune responses induced by hepatitis B virus core gene DNA vaccine. METHODS: We used RT-PCR based strategies to develop IL-15 expression constructs. We first confirmed that the gene could be expressed in Escherichia coli due to the poor expression of IL-15. Then the bioactivity of IL-15 plasmid expression product was identified by CTLL-2 proliferation assay. One hundred micrograms of DNA from each of the IL-15 eukaryotic expressed plasmid and the recombinant plasmid harboring DNA encoding the 144 amino acids of the N-terminus of HBV core gene (abbreviated pHBc144) was used to co-immunize C57 BL/6 mice. The titer of anti-HBcIgG was detected by ELISA and the antigen-specific CD8+ T cells (CD8+IFN-γ+ T cells) were detected by intracellular cytokine staining at different time points. RESULTS: After co-immunization by pIL-15 and pHBc144 DNA vaccine the antigen-specific CD8+ cells of mice increased gradually, the first peak of immune response appeared 14 d later, then the number of antigen-specific CD8+ Ts cells decreased gradually and maintained at a steady level in 3 mo. After boosting, the number of antigen-specific CD8+ T cells reached the second peak 10 d later with a double of the 1st peak, then the number of antigen-specific CD8+ T cells decreased slowly. IL-15 as a gene adjuvant had no significant effect on humoral immune responses induced by hepatitis B virus core gene DNA vaccine, but increased the memory antigen-specific CD8+ T cells induced by hepatitis B virus core gene DNA vaccine. CONCLUSION: DNA vaccine constructed by HBc Ag 1-144 amino acid induces effective cell immunity, and cytokine plasmid-delivered IL-15 enhances the longevity of CD8+ T cells. PMID:16937447

  12. 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.

  13. Dynamico-FE: A Structure-Preserving Hydrostatic Dynamical Core

    NASA Astrophysics Data System (ADS)

    Eldred, Christopher; Dubos, Thomas; Kritsikis, Evaggelos

    2017-04-01

    It is well known that the inviscid, adiabatic equations of atmospheric motion constitute a non-canonical Hamiltonian system, and therefore posses many important conserved quantities such as as mass, potential vorticity and total energy. In addition, there are also key mimetic properties (such as curl grad = 0) of the underlying continuous vector calculus. Ideally, a dynamical core should have similar properties. A general approach to deriving such structure-preserving numerical schemes has been developed under the frameworks of Hamiltonian methods and mimetic discretizations, and over the past decade, there has been a great deal of work on the development of atmospheric dynamical cores using these techniques. An important example is Dynamico, which conserves mass, potential vorticity and total energy; and possesses additional mimetic properties such as a curl-free pressure gradient. Unfortunately, the underlying finite-difference discretization scheme used in Dynamico has been shown to be inconsistent on general grids. To resolve these accuracy issues, a scheme based on mimetic Galerkin discretizations has been developed that achieves higher-order accuracy while retaining the structure-preserving properties of the existing discretization. This presentation will discuss the new dynamical core, termed Dynamico-FE, and show results from a standard set of test cases on both the plane and the sphere.

  14. 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.

  15. Nanocrystalline Aluminum Truss Cores for Lightweight Sandwich Structures

    NASA Astrophysics Data System (ADS)

    Schaedler, Tobias A.; Chan, Lisa J.; Clough, Eric C.; Stilke, Morgan A.; Hundley, Jacob M.; Masur, Lawrence J.

    2017-08-01

    Substitution of conventional honeycomb composite sandwich structures with lighter alternatives has the potential to reduce the mass of future vehicles. Here we demonstrate nanocrystalline aluminum-manganese truss cores that achieve 2-4 times higher strength than aluminum alloy 5056 honeycombs of the same density. The scalable fabrication approach starts with additive manufacturing of polymer templates, followed by electrodeposition of nanocrystalline Al-Mn alloy, removal of the polymer, and facesheet integration. This facilitates curved and net-shaped sandwich structures, as well as co-curing of the facesheets, which eliminates the need for extra adhesive. The nanocrystalline Al-Mn alloy thin-film material exhibits high strength and ductility and can be converted into a three-dimensional hollow truss structure with this approach. Ultra-lightweight sandwich structures are of interest for a range of applications in aerospace, such as fairings, wings, and flaps, as well as for the automotive and sports industries.

  16. Assessing intern core competencies with an objective structured clinical examination.

    PubMed

    Short, Matthew W; Jorgensen, Jennifer E; Edwards, John A; Blankenship, Robert B; Roth, Bernard J

    2009-09-01

    Residents are evaluated using Accreditation Council for Graduate Medical Education (ACGME) core competencies. An Objective Structured Clinical Examination (OSCE) is a potential evaluation tool to measure these competencies and provide outcome data. Create an OSCE to evaluate and demonstrate improvement in intern core competencies of patient care, medical knowledge, practice-based learning and improvement, interpersonal and communication skills, professionalism, and systems-based practice before and after internship. From 2006 to 2008, 106 interns from 10 medical specialties were evaluated with a preinternship and postinternship OSCE at Madigan Army Medical Center. The OSCE included eight 12-minute stations that collectively evaluated the 6 ACGME core competencies using human patient simulators, standardized patients, and clinical scenarios. Interns were scored using objective and subjective criteria, with a maximum score of 100 for each competency. Stations included death notification, abdominal pain, transfusion consent, suture skills, wellness history, chest pain, altered mental status, and computer literature search. These stations were chosen by specialty program directors, created with input from board-certified specialists, and were peer reviewed. All OSCE testing on the 106 interns (ages 25 to 44 [average, 28.6]; 70 [66%] men; 65 [58%] allopathic medical school graduates) resulted in statistically significant improvement in all ACGME core competencies: patient care (71.9% to 80.0%, P < .001), medical knowledge (59.6% to 78.6%, P < .001), practice-based learning and improvement (45.2% to 63.0%, P < .001), interpersonal and communication skills (77.5% to 83.1%, P < .001), professionalism (74.8% to 85.1%, P < .001), and systems-based practice (56.6% to 76.5%, P < .001). An OSCE during internship can evaluate incoming baseline ACGME core competencies and test for interval improvement. The OSCE is a valuable assessment tool to provide

  17. 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.

  18. Structural Analysis to Determine the Core of Hypoxia Response Network

    PubMed Central

    Heiner, Monika; Sriram, K.

    2010-01-01

    The advent of sophisticated molecular biology techniques allows to deduce the structure of complex biological networks. However, networks tend to be huge and impose computational challenges on traditional mathematical analysis due to their high dimension and lack of reliable kinetic data. To overcome this problem, complex biological networks are decomposed into modules that are assumed to capture essential aspects of the full network's dynamics. The question that begs for an answer is how to identify the core that is representative of a network's dynamics, its function and robustness. One of the powerful methods to probe into the structure of a network is Petri net analysis. Petri nets support network visualization and execution. They are also equipped with sound mathematical and formal reasoning based on which a network can be decomposed into modules. The structural analysis provides insight into the robustness and facilitates the identification of fragile nodes. The application of these techniques to a previously proposed hypoxia control network reveals three functional modules responsible for degrading the hypoxia-inducible factor (HIF). Interestingly, the structural analysis identifies superfluous network parts and suggests that the reversibility of the reactions are not important for the essential functionality. The core network is determined to be the union of the three reduced individual modules. The structural analysis results are confirmed by numerical integration of the differential equations induced by the individual modules as well as their composition. The structural analysis leads also to a coarse network structure highlighting the structural principles inherent in the three functional modules. Importantly, our analysis identifies the fragile node in this robust network without which the switch-like behavior is shown to be completely absent. PMID:20098728

  19. 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

  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. 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

  2. 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.

  3. 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.

  4. Structure and serology of the native polysaccharide antigen of type Ia group B Streptococcus

    PubMed Central

    Jennings, Harold J.; Rosell, Karl-Gunnar; Kasper, Dennis L.

    1980-01-01

    The native polysaccharide antigen isolated from type Ia group B Streptococcus by using pH-controlled growth conditions and extraction procedures contains D-galactose, D-glucose, 2-acetamido-2-deoxy-D-glucose, and sialic acid in the molar ratio of 2:1:1:1. The structure of the native type Ia antigen has been elucidated; it can be represented by the following repeating unit in which all the side-chain β-D-galactopyranose units are masked by sialic acid residues: [Formula: see text] Removal of all the sialic acid groups yields the incomplete type Ia polysacharide antigen with exposed terminal β-D-galactopyranose residues. Antisera to type Ia organisms produced in rabbits according to the Lancefield procedures contain antibodies specific for both the native and incomplete antigens. Although sialic acid is not itself a determinant in the formation of antibodies to the native polysaccharide, it is an essential part of a larger determinant. In order to maintain the high degree of immunologic specificity of the native antigen, this determinant must be at least a trisaccharide unit, because the native polysaccharide as isolated has terminal disaccharide units [α-D-NeuAcp-(2→3)-β-D-Galp] identical to those found in the human M and N blood group substances and fetuin. Formation of antibodies to the incomplete antigen is due to determinants terminating in β-D-galactopyranose residues. These determinants are probably generated by the removal of the masking sialic acid residues from the cell-associated native polysaccharide by degradative processes that occur in organisms grown without pH control. Images PMID:6156459

  5. 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.

  6. 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

  7. 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

  8. Electronic structure study of screw dislocation core energetics in Aluminum and core energetics informed forces in a dislocation aggregate

    NASA Astrophysics Data System (ADS)

    Das, Sambit; Gavini, Vikram

    2017-07-01

    We use a real-space formulation of orbital-free DFT to study the core energetics and core structure of an isolated screw dislocation in Aluminum. Using a direct energetics based approach, we estimate the core size of a perfect screw dislocation to be ≈ 7 |b|, which is considerably larger than previous estimates of 1-3 |b| based on displacement fields. The perfect screw upon structural relaxation dissociates into two Shockley partials with partial separation distances of 8.2 Å and 6.6 Å measured from the screw and edge component differential displacement plots, respectively. Similar to a previous electronic structure study on edge dislocation, we find that the core energy of the relaxed screw dislocation is not a constant, but strongly dependent on macroscopic deformations. Next, we use the edge and screw dislocation core energetics data with physically reasonable assumptions to develop a continuum energetics model for an aggregate of dislocations that accounts for the core energy dependence on macroscopic deformations. Further, we use this energetics model in a discrete dislocation network, and from the variations of the core energy with respect to the nodal positions of the network, we obtain the nodal core force which can directly be incorporated into discrete dislocation dynamics frameworks. We analyze and classify the nodal core force into three different contributions based on their decay behavior. Two of these contributions to the core force, both arising from the core energy dependence on macroscopic deformations, are not accounted for in currently used discrete dislocation dynamics models which assume the core energy to be a constant excepting for its dependence on the dislocation line orientation. Using case studies involving simple dislocation structures, we demonstrate that the contribution to the core force from the core energy dependence on macroscopic deformations can be significant in comparison to the elastic Peach-Koehler force even up to

  9. Space Launch System, Core Stage, Structural Test Design and Implementation

    NASA Technical Reports Server (NTRS)

    Shaughnessy, Ray

    2017-01-01

    As part of the National Aeronautics and Space Administration's (NASA) Space Launch System (SLS) Program, engineers at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama are working to design, develop and implement the SLS Core Stage structural testing. The SLS will have the capability to return humans to the Moon and beyond and its first launch is scheduled for December of 2017. The SLS Core Stage consist of five major elements; Forward Skirt, Liquid Oxygen (LOX) tank, Intertank (IT), Liquid Hydrogen (LH2) tank and the Engine Section (ES). Structural Test Articles (STA) for each of these elements are being designed and produced by Boeing at Michoud Assembly Facility located in New Orleans, La. The structural test for the Core Stage STAs (LH2, LOX, IT and ES) are to be conducted by the MSFC Test Laboratory. Additionally, the MSFC Test Laboratory manages the Structural Test Equipment (STE) design and development to support the STAs. It was decided early (April 2012) in the project life that the LH2 and LOX tank STAs would require new test stands and the Engine Section and Intertank would be tested in existing facilities. This decision impacted schedules immediately because the new facilities would require Construction of Facilities (C of F) funds that require congressional approval and long lead times. The Engine Section and Intertank structural test are to be conducted in existing facilities which will limit lead times required to support the first launch of SLS. With a SLS launch date of December, 2017 Boeing had a need date for testing to be complete by September of 2017 to support flight certification requirements. The test facilities were required to be ready by October of 2016 to support test article delivery. The race was on to get the stands ready before Test Article delivery and meet the test complete date of September 2017. This paper documents the past and current design and development phases and the supporting processes, tools, and

  10. New approach to the design of core support structures for large LMFBR plants

    SciTech Connect

    Burelbach, J.P.; Kann, W.J.; Pan, Y.C.; Saiveau, J.G.; Seidensticker, R.W.

    1984-01-01

    The paper describes an innovative design concept for a LMFBR Core Support Structure. A hanging Core Support Structure is described and analyzed. The design offers inherent safety features, constructibility advantages, and potential cost reductions.

  11. Inner Core Structure of Hurricane Patricia Observed During TCI-2015

    NASA Astrophysics Data System (ADS)

    Bell, M. M.; Martinez, J.; Doyle, J. D.; Rogers, R. F.

    2016-12-01

    Hurricane Patricia (2015) rapidly intensified from a tropical storm to an estimated 185 kt intensity in 36 hours, making it the strongest tropical cyclone in the western hemisphere on record. Four high-altitude research flights with the NASA WB-57 aircraft were conducted into Patricia as part of the Office of Naval Research (ONR) sponsored Tropical Cyclone Intensity (TCI) field experiment from 20 to 23 October. The WB-57 was equipped with a new high-density sounding system (HDSS) developed by Yankee Environmental Systems, enabling full-tropospheric profiling of temperature, humidity, and winds throughout Patricia's inner and outer core. A total of 257 dropsondes were released from the HDSS over the four day intensive observing period, spanning the development from a tropical depression to category 5 intensity. Doppler radar observations were obtained by the NOAA WP-3D aircraft reconnaissance from 21 to 23 October, allowing for complementary observations of the precipitation and kinematic structure during the rapid intensification period. Additional dropsonde observations from the Airborne Vertical Atmospheric Profiling System (AVAPS) and in situ instrumentation aboard the NOAA WP-3D and USAF C-130 aircraft are also used to complement the HDSS observations. Integrated kinematic and thermodynamic analyses of the full-tropospheric structure derived from dropsonde, radar, in situ, and satellite observations using a variational spline-based mesoscale analysis technique will be presented. The evolution of Patricia's inner core structure during the extreme rapid intensification period will be discussed.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Antigen-antibody interactions and structural flexibility of a femtomolar-affinity antibody.

    PubMed

    Fukunishi, Hiroaki; Shimada, Jiro; Shiraishi, Kenji

    2012-03-27

    The femtomolar-affinity mutant antibody (4M5.3) generated by directed evolution is interesting because of the potential of antibody engineering. In this study, the mutant and its wild type (4-4-20) were compared in terms of antigen-antibody interactions and structural flexibility to elucidate the effects of directed evolution. For this purpose, multiple steered molecular dynamics (SMD) simulations were performed. The pulling forces of SMD simulations elucidated the regions that form strong attractive interactions in the binding pocket. Structural analysis in these regions showed two important mutations for improving attractive interactions. First, mutation of Tyr102(H) to Ser (sequence numbering of Protein Data Bank entry 1FLR ) played a role in resolving the steric hindrance on the pathway of the antigen in the binding pocket. Second, mutation of Asp31(H) to His played a role in resolving electrostatic repulsion. Potentials of mean force (PMFs) of both the wild type and the mutant showed landscapes that do not include obvious intermediate states and go directly to the bound state. These landscapes were regarded as funnel-like binding free energy landscapes. Furthermore, the structural flexibility based on the fluctuations of the positions of atoms was analyzed. It was shown that the fluctuations in the positions of the antigen and residues in contact with antigen tend to be smaller in the mutant than in the wild type. This result suggested that structural flexibility decreases as affinity is improved by directed evolution. This suggestion is similar to the relationship between affinity and flexibility for in vivo affinity maturation, which was suggested by Romesberg and co-workers [Jimenez, R., et al. (2003) Proc. Natl. Acad. Sci. U.S.A.100, 92-97]. Consequently, the relationship was found to be applicable up to femotomolar affinity levels.

  19. Structural Characterization of Closely Related O-antigen Lipopolysaccharide (LPS) Chain Length Regulators*

    PubMed Central

    Kalynych, Sergei; Yao, Deqiang; Magee, James; Cygler, Miroslaw

    2012-01-01

    The surface O-antigen polymers of Gram-negative bacteria exhibit a modal length distribution that depends on dedicated chain length regulator periplasmic proteins (polysaccharide co-polymerases, PCPs) anchored in the inner membrane by two transmembrane helices. In an attempt to determine whether structural changes underlie the O-antigen modal length specification, we have determined the crystal structures of several closely related PCPs, namely two chimeric PCP-1 family members solved at 1.6 and 2.8 Å and a wild-type PCP-1 from Shigella flexneri solved at 2.8 Å. The chimeric proteins form circular octamers, whereas the wild-type WzzB from S. flexneri was found to be an open trimer. We also present the structure of a WzzFepE mutant, which exhibits severe attenuation in its ability to produce very long O-antigen polymers. Our findings suggest that the differences in the modal length distribution depend primarily on the surface-exposed amino acids in specific regions rather than on the differences in the oligomeric state of the PCP protomers. PMID:22437828

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. Assessing Intern Core Competencies With an Objective Structured Clinical Examination

    PubMed Central

    Short, Matthew W.; Jorgensen, Jennifer E.; Edwards, John A.; Blankenship, Robert B.; Roth, Bernard J.

    2009-01-01

    Background Residents are evaluated using Accreditation Council for Graduate Medical Education (ACGME) core competencies. An Objective Structured Clinical Examination (OSCE) is a potential evaluation tool to measure these competencies and provide outcome data. Objective Create an OSCE to evaluate and demonstrate improvement in intern core competencies of patient care, medical knowledge, practice-based learning and improvement, interpersonal and communication skills, professionalism, and systems-based practice before and after internship. Methods From 2006 to 2008, 106 interns from 10 medical specialties were evaluated with a preinternship and postinternship OSCE at Madigan Army Medical Center. The OSCE included eight 12-minute stations that collectively evaluated the 6 ACGME core competencies using human patient simulators, standardized patients, and clinical scenarios. Interns were scored using objective and subjective criteria, with a maximum score of 100 for each competency. Stations included death notification, abdominal pain, transfusion consent, suture skills, wellness history, chest pain, altered mental status, and computer literature search. These stations were chosen by specialty program directors, created with input from board-certified specialists, and were peer reviewed. Results All OSCE testing on the 106 interns (ages 25 to 44 [average, 28.6]; 70 [66%] men; 65 [58%] allopathic medical school graduates) resulted in statistically significant improvement in all ACGME core competencies: patient care (71.9% to 80.0%, P < .001), medical knowledge (59.6% to 78.6%, P < .001), practice-based learning and improvement (45.2% to 63.0%, P < .001), interpersonal and communication skills (77.5% to 83.1%, P < .001), professionalism (74.8% to 85.1%, P < .001), and systems-based practice (56.6% to 76.5%, P < .001). Conclusion An OSCE during internship can evaluate incoming baseline ACGME core competencies and test for interval improvement. The

  5. 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

  6. Structural properties of superplastically formed/diffusion-bonded orthogonally corrugated core sandwich plates

    NASA Technical Reports Server (NTRS)

    Ko, W. L.

    1980-01-01

    This paper describes a new superplastically formed/diffusion-bonded (SPF/DB) orthogonally corrugated sandwich structure, and presents formulae and the associated plots for evaluating the effective elastic constants for the core of this new sandwich structure. Comparison of structural properties of this new sandwich structure with the conventional honeycomb core sandwich structure was made under the condition of equal sandwich density. It was found that the SPF/DB orthogonally corrugated sandwich core has higher transverse shear stiffness than the conventional honeycomb sandwich core. However, the former has lower stiffness in the sandwich core thickness direction than the latter.

  7. 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.

  8. 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

  9. 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

  10. Uncommon Structural Motifs Dominate the Antigen Binding Site in Human Autoantibodies Reactive with Basement Membrane Collagen

    PubMed Central

    Foster, Mary H.; Buckley, Elizabeth S.; Chen, Benny J.; Hwang, Kwan-Ki; Clark, Amy G.

    2016-01-01

    Autoantibodies mediate organ destruction in multiple autoimmune diseases, yet their origins in patients remain poorly understood. To probe the genetic origins and structure of disease-associated autoantibodies, we engrafted immunodeficient mice with human CD34+ hematopoietic stem cells and immunized with the non-collagenous-1 (NC1) domain of the alpha3 chain of type IV collagen. This antigen is expressed in lungs and kidneys and is targeted by autoantibodies in anti-glomerular basement membrane (GBM) nephritis and Goodpasture syndrome (GPS), prototypic human organ-specific autoimmune diseases. Using Epstein Barr virus transformation and cell fusion, six human anti-alpha3(IV)NC1 collagen monoclonal autoantibodies (mAb) were recovered, including subsets reactive with human kidney and with epitopes recognized by patients’ IgG. Sequence analysis reveals a long to exceptionally long heavy chain complementarity determining region3 (HCDR3), the major site of antigen binding, in all six mAb. Mean HCDR3 length is 25.5 amino acids (range 20–36), generated from inherently long DH and JH genes and extended regions of non-templated N-nucleotides. Long HCDR3 are suited to forming noncontiguous antigen contacts and to binding recessed, immunologically silent epitopes hidden from conventional antibodies, as seen with self-antigen crossreactive broadly neutralizing anti-HIV Ig (bnAb). The anti-alpha3(IV)NC1 collagen mAb also show preferential use of unmutated variable region genes that are enriched among human chronic lymphocytic leukemia antibodies that share features with natural polyreactive Ig. Our findings suggest unexpected relationships between pathogenic anti-collagen Ig, bnAb, and autoreactive Ig associated with malignancy, all of which arise from B cells expressing unconventional structural elements that may require transient escape from tolerance for successful expansion. PMID:27450516

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  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. 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.

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. Humoral Immune Response in Mice Elicited by Combined Yeast-Derived Hepatitis B Virus Core, Surface, and Mosaic Surface Antigens.

    PubMed

    Granovski, Vladimir; Yokosawa, Jonny; Rodrigues-Granovski, Vanessa; Castro, Carlos Cueto; Urbina, Alfonso Camacho; Granovski, Nikolai

    2017-09-29

    Although successful, the second-generation hepatitis B vaccine programs around the world have a small group of immunized individuals that does not respond efficiently to the vaccination. Other issues of these vaccines are individuals that are low or nonresponders and/or have incomplete protection against heterologous hepatitis B virus (HBV) genotypes/subtypes and against HBV escape mutants. In addition, there are approximately 240 million people chronically infected with HBV worldwide and 620,000 deaths per year caused by the infection. In this study we developed three Hansenula polymorpha plasmids containing the following sequences: (a) HBsAg subtype ayw, (b) HBcAg sequence subtype adw2, and (c) chimeric HBsAg (adw4/ ayw) - preS1 (adw2) - 3 repetitions of preS2 (genotypes A, B, and C). The sequences were successfully expressed and the antigens purified. Using Balb/c mice the antigens were tested in different dosage combinations. Three antigens were obtained at a high purity level and with high reproducibility. We also assessed their immunogenic properties, showing that the antigens, individually or in combination, generated anti-HBs, anti-preS1, anti-preS2, and anti-HBc antibodies efficiently in mice. The formulation tests showed that a combination of 0.02 μg of HBs, 0.2 μg of preS1-preS2-HBs, and 0.02 μg of HBc was effective in eliciting specific antibodies in mice. © 2017 S. Karger AG, Basel.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. Major Immunodominant Region of Hepatitis B Virus Core Antigen as a Delivery Vector to Improve the Immunogenicity of the Fusion Antigen ROP2-SAG1 Multiepitope from Toxoplasma gondii in Mice.

    PubMed

    Wang, Wenhuan; Feng, Fangfang; Lv, Jinhui; Xie, Zixin; Chen, Jun; Zhang, Lifang; Li, Wenshu

    2017-09-01

    To prepare the dominant multiepitope fusion antigen ROP2-SAG1 (RSmultiepitope) from Toxoplasma gondii in a prokaryotic system, the major immunodominant region (MIR) of the human hepatitis B virus core antigen (HBcAg(MIR)) was used as a delivery vector. The gene encoding the RSmultiepitope was inserted into HBcAg(MIR), and rHBcAg(MIR)-RSmultiepitope was prepared, purified, and administered to BALB/c mice through intradermal injection. An indirect enzyme-linked immunosorbent assay analysis based on a multiepitope peptide facilitated the specific differentiation of sera obtained from mice immunized with the rHBcAg(MIR)-RSmultiepitope protein, and high titers (greater than 1:6,400) of specific anti-RSmultiepitope antibodies were obtained. Immunized splenocytes demonstrated enhanced IFN-γ production. Based on these results, the HBcAg(MIR) vector is easily applied in vitro for targeting the RSmultiepitope and efficiently presents this target epitope for the induction of significant humoral and cellular immune responses. This study offers a novel strategy for the design of a target epitope delivery system for a toxoplasmosis vaccine.

  13. 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

  14. Aspherical structural heterogeneity within the uppermost inner core: Insights into the hemispherical boundaries and core formation

    NASA Astrophysics Data System (ADS)

    Miller, Meghan S.; Niu, Fenglin; Vanacore, Elizabeth A.

    2013-10-01

    Lateral heterogeneities at the top of the inner core are investigated using earthquakes that occurred in Indonesia and southeast Asia and were recorded in the southeastern Caribbean. Using seismic observations of attenuation and seismic velocity, we were able to constrain the characteristics of the boundary between the inner and outer core to further investigate the dynamics and evolution of the Earth’s core. Our seismic observations from core phases confirm that the outermost inner core is asymmetrically heterogeneous and we are able to further constrain the morphology and physical properties of this layer. Comparison of data from earthquakes with ray paths traversing from east to the west versus those with ray paths from west to east allow us to map the aspherical heterogeneity of the boundary layer and specifically image the boundary between the proposed quasi-eastern and western hemispheres of the inner core. The variation of differential travel times between PKPdf and PKPbc, attenuation in terms of Q factor, and latitudinal changes for both of these observations, can be attributed to localized heterogeneity at the quasi-hemispherical boundaries of the inner core. We constrain the change in the thickness of outermost core boundary layer from 100 to 250 km within a distance of a few 10s of kilometers at 45°E ± 2°, for the western boundary, with an overall P-wave velocity decrease in the western hemisphere of 0.5% and increase of 0.5% in the eastern hemisphere. We constrain the eastern boundary at latitudes greater than 45°N to 173°E ± 4° with an overall P-wave velocity decrease in the western hemisphere of 1.0% in the uppermost 200 km of the inner core. The eastern boundary at equatorial latitudes is constrained to a region <170°E with a western hemisphere with a 0.5% drop in P-wave velocity in the uppermost 250 km.

  15. Structural and Biochemical Analysis of a Single Amino-Acid Mutant of WzzBSF That Alters Lipopolysaccharide O-Antigen Chain Length in Shigella flexneri

    PubMed Central

    Casey, Lachlan W.; Lonhienne, Thierry; Benning, Friederike; Morona, Renato; Kobe, Bostjan

    2015-01-01

    Lipopolysaccharide (LPS), a surface polymer of Gram-negative bacteria, helps bacteria survive in different environments and acts as a virulence determinant of host infection. The O-antigen (Oag) component of LPS exhibits a modal chain-length distribution that is controlled by polysaccharide co-polymerases (PCPs). The molecular basis of the regulation of Oag chain-lengths remains unclear, despite extensive mutagenesis and structural studies of PCPs from Escherichia coli and Shigella. Here, we identified a single mutation (A107P) of the Shigella flexneri WzzBSF, by a random mutagenesis approach, that causes a shortened Oag chain-length distribution in bacteria. We determined the crystal structures of the periplasmic domains of wild-type WzzBSF and the A107P mutant. Both structures form a highly similar open trimeric assembly in the crystals, and show a similar tendency to self-associate in solution. Binding studies by bio-layer interferometry reveal cooperative binding of very short (VS)-core-plus-O-antigen polysaccharide (COPS) to the periplasmic domains of both proteins, but with decreased affinity for the A107P mutant. Our studies reveal that subtle and localized structural differences in PCPs can have dramatic effects on LPS chain-length distribution in bacteria, for example by altering the affinity for the substrate, which supports the role of the structure of the growing Oag polymer in this process. PMID:26378781

  16. 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.

  17. Structural Analysis of Determinants of Histo-Blood Group Antigen Binding Specificity in Genogroup I Noroviruses

    PubMed Central

    Shanker, Sreejesh; Czako, Rita; Sankaran, Banumathi; Atmar, Robert L.; Estes, Mary K.

    2014-01-01

    ABSTRACT Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Susceptibility to the majority of NoV infections is determined by genetically controlled secretor-dependent expression of histo-blood group antigens (HBGAs), which are also critical for NoV attachment to host cells. Human NoVs are classified into two major genogroups (genogroup I [GI] and GII), with each genogroup further divided into several genotypes. GII NoVs are more prevalent and exhibit periodic emergence of new variants, suggested to be driven by altered HBGA binding specificities and antigenic drift. Recent epidemiological studies show increased activity among GI NoVs, with some members showing the ability to bind nonsecretor HBGAs. NoVs bind HBGAs through the protruding (P) domain of the major capsid protein VP1. GI NoVs, similar to GII, exhibit significant sequence variations in the P domain; it is unclear how these variations affect HBGA binding specificities. To understand the determinants of possible strain-specific HBGA binding among GI NoVs, we determined the structure of the P domain of a GI.7 clinical isolate and compared it to the previously determined P domain structures of GI.1 and GI.2 strains. Our crystallographic studies revealed significant structural differences, particularly in the loop regions of the GI.7 P domain, altering its surface topography and electrostatic landscape and potentially indicating antigenic variation. The GI.7 strain bound to H- and A-type, Lewis secretor, and Lewis nonsecretor families of HBGAs, allowing us to further elucidate the structural determinants of nonsecretor HBGA binding among GI NoVs and to infer several contrasting and generalizable features of HBGA binding in the GI NoVs. IMPORTANCE Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Recent epidemiological studies have shown increased prevalence of genogroup I (GI) NoVs. Although secretor-positive status is strongly correlated with NoV infection, cases of NoV infection

  18. Naturally occurring core immune-escape and carboxy-terminal mutations\\truncations in patients with e antigen negative chronic hepatitis B.

    PubMed

    Chauhan, Ranjit; Sarin, Shiv K; Kumar, Manoj; Bhattacharjee, Jayashree

    2012-10-01

    Hepatocellular injury is often progressive in patients with hepatitis B e antigen negative chronic hepatitis B (HBeAg -ve CHB). There is scant data on association of core mutations occurring in patients with HBeAg -ve CHB with severity of liver disease. Hundred and eighteen patients with chronic infection who were HBeAg negative, anti-HBe, and HBV DNA positive were enrolled. Precore and core regions were amplified, sequenced, and analyzed for precore, T helper, cytotoxic T lymphocytes (CTLs), B-cell epitope, and core carboxy-terminal region mutations. Majority of patients were infected with HBV genotype D: 96 (81%) [D1: 16, D2: 55 and D5: 25] followed by genotype A1: 15 (13%) and genotype C: 7 (6%) [C1: 5 and unidentified subgenotype C: 2]. Classical (A1896) as well as nonclassical precore region mutations were detected in 30 (25%) and in 9 (7.6%) patients, respectively. Core immune escape, core carboxy-terminal mutations and truncations were detected in 61 (52%), 11 (9.3%), and 14 (12%) patients, respectively. Three core immune escape mutations were significantly higher in patients with coexisting precore stop codon compared with patients without precore stop codon mutation, cT12S (43 vs. 8%, p < 0.001), cS21T (16 vs. 3.4%, p < 0.026), and cE77D (30 vs. 4.5%, p < 0.002). When frequency of core immune escape mutations was compared among CHB and decompensated patients, and cT12S: (27 vs. 10%, p < 0.05), cS21T (16 vs. 1.35%, p < 0.01), cT67P/N: (20 vs. 4%, p < 0.001), cE113D (11.37 vs. 1.35%, p < 0.05), and cP130T/Q (7 vs. 0%, p < 0.001) mutations were found to be significantly higher in decompensated patients. Core immune-escape mutations cT12S, cS21T, cT67P, cE113D, and cP130T/Q are significantly higher in decompensated liver disease patients and could influence the severity of liver disease in HBeAg -ve CHB patients.

  19. Predicted philogeny, secondary conformational structure, and epitope antigenicity of immunological sequences in poultry.

    PubMed

    Lara, L J; Peconick, A P; Fassani, É J; Júnior, A M P; Chalfun, P R B; Raymundo, D L; Barçante, T A; Barçante, J M de P

    2017-05-18

    Poultry production is faced with different types of stresses that are responsible for issues of animal welfare as well as for economic losses. Moreover, the immunity decreases when animals are stressed. In silico analyses are important in reducing the cost and in increasing the accuracy of scientific results. A bioinformatics tool was used to perform ontology studies on 15 different immunological sequences of poultry. The mRNA structures and sequences with maximum antigenic residues were also predicted. No homology was found between the sequences of poultry and mammals. These results helped in the prediction of new potential molecular markers. Of the 15 sequences that were analyzed, predictions could not be made for five because they were longer than 2500 nucleotides; for the remaining 10 sequences, 20 conformational structures per sequence were predicted and the most stable sequences were identified by their minimum free energy values. The highest antigenic epitopes were accepted by the maximum scores; 15 of the total 8934 epitopes that were predicted were analyzed. These results would aid future studies that use synthetic peptides or recombinants as markers or immunomodulators and would expand our understanding on how stress can modulate the immune system. These would also help in developing rapid diagnostic tools, in increasing animal welfare, biosecurity, and productivity, and also in developing of food additives and environmental enrichment for stress control, thereby, making animal production more sustainable.

  20. 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

  1. Structural, Antigenic, and Evolutionary Characterizations of the Envelope Protein of Newly Emerging Duck Tembusu Virus

    PubMed Central

    Huang, Bing; Ma, Xiuli; Li, Yufeng; Yuan, Xiaoyuan; Qin, Zhuoming; Wang, Dan; Chakravarty, Suvobrata; Li, Feng; Song, Minxun; Sun, Huaichang

    2013-01-01

    Since the first reported cases of ducks infected with a previously unknown flavivirus in eastern China in April 2010, the virus, provisionally designated Duck Tembusu Virus (DTMUV), has spread widely in domestic ducks in China and caused significant economic losses to poultry industry. In this study, we examined in detail structural, antigenic, and evolutionary properties of envelope (E) proteins of six DTMUV isolates spanning 2010–2012, each being isolated from individual farms with different geographical locations where disease outbreaks were documented. Structural analysis showed that E proteins of DTMUV and its closely related flavivirus (Japanese Encephalitis Virus) shared a conserved array of predicted functional domains and motifs. Among the six DTMUV strains, mutations were observed only at thirteen amino acid positions across three separate domains of the E protein. Interestingly, these genetic polymorphisms resulted in no detectable change in viral neutralization properties as demonstrated in a serum neutralization assay. Furthermore, phylogenetic analysis of the nucleotide sequences of the E proteins showed that viruses evolved into two distinct genotypes, termed as DTMUV.I and DTMUV.II, with II emerging as the dominant genotype. New findings described here shall give insights into the antigenicity and evolution of this new pathogen and provide guidance for further functional studies of the E protein for which no effective vaccine has yet been developed. PMID:23990944

  2. 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.

  3. 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

  4. 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.

  5. Non-enveloped HCV core protein as constitutive antigen of cold-precipitable immune complexes in type II mixed cryoglobulinaemia

    PubMed Central

    SANSONNO, D; LAULETTA, G; NISI, L; GATTI, P; PESOLA, F; PANSINI, N; DAMMACCO, F

    2003-01-01

    Hepatitis C virus (HCV) infection has been detected in a large proportion of patients with mixed cryoglobulinaemia (MC). Circulating ‘free’ non-enveloped HCV core protein has been demonstrated in HCV-infected patients, and this suggests its possible involvement in the formation of cryoprecipitable immune complexes (ICs). Thirty-two anti-HCV, HCV RNA-positive patients with type II MC were evaluated. Non-enveloped HCV core protein, HCV RNA sequences, total IgM, rheumatoid factor (RF) activity, IgG and IgG subclasses, C3 and C4 fractions, C1q protein and C1q binding activity were assessed in both cryoprecipitates and supernatants. Non-enveloped HCV core protein was demonstrated in 30 of 32 (93·7%) type II MC patients. After separation of cold-precipitable material, the protein was removed completely from supernatant in 12 patients (40%), whereas it was enriched in the cryoprecipitates of the remaining 18. In addition, HCV RNA and IgM molecules with RF activity were concentrated selectively in the cryoprecipitates. Differential precipitation was found for both total IgG and IgG subclasses, as they were less represented in the cryoglobulins and no selective enrichment was noted. Immunological characterization of HCV core protein-containing cryoprecipitating ICs after chromatographic fractionation showed that the IgM monoclonal component had RF activity, whereas anti-HCV core reactivity was confined to the IgG fraction. C1q enrichment in addition to high avidity of ICs for C1q binding in the cryoprecipitates suggest that complement activation may occur through the C1q protein pathway. The present data demonstrate that non-enveloped HCV core protein is a constitutive component of cryoprecipitable ICs in type II MC patients. PMID:12869035

  6. 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

  7. Population genetic structure and natural selection of apical membrane antigen-1 in Plasmodium vivax Korean isolates.

    PubMed

    Kang, Jung-Mi; Lee, Jinyoung; Cho, Pyo-Yun; Moon, Sung-Ung; Ju, Hye-Lim; Ahn, Seong Kyu; Sohn, Woon-Mok; Lee, Hyeong-Woo; Kim, Tong-Soo; Na, Byoung-Kuk

    2015-11-16

    Plasmodium vivax apical membrane antigen-1 (PvAMA-1) is a leading candidate antigen for blood stage malaria vaccine. However, antigenic variation is a major obstacle in the development of an effective vaccine based on this antigen. In this study, the genetic structure and the effect of natural selection of PvAMA-1 among Korean P. vivax isolates were analysed. Blood samples were collected from 66 Korean patients with vivax malaria. The entire PvAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. The PvAMA-1 sequence of each isolate was sequenced and the polymorphic characteristics and effect of natural selection were analysed using the DNASTAR, MEGA4, and DnaSP programs. Thirty haplotypes of PvAMA-1, which were further classified into seven different clusters, were identified in the 66 Korean P. vivax isolates. Domain II was highly conserved among the sequences, but substantial nucleotide diversity was observed in domains I and III. The difference between the rates of non-synonymous and synonymous mutations suggested that the gene has evolved under natural selection. No strong evidence indicating balancing or positive selection on PvAMA-1 was identified. Recombination may also play a role in the resulting genetic diversity of PvAMA-1. This study is the first comprehensive analysis of nucleotide diversity across the entire PvAMA-1 gene using a single population sample from Korea. Korean PvAMA-1 had limited genetic diversity compared to PvAMA-1 in global isolates. The overall pattern of genetic polymorphism of Korean PvAMA-1 differed from other global isolates and novel amino acid changes were also identified in Korean PvAMA-1. Evidences for natural selection and recombination event were observed, which is likely to play an important role in generating genetic diversity across the PvAMA-1. These results provide useful information for the understanding the population structure of P. vivax circulating in Korea and have important

  8. Seropositivity for Anti-HCV Core Antigen is Independently Associated With Increased All-Cause, Cardiovascular, and Liver Disease-Related Mortality in Hemodialysis Patients

    PubMed Central

    Ohsawa, Masaki; Kato, Karen; Tanno, Kozo; Itai, Kazuyoshi; Fujishima, Yosuke; Okayama, Akira; Turin, Tanvir Chowdhury; Onoda, Toshiyuki; Suzuki, Kazuyuki; Nakamura, Motoyuki; Kawamura, Kazuko; Akiba, Takashi; Sakata, Kiyomi; Fujioka, Tomoaki

    2011-01-01

    Background It is not known whether chronic or past hepatitis C virus (HCV) infection contributes to the high mortality rate in hemodialysis patients. Methods This prospective study of 1077 adult hemodialysis patients without hepatitis B virus infection used Poisson regression analysis to estimate crude and sex- and age-adjusted rates (per 1000 patient-years) of all-cause, cardiovascular, infectious disease-related and liver disease-related mortality in patients negative for HCV antibody (group A), patients positive for HCV antibody and negative for anti-HCV core antigen (group B), and patients positive for anti-HCV core antigen (group C). The relative risks (RRs) for each cause of death in group B vs group C as compared with those in group A were also estimated by Poisson regression analysis after multivariate adjustment. Results A total of 407 patients died during the 5-year observation period. The sex- and age-adjusted mortality rate was 71.9 in group A, 80.4 in group B, and 156 in group C. The RRs (95% CI) for death in group B vs group C were 1.23 (0.72 to 2.12) vs 1.60 (1.13 to 2.28) for all-cause death, 0.75 (0.28 to 2.02) vs 1.64 (0.98 to 2.73) for cardiovascular death, 1.64 (0.65 to 4.15) vs 1.58 (0.81 to 3.07) for infectious disease-related death, and 15.3 (1.26 to 186) vs 28.8 (3.75 to 221) for liver disease-related death, respectively. Conclusions Anti-HCV core antigen seropositivity independently contributes to elevated risks of all-cause and cause-specific death. Chronic HCV infection, but not past HCV infection, is a risk for death among hemodialysis patients. PMID:22001541

  9. 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.

  10. Structure binding relationship of human surfactant protein D and various lipopolysaccharide inner core structures.

    PubMed

    Reinhardt, Anika; Wehle, Marko; Geissner, Andreas; Crouch, Erika C; Kang, Yu; Yang, You; Anish, Chakkumkal; Santer, Mark; Seeberger, Peter H

    2016-09-01

    As a major player of the innate immune system, surfactant protein D (SP-D) recognizes and promotes elimination of various pathogens such as Gram-negative bacteria. SP-D binds to l-glycero-d-manno-heptose (Hep), a constituent of the partially conserved lipopolysaccharide (LPS) inner core of many Gram-negative bacteria. Binding and affinity of trimeric human SP-D to Hep in distinct LPS inner core glycans differing in linkages and adjacent residues was elucidated using glycan array and surface plasmon resonance measurements that were compared to in silico interaction studies. The combination of in vitro assays using defined glycans and molecular docking and dynamic simulation approaches provides insights into the interaction of trimeric SP-D with those glycan ligands. Trimeric SP-D wildtype recognized larger LPS inner core oligosaccharides with slightly enhanced affinity than smaller compounds suggesting the involvement of stabilizing secondary interactions. A trimeric human SP-D mutant D324N+D325N+R343K resembling rat SP-D bound to various LPS inner core structures in a similar pattern as observed for the wildtype but with higher affinity. The selective mutation of SP-D promotes targeting of LPS inner core oligosaccharides on Gram-negative bacteria to develop novel therapeutic agents. Copyright © 2016. Published by Elsevier Inc.

  11. 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.

  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. 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.

  14. O-antigen structure of Shigella flexneri serotype Yv and effect of the lpt-O gene variation on phosphoethanolamine modification of S. flexneri O-antigens.

    PubMed

    Knirel, Yuriy A; Lan, Ruiting; Senchenkova, Sof'ya N; Wang, Jianping; Shashkov, Alexander S; Wang, Yan; Perepelov, Andrei V; Xiong, Yanwen; Xu, Jianguo; Sun, Qiangzheng

    2013-04-01

    Shigella flexneri is the major human pathogen causing shigellosis. O-antigens of all S. flexneri serotypes (except for serotype 6) share the →2)-α-l-Rhap(III)-(1 → 2)-α-l-Rhap(II)-(1 → 3)-α-l-Rhap(I)-(1 → 3)-β-d-GlcpNAc-(1→ basic O-unit, whereas differences between the serotypes are conferred by phage-encoded glucosylation and/or O-acetylation at various positions. Recently, in serotype X and 4a variants called Xv and 4av, respectively, O-antigen modification with phosphoethanolamine (PEtN) has been identified, which is encoded by a plasmid-borne gene (lpt-O) for a PEtN-transferase and confers the monoclonal antibody IV-1(MASF IV-1) determinant to the bacteria. In this study, we elucidated the O-antigen structure of serotype Yv, another MASF IV-1-positive novel variant of S. flexneri. The serotype Yv O-antigen has the same basic carbohydrate backbone structure as that of the "classical" serotype Y, but differs in the presence of PEtN at position 3 of Rha(III) (major) or both Rha(II) and Rha(III) (minor). This pattern is similar to that of serotype 4av, but different from the pattern of serotype Xv, which is characterized by major PEtN modification on Rha(II). In serotype Yv, mono- and bisphosphorylated O-units generate a block-copolymeric structure, the former being partially O-acetylated at position 6 of GlcNAc and the latter lacking O-acetylation. Functional analysis revealed a correlation between the serotype-specific PEtN modification pattern and the lpt-O variation in different serotypes: lpt-O(RII) in serotype Xv is better tuned for phosphorylation of Rha(II) and lpt-O(RIII) in serotypes Yv and 4av for phosphorylation of Rha(III). These data enhance our knowledge of S. flexneri serotype conversion mechanisms and help to understand the biosynthesis process of the new O-antigen variants.

  15. 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.

  16. 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

  17. 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

  18. Candidate Structural Materials for In-Core VHTR Application

    SciTech Connect

    Snead, Lance Lewis; Katoh, Yutai; Windes, Will; Smit, Kobus

    2008-01-01

    Graphite moderated gas cooled reactors led the way into the nuclear age with the Chicago Pile-1 reactor, which provided the first sustained critical reaction in December, 1942. The first commercial nuclear plant, Calder Hall in the UK, went critical in 1956 with an outlet gas temperature of {approx}345 C. As depicted in Fig. 1, in five decades since Calder Hall, outlet temperature increased rapidly, reaching a plateau of {approx}950 C. This apparent ceiling is in large part due to limitations in the structural materials utilized within the core (e.g. control systems) and primary loop (hot duct, heat-exchangers etc.) Simply, the operating temperatures of Generation III (HTGR's) are very near performance limits of the structural alloys used, both in terms of elevated temperature and as-irradiated properties. This limitation remains today and is the reason the outlet temperature of the Generation IV Very High Temperature Reactor (VHTR) continues to be revised downward from the original optimistic goal of {approx}1200 C, to it's current target outlet temperature of {approx}950 C, a temperature consistent with the previous generation of HTGR's. An example of the challenges facing Generation IV VHTR is found by considering the control rods. For the Fort St. Vrain Reactor the control system consisted of thirty tubes each containing B4C control material. Alloy 800, originally developed by Inco in the 1950's under the trade-name Incoloy 800 and 800H had found widespread application is steam generators, turbines and was selected for this control rod application. These materials are included for Class 1 Nuclear Component by ASME section III. In addition to Ft. St Vrain, alloy 800H has found control rod application in the German HTR and Japanese HTTR reactors and is the primary choice Pebble Bed Modular Reactor (a HTGR) reactivity control system. Figure 2 gives the ASME allowed stress for Alloy 800H. Due to the loss in creep rupture strength, the allowed design stress for

  19. A new label-free electrochemical immunosensor based on dendritic core-shell AuPd@Au nanocrystals for highly sensitive detection of prostate specific antigen.

    PubMed

    Wang, Rui; Liu, Wei-Dong; Wang, Ai-Jun; Xue, Yadong; Wu, Liang; Feng, Jiu-Ju

    2018-01-15

    Herein, bimetallic dendritic core-shell AuPd@Au nanocrystals (AuPd@Au NCs) were prepared by a simple one-pot aqueous method using xanthine as a green growth-directing agent. By virtue of the enhanced peak currents in the H2O2 reduction catalyzed by AuPd@Au NCs, a label-free immunosensor was constructed for the detection of prostate specific antigen (PSA). The immunosensor exhibited significantly improved analytical performance for the assay of PSA with wide linear range of 0.1-50ngmL(-1) and low detection limit of 0.078ngmL(-1) (S/N = 3), coupled with the improved stability, reproducibility and selectivity. It provides a promising platform for clinical research and diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Magneto-controlled bioelectronics for the antigen-antibody interaction based on magnetic-core/gold-shell nanoparticles functionalized biomimetic interface.

    PubMed

    Tang, Dianping; Yuan, Ruo; Chai, Yaqin

    2008-02-01

    A new protein assay system for the antigen-antibody interaction was developed by immobilization of carcinoembryonic antibody (anti-CEA) onto magnetic-core/gold-shell nanoparticles-functionalized biomimetic interface on multiporous polythionine modified magnetic carbon paste electrodes (MCPE). Differential pulse voltammetric (DPV) technique was employed to investigate the antigen-antibody interaction in pH 6.8 acetate acid buffer solution after incubation with various CEA samples for 50 min at room temperature. The peak currents decreased with increased CEA concentration, and were proportional to the CEA concentration in the range of 1.5-60 ng/ml with a detection limit of 0.3 ng/ml at a signal-to-noise ratio of 3. Moreover, the selectivity, reproducibility and stability of the proposed immunoassay system were acceptable. Compared with the conventional immunoassays, the developed immunoassay system was simple and rapid without multiple labeling and separation steps. Importantly, the proposed methodology would be valuable for diagnosis and monitoring of carcinoma and its metastasis.

  1. 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.

  2. A Comprehensive Phylogenetic and Structural Analysis of the Carcinoembryonic Antigen (CEA) Gene Family

    PubMed Central

    Pavlopoulou, Athanasia; Scorilas, Andreas

    2014-01-01

    The carcinoembryonic antigen (CEA) gene family belongs to the immunoglobulin (Ig) superfamily and codes for a vast number of glycoproteins that differ greatly both in amino acid composition and function. The CEA family is divided into two groups, the carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the pregnancy-specific glycoproteins. The CEA family members are implicated in pleiotropic (patho)physiological functions including cell–cell adhesion, pregnancy, immunity, neovascularization, regulation of insulin homeostasis, and carcinogenesis. In general, the CEA-encoded proteins are composed of an extracellular region with Ig variable and constant-like domains and a cytoplasmic region containing signaling motifs. Of particular interest, the well-studied human and mouse CEA genes are arranged in clusters in a single chromosome. Taking into account this characteristic, we made an effort to reconstruct the evolutionary history of the CEA gene family. Toward this end, the publicly available genomes were searched extensively for CEA homologs. The domain organization of the retrieved protein sequences was analyzed, and, subsequently, comprehensive phylogenetic analyses of the entire length CEA homologous proteins were performed. A series of evolutionarily conserved amino acid residues, functionally important, were identified. The relative positioning of these residues on the modeled tertiary structure of novel CEA protein domains revealed that they are, also, spatially conserved. Furthermore, the chromosomal arrangement of CEA genes was examined, and it was found that the CEA genes are preserved in terms of position, transcriptional orientation, and number in all species under investigation. PMID:24858421

  3. 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.

  4. 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.

  5. Structural reorganization of the antigen-binding groove of human CD1b for presentation of mycobacterial sulfoglycolipids

    PubMed Central

    Garcia-Alles, Luis F.; Collmann, Anthony; Versluis, Cees; Lindner, Buko; Guiard, Julie; Maveyraud, Laurent; Huc, Emilie; Im, Jin S.; Sansano, Sebastiano; Brando, Thérèse; Julien, Sylviane; Prandi, Jacques; Gilleron, Martine; Porcelli, Steven A.; de la Salle, Henri; Heck, Albert J. R.; Mori, Lucia; Puzo, Germain; Mourey, Lionel; De Libero, Gennaro

    2011-01-01

    The mechanisms permitting nonpolymorphic CD1 molecules to present lipid antigens that differ considerably in polar head and aliphatic tails remain elusive. It is also unclear why hydrophobic motifs in the aliphatic tails of some antigens, which presumably embed inside CD1 pockets, contribute to determinants for T-cell recognition. The 1.9-Å crystal structure of an active complex of CD1b and a mycobacterial diacylsulfoglycolipid presented here provides some clues. Upon antigen binding, endogenous spacers of CD1b, which consist of a mixture of diradylglycerols, moved considerably within the lipid-binding groove. Spacer displacement was accompanied by F’ pocket closure and an extensive rearrangement of residues exposed to T-cell receptors. Such structural reorganization resulted in reduction of the A’ pocket capacity and led to incomplete embedding of the methyl-ramified portion of the phthioceranoyl chain of the antigen, explaining why such hydrophobic motifs are critical for T-cell receptor recognition. Mutagenesis experiments supported the functional importance of the observed structural alterations for T-cell stimulation. Overall, our data delineate a complex molecular mechanism combining spacer repositioning and ligand-induced conformational changes that, together with pocket intricacy, endows CD1b with the required molecular plasticity to present a broad range of structurally diverse antigens. PMID:22006319

  6. 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.

  7. 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

  8. The Structure and Properties of Iron in the Core

    NASA Astrophysics Data System (ADS)

    Price, G. D.; Vocadlo, L.; Alfe, D.; Wood, I. G.; Gillan, M. J.

    2002-12-01

    In his 1952 paper, Birch observed that the interior of the Earth is a problem at once fascinating and baffling. This is especially true of the Earth's inner core, and in the fifty years since Birch's work, many subsequent papers have been published with the aim of constraining its nature and composition. Birch concluded the inner core is most simply interpreted as crystalline iron, perhaps alloyed with a small fraction of lighter elements. This inference has stood the test of time, but the exact nature of the stable phase of iron in the Earth's solid inner core is still highly controversial. Recent research has indicated that the hexagonal-close-packed (hcp) phase of Fe exists at Earth's core conditions. This is supported by theoretical studies suggesting that the body-centred-cubic (bcc) phase is unlikely to be found in the core since it becomes unstable at high pressures. Yet in other hcp metals (e.g. Ti, Zr..) a high-pressure bcc form is stabilized at high temperatures. We recently reported the results of the first ab initio, finite-temperature, molecular dynamics free-energy calculations on the bcc phase of Fe at core conditions. We found that this phase becomes entropically stabilised at core temperatures, with a transition on cooling to a low temperature omega phase occurring at ~3000-4000K. Although we find that in all cases along the melting curve the free energy of the hcp phase is thermodynamically more favourable, the free energy difference between the two phases is very small. The inner core is not, however, pure Fe. Our calculations also show that if S and/or Si are the light elements in the core, then they may stabilize the bcc phase of Fe at the expense of the hcp form. This will have profound implications for the interpretation of the origin of the seismic anisotropy of the inner core. We will review our current understanding of the high P and T stabilities and elastic properties of Fe polymorphs and their alloys, and will conclude that after fifty

  9. Normal mode constraints on inner core structure: a trans­-dimensional Bayesian approach

    NASA Astrophysics Data System (ADS)

    Robson, A.; Romanowicz, B. A.

    2016-12-01

    Obtaining accurate constraints on the elastic structure of the inner core is key to gaining better understanding of it's composition and dynamics. While observations of body wave phases provide information on inner core P velocity and anisotropy structure, constraining shear velocity and density currently relies entirely on core-sensitive normal mode observations. The PREM model (Dziewonski and Anderson, 1981) relied on constraints from core-sensitive modes and is still widely used as a reference for Vs and density in the inner core. However, since then, the normal mode database has grown significantly and new applicable inversion methodologies have become feasible due to increases in computation power. Our goal is to build a probabilistic 1D model of core structure in Vp, Vs and density, taking advantage of an augmented mode center frequency catalog and advances in computational resources. We use the REM catalog of observed frequencies of core sensitive normal modes (http://igppweb.ucsd.edu/ gabi/rem.html), together with the dataset of Deuss (2008), augmented with data from more recent large and deep earthquakes. We also include constraints on the mass and moment of inertia of the Earth. We have implemented a Trans-dimensional Markov chain Monte Carlo method, exploring the model space more fully than ever before while minimizing a-priori inputs and allowing the data to exercise maximum control on the result. In this approach, the number of layers and the properties of each layer are allowed to vary freely to match observations. In a first step, we keep mantle and outer core structure fixed to that of PREM, and explore the space of acceptable models in Vs, Vp and rho in the inner core alone. In a second step, we will allow adjustments in lowermost outer core structure. Ultimately, we will add constraints from mantle modes to investigate trade­offs between mantle and core structure. Here we present preliminary results on structure in the inner core and its vicinity.

  10. 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.

  11. [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.

  12. 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.

  13. Structure of Hepatitis C Virus Envelope Glycoprotein E2 Antigenic Site 412 to 423 in Complex with Antibody AP33

    PubMed Central

    Kong, Leopold; Giang, Erick; Nieusma, Travis; Robbins, Justin B.; Deller, Marc C.; Stanfield, Robyn L.

    2012-01-01

    We have determined the crystal structure of the broadly neutralizing antibody (bnAb) AP33, bound to a peptide corresponding to hepatitis C virus (HCV) E2 envelope glycoprotein antigenic site 412 to 423. Comparison with bnAb HCV1 bound to the same epitope reveals a different angle of approach to the antigen by bnAb AP33 and slight variation in its β-hairpin conformation of the epitope. These structures establish two different modes of binding to E2 that antibodies adopt to neutralize diverse HCV. PMID:22973046

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

    PubMed Central

    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. WIREs RNA 2015, 6:157–171. doi: 10.1002/wrna.1262 PMID:25264139

  15. 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.

  16. Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen.

    PubMed

    Pallesen, Jesper; Wang, Nianshuang; Corbett, Kizzmekia S; Wrapp, Daniel; Kirchdoerfer, Robert N; Turner, Hannah L; Cottrell, Christopher A; Becker, Michelle M; Wang, Lingshu; Shi, Wei; Kong, Wing-Pui; Andres, Erica L; Kettenbach, Arminja N; Denison, Mark R; Chappell, James D; Graham, Barney S; Ward, Andrew B; McLellan, Jason S

    2017-08-29

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines.

  17. Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen

    PubMed Central

    Pallesen, Jesper; Wang, Nianshuang; Corbett, Kizzmekia S.; Wrapp, Daniel; Kirchdoerfer, Robert N.; Turner, Hannah L.; Cottrell, Christopher A.; Becker, Michelle M.; Wang, Lingshu; Shi, Wei; Kong, Wing-Pui; Andres, Erica L.; Kettenbach, Arminja N.; Denison, Mark R.; Chappell, James D.; Graham, Barney S.; Ward, Andrew B.

    2017-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines. PMID:28807998

  18. 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

  19. Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex.

    PubMed Central

    Padlan, E A; Silverton, E W; Sheriff, S; Cohen, G H; Smith-Gill, S J; Davies, D R

    1989-01-01

    The crystal structure of the complex of the anti-lysozyme HyHEL-10 Fab and hen egg white lysozyme has been determined to a nominal resolution of 3.0 A. The antigenic determinant (epitope) on the lysozyme is discontinuous, consisting of residues from four different regions of the linear sequence. It consists of the exposed residues of an alpha-helix together with surrounding amino acids. The epitope crosses the active-site cleft and includes a tryptophan located within this cleft. The combining site of the antibody is mostly flat with a protuberance made up of two tyrosines that penetrate the cleft. All six complementarity-determining regions of the Fab contribute at least one residue to the binding; one residue from the framework is also in contact with the lysozyme. The contacting residues on the antibody contain a disproportionate number of aromatic side chains. The antibody-antigen contact mainly involves hydrogen bonds and van der Waals interactions; there is one ion-pair interaction but it is weak. Images PMID:2762305

  20. Seismological evidence for mosaic structure of the surface of the Earth's inner core.

    PubMed

    Krasnoshchekov, Dmitry N; Kaazik, Peter B; Ovtchinnikov, Vladimir M

    2005-05-26

    The transition from the Earth's solid inner core to liquid outer core is the location where the inner core grows and from which compositional convection in the outer core originates. Most seismological models of the Earth describe the inner-core boundary as sharp and simple, although experimental data requiring the presence of a thin transition layer at the bottom of the outer core have been reported. The density jump at the inner-core boundary--an important parameter determining gravitational energy release and constraining the compositional difference between the inner and outer core-is also not well known. Estimates of this density jump obtained using free-oscillation eigenfrequencies give low values of 0.25-1.0 g cm(-3), whereas a method using the amplitude ratio of core-reflected phases yielded values of 0.6-1.8 g cm(-3) (refs 14, 15, 16-17). Here we analyse properties of waves precritically reflected from the Earth's inner core (PKiKP phases) that show significant variability in amplitude, consistent high-frequency content and stable travel times with respect to a standard Earth model. We infer that the data are best explained by a mosaic structure of the inner core's surface. Such a mosaic may be composed of patches in which the transition from solid inner to liquid outer core includes a thin partially liquid layer interspersed with patches containing a sharp transition.

  1. Secondary structure and 3D homology modeling of swine leukocyte antigen class 2 (SLA-2) molecules.

    PubMed

    Gao, Feng-Shan; Xu, Chong-bo; Long, Yi-hou; Xia, Chun

    2009-01-01

    No information to date is available to elucidate the structure of swine leukocyte antigen class I (SLA-I) molecule which is comprised by a heavy chain of SLA-I non-covalently associated with a light chain, beta(2)-microglobulin (beta(2)m) proteins. Presently, one of SLA-I gene SLA-2 and beta(2)m gene were expressed as soluble maltose binding proteins (MBP-proteins) in a pMAL-p2X/Escherichia coli TB1 system and identified by western blotting with anti-MBP polyclonal antibodies. The expressed proteins MBP-SLA-2 and MBP-beta(2)m were purified on amylose affinity columns followed by DEAE-Sepharose. The purified products were cleaved by Factor Xa, respectively, and the interest of proteins SLA-2 and beta(2)m were purified on amylose affinity columns followed by separation from MBP on DEAE-Sepharose. The secondary structures of SLA-2 and beta(2)m were analyzed by circular dichroism (CD) spectrophotometry. The three-dimensional (3D) structure of their peptide-binding domain (PBD) was modeled-based sequence homology. The content of the alpha-helix, beta-sheet, turn, and random coil in the SLA-2 protein were 76, 95, 36, and 67aa, respectively. In the 98aa of beta(2)m, the contents of the alpha-helix, beta-sheet, turn, and random coil were 0, 45, 8, and 45aa, respectively. The SLA-2 protein displayed a typical alpha-helix structure while beta(2)m protein displayed a typical beta-sheet structure. Homology modeling of the SLA-2 and beta(2)m proteins demonstrated similarities with the structure of human and mouse MHC (major histocompatibility complex) class I proteins.

  2. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Synthesis of polyacrylate core-shell structure latex by radiation techniques

    NASA Astrophysics Data System (ADS)

    Minghong, Wu; Weiping, Shen; Zueteh, Ma

    1993-07-01

    A series of poly(butyl acrylate-co-methyl methacrylate)/poly (ethyl acrylate-co-acrylic acid) interpenetrating polymer network (IPN) was synthesized in latex form by emulsion polymerization. The multiphase morphology of the latex particles was studied after two-stage polymerization by using transimission electron microscope (TEM), the result indicated that the morphology of the particles comprises gradient shell structure, cellular structure and core-shell structure. The change of morphology might stem from emulsion polymerization by radiation initiation or chemical initiation and the weight composition of poly(EA-co-MMA) seed latex which formed the core. By radiation techniques, we successfully synthesized poly( BA-co-MMA)/poly(EA-co-AA) latex of core-shell structure having (42-8)/(46-4) weight compositions. The PA core-shell structure latex applied to textile as a water proofing coating showed higher water-pressure and easier handling than that with PA homogeneous phase structure latex.

  9. Structural and Immunological Analysis of Anthrax Recombinant Protective Antigen Adsorbed to Aluminum Hydroxide Adjuvant

    PubMed Central

    Wagner, Leslie; Verma, Anita; Meade, Bruce D.; Reiter, Karine; Narum, David L.; Brady, Rebecca A.; Little, Stephen F.

    2012-01-01

    New anthrax vaccines currently under development are based on recombinant protective antigen (rPA) and formulated with aluminum adjuvant. Because long-term stability is a desired characteristic of these vaccines, an understanding of the effects of adsorption to aluminum adjuvants on the structure of rPA is important. Using both biophysical and immunological techniques, we compared the structure and immunogenicity of freshly prepared rPA-Alhydrogel formulations to that of formulations stored for 3 weeks at either room temperature or 37°C in order to assess the changes in rPA structure that might occur upon long-term storage on aluminum adjuvant. Intrinsic fluorescence emission spectra of tryptophan residues indicated that some tertiary structure alterations of rPA occurred during storage on Alhydrogel. Using anti-PA monoclonal antibodies to probe specific regions of the adsorbed rPA molecule, we found that two monoclonal antibodies that recognize epitopes located in domain 1 of PA exhibited greater reactivity to the stored formulations than to freshly prepared formulations. Immunogenicity of rPA-Alhydrogel formulations in mice was assessed by measuring the induction of toxin-neutralizing antibodies, as well as antibodies reactive to 12-mer peptides spanning the length of PA. Mice immunized with freshly prepared formulations developed significantly higher toxin-neutralizing antibody titers than mice immunized with the stored preparations. In contrast, sera from mice immunized with stored preparations exhibited increased reactivity to nine 12-mer peptides corresponding to sequences located throughout the rPA molecule. These results demonstrate that storage of rPA-Alhydrogel formulations can lead to structural alteration of the protein and loss of the ability to elicit toxin-neutralizing antibodies. PMID:22815152

  10. Measurement of hepatitis B virus core-related antigen is valuable for identifying patients who are at low risk of lamivudine resistance.

    PubMed

    Tanaka, Eiji; Matsumoto, Akihiro; Suzuki, Fumitaka; Kobayashi, Mariko; Mizokami, Masashi; Tanaka, Yasuhito; Okanoue, Takeshi; Minami, Masahito; Chayama, Kazuaki; Imamura, Michio; Yatsuhashi, Hiroshi; Nagaoka, Shinya; Yotsuyanagi, Hiroshi; Kawata, Sumio; Kimura, Tatsuji; Maki, Noboru; Iino, Shiro; Kiyosawa, Kendo

    2006-02-01

    The clinical usefulness of hepatitis B virus core-related antigen (HBVcrAg) assay was compared with that of HBV DNA assay in predicting the occurrence of lamivudine resistance in patients with chronic hepatitis B. Of a total of 81 patients who were treated with lamivudine, 25 (31%) developed lamivudine resistance during a median follow-up period of 19.3 months. The pretreatment positive rate of HBe antigen, or pretreatment levels of HBVcrAg or HBV DNA did not differ between patients with and without lamivudine resistance. Levels of both HBVcrAg and HBV DNA decreased after the initiation of lamivudine administration; however, the level of HBVcrAg decreased significantly more slowly than that of HBV DNA. The occurrence of lamivudine resistance was significantly less frequent in the 56 patients whose HBV DNA level was less than 2.6 log copy/ml at 6 months of treatment than in the remaining 25 patients. The cumulative rate of lamivudine resistance was as high as 70% within 2 years in the latter group, while it was only 28% in the former group. Lamivudine resistance did not occur during the follow-up period in the 19 patients whose HBVcrAg level was less than 4.6 log U/ml at 6 months of treatment, while it did occur in 50% of the remaining patients within 2 years. These results suggest that measurement of HBV DNA is valuable for identifying patients who are at high risk of developing lamivudine resistance, and that, conversely, measurement of HBVcrAg is valuable for identifying those who are at low risk of lamivudine resistance.

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

    PubMed

    Uchiyama, Ikuo

    2008-10-31

    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. 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. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

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

    PubMed

    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

    2014-12-02

    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.

  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. 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

  3. 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.

  4. Structure of hepatitis B surface antigen from subviral tubes determined by electron cryomicroscopy.

    PubMed

    Short, Judith M; Chen, Shaoxia; Roseman, Alan M; Butler, P Jonathan G; Crowther, R Anthony

    2009-07-03

    Hepatitis B virus consists of an icosahedral core containing the double-stranded DNA genome, enveloped by a membrane with embedded surface proteins. The crystal structure of the core protein has been solved but little information about the structure of the surface proteins has so far been available. There are three sizes of surface protein, small (S), medium (M) and large (L), which form disulfide-bonded homo- and heterodimers. The three proteins, expressed from different start sites in the coding sequence, share the common C-terminal S region; the M protein contains an additional preS2 sequence N-terminal to S, and the L protein a further preS1 sequence N-terminal to M. In infected individuals, the surface proteins are produced in huge excess over the amount needed for viral envelopment and are secreted as a heterogeneous mixture of isometric and tubular subviral particles. We have used electron cryomicroscopy to study tubular particles extracted from human serum. Helical Fourier-Bessel analysis was used to calculate a low-resolution map, although it showed that the tubes were quite disordered. From the symmetry derived from this analysis, we used single-particle methods to improve the resolution. We found that the tubes had a diameter of approximately 250 A, with spike-like features projecting from the membrane. In the plane of the membrane the proteins appear to be close packed. We propose a model for the packing arrangement of surface protein dimers in the tubes.

  5. 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.

  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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins.

    PubMed

    Leen, Eoin N; Kwok, K Y Rex; Birtley, James R; Simpson, Peter J; Subba-Reddy, Chennareddy V; Chaudhry, Yasmin; Sosnovtsev, Stanislav V; Green, Kim Y; Prater, Sean N; Tong, Michael; Young, Joanna C; Chung, Liliane M W; Marchant, Jan; Roberts, Lisa O; Kao, C Cheng; Matthews, Stephen; Goodfellow, Ian G; Curry, Stephen

    2013-05-01

    We report the solution structures of the VPg proteins from feline calicivirus (FCV) and murine norovirus (MNV), which have been determined by nuclear magnetic resonance spectroscopy. In both cases, the core of the protein adopts a compact helical structure flanked by flexible N and C termini. Remarkably, while the core of FCV VPg contains a well-defined three-helix bundle, the MNV VPg core has just the first two of these secondary structure elements. In both cases, the VPg cores are stabilized by networks of hydrophobic and salt bridge interactions. The Tyr residue in VPg that is nucleotidylated by the viral NS7 polymerase (Y24 in FCV, Y26 in MNV) occurs in a conserved position within the first helix of the core. Intriguingly, given its structure, VPg would appear to be unable to bind to the viral polymerase so as to place this Tyr in the active site without a major conformation change to VPg or the polymerase. However, mutations that destabilized the VPg core either had no effect on or reduced both the ability of the protein to be nucleotidylated and virus infectivity and did not reveal a clear structure-activity relationship. The precise role of the calicivirus VPg core in virus replication remains to be determined, but knowledge of its structure will facilitate future investigations.

  8. Core-Shell-structured Dendritic Mesoporous Silica Nanoparticles for Combined Photodynamic Therapy and Antibody Delivery.

    PubMed

    Abbaraju, Prasanna Lakshmi; Yang, Yannan; Yu, Meihua; Fu, Jianye; Xu, Chun; Yu, Chengzhong

    2017-07-04

    Multifunctional core-shell-structured dendritic mesoporous silica nanoparticles with a fullerene-doped silica core, a dendritic silica shell and large pores have been prepared. The combination of photodynamic therapy and antibody therapeutics significantly inhibits the cancer cell growth by effectively reducing the level of anti-apoptotic proteins. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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…

  10. Acetylation (O-factor 5) affects the structural and immunological properties of Salmonella typhimurium lipopolysaccharide O antigen.

    PubMed Central

    Slauch, J M; Mahan, M J; Michetti, P; Neutra, M R; Mekalanos, J J

    1995-01-01

    The lipopolysaccharide (LPS) of gram-negative bacteria serves as a barrier between the cell and its environment. The LPS O antigen is the immunodominant portion of the molecule and thus has a significant effect on the interaction between a bacterial pathogen and the host organism. Antibodies directed against O antigen are vital to the immune response to infection. In this study, we have characterized the interaction between a series of monoclonal immunoglobulin A antibodies and the LPS of Salmonella typhimurium. Using one of these antibodies, we have previously shown that monoclonal immunoglobulin A is sufficient to protect against S. typhimurium infection, both in vivo and in vitro. Here, we show that recognition of LPS by the monoclonal antibodies is affected by acetylation of the O antigen on the abequose moiety, the determinant of the O5 epitope. Although recognition of LPS by several of the monoclonal antibodies is completely dependent on acetylation, the antibodies recognize clearly separable epitopes. This suggests that acetylation of O antigen affects the three-dimensional structure of the molecule and thus creates and destroys a series of conformational antigenic determinants. We have shown that a change in the acetylation state of LPS has no effect on virulence. However, acetylation has important consequences for the mucosal immune response and thus could potentially have profound implications for the ability of an immune host to respond to a subsequent infection. PMID:7529745

  11. Constraints on Inner Core structure from P'P' array-based observations

    NASA Astrophysics Data System (ADS)

    Frost, D. A.; Romanowicz, B. A.

    2016-12-01

    Seismic analysis of the inner core has revealed complicated physical properties. Seismic wavespeeds are observed to be anisotropic, with the fast axis oriented roughly parallel to the rotation axis. Further analysis reveals hemispherical and radial variations in seismic velocity anisotropy. Most previous studies of inner core structure have employed the wave PKIKP that samples the inner core, and referenced measurements to PKP "branches" which sample only the outer core. However, high-resolution study of the inner core with body waves is significantly limited by the paucity of appropriate "polar" ray paths that sample the inner core along the fast axis of the anisotropy. Consequently, there is disagreement over the magnitude of the anisotropy, its spatial variation, and the influence of mantle structure on inner core observations that requires further data to assess. We present analysis of the PKIKPPKIKP wave, also written P'P', and its branches observed at small aperture, high-latitude seismic arrays. The wave travels through the core and up to the surface as a PKIKP wave, and then reflects from the underside of the surface, back onto a second PKIKP path, thus twice samples inner core structure. We analyse paths through the core inaccessible to those used in PKP studies. We use arrays to amplify this strongly attenuated phase relative to the noise level and distinguish it from contaminating waves. A previous study based on a limited amount of data had shown much smaller P'P' travel time anomalies on polar paths than expected from previously derived models. We expand on past P'P' studies with over 100 observations from two new seismic arrays sampling many new polar paths that are complementary to those sampled in previous PKP studies in an attempt to further constrain the strength of inner-core anisotropy. Here, we also evaluate possible contamination of P'P' travel times by 3D mantle structure based on available models

  12. Independent Effects of Protein Core Size and Expression on Residue-Level Structure-Evolution Relationships

    PubMed Central

    Franzosa, Eric A.; Xia, Yu

    2012-01-01

    Recently, we demonstrated that yeast protein evolutionary rate at the level of individual amino acid residues scales linearly with degree of solvent accessibility. This residue-level structure-evolution relationship is sensitive to protein core size: surface residues from large-core proteins evolve much faster than those from small-core proteins, while buried residues are equally constrained independent of protein core size. In this work, we investigate the joint effects of protein core size and expression on the residue-level structure-evolution relationship. At the whole-protein level, protein expression is a much more dominant determinant of protein evolutionary rate than protein core size. In contrast, at the residue level, protein core size and expression both have major impacts on protein structure-evolution relationships. In addition, protein core size and expression influence residue-level structure-evolution relationships in qualitatively different ways. Protein core size preferentially affects the non-synonymous substitution rates of surface residues compared to buried residues, and has little influence on synonymous substitution rates. In comparison, protein expression uniformly affects all residues independent of degree of solvent accessibility, and affects both non-synonymous and synonymous substitution rates. Protein core size and expression exert largely independent effects on protein evolution at the residue level, and can combine to produce dramatic changes in the slope of the linear relationship between residue evolutionary rate and solvent accessibility. Our residue-level findings demonstrate that protein core size and expression are both important, yet qualitatively different, determinants of protein evolution. These results underscore the complementary nature of residue-level and whole-protein analysis of protein evolution. PMID:23056364

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  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. 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.

  20. 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.

  1. [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.

  2. 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.

  3. 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.

  4. HCV core-antigen assay as an alternative to HCV RNA quantification: A correlation study for the assessment of HCV viremia.

    PubMed

    Alonso, Roberto; Pérez-García, Felipe; López-Roa, Paula; Alcalá, Luis; Rodeño, Pilar; Bouza, Emilio

    2017-02-25

    Detection of hepatitis C virus (HCV) RNA and the HCV core antigen assay (HCV-Ag) are reliable techniques for the diagnosis of active and chronic HCV infection. Our aim was to evaluate the HCV-Ag assay as an alternative to quantification of HVC RNA. A comparison was made of the sensitivity and specificity of an HCV-Ag assay (204 serum samples) with those of a PCR assay, and the correlation between the two techniques was determined. The sensitivity and specificity of HCV-Ag was 76.6% and 100%, respectively. Both assays were extremely well correlated (Pearson coefficient=0.951). The formula (LogCV=1.15*LogAg+2.26) was obtained to calculate the viral load by PCR from HCV-Ag values. HCV-Ag was unable to detect viral loads below 5000IU/mL. Although the HCV-Ag assay was less sensitive than the PCR assay, the correlation between both assays was excellent. HCV-Ag can be useful as a first step in the diagnosis of acute or chronic HCV infection and in emergency situations. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  5. 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

  6. 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.

  7. Seroprevalence of antibodies specific for gram-negative core antigens in chickens on the basis of an Escherichia coli J5 enzyme-linked immunosorbent assay.

    PubMed

    Ruble, Randall P; Wakenell, Patricia S; Cullor, James S

    2002-01-01

    Antibodies directed toward gram-negative core antigens (GNCAs) have been demonstrated in many mammalian species but to date are unexamined in any avian species. An enzyme-linked immunosorbent assay with phenol-killed whole cell Escherichia coli J5 was used to assess the presence of serum antibodies directed toward GNCAs in chickens. The first experiment consisted of collecting blood samples from randomly selected hens at egg laying ranches in northern California. The ages ranged from several days of age to 77 wk of age. Birds were classified into age groups (hatchling [1 day-4 wk], pullet [4-18 wk], pullet cycle [18-60 wk], and postmolt [>60 wk]) and husbandry style for titer comparison. The geometric mean titer (GMT) for all adult hens regardless of age was 2147. The geometric mean titers were 220, 5691, 2304, and 1776 for hatchlings, pullets, pullet cycle hens, and postmolt hens, respectively. The age group titer trends were similar to those of humans rather than those of farm animals in that the highest titers occurred during "adolescence" (pullets) and titers decreased slightly with maturity. The GMTs were 2870 for hens housed intensively and 1872 for those housed extensively. The second experiment looked at the progression of GNCA titers within individual birds over a 1-yr period. Individual titers increased slightly throughout the study time of the second experiment.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. The influence of glycosylation on the antigenicity, allergenicity, and structural properties of 11S-lactose conjugates.

    PubMed

    Bu, Guanhao; Zhang, Nan; Chen, Fusheng

    2015-10-01

    Soybean is nutritious and is an excellent source of high-quality protein for human food and animal feed. However, glycinin (11S) is considered as the major allergenic protein that causes soybean allergies. Glycosylation is widely used to remove food protein allergens. In this study, soybean 11S was isolated and used in a glycation reaction with lactose at a weight ratio of 4:1 at 55°C and 79% relative humidity for different periods of time. The effects of glycosylation on the antigenicity and residual allergenicity of 11S were investigated, using the specific IgG polyclonal antibodies for glycinin and soy-allergic patient sera by indirect competitive, enzyme-linked immunosorbent assay (indirect competitive ELISA). Meanwhile, the degree of glycation was determined by the trinitrobenzene sulfonic acid (TNBS) method. The structural properties of 11S-lactose conjugates were characterized by SDS-PAGE, Fourier transform infrared spectrum (FTIR), and ultraviolet spectroscopy. Glycosylation effectively decreased the antigenicity and allergenicity of 11S if we increased the reaction time. The antigenicity of 11S after glycosylation was reduced by approximately 30% compared with raw 11S, while allergenicity of 11S was reduced by 9%. The changes in secondary structures of glycated 11S may have influenced the allergic epitopes of protein. Therefore, we suggest that introducing lactose in 11S is an effective method to remove the antigenicity and allergenicity of glycinin. Copyright © 2015. Published by Elsevier Ltd.

  14. 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.

  15. Core-Shell Structured Electro- and Magneto-Responsive Materials: Fabrication and Characteristics

    PubMed Central

    Choi, Hyoung Jin; Zhang, Wen Ling; Kim, Sehyun; Seo, Yongsok

    2014-01-01

    Core-shell structured electrorheological (ER) and magnetorheological (MR) particles have attracted increasing interest owing to their outstanding field-responsive properties, including morphology, chemical and dispersion stability, and rheological characteristics of shear stress and yield stress. This study covers recent progress in the preparation of core-shell structured materials as well as their critical characteristics and advantages. Broad emphasises from the synthetic strategy of various core-shell particles to their feature behaviours in the magnetic and electric fields have been elaborated. PMID:28788258

  16. Cascading failures of interdependent networks with different k-core structures

    NASA Astrophysics Data System (ADS)

    Dong, Zhengcheng; Fang, Yanjun; Tian, Meng

    2017-04-01

    As one of the most common mesoscale structures in real-life networks, k-core hierarchical structure has attracted a lot of attention. Recent research about k-core always focuses on detecting influential nodes determining failure or epidemic propagation. However, few studies have attempted to understand how k-core structural properties can affect dynamic characteristics of network. In this paper, the influences of depth and coupling preferences of k-core on the cascading failures of interdependent scale-free networks are investigated. First, k-core structures of some real-life networks are analyzed, and a scale-free network evolution model with rich and successive k-core layers is proposed. Then, based on a load-based cascading model, the influence of the depth of k-core is investigated with a new evaluation index. In the end, two coupling preferences are analyzed, i.e. random coupling (RC) and assortative coupling (AC). Results show that the lower the depth is, the more robust the interdependent networks will be, and we find AC and RC perform dissimilarly when the capacity varies. Furthermore, all the effects will be affected by the initial load.

  17. Solution Structure and Characterisation of the Human Pyruvate Dehydrogenase Complex Core Assembly

    PubMed Central

    Vijayakrishnan, S.; Kelly, S.M.; Gilbert, R.J.C.; Callow, P.; Bhella, D.; Forsyth, T.; Lindsay, J.G.; Byron, O.

    2010-01-01

    Mammalian pyruvate dehydrogenase complex (PDC) is a key multi-enzyme assembly that is responsible for glucose homeostasis maintenance and conversion of pyruvate into acetyl-CoA. It comprises a central pentagonal dodecahedral core consisting of two subunit types (E2 and E3BP) to which peripheral enzymes (E1 and E3) bind tightly but non-covalently. Currently, there are two conflicting models of PDC (E2 + E3BP) core organisation: the ‘addition’ model (60 + 12) and the ‘substitution’ model (48 + 12). Here we present the first ever low-resolution structures of human recombinant full-length PDC core (rE2/E3BP), truncated PDC core (tE2/E3BP) and native bovine heart PDC core (bE2/E3BP) obtained by small-angle X-ray scattering and small-angle neutron scattering. These structures, corroborated by negative-stain and cryo electron microscopy data, clearly reveal open pentagonal core faces, favouring the ‘substitution’ model of core organisation. The native and recombinant core structures are all similar to the truncated bacterial E2 core crystal structure obtained previously. Cryo-electron microscopy reconstructions of rE2/E3BP and rE2/E3BP:E3 directly confirm that the core has open pentagonal faces, agree with scattering-derived models and show density extending outwards from their surfaces, which is much more structurally ordered in the presence of E3. Additionally, analytical ultracentrifugation characterisation of rE2/E3BP, rE2 (full-length recombinant E2-only) and tE2/E3BP supports the substitution model. Superimposition of the small-angle neutron scattering tE2/E3BP and truncated bacterial E2 crystal structures demonstrates conservation of the overall pentagonal dodecahedral morphology, despite evolutionary diversity. In addition, unfolding studies using circular dichroism and tryptophan fluorescence spectroscopy show that the rE2/E3BP is less stable than its rE2 counterpart, indicative of a role for E3BP in core destabilisation. The architectural

  18. Measurement and Analysis of Structural Integrity of Reactor Core Support Structure in Pressurized Water Reactor (PWR) Plant

    NASA Astrophysics Data System (ADS)

    Ansari, Saleem A.; Haroon, Muhammad; Rashid, Atif; Kazmi, Zafar

    2017-02-01

    Extensive calculation and measurements of flow-induced vibrations (FIV) of reactor internals were made in a PWR plant to assess the structural integrity of reactor core support structure against coolant flow. The work was done to meet the requirements of the Fukushima Response Action Plan (FRAP) for enhancement of reactor safety, and the regulatory guide RG-1.20. For the core surveillance measurements the Reactor Internals Vibration Monitoring System (IVMS) has been developed based on detailed neutron noise analysis of the flux signals from the four ex-core neutron detectors. The natural frequencies, displacement and mode shapes of the reactor core barrel (CB) motion were determined with the help of IVMS. The random pressure fluctuations in reactor coolant flow due to turbulence force have been identified as the predominant cause of beam-mode deflection of CB. The dynamic FIV calculations were also made to supplement the core surveillance measurements. The calculational package employed the computational fluid dynamics, mode shape analysis, calculation of power spectral densities of flow & pressure fields and the structural response to random flow excitation forces. The dynamic loads and stiffness of the Hold-Down Spring that keeps the core structure in position against upward coolant thrust were also determined by noise measurements. Also, the boron concentration in primary coolant at any time of the core cycle has been determined with the IVMS.

  19. Predictive Value of Hepatitis B Core-Related Antigen (HBcrAg) During the Natural History of Hepatitis B Virus Infection.

    PubMed

    Gou, Yu; Zhao, Yanhua; Rao, Chenli; Feng, Shu; Wang, Tingting; Li, Dongdong; Tao, Chuanmin

    2017-07-01

    The natural history of HBV infection includes immune tolerance (IT), immune clearance (IC), HBeAg-negative inactive/quiescent carrier (ENQ), and HBeAg-negative hepatitis (ENH) phases. As the current biomarkers for discriminating the four phases still have some weaknesses, additional serological indicators are needed. Hepatitis B core-related antigen (HBcrAg) encoded with the precore/core gene contains denatured HBeAg, HBV core antigen (HBcAg), and a 22-KDa precore protein (p22cr) and has been demonstrated to have a close association with the natural history of hepatitis B infection. However, no specific cutoff values and diagnostic parameters have been identified to evaluate the diagnostic efficacy. This study aimed to clarify the distribution of HBcrAg levels and evaluate the diagnostic performance during the natural history of HBV infection in a Western Chinese population. In this study, 294 samples were collected from treatment-naive HBV infection patients in different phases (IT = 64; IC = 72; ENQ = 100, and ENH = 58). We detected the HBcrAg values and analyzed the relationship between HBcrAg and HBV DNA. HBsAg and other clinical parameters were quantitatively detected. The HBcrAg levels of IT, IC, ENQ, and ENH were 9.30 log U/mL, 8.80 log U/mL, 3.00 log U/mL, and 5.10 log U/mL, respectively (p < 0.0001). Receiver operating characteristic curve analysis demonstrated that the areas under the curves (AUCs) for HBcrAg and quantitative HBsAg at cutoff values of 9.25 log U/mL and 4.355 log IU/mL for distinguishing the IT phase from the IC phase were 0.704 and 0.694, with a sensitivity of 53.13% and 79.69% and specificity of 76.39% and 59.72%, respectively. AUCs of HBcrAg and quantitative HBsAg at cutoff values of 4.15 log U/mL and 2.395 log IU/mL for discriminating between the ENQ and ENH phases were 0.931 and 0.653, with a sensitivity of 87.93% and 91.38% and specificity of 84.00% and 39.00%, respectively. HBcrAg levels varied significantly among the four natural

  20. Core American values and the structure of antigay prejudice.

    PubMed

    Callahan, Matthew Paolucci; Vescio, Theresa K

    2011-01-01

    This work presents a new scale to measure conflicting attitudes toward sexual minorities. This scale parallels existing measures of conflicting racial attitudes (anti-Black and pro-Black attitudes; Katz & Hass, 1988). After constructing and validating measures of antigay and progay attitudes, we tested relationships among core American values with racial and sexual minority attitudes. We examined relations among the Protestant Work Ethic (PWE), Traditional Family Ideology (TFI), and egalitarian values with attitudes toward racial outgroups and sexual minorities. The results revealed that both PWE values and egalitarian values predicted anti-Black attitudes. By contrast, endorsement of egalitarian values, but not PWE values, predicted pro-Black attitudes. Results also revealed a similar but distinct pattern among values and heterosexuals' attitudes toward sexual minorities. TFI, but not egalitarian value endorsement, predicted antigay attitudes, whereas both TFI and egalitarian value endorsement predicted progay attitudes. The implications of these findings are discussed.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Research advances in polymer emulsion based on "core-shell" structure particle design.

    PubMed

    Ma, Jian-zhong; Liu, Yi-hong; Bao, Yan; Liu, Jun-li; Zhang, Jing

    2013-09-01

    In recent years, quite many studies on polymer emulsions with unique core-shell structure have emerged at the frontier between material chemistry and many other fields because of their singular morphology, properties and wide range of potential applications. Organic substance as a coating material onto either inorganic or organic internal core materials promises an unparalleled opportunity for enhancement of final functions through rational designs. This contribution provides a brief overview of recent progress in the synthesis, characterization, and applications of both inorganic-organic and organic-organic polymer emulsions with core-shell structure. In addition, future research trends in polymer composites with core-shell structure are also discussed in this review. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. A study of the structural efficiency of fluted core graphite-epoxy panels

    NASA Technical Reports Server (NTRS)

    Jegley, Dawn C.

    1990-01-01

    The structural efficiency of compression-loaded graphite-epoxy sandwich panels with fluted cores is studied to determine their weight saving potential. Graphite-epoxy equilateral triangular elements are used to construct the fluted cores for the sandwich panels. Two panel configurations are considered. One configuration has two layers of triangular elements in the fluted core and the second configuration has only one layer of triangular elements in the core. An optimization code is used to find the minimum weight design for each panel configuration. Laminate ply orientations are limited to approx. 45, 0, and 90 deg. A constraint on the axial stiffness is included in the design process so the panel will conform to typical constraints for aircraft wing structures. Minimum thickness requirements for each laminate and maximum allowable strains are also included. A comparison is made of the calculated structural efficiency of the fluted core panels to the structural efficiency of aluminum transport aircraft structures and simple blade-stiffened graphite-epoxy panels. Limited experimental results are also included for comparison with the analytical predictions and to identify the critical failure mechanisms of graphite-epoxy fluted-core sandwich panels.

  7. Anti-hepatits B core antigen testing, viral markers, and occult hepatitis B virus infection in Pakistani blood donors: implications for transfusion practice.

    PubMed

    Bhatti, Farhat Abbas; Ullah, Zia; Salamat, Nuzhat; Ayub, Muhammad; Ghani, Ejaz

    2007-01-01

    The purpose of this study was to determine the seroprevalence of anti-hepatitis B core antigen (HBc) and the impact of its testing along with other markers of hepatitis B, hepatitis B virus (HBV) DNA, hepatitis C virus antibody (anti-HCV), and syphilis in Pakistani blood donors. The study design was cross-sectional. A total of 966 donors were selected randomly for testing of anti-HBc and HBV markers, including HBV DNA, of 94,177 blood donors who were routinely screened for hepatitis B surface antigen (HBsAg), anti-HCV, human immunodeficiency virus antibody (anti-HIV), Treponema pallidum hemagglutination assay (TPHA), and malarial parasites from 2003 to October 2005. The seroprevalence of various infectious markers was as follows: HBsAg, 2.16 percent; anti-HCV, 4.16 percent; anti-HIV, 0.004 percent; TPHA, 0.75 percent; and malaria, 0.002 percent. Anti-HBc prevalence in HBsAg-negative, HBV DNA-negative blood donors was 167 of 966 (17.28%), with 76 percent demonstrating anti-HBs positivity. Younger donors with mean age of 25 years were exposed to HBV to a lesser extent compared to those with a mean age of 29 years. Anti-HBc positivity was significantly higher in anti-HCV-reactive individuals. HBV DNA was detectable in 5 blood donors who were HBsAg-, anti-HBc-positive and were categorized as having occult HBV infection. The study shows that more than 17 percent of healthy, young blood donors in Pakistan are already exposed to HBV, with two-thirds showing anti-HBs levels of greater than 100 mIU per mL. One in 200 blood donors who are HBsAg-, anti-HBc-positive, however, have occult HBV infection, with likelihood of transmission of hepatitis B in recipients of blood components derived from them. HBsAg-negative individuals who are anti-HBc-negative and those who are anti-HBc-positive, anti-HBs-positive, and HBV DNA-negative should be selected as regular blood donors to minimize transmission due to occult hepatitis B infection.

  8. 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.

  9. 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

  10. 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.

  11. Amygdala structure and core dimensions of the affective personality.

    PubMed

    Frühholz, Sascha; Schlegel, Katja; Grandjean, Didier

    2017-05-16

    While biological models of human personality propose that socio-affective traits and skills are rooted in the structure of the amygdala, empirical evidence remains sparse and inconsistent. Here, we used a comprehensive assessment of the affective personality and tested its association with global, local, and laterality measures of the amygdala structure. Results revealed three broad dimensions of the affective personality that were differentially related to bilateral amygdala structures. Dysfunctional and maladaptive affective traits were associated with a global size and local volume reduction of the amygdala, whereas adaptive emotional skills were linked to an increased size of the left amygdala. Furthermore, reduced asymmetry in the bilateral global amygdala volume was linked to higher affective instability and might be a potential precursor of psychiatric disorders. This study demonstrates that structural amygdala measures provide a neural basis for all major dimensions of the human personality related to adaptive and maladaptive socio-affective functioning.

  12. The Warm Core Structure of Hurricane Earl (2010): Observations and Simulations

    NASA Astrophysics Data System (ADS)

    Stern, Daniel; Zhang, Fuqing

    2014-05-01

    In a series of recent studies, we have examined the warm core structure of tropical cyclones in the context of idealized numerical simulations. In those studies, we found that the maximum in perturbation temperature was consistently at mid-levels (4-8 km height), in contrast to the conventional wisdom that the warm core is a maximum at upper-levels. We argued that due to the scarcity of observations, the "true" characteristic warm core structure of tropical cyclones remains unknown. In this study, we aim to further our understanding of the thermal structure of the eye, using a combination of observations and numerical simulations for Hurricane Earl (2010). We use dropsondes released at 11-12 km height by the NASA DC-8 aircraft into the inner-core of Hurricane Earl to determine the temperature profile in and near the eye. In order to calculate the perturbation temperature, we composite NOAA-GIV sondes that were dropped in the environment (> 200 km from the storm center) of Earl, and subtract this environmental profile from the inner-core sondes. As Earl was sampled by the DC-8 on four different days, we are able to characterize the warm core structure during different parts of the TC lifecycle. We further investigate the warm core structure of Hurricane Earl with 3-km WRF simulations produced using the 2013 version of the PSU EnKF system. Both the inner-core and environmental temperature structures are compared between the analyses/forecasts and the dropsonde observations.

  13. 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.

  14. Polymeric Structure and Host Toll-like Receptor 4 Dictate Immunogenicity of NY-ESO-1 Antigen in Vivo*

    PubMed Central

    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

    2011-01-01

    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. PMID:21900253

  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. [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.

  17. 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

  18. Effects of pressure on maghemite nanoparticles with a core/shell structure

    NASA Astrophysics Data System (ADS)

    Komorida, Y.; Mito, M.; Deguchi, H.; Takagi, S.; Tajiri, T.; Millán, A.; Silva, N. J. O.; Laguna, M. A.; Palacio, F.

    2010-08-01

    The magnetic property and intraparticle structure of the γ phase of Fe 2O 3 (maghemite) nanoparticles with a diameter ( D) of 5.1±0.5 nm were investigated through AC and DC magnetic measurements and powder X-ray diffraction (XRD) measurements at pressures ( P) up to 27.7 kbar. Maghemite originally exhibits ferrimagnetic ordering below 918 K, and has an inverse-spinel structure with vacancies. Maghemite nanoparticles studied here consist of a core with structural periodicity and a disordered shell without the periodicity, and core shows superparamagnetism. The DC and AC susceptibilities reveal that the anisotropy energy barrier (Δ E/ kB) and the effective value of the core moment decrease against the initial pressure ( P≤3.8 kbar), recovering at P≥3.8 kbar. The change of Δ E/ kB with P is qualitatively identical with that of the core moment, suggesting a down-and-up fluctuation of the number of Fe 3+ ions constituting the core at the pressure threshold of about 4 kbar. This phenomenon was confirmed by the analysis of the XRD measurement using Scherrer's formula. The core volume decreased for P≤2.5 kbar, whereas at higher pressure the core was restructured. For 2.5≤ P≤10.7 kbar, the volume shrinkage of particle hardly occurs. There, Δ E/ kB is approximately proportional to the volume associated to the ordered fraction of the nanoparticles as seen from XRD, Vcore. From this dependence it is possible to separate the core/shell contribution to Δ E/ kB and estimate core and surface anisotropy constants. As for the structural experiments, similar experimental data have been obtained for D=12.8±3.2 nm as well.

  19. Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site.

    PubMed

    Julien, Jean-Philippe; Bryson, Steve; Nieva, Jose L; Pai, Emil F

    2008-12-12

    2F5 is a monoclonal antibody with potent and broadly neutralizing activity against HIV-1. It targets the membrane-proximal external region (MPER) of the gp41 subunit of the envelope glycoprotein and interferes with the process of fusion between viral and host cell membranes. This study presents eight 2F5 F(ab)' crystal structures in complex with various gp41 peptide epitopes. These structures reveal several key features of this antibody-antigen interaction. (1) Whenever free of contacts caused by crystal artifacts, the extended complementarity-determining region H3 loop is mobile; this is true for ligand-free and epitope-bound forms. (2) The interaction between the antibody and the gp41 ELDKWA epitope core is absolutely critical, and there are also close and specific contacts with residues located N-terminal to the epitope core. (3) Residues located at the C-terminus of the gp41 ELDKWA core do not interact as tightly with the antibody. However, in the presence of a larger peptide containing the gp41 fusion peptide segment, these residues adopt a conformation consistent with the start of an alpha-helix. (4) At high sulfate concentrations, the electron density maps of 2F5 F(ab)'-peptide complexes contain a peak that may mark a binding site for phosphate groups of negatively charged lipid headgroups. The refined atomic-level details of 2F5 paratope-epitope interactions revealed here should contribute to a better understanding of the mechanism of 2F5-based virus neutralization, in general, and prove important for the design of potential vaccine candidates intended to elicit 2F5-like antibody production.

  20. 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.

  1. 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.

  2. Periodic mesoporous organosilica (PMO) materials with uniform spherical core-shell structure.

    PubMed

    Haffer, Stefanie; Tiemann, Michael; Fröba, Michael

    2010-09-10

    We report the synthesis of monodisperse, spherical periodic mesoporous organosilica (PMO) materials. The particles have diameters between about 350 and 550 nm. They exhibit a regular core-shell structure with a solid, non-porous silica core and a mesoporous PMO shell with a thickness of approximately 75 nm and uniform pores of about 1.7 nm. The synthesis of the core and the shell is carried out in a one-pot, two-stage synthesis and can be accomplished at temperatures between 25 and 100 °C. Higher synthesis temperatures lead to substantial shrinking of the solid core, generating an empty void between core and shell. This leads to interesting cavitation phenomena in the nitrogen physisorption analysis at 77.4 K.

  3. 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.

  4. Coupled rows of PBS cores and PSII dimers in cyanobacteria: symmetry and structure.

    PubMed

    Zlenko, Dmitry V; Galochkina, Tatiana V; Krasilnikov, Pavel M; Stadnichuk, Igor N

    2017-09-01

    Phycobilisome (PBS) is a giant water-soluble photosynthetic antenna transferring the energy of absorbed light mainly to the photosystem II (PSII) in cyanobacteria. Under the low light conditions, PBSs and PSII dimers form coupled rows where each PBS is attached to the cytoplasmic surface of PSII dimer, and PBSs come into contact with their face surfaces (state 1). The model structure of the PBS core that we have developed earlier by comparison and combination of different fine allophycocyanin crystals, as reported in Zlenko et al. (Photosynth Res 130(1):347-356, 2016b), provides a natural way of the PBS core face-to-face stacking. According to our model, the structure of the protein-protein contact between the neighboring PBS cores in the rows is the same as the contact between the APC hexamers inside the PBS core. As a result, the rates of energy transfer between the cores can occur, and the row of PBS cores acts as an integral PBS "supercore" providing energy transfer between the individual PBS cores. The PBS cores row pitch in our elaborated model (12.4 nm) is very close to the PSII dimers row pitch obtained by the electron microscopy (12.2 nm) that allowed to unite a model of the PBS cores row with a model of the PSII dimers row. Analyzing the resulting model, we have determined the most probable locations of ApcD and ApcE terminal emitter subunits inside the bottom PBS core cylinders and also revealed the chlorophyll molecules of PSII gathering energy from the PBS.

  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. SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

    PubMed Central

    Sircar, Aroop; Gray, Jeffrey J.

    2010-01-01

    High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering. When a crystallographic structure of a complex is unavailable, the structure must be predicted using computational tools. In this work, we illustrate a novel approach, named SnugDock, to predict high-resolution antibody-antigen complex structures by simultaneously structurally optimizing the antibody-antigen rigid-body positions, the relative orientation of the antibody light and heavy chains, and the conformations of the six complementarity determining region loops. This approach is especially useful when the crystal structure of the antibody is not available, requiring allowances for inaccuracies in an antibody homology model which would otherwise frustrate rigid-backbone docking predictions. Local docking using SnugDock with the lowest-energy RosettaAntibody homology model produced more accurate predictions than standard rigid-body docking. SnugDock can be combined with ensemble docking to mimic conformer selection and induced fit resulting in increased sampling of diverse antibody conformations. The combined algorithm produced four medium (Critical Assessment of PRediction of Interactions-CAPRI rating) and seven acceptable lowest-interface-energy predictions in a test set of fifteen complexes. Structural analysis shows that diverse paratope conformations are sampled, but docked paratope backbones are not necessarily closer to the crystal structure conformations than the starting homology models. The accuracy of SnugDock predictions suggests a new genre of general docking algorithms with flexible binding interfaces targeted towards making homology models useful for further high-resolution predictions. PMID:20098500

  7. 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.

  8. 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

  9. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Coarse graining of NN inelastic interactions up to 3 GeV: Repulsive versus structural core

    NASA Astrophysics Data System (ADS)

    Fernández-Soler, P.; Ruiz Arriola, E.

    2017-07-01

    The repulsive short-distance core is one of the main paradigms of nuclear physics which even seems confirmed by QCD lattice calculations. On the other hand nuclear potentials at short distances are motivated by high energy behavior where inelasticities play an important role. We analyze NN interactions up to 3 GeV in terms of simple coarse grained complex and energy dependent interactions. We discuss two possible and conflicting scenarios which share the common feature of a vanishing wave function at the core location in the particular case of S waves. We find that the optical potential with a repulsive core exhibits a strong energy dependence whereas the optical potential with the structural core is characterized by a rather adiabatic energy dependence which allows one to treat inelasticity perturbatively. We discuss the possible implications for nuclear structure calculations of both alternatives.

  11. 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.

  12. Vortex-core structure in a mixture of Bose and Fermi superfluids

    NASA Astrophysics Data System (ADS)

    Pan, Jian-Song; Zhang, Wei; Yi, Wei; Guo, Guang-Can

    2017-06-01

    We study a single quantized vortex in the fermionic component of a mixture of Fermi superfluid and Bose-Einstein condensate. As the density ratio between the boson and the fermion components is tuned, we identify a transition in the vortex-core structure, across which fermions in the vortex core become completely depleted even in the weak-coupling Bardeen-Cooper-Schrieffer regime. This is accompanied by changes in key properties of the vortex state, as well as by the localization of the Bose-Einstein condensate in the vortex core. The transition in the vortex-core structure can be experimentally probed in Bose-Fermi superfluid mixtures by detecting the size and visibility of the vortices.

  13. 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.

  14. Simple structural unit model for core-dependent properties of symmetrical tilt boundaries

    SciTech Connect

    Balluffi, R.W.; Brokman, A.

    1983-08-01

    Any physical property, p, of a grain boundary, which depends primarily on the atomic structure of the core, e.g., boundary diffusivity or core energy. The purpose of the present note is to demonstrate that the recently determined structural unit model for the core structure allows one to estimate p for any boundary in a series of symmetrical tilt boundaries possessing a range of tilt angles if values of p for a few particular boundaries in the series are known. More specifically, that p for all boundaries with misorientations between those of two so-called ''favored boundaries'' can be estimated from a knowledge of the values of p for the two favored boundaries and the intermediate boundary made up of equal numbers of the structural units comprising the two favored boundaries. Applications of the results to measurements of boundary diffusivities and boundary energies are indicated.

  15. Simple structural unit model for core-dependent properties of symmetrical tilt boundaries

    SciTech Connect

    Balluffi, R.W.; Brokman, A.

    1983-04-01

    Consider any physical property, p, of a grain boundary, which depends primarily on the atomic structure of the core, e.g., the boundary diffusivity or the core energy. This note demonstrates that the recently determined structural unit model for the core structure allows one to estimate p for any boundary in a series of symmetrical tilt boundaries possessing a range of tilt angles if values of p for a few particular boundaries in the series are known. P for all boundaries with misorientations between those of two so-called favored boundaries can be estimated from a knowledge of the values of p for the two favored boundaries and the intermediate boundary made up of equal numbers of the structural units comprising the two favored boundaries. Applications of the results to measurements of boundary diffusivities and boundary energies are indicated briefly.

  16. Simple structural unit model for core-dependent properties of symmetrical tilt boundaries

    SciTech Connect

    Balluffi, R.W.; Brokman, A.

    1983-08-01

    Consider any physical property, p, of a grain boundary, which depends primarily on the atomic structure of the core, e.g., the boundary diffusivity or the core energy. This paper demonstrates that the recently determined structural unit model for the core structure allows one to estimate p for any boundary in a series of symmetrical tilt boundaries possessing a range of tilt angles if values of p for a few particular boundaries in the series are known. More specifically, we shall show that p for all boundaries with misorientations between those of two so-called ''favored boundaries'' can be estimated from a knowledge of the values of p for the two favored boundaries and the intermediate boundary made up of equal numbers of the structural units comprising the two favored boundaries. Applications of the results to measurements of boundary diffusivities and boundary energies are indicated briefly.

  17. 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.

  18. Structural basis of core promoter recognition in a primitive eukaryote.

    PubMed

    Schumacher, Maria A; Lau, Audrey O T; Johnson, Patricia J

    2003-11-14

    Transcription start site selection in eukaryotes is mediated through combinations of the TATA, initiator (Inr), and downstream promoter elements (DPE). In Trichomonas vaginalis, a parabasalian flagellate thought to represent an ancient eukaryote lineage, the Inr appears to be solely responsible for start site selection and is recognized by the initiator binding protein 39 kDa (IBP39). IBP39 contains an N-terminal Inr binding domain (IBD) connected via a flexible linker to a C-terminal domain (C domain). Here we present crystal structures of the apoIBD and IBD-Inr complexes and the C domain. The IBD structures reveal a winged-helix motif with prokaryotic and eukaryotic features and a scaffold similar to that of ETS-family proteins. The C domain structure and biochemical studies indicate that it interacts with the T. vaginalis RNAP II large subunit C-terminal domain. These data suggest that binding of IBP39 to the Inr directly recruits RNAP II and in this way initiates transcription.

  19. 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.

  20. Solution structure of the core SMN–Gemin2 complex

    SciTech Connect

    Sarachan, Kathryn L.; Valentine, Kathleen G.; Gupta, Kushol; Moorman, Veronica R.; Gledhill, John M.; Bernens, Matthew; Tommos, Cecilia; Wand, A.  Joshua; Van Duyne, Gregory D.

    2012-08-01

    In humans, assembly of spliceosomal snRNPs (small nuclear ribonucleoproteins) begins in the cytoplasm where the multi-protein SMN (survival of motor neuron) complex mediates the formation of a seven-membered ring of Sm proteins on to a conserved site of the snRNA (small nuclear RNA). The SMN complex contains the SMN protein Gemin2 and several additional Gemins that participate in snRNP biosynthesis. SMN was first identified as the product of a gene found to be deleted or mutated in patients with the neurodegenerative disease SMA (spinal muscular atrophy), the leading genetic cause of infant mortality. In the present study, we report the solution structure of Gemin2 bound to the Gemin2-binding domain of SMN determined by NMR spectroscopy. This complex reveals the structure of Gemin2, how Gemin2 binds to SMN and the roles of conserved SMN residues near the binding interface. Surprisingly, several conserved SMN residues, including the sites of two SMA patient mutations, are not required for binding to Gemin2. Instead, they form a conserved SMN/Gemin2 surface that may be functionally important for snRNP assembly. The SMN–Gemin2 structure explains how Gemin2 is stabilized by SMN and establishes a framework for structure–function studies to investigate snRNP biogenesis as well as biological processes involving Gemin2 that do not involve snRNP assembly.

  1. 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.

  2. Structural Color Palettes of Core-Shell Photonic Ink Capsules Containing Cholesteric Liquid Crystals.

    PubMed

    Lee, Sang Seok; Seo, Hyeon Jin; Kim, Yun Ho; Kim, Shin-Hyun

    2017-06-01

    Photonic microcapsules with onion-like topology are microfluidically designed to have cholesteric liquid crystals with opposite handedness in their core and shell. The microcapsules exhibit structural colors caused by dual photonic bandgaps, resulting in a rich variety of color on the optical palette. Moreover, the microcapsules can switch the colors from either core or shell depending on the selection of light-handedness. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Structure and binding studies of proliferating cell nuclear antigen from Leishmania donovani.

    PubMed

    Yadav, Satya Prakash; Singh, Prashant Kumar; Sharma, Pradeep; Iqbal, Naseer; Kaur, Punit; Sharma, Sujata; Singh, Tej P

    2017-11-01

    Proliferating cell nuclear antigen (PCNA) acts as a sliding clamp to support DNA replication and repair. The structure of PCNA from Leishmania donovani (LdPCNA) has been determined at 2.73Å resolution. Structure consists of six crystallographically independent molecules which form two trimeric rings. The pore diameter of the individual trimeric ring is of the order of 37Å. The two rings are stacked through their front to front faces. In order to gain a stable packing, the rings are rotated by 42° about the pore axis and shifted by 7Å and tilted by 16° along the perpendicular direction to pore axis. This form of stacking reduced the effective diameter of the pore to 32Å. The sequence of LdPCNA consists of a long segment of 41 amino acid residues (186-Gly-Val-Ser-Asp-Arg-Ser-Thr-Lys-Ser-Glu-Val-Lys-Ala-Glu-Val-Lys-Ala-Glu-Ala-Arg-Asp-Asp-Asp-Glu-Glu-Pro-Leu-Ser-Arg-Lys-Tyr-Gly-Lys-Ala-Asp-Ser-Ser-Ala-Asn-Ala-Ile-226) whereas the corresponding segments in other PCNAs contain only eight residues corresponding to 186-Gly-Val-Ser-Asp-Arg------224-Asn-Ala-Ile-226. The enhanced length of this segment in LdPCNA may influence its mode of interaction with DNA and other proteins. The dissociation constants obtained using real time binding studies with surface plasmon resonance (SPR) for two peptides, Lys-Arg-Arg-Gln-Thr-Ser-Met-Thr-Asp-Phe-Tyr-His (P1) from human cyclin-dependent kinase inhibitor-1(CKI-1) and Lys-Thr-Gln-Gly-Arg-Leu-Asp-Ser-Phe-Phe-Thr-Val (P2) from flap endonuclease 1 (Fen-1) as well as with two small molecule inhibitors, (S)-4-(4-(2-amino-3-hydroxypropyl)-2, 6-diiodophenoxy) phenol hydrochloride (ADPH) and N-(3-methylthiophene-2-carboxylicacid)-N'-((3-hydroxy-2-naphthalenyl) methylene) hydrazide (MCMH) are 0.29±0.09μM, 0.37±0.08μM, 0.35±0.09μM and 1.20±0.08μM respectively. The corresponding values obtained using fluorescence spectroscopic methods were 0.22±0.06μM, 0.68±0.07μM, 0.44±0.07μM and 0.75±0.05μM respectively. Copyright © 2017

  4. 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.

  5. Effect of the parameters of a sandwich structure with a honeycomb core on its soundproofing capacity

    NASA Astrophysics Data System (ADS)

    Tkachev, A. A.

    Expressions for estimating the soundproofing capacity of sandwich structures with a honeycomb core are obtained by using equations of transverse vibrations of a plate with allowance for the flexural and shear waves. The expressions provide an adequate description of the experimentally observed effects and make it possible to predict the effect of the parameters of a structure on its soundproofing efficiency.

  6. In situ preparation of nickel/carbon core-shell structure by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Cao, Fuyang; Jiang, Qi; Fang, Yuan; Ban, Shengguang; Ou, Shisheng; Qian, Hongxia; Zhao, Yong

    2013-10-01

    Nickel/carbon core-shell structure with uniform diameter has been synthesized by galvanostatic electrodeposition nickel on its surface followed by chemical vapor deposition. We proposed the growth mechanism of the core-shell structure that the precipitation of carbon from metal catalysts during the high temperature growth period lifts up metal particles leading to the formation of core-shell structure or carbon nanotubes with respect to the diameter of catalyst particles. The substrate with deposited nickel was characterized by optical microscope. The elements and features of the substrate were studied by energy dispersive X-ray spectroscopy and X-ray diffraction respectively. The morphology of the resulting material was examined by field emitting scanning electron microscopy. In addition, the electrochemical performance of the core-shell structure modified electrodes was also investigated. The result shows that electrodes modified with core structure have better electrochemical property than the bare electrodes in the [Fe(CN)6]3-/[Fe(CN)6]4- solution at a scan rate of 20 mV s-1.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Structural synergy in a core-shell spin crossover nanoparticle investigated by an electroelastic model

    NASA Astrophysics Data System (ADS)

    Slimani, Ahmed; Khemakhem, Hamadi; Boukheddaden, Kamel

    2017-05-01

    Understanding how surrounding environments act on the functional properties of switchable nano-objects across extended and multiple length scales is of growing interest in many areas of material science. Here, we examine in details, using a microscopic model, the interplay between the structural properties of an inert shell and a spin-active spin-crossover (SCO) core, composed of atoms which can switch thermally between the low-spin (LS) and high-spin (HS) states, a transition which is accompanied with a volume expansion. To come closer to realistic experimental data, we considered a shell having the lattice parameter of the HS state. Intensive Monte Carlo simulations, running on the spin states and atomic positions, are performed on the core-shell spin-crossover nanoparticle using an electroelastic model based on a compressible 2D lattice. A detailed analysis of the effect of the shell's size and rigidity on the magnetostructural properties of the core allows us to address the following issues: (i) the heteroelastic properties of the lattice induce a spatially inhomogeneous pressure (negative in the shell and positive in the core) which strongly distorts the lattice when the core is in the LS state, creating a visible spatial deflection of the shell/core interface; (ii) the thermally-induced first-order SCO transition of the core is significantly affected by the increase of the shell size, which lowers the transition temperature and reduces the thermal hysteresis width; (iii) the shell's rigidity dependence of the thermal hysteresis of the nanoparticle exhibited a resonance behavior when the shell's rigidity equals that of the core, a feature that is analyzed on the basis of acoustic impedance mismatch between the core and the shell. All these outcomes reflect the crucial influence of the surrounding environment on the structural properties of the nanoparticle and provide potentialities in the control of the bistability and cooperativity of the SCO nanoparticles

  13. Unveiling the Detailed Density and Velocity Structures of the Protostellar Core B335

    NASA Astrophysics Data System (ADS)

    Kurono, Yasutaka; Saito, Masao; Kamazaki, Takeshi; Morita, Koh-Ichiro; Kawabe, Ryohei

    2013-03-01

    We present an observational study of the protostellar core B335 harboring a low-mass Class 0 source. The observations of the H13CO+(J = 1-0) line emission were carried out using the Nobeyama 45 m telescope and Nobeyama Millimeter Array. Our combined image of the interferometer and single-dish data depicts detailed structures of the dense envelope within the core. We found that the core has a radial density profile of n(r)vpropr -p and a reliable difference in the power-law indices between the outer and inner regions of the core: p ≈ 2 for r >~ 4000 AU and p ≈ 1.5 for r <~ 4000 AU. The dense core shows a slight overall velocity gradient of ~1.0 km s-1 over the scale of 20, 000 AU across the outflow axis. We believe that this velocity gradient represents a solid-body-like rotation of the core. The dense envelope has a quite symmetrical velocity structure with a remarkable line broadening toward the core center, which is especially prominent in the position-velocity diagram across the outflow axis. The model calculations of position-velocity diagrams do a good job of reproducing observational results using the collapse model of an isothermal sphere in which the core has an inner free-fall region and an outer region conserving the conditions at the formation stage of a central stellar object. We derived a central stellar mass of ~0.1 M ⊙, and suggest a small inward velocity, v_{r ≥ r_inf}˜ 0 km s^{-1} in the outer core at >~ 4000 AU. We concluded that our data can be well explained by gravitational collapse with a quasi-static initial condition, such as Shu's model, or by the isothermal collapse of a marginally critical Bonnor-Ebert sphere.

  14. 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

  15. Course of hepatitis C virus (HCV) RNA and HCV core antigen testing are predictors for reaching sustained virologic response in liver transplant recipients undergoing sofosbuvir treatment in a real-life setting.

    PubMed

    Pischke, S; Polywka, S; Proske, V M; Lang, M; Jordan, S; Nashan, B; Lohse, A W; Sterneck, M

    2016-02-01

    Hepatitis C virus (HCV) infection is associated with reduced graft survival in orthotopic liver transplant recipients. Treatment with the new direct-acting antivirals (DAAs) is safe and efficient, but no reliable predictive factors for sustained virologic response (SVR) have been identified so far. The HCV core antigen assay (HCV-core-Ag) is a new, inexpensive, and efficient method to detect viral antigens, but the value of this technique to predict treatment response in orthotopic liver transplantation (OLT) patients is still unclear. All OLT patients who were treated with a sofosbuvir-based antiviral regimen at our center between March 2014 and August 2014 were included in the analysis (n = 20). HCV-core-Ag and HCV RNA (polymerase chain reaction [PCR]) were determined at each visit. Primary endpoints of this study were SVR at 4 or 12 weeks after end of treatment (SVR 4 and SVR 12). HCV-core-Ag tested negative after a median of 2 weeks (range 1-16 weeks) while PCR tests became negative after a median of 4 weeks (range 2-12 weeks). Time until PCR negativity and until HCV-core-Ag negativity showed a good correlation (R = 0.711, P < 0.001, Fig. ). Seventeen of 20 patients (85%) achieved SVR 12. SVR 12 was associated with a short time interval between treatment start and HCV PCR negativity (P = 0.005) or HCV-core-Ag negativity (P = 0.003, Mann-Whitney test). No severe side effects were observed. DAA treatment is safe and well tolerated in OLT. The time points of HCV-core-Ag loss and PCR negativity were predictors of SVR 12. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Electronic structure and transport properties of III-V core/shell nanowires

    NASA Astrophysics Data System (ADS)

    Viñas, Florinda; Leijnse, Martin

    We have modeled electron structure and low-temperature transport in III-V core/shell nanowires to establish a relationship between electron-hole hybridization and signatures in thermoelectrical measurements. Nanowires with a GaSb core and an InAs shell (and inverted) are interesting for studies of hybridization effects due to the bulk broken band gap alignment at the material interface. By varying the core radius and shell thickness of such wires we can modify the size of the band gap and create wires with band structures that exhibit hole-electron hybridization states. The band structures are obtained using 8-band k . p theory together with the envelope function approximation. The calculated energy dispersions are used as input to the Boltzmann equation to study thermoelectric transport quantities such as the Seebeck coefficient, in the diffusive limit.

  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. Seismic Structures of the Earth's Inner Core Boundary Beneath the Bearing Sea and Mexico

    NASA Astrophysics Data System (ADS)

    Tian, D.; Wen, L.

    2016-12-01

    The detailed structure of the Earth's inner core boundary is vital for the understanding of dynamic processes in the Earth's core. In this study, we perform a systematic search of events (with magnitude greater than 5.8 and event depth great than 30 km) recorded by USArray Transportable Aarry (TA) stations. We are able to find clear pre-critical PKiKP records, which sample the inner core boundary (ICB) beneath the Bearing Sea and Mexico. The PKiKP records which sample the ICB beneath the Bearing Sea, exhibit small lateral variations of PKiKP-PcP differential travel time residuals and high similarity between PKiKP and PcP waveforms, indicating a flat and sharp ICB. However, the PKiKP records which sample the ICB beneath Mexico, exhibit lateral varying PKiKP-PcP differential travel time residuals and PKiKP/PcP amplitude ratios, and anomalous PKiKP waveforms. We estimate contributions from the CMB structures using neighboring events and constrain the complex ICB structure based on fittings of observations and numerical simulations. We also observe reliable PKiKP coda signals on individual seismograms and use them to determine the locations of seismic scatters in the Earth's inner core. These observations suggest complicated seismic structures in the vicinity of the ICB and complex dynamic processes in the Earth's core.

  4. Effect of annealing temperature on the stress and structural properties of Ge core fibre

    NASA Astrophysics Data System (ADS)

    Zhao, Ziwen; Cheng, Xueli; Xue, Fei; He, Ting; Wang, Tingyun

    2017-09-01

    Effect of annealing temperature on the stress and structural properties of a Ge core fibre via the molten core drawing (MCD) method is investigated using Raman spectroscopy, Scanning electronic microscopy (SEM), and X-ray diffraction. The experimental results showed that the Raman peak position of the Ge fibre shifted from 297.6 cm-1 to 300.5 cm-1, and the FWHM value decreased from 4.53 cm-1 to 4.31 cm-1, when the annealing is carried out at 700 °C, 800 °C, and 900 °C, respectively. For the Ge core annealed at 900 °C, an apparent crystal grain can be seen in the SEM image, and the diffraction peaks of the (3 3 1) plane are generated in the X-ray diffraction spectra. These results show that optimising the annealing temperature allows the release of the residual stress in the Ge core. When the Ge core fibre is annealed at 900 °C, it exhibits the lowest residual stress and the highest crystal quality, and the quality improvement relative to that of the sample annealed at 800 °C is significant. Hence, annealing at around 900 °C can greatly improve the quality of a Ge core fibre. Further performance improvement of the Ge core fibre by annealing techniques can be anticipated.

  5. Probing atomic structure in magnetic core/shell nanoparticles using synchrotron radiation.

    PubMed

    Baker, S H; Roy, M; Thornton, S C; Qureshi, M; Binns, C

    2010-09-29

    Core/shell Fe/Cu and Fe/Au nanoparticles were prepared directly by deposition from the gas phase. A detailed study of the atomic structure in both the cores and shells of the nanoparticles was undertaken by means of extended absorption fine structure (EXAFS) measurements. For Fe/Cu nanoparticles, a Cu shell ∼ 20 monolayers thick appears similar in structure to bulk Cu and is sufficient to cause the structure in the Fe core to switch from body centred cubic (bcc; as in bulk Fe) to face centred cubic. This is not the case for thinner Cu shells, 1-2 monolayers in thickness, in which there is a considerable contraction in nearest-neighbour interatomic distance as the shell structure changes to bcc. In Fe/Au nanoparticles, the crystal structure in the Fe core remains bcc for all Au thicknesses although there is some stretching of the lattice. In thin Au shells ∼ 2 monolayers thick, there is strong contraction in interatomic distances. There does not appear to be significant alloying at the Fe/Au interface.

  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. 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.

  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. 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

  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. 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.

  12. Flux-flow resistivity in UPt3: Evidence for nonsingular vortex-core structure

    NASA Astrophysics Data System (ADS)

    Lütke-Entrup, N.; Blaauwgeers, R.; Plaçais, B.; Huxley, A.; Kambe, S.; Krusius, M.; Mathieu, P.; Simon, Y.

    2001-07-01

    We have investigated the core structure of B-phase vortex lines in two clean UPt3 crystals, using flux-flow dissipation as the probe. The flux-flow resistivity is determined from the skin depth of the high-frequency oscillations of the vortex lines in the pinned state. With Ĥ⊥ĉ, our data agree with the previously established scaling law of the moderately clean limit with anisotropic gap. When Ĥ||ĉ, the resistivity is three times larger. We interpret this increase as evidence for a vortex-core structure with two length scales, as predicted for UPt3 with a two-component order parameter.

  13. 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.

  14. Potential of electrospun core-shell structured gelatin-chitosan nanofibers for biomedical applications.

    PubMed

    Jalaja, K; Naskar, Deboki; Kundu, Subhas C; James, Nirmala R

    2016-01-20

    Coaxial electrospinning is an upcoming technology that has emerged from the conventional electrospinning process in order to realize the production of nanofibers of less spinnable materials with potential applications. The present work focuses on the production of chitosan nanofibers in a benign route, using natural polymer as core template, mild solvent system and naturally derived cross-linkers. Nanofibers with chitosan as shell are fabricated by coaxial electrospinning with highly spinnable gelatin as core using aqueous acetic acid as solvent. For maintaining the biocompatibility and structural integrity of the core-shell nanofibers, cross-linking is carried out using naturally derived cross-linking agents, dextran aldehyde and sucrose aldehyde. The biological evaluation of gelatin/chitosan mat is carried out using human osteoblast like cells. The results show that the cross-linked core-shell nanofibers are excellent matrices for cell adhesion and proliferation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. 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.

  16. Magnetic properties of mixed spin (1, 3/2) Ising nanoparticles with core-shell structure

    NASA Astrophysics Data System (ADS)

    Deviren, Bayram; Şener, Yunus

    2015-07-01

    The magnetic properties of mixed spin-1 and spin-3/2 Ising nanoparticles with core/shell structure are studied by using the effective-field theory with correlations. We investigate the thermal variations of the core, shell and total magnetizations and the Q-, R-, P-, S-, N- and L-types of compensation behavior in Néel classification nomenclature exists in the system. The effects of the crystal-field, core and shell interactions and interface coupling, on the phase diagrams are investigated in detail and the obtained phase diagrams are presented in three different planes. The system exhibits both second- and first-order phase transitions besides tricritical point, double critical end point, triple point and critical end point depending on the appropriate values of the interaction parameters. The system strongly affected by the surface situations and some characteristic phenomena are found depending on the ratio of the physical parameters in the surface shell and the core.

  17. 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).

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

    PubMed

    Wen, Cai

    2017-06-01

    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.

  19. Mapping the Atomistic Structure of Graded Core/Shell Colloidal Nanocrystals.

    PubMed

    Yarema, Maksym; Xing, Yunhua; Lechner, Rainer T; Ludescher, Lukas; Dordevic, Nikola; Lin, Weyde M M; Yarema, Olesya; Wood, Vanessa

    2017-09-15

    Engineering the compositional gradient for core/shell semiconductor nanocrystals improves their optical properties. To date, however, the structure of graded core/shell nanocrystal emitters has only been qualitatively described. In this paper, we demonstrate an approach to quantify nanocrystal structure, selecting graded Ag-In-Se/ZnSe core/shell nanocrystals as a proof-of-concept material. A combination of multi-energy small-angle X-ray scattering and electron microscopy techniques enables us to establish the radial distribution of ZnSe with sub-nanometer resolution. Using ab initio shape-retrieval analysis of X-ray scattering spectra, we further determine the average shape of nanocrystals. These results allow us to generate three-dimensional, atomistic reconstructions of graded core/shell nanocrystals. We use these reconstructions to calculate solid-state Zn diffusion in the Ag-In-Se nanocrystals and the lattice mismatch between nanocrystal monolayers. Finally, we apply these findings to propose design rules for optimal shell structure and record-luminescent core/shell nanocrystals.

  20. 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.

  1. 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.

  2. Fragmentation of Massive Dense Cores Down to <~ 1000 AU: Relation between Fragmentation and Density Structure

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    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. The James Clerk Maxwell Telescope is operated by the Joint Astronomy Centre on behalf of the Science and Technology Facilities Council of the United Kingdom, the Netherlands Organisation for Scientific Research, and the National Research Council of Canada.

  3. 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

  4. 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

  5. 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.

  6. Comparison of Serum Hepatitis C Virus (HCV) RNA and Core Antigen Levels in Patients Coinfected with Human Immunodeficiency Virus and HCV and Treated with Interferon plus Ribavirin

    PubMed Central

    Pivert, A.; Payan, C.; Morand, P.; Fafi-Kremer, S.; Deshayes, J.; Carrat, F.; Pol, S.; Cacoub, P.; Perronne, C.; Lunel, F.

    2006-01-01

    Trak-C (Ortho-Clinical Diagnostics) is an enzyme-linked immunosorbent assay-based method capable of quantifying hepatitis C virus (HCV) core antigen (CA) in serum and could be an alternative to molecular detection and quantification of HCV RNA. We have evaluated the Trak-C assay in comparison with an HCV RNA quantitative assay (Versant HCV v3.0; Bayer Diagnostics) in the follow-up of 348 treated, human immunodeficiency virus (HIV)/HCV-coinfected patients included in the ANRS HC02 RIBAVIC trial. ANRS HC02 RIBAVIC is a therapeutic, multicenter, randomized protocol comparing the efficacy of alpha interferon 2b (IFN-α2b) (3 million units three times a week)-ribavirin (800 mg/day) to that of pegylated IFN-α2b (1.5 μg/kg of body weight/week)-ribavirin (800 mg/day) during 48 weeks of treatment of HIV/HCV-coinfected patients naïve to HCV treatment. Patients were assessed for virological analysis at day 0 and weeks 4, 12, 24, 48, and 72. Correlation of HCV RNA and HCV CA at the initiation of treatment was excellent (r = 0.92). HCV RNA and CA kinetics were similar during follow-up of HCV treatment from day 0 to week 72 whatever the group of response and genotype. The positive and negative predictive values of response to the treatment at week 4 were 59 and 94%, respectively, for HCV RNA load reduction of >2 log and 54 and 94%, respectively, for HCV CA below the threshold value (4.18 log10 pg/ml · 104). Trak-C, a new assay able to quantify CA in HIV/HCV-coinfected patients, correlates well with quantitative HCV RNA assays and is cheaper and easier to perform than molecular technology. HCV CA could be a valuable alternative test for therapeutic follow-up of coinfected patients treated with IFN plus ribavirin in developing countries. PMID:16455894

  7. 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.

  8. 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.

  9. 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.

  10. Fine structure of the topological defect cores studied for disclinations in lyotropic chromonic liquid crystals

    PubMed Central

    Zhou, Shuang; Shiyanovskii, Sergij V.; Park, Heung-Shik; Lavrentovich, Oleg D.

    2017-01-01

    The detailed structure of singularities of ordered field represents a fundamental problem in diverse areas of physics. At the defect cores, the deformations are so strong that the system explores states with symmetry different from that of an undistorted material. These regions are difficult to explore experimentally as their spatial extension is very small, a few molecular lengths in the condensed matter. Here we explore the cores of disclinations in the so-called chromonic nematics that extend over macroscopic length scales accessible for optical characterization. We demonstrate that the amplitude S and the phase (the director) of the order parameter vary along both the radial and azimuthal directions, in contrast to the classic models in which S varies only with the distance from the centre and depends only on the azimuthal coordinate. This unexpected core structure is explained by a strong coupling of the phase and amplitude of the order parameter in the free energy. PMID:28429783

  11. Rift Valley fever phlebovirus NSs protein core domain structure suggests molecular basis for nuclear filaments.

    PubMed

    Barski, Michal; Brennan, Benjamin; Miller, Ona K; Potter, Jane A; Vijayakrishnan, Swetha; Bhella, David; Naismith, James H; Elliott, Richard M; Schwarz-Linek, Ulrich

    2017-09-15

    Rift Valley fever phlebovirus (RVFV) is a clinically and economically important pathogen increasingly likely to cause widespread epidemics. RVFV virulence depends on the interferon antagonist non-structural protein (NSs), which remains poorly characterized. We identified a stable core domain of RVFV NSs (residues 83-248), and solved its crystal structure, a novel all-helical fold organized into highly ordered fibrils. A hallmark of RVFV pathology is NSs filament formation in infected cell nuclei. Recombinant virus encoding the NSs core domain induced intranuclear filaments, suggesting it contains all essential determinants for nuclear translocation and filament formation. Mutations of key crystal fibril interface residues in