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  • 1
    Publication Date: 2014-02-07
    Description: Vaccines prevent infectious disease largely by inducing protective neutralizing antibodies against vulnerable epitopes. Several major pathogens have resisted traditional vaccine development, although vulnerable epitopes targeted by neutralizing antibodies have been identified for several such cases. Hence, new vaccine design methods to induce epitope-specific neutralizing antibodies are needed. Here we show, with a neutralization epitope from respiratory syncytial virus, that computational protein design can generate small, thermally and conformationally stable protein scaffolds that accurately mimic the viral epitope structure and induce potent neutralizing antibodies. These scaffolds represent promising leads for the research and development of a human respiratory syncytial virus vaccine needed to protect infants, young children and the elderly. More generally, the results provide proof of principle for epitope-focused and scaffold-based vaccine design, and encourage the evaluation and further development of these strategies for a variety of other vaccine targets, including antigenically highly variable pathogens such as human immunodeficiency virus and influenza.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260937/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260937/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Correia, Bruno E -- Bates, John T -- Loomis, Rebecca J -- Baneyx, Gretchen -- Carrico, Chris -- Jardine, Joseph G -- Rupert, Peter -- Correnti, Colin -- Kalyuzhniy, Oleksandr -- Vittal, Vinayak -- Connell, Mary J -- Stevens, Eric -- Schroeter, Alexandria -- Chen, Man -- Macpherson, Skye -- Serra, Andreia M -- Adachi, Yumiko -- Holmes, Margaret A -- Li, Yuxing -- Klevit, Rachel E -- Graham, Barney S -- Wyatt, Richard T -- Baker, David -- Strong, Roland K -- Crowe, James E Jr -- Johnson, Philip R -- Schief, William R -- 1R01AI102766-01A1/AI/NIAID NIH HHS/ -- 1UM1AI100663/AI/NIAID NIH HHS/ -- 2T32GM007270/GM/NIGMS NIH HHS/ -- 5R21AI088554/AI/NIAID NIH HHS/ -- P01 AI094419/AI/NIAID NIH HHS/ -- P01AI094419/AI/NIAID NIH HHS/ -- P30 AI036214/AI/NIAID NIH HHS/ -- P30 AI045008/AI/NIAID NIH HHS/ -- P30AI36214/AI/NIAID NIH HHS/ -- R01 AI102766/AI/NIAID NIH HHS/ -- R21 AI088554/AI/NIAID NIH HHS/ -- T32 CA080416/CA/NCI NIH HHS/ -- T32 GM007270/GM/NIGMS NIH HHS/ -- T32CA080416/CA/NCI NIH HHS/ -- U54 AI 005714/AI/NIAID NIH HHS/ -- U54 AI057141/AI/NIAID NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2014 Mar 13;507(7491):201-6. doi: 10.1038/nature12966. Epub 2014 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] PhD Program in Computational Biology, Instituto Gulbenkian Ciencia and Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal [3] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA. ; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA. ; The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania 19104, USA. ; Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA. ; Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA. ; 1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA [3] IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [4] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA. ; 1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [3] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA. ; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. ; 1] Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA [2]. ; 1] Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA [2] IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [3] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA. ; 1] The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA [2] Department of Pathology, Microbiology and Immunology, Vanderbilt Medical Center, Nashville, Tennessee 37232, USA [3] Department of Pediatrics, Vanderbilt Medical Center, Nashville, Tennessee 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24499818" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Antibodies, Monoclonal/analysis/immunology ; Antibodies, Neutralizing/analysis/immunology ; Antibodies, Viral/analysis/immunology ; Antigens, Viral/chemistry/immunology ; Crystallography, X-Ray ; *Drug Design ; Enzyme-Linked Immunosorbent Assay ; Epitopes/*chemistry/*immunology ; Macaca mulatta/immunology ; Male ; Mice ; Mice, Inbred BALB C ; Models, Molecular ; Neutralization Tests ; Protein Conformation ; *Protein Stability ; Respiratory Syncytial Virus Vaccines/*chemistry/*immunology ; Respiratory Syncytial Viruses/chemistry/immunology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2016-11-02
    Description: Palivizumab was the first antiviral monoclonal antibody (mAb) approved for therapeutic use in humans, and remains a prophylactic treatment for infants at risk for severe disease because of respiratory syncytial virus (RSV). Palivizumab is an engineered humanized version of a murine mAb targeting antigenic site II of the RSV fusion...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 3
  • 4
    Publication Date: 2011-05-29
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2015-11-04
    Description: The ability of certain components of particulate matter to induce oxidative stress through catalytic generation of reactive oxygen species (ROS) in vivo may be one mechanism accounting for observed linkages between ambient aerosols and adverse health outcomes. A variety of assays have been used to measure this so-called aerosol oxidative potential. We developed a semi-automated system to quantify oxidative potential of filter aqueous extracts utilizing the dithiothreitol (DTT) assay and have recently developed a similar semi-automated system using the ascorbic acid (AA) assay. Approximately 500 PM2.5 filter samples collected in contrasting locations in the southeastern US were analyzed using both assays. We found that water-soluble DTT activity on a per air volume basis was more spatially uniform than water-soluble AA activity. DTT activity was higher in winter than in summer/fall, whereas AA activity was higher in summer/fall compared to winter, with highest levels near highly trafficked highways. DTT activity was correlated with organic and metal species, whereas AA activity was correlated with water-soluble metals (especially water-soluble Cu, r=0.70–0.91 at most sites). Source apportionment models, Positive Matrix Factorization (PMF) and a Chemical Mass Balance Method with ensemble-averaged source impact profiles (CMB-E), suggest a strong contribution from secondary processes (e.g., organic aerosol oxidation or metal mobilization by formation of an aqueous particle with secondary acids) and traffic emissions to both DTT and AA activities in urban Atlanta. Biomass burning was a large source for DTT activity, but insignificant for AA. DTT activity was well correlated with PM2.5 mass (r=0.49–0.86 across sites/seasons), while AA activity did not co-vary strongly with mass. A linear model was developed to estimate DTT and AA activities for the central Atlanta Jefferson Street site, based on the CMB-E sources that are statistically significant with positive coefficients. The model was used to estimate oxidative potential at this site over the period 1998–2009. Time-series epidemiological analyses were conducted to assess daily emergency department (ED) visits data for the five-county Atlanta metropolitan area based on the estimated 10 year backcast oxidative potential. Results suggest that estimated DTT activity was associated with ED visits for both asthma/wheeze and congestive heart failure, while AA activity was not linked to any health outcomes. The findings point to the importance of both organic components and transition metals from biomass burning and mobile sources to adverse health outcomes in this region.
    Electronic ISSN: 1680-7375
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 6
    Publication Date: 2014-07-30
    Description: We assess the potential of the water-soluble fraction of atmospheric fine aerosols in the southeastern US to generate reactive oxygen species (ROS) and identify major ROS-associated emission sources. ROS-generation potential of particles was quantified by the dithiothreitol (DTT) assay and involved analysis of fine particulate matter (PM) extracted from high-volume quartz filters (23 h integrated samples) collected at various sites in different environmental settings in the southeast, including three urban Atlanta sites, in addition to a rural site. Paired sampling was conducted with one fixed site in Atlanta (Jefferson Street), representative of the urban environment, with the others rotating among different sites, for ~250 days between June 2012 and September 2013 (N = 483). A simple linear regression between the DTT activity and aerosol chemical components revealed strong associations between PM ROS generation potential and secondary organic aerosol (WSOC) in summer, and biomass burning markers in winter. Redox-active metals were also correlated with the DTT activity, but mostly at urban and roadside sites. Positive matrix factorization (PMF) was applied to apportion the relative contribution of various sources to the ROS generation potential of water-soluble PM2.5 in urban Atlanta. PMF showed that vehicular emissions contribute uniformly throughout the year (12 to 25%), while secondary oxidation processes dominated the DTT activity in summer (46%) and biomass burning in winter (47%). Mineral dust was significant only during drier periods (~12% in summer and fall). Source apportionment by chemical mass balance (CMB) was reasonably consistent with PMF, but with higher contribution from vehicular emissions (32%). Given the spatially large data set of PM sampled over an extended period, the study reconciles the results from previous work that showed only region- or season-specific aerosol components or sources contributing to PM ROS activity, possibly due to smaller sample sizes. Our results indicate that the ability to generate ROS is a generic property of fine PM to which almost all major emission sources contribute to variable extents. The ubiquitous nature of the ROS generation property of ambient particulate matter suggests widespread population exposures to aerosol components that have the ability to catalyze the production of oxidants in vivo.
    Electronic ISSN: 1680-7375
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 7
    Publication Date: 2014-12-08
    Description: We assess the potential of the water-soluble fraction of atmospheric fine aerosols in the southeastern United States to generate reactive oxygen species (ROS) and identify major ROS-associated emission sources. ROS-generation potential of particles was quantified by the dithiothreitol (DTT) assay and involved analysis of fine particulate matter (PM) extracted from high-volume quartz filters (23 h integrated samples) collected at various sites in different environmental settings in the southeast, including three urban-Atlanta sites, in addition to a rural site. Paired sampling was conducted with one fixed site in Atlanta (Jefferson Street), representative of the urban environment, with the others rotating among different sites, for ~250 days between June 2012 and September 2013 (N=483). A simple linear regression between the DTT activity and aerosol chemical components revealed strong associations between PM ROS-generation potential and secondary organic aerosol (WSOC – water-soluble organic carbon) in summer, and biomass burning markers in winter. Redox-active metals were also somewhat correlated with the DTT activity, but mostly at urban and roadside sites. Positive matrix factorization (PMF) was applied to apportion the relative contribution of various sources to the ROS-generation potential of water-soluble PM2.5 in urban Atlanta. PMF showed that vehicular emissions contribute uniformly throughout the year (12–25%), while secondary oxidation processes dominated the DTT activity in summer (46%) and biomass burning in winter (47%). Road dust was significant only during drier periods (~12% in summer and fall). Source apportionment by chemical mass balance (CMB) was reasonably consistent with PMF, but with higher contribution from vehicular emissions (32%). Given the spatially large data set of PM sampled over an extended period, the study reconciles the results from previous work that showed only region- or season-specific aerosol components or sources contributing to PM ROS activity, possibly due to smaller sample sizes. The ubiquitous nature of the major sources of PM-associated ROS suggests widespread population exposures to aerosol components that have the ability to catalyze the production of oxidants in vivo.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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