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Sample records for outsmarting flu viruses

  1. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Toward Design of a Universal Flu Vaccine Print Worldwide, influenza causes substantial deaths and yearly economic burdens, but the highly changeable nature of the flu virus ...

  2. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Toward Design of a Universal Flu Vaccine Print Worldwide, influenza causes substantial deaths and yearly economic burdens, but the highly changeable nature of the flu virus...

  3. Avian Flu

    SciTech Connect (OSTI)

    Eckburg, Paul

    2006-11-06

    Since 2003, a severe form of H5N1 avian influenza has rapidly spread throughout Asia and Europe, infecting over 200 humans in 10 countries. The spread of H5N1 virus from person-to-person has been rare, thus preventing the emergence of a widespread pandemic. However, this ongoing epidemic continues to pose an important public health threat. Avian flu and its pandemic potential in humans will be discussed.

  4. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Toward Design of a Universal Flu Vaccine Toward Design of a Universal Flu Vaccine Print Wednesday, 30 January 2013 00:00 Worldwide, influenza causes substantial deaths and yearly economic burdens, but the highly changeable nature of the flu virus complicates the production of an effective vaccine. The Centers for Disease Control and Prevention (CDC) estimates that the effectiveness of this year's flu vaccine is about 62%. For comparison, this number for childhood vaccines is routinely well over

  5. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Toward Design of a Universal Flu Vaccine Print Worldwide, influenza causes substantial deaths and yearly economic burdens, but the highly changeable nature of the flu virus complicates the production of an effective vaccine. The Centers for Disease Control and Prevention (CDC) estimates that the effectiveness of this year's flu vaccine is about 62%. For comparison, this number for childhood vaccines is routinely well over 90%. One factor in determining the vaccine's effectiveness is how closely

  6. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Toward Design of a Universal Flu Vaccine Print Worldwide, influenza causes substantial deaths and yearly economic burdens, but the highly changeable nature of the flu virus complicates the production of an effective vaccine. The Centers for Disease Control and Prevention (CDC) estimates that the effectiveness of this year's flu vaccine is about 62%. For comparison, this number for childhood vaccines is routinely well over 90%. One factor in determining the vaccine's effectiveness is how closely

  7. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Toward Design of a Universal Flu Vaccine Print Worldwide, influenza causes substantial deaths and yearly economic burdens, but the highly changeable nature of the flu virus complicates the production of an effective vaccine. The Centers for Disease Control and Prevention (CDC) estimates that the effectiveness of this year's flu vaccine is about 62%. For comparison, this number for childhood vaccines is routinely well over 90%. One factor in determining the vaccine's effectiveness is how closely

  8. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Toward Design of a Universal Flu Vaccine Print Worldwide, influenza causes substantial deaths and yearly economic burdens, but the highly changeable nature of the flu virus complicates the production of an effective vaccine. The Centers for Disease Control and Prevention (CDC) estimates that the effectiveness of this year's flu vaccine is about 62%. For comparison, this number for childhood vaccines is routinely well over 90%. One factor in determining the vaccine's effectiveness is how closely

  9. The forecast calls for flu

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The forecast calls for flu Science on the Hill: The forecast calls for flu Using mathematics, computer programs, statistics and information about how disease develops and spreads, a research team at Los Alamos National Laboratory found a way to forecast the flu season and even next week's sickness trends. January 15, 2016 Forecasting flu A team from Los Alamos has developed a method to predict flu outbreaks based in part on influenza-related searches of Wikipedia. The forecast calls for flu

  10. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three...

  11. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents,...

  12. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Structure and Receptor Specificity of an Avian Flu Antigen Print Wednesday, 25 July 2007 00:00 To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of

  13. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of genetic material from similar viruses) or mutation, is seen as a major threat to public

  14. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of genetic material from similar viruses) or mutation, is seen as a major threat to public

  15. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of genetic material from similar viruses) or mutation, is seen as a major threat to public health

  16. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Toward Design of a Universal Flu Vaccine Toward Design of a Universal Flu Vaccine Print Wednesday, 30 January 2013 00:00 Worldwide, influenza causes substantial deaths and yearly ...

  17. Our view: Vaccinate now, prevent flu later

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Our view: Vaccinate now, prevent flu later Our view: Vaccinate now, prevent flu later Los Alamos National Laboratory scientists are predicting that this winter's flu season is most likely to peak in February across much of the United States. The scientists can say this because of the model they have constructed. December 24, 2015 Man sneezing Model suggests still time to get your flu shot and be protected. "There's no crystal ball when it comes to predicting disease outbreaks," said

  18. Picture of the Week: Forecasting Flu

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    3 Forecasting Flu What if we could forecast infectious diseases the same way we forecast the weather, and predict how diseases like Dengue, Typhus or Zika were going to spread? March 6, 2016 flu epidemics modellled using social media Watch the video on YouTube. Forecasting Flu What if we could forecast infectious diseases the same way we forecast the weather, and predict how diseases like Dengue, Typhus or Zika were going to spread? Using real-time data from Wikipedia and social media, Sara del

  19. From biofuels to predicting the flu

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    May » From biofuels to predicting the flu From biofuels to predicting the flu WHEN: May 14, 2016 11:00 AM - 1:00 PM WHERE: Bradbury Science Museum 1350 Central Ave, Los Alamos, NM 87544, USA CONTACT: Linda Anderman (505) 665-9196 CATEGORY: Bradbury INTERNAL: Calendar Login Event Description Scientist in the Spotlight: A chance to chat with scientists about their work Is the flu in your future? Los Alamos scientists are using supercomputing to monitor and even forecast the spread of diseases.

  20. Occ. Med. Offers Staff Flu Vaccines by Appointment | Jefferson...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Occ. Med. Offers Staff Flu Vaccines by Appointment Occupational Medicine is now accepting appointments from Jefferson Lab staff for Influenza vaccinations. If you would like to be...

  1. Flu shots available beginning Oct. 5 | The Ames Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    battle the flu Wash hands regularly with soap and water, use hand sanitizer Sneeze and cough into a sleeve or tissue Stay home when sick Regularly sanitize work surfaces and...

  2. Toward Design of a Universal Flu Vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    large structural differences from CR9114, indicating that, while they bind to a similar region on various viruses, they employ different strategies for neutralizing those...

  3. City of Chicago won't sweat the flu with Argonne's help | Argonne...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    on their toes." This particular exercise followed the spread of an imaginary flu from Egypt. By the time the flu "arrived" in Chicago, more than 15,000 cases had been reported...

  4. Full-spectrum disease response : beyond just the flu.

    SciTech Connect (OSTI)

    Knazovich, Michael Ward; Cox, Warren B.; Henderson, Samuel Arthur

    2010-04-01

    Why plan beyond the flu: (1) the installation may be the target of bioterrorism - National Laboratory, military base collocated in large population center; and (2) International Airport - transport of infectious agents to the area - Sandia is a global enterprise and staff visit many foreign countries. In addition to the Pandemic Plan, Sandia has developed a separate Disease Response Plan (DRP). The DRP addresses Category A, B pathogens and Severe Acute Respiratory Syndrome (SARS). The DRP contains the Cities Readiness Initiative sub-plan for disbursement of Strategic National Stockpile assets.

  5. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    combined effects could allow the Viet04 virus to escape entrapment by mucins in the lungs and increase binding to susceptible human epithelial cells. These mutations therefore...

  6. Structural Basis of Preexisting Immunity to the 2009 H1N1 Pandemic Influenza Virus

    SciTech Connect (OSTI)

    Xu, Rui; Ekiert, Damian C.; Krause, Jens C.; Hai, Rong; Crowe, Jr., James E.; Wilson, Ian A.

    2010-05-25

    The 2009 H1N1 swine flu is the first influenza pandemic in decades. The crystal structure of the hemagglutinin from the A/California/04/2009 H1N1 virus shows that its antigenic structure, particularly within the Sa antigenic site, is extremely similar to those of human H1N1 viruses circulating early in the 20th century. The cocrystal structure of the 1918 hemagglutinin with 2D1, an antibody from a survivor of the 1918 Spanish flu that neutralizes both 1918 and 2009 H1N1 viruses, reveals an epitope that is conserved in both pandemic viruses. Thus, antigenic similarity between the 2009 and 1918-like viruses provides an explanation for the age-related immunity to the current influenza pandemic.

  7. Forecasting Flu

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    introduction in 1992 of an American-made truck with a fully factory-installed/war- ranted liquefied petroleum gas (LPG) engine represents another "Ford first" in the alternative fuel arena. Now the company has introduced an LPG- powered F-700, a medium/heavy- duty truck. According to Tom Steckel, Ford's medium-duty marketing man- ager, Ford's latest sales figures already prove the alternative fuel F-700's popularity. With a little more than 10 months of the model year finished, Ford

  8. Science Summary

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    that can take out an unprecedented number of different types of flu viruses, including H5N1 'bird flu' and the 1918 H1N1 'Spanish flu', which killed millions around the world...

  9. Generating electricity from viruses

    SciTech Connect (OSTI)

    Lee, Seung-Wuk

    2013-10-31

    Berkeley Lab's Seung-Wuk Lee discusses "Generating electricity from viruses" in this Oct. 28, 2013 talk, which is part of a Science at the Theater event entitled Eight Big Ideas.

  10. Generating electricity from viruses

    ScienceCinema (OSTI)

    Lee, Seung-Wuk

    2014-06-23

    Berkeley Lab's Seung-Wuk Lee discusses "Generating electricity from viruses" in this Oct. 28, 2013 talk, which is part of a Science at the Theater event entitled Eight Big Ideas.

  11. Production of virus resistant plants

    DOE Patents [OSTI]

    Dougherty, William G.; Lindbo, John A.

    1996-01-01

    A method of suppressing virus gene expression in plants using untranslatable plus sense RNA is disclosed. The method is useful for the production of plants that are resistant to virus infection.

  12. Production of virus resistant plants

    DOE Patents [OSTI]

    Dougherty, W.G.; Lindbo, J.A.

    1996-12-10

    A method of suppressing virus gene expression in plants using untranslatable plus sense RNA is disclosed. The method is useful for the production of plants that are resistant to virus infection. 9 figs.

  13. From Shakespeare to Viruses

    ScienceCinema (OSTI)

    Sung-Hou Kim

    2010-01-08

    Berkeley Lab scientists have created a unique new tool for analyzing and comparing long sets of data, be it the genomes of mammals or viruses, or the works of Shakespeare. The results of the Shakespeare analysis surprised scholars with their accuracy

  14. From Shakespeare to Viruses

    ScienceCinema (OSTI)

    Kim, Sung-Hou

    2013-05-29

    Berkeley Lab scientists have created a unique new tool for analyzing and comparing long sets of data, be it the genomes of mammals or viruses, or the works of Shakespeare. The results of the Shakespeare analysis surprised scholars with their accuracy.

  15. Computer virus information update CIAC-2301

    SciTech Connect (OSTI)

    Orvis, W.J.

    1994-01-15

    While CIAC periodically issues bulletins about specific computer viruses, these bulletins do not cover all the computer viruses that affect desktop computers. The purpose of this document is to identify most of the known viruses for the MS-DOS and Macintosh platforms and give an overview of the effects of each virus. The authors also include information on some windows, Atari, and Amiga viruses. This document is revised periodically as new virus information becomes available. This document replaces all earlier versions of the CIAC Computer virus Information Update. The date on the front cover indicates date on which the information in this document was extracted from CIAC`s Virus database.

  16. OSTI, US Dept of Energy, Office of Scientific and Technical Informatio...

    Office of Scientific and Technical Information (OSTI)

    step toward developing a new drug and encourages further research to crystallize proteins relevant to other parasites and viruses, including strains of hepatitis and flu. ...

  17. Stanford Synchrotron Radiation Lightsource

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    the design principles of natural functional sites. The team targeted a surface on the influenza hemagglutinin protein that enables flu viruses to attach to and invade cells lining...

  18. Immunogenic compositions comprising human immunodeficiency virus...

    Office of Scientific and Technical Information (OSTI)

    Patent: Immunogenic compositions comprising human immunodeficiency virus (HIV) mosaic Nef proteins Citation Details In-Document Search Title: Immunogenic compositions comprising...

  19. Structure and Mutagenesis of the Parainfluenza Virus 5Hemagglutinin...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Structure and Mutagenesis of the Parainfluenza Virus 5 ... Title: Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase ...

  20. Recombinant herpes simplex virus useful for treating neoplastic disease

    DOE Patents [OSTI]

    Whitley, Richard J.; Roizman, Bernard

    2010-06-29

    Recombinant herpes simplex viruses comprising DNA encoding cytokines and methods for treating neoplastic diseases using the inventive recombinant viruses are disclosed.

  1. Structure of the Newcastle disease virus hemagglutinin-neuraminidase...

    Office of Scientific and Technical Information (OSTI)

    virus hemagglutinin-neuraminidase (HN) ectodomain reveals a four-helix bundle stalk Citation Details In-Document Search Title: Structure of the Newcastle disease virus ...

  2. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Wednesday, 03 December 2014 00:00 Immortality is...

  3. Battling bird flu by the numbers

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and crisis managers determine in real time whether an emerging infectious disease ... and crisis managers determine in real time whether an emerging infectious disease ...

  4. Better predicting flu outbreaks with Wikipedia

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Del Valle said. Del Valle and her team recently published "Forecasting the 2013-2014 Influenza Season using Wikipedia," in the Public Library of Science. "Infectious diseases are...

  5. Microsoft Word - 1918flu.doc

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    required for influenza infection. One patch, unique to both human and avian H1, H2 and H5 subtypes, is adjacent to the cleavage site, and may be involved in either trimer...

  6. Presentation, Zika Virus Disease and Prevention

    Broader source: Energy.gov [DOE]

    “Zika Virus Disease and Prevention” presentation was made by Bonnie S. Richter, MPH, PhD, at the May 19 Office of Environment, Health, Safety and Security (EHSS) All Hands Meeting.

  7. Shutting Out Ebola and Other Viruses

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Shutting Out Ebola and Other Viruses Shutting Out Ebola and Other Viruses Print Wednesday, 27 April 2016 14:05 Throughout the summer and fall of 2014, a tragic outbreak of Ebola hemorrhagic fever in West Africa reminded us of how interconnected the world is and how vulnerable we can be to the spread of virulent diseases. Science, however, gives us powerful tools for gaining insight into how pathogens operate and, consequently, how to design strategies to defeat them. Here we report on

  8. OSTI, US Dept of Energy, Office of Scientific and Technical Informatio...

    Office of Scientific and Technical Information (OSTI)

    played a key role in building the world's first atomic bomb. It's the place where vitamin E and K were discovered, the human polio virus isolated, and the flu virus identified. ...

  9. Treatment of tumors with genetically engineered herpes virus

    DOE Patents [OSTI]

    Weichselbaum, Ralph R; Roizman, Bernard; Whitley, Richard J

    2012-11-27

    Disclosed are methods for treating cancer by administering an effective amount of a modified Herpes simplex virus.

  10. Shutting Out Ebola and Other Viruses

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Shutting Out Ebola and Other Viruses Print Throughout the summer and fall of 2014, a tragic outbreak of Ebola hemorrhagic fever in West Africa reminded us of how interconnected the world is and how vulnerable we can be to the spread of virulent diseases. Science, however, gives us powerful tools for gaining insight into how pathogens operate and, consequently, how to design strategies to defeat them. Here we report on researchers from UC San Francisco who used protein crystallography at the ALS

  11. Shutting Out Ebola and Other Viruses

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Shutting Out Ebola and Other Viruses Print Throughout the summer and fall of 2014, a tragic outbreak of Ebola hemorrhagic fever in West Africa reminded us of how interconnected the world is and how vulnerable we can be to the spread of virulent diseases. Science, however, gives us powerful tools for gaining insight into how pathogens operate and, consequently, how to design strategies to defeat them. Here we report on researchers from UC San Francisco who used protein crystallography at the ALS

  12. Shutting Out Ebola and Other Viruses

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Shutting Out Ebola and Other Viruses Print Throughout the summer and fall of 2014, a tragic outbreak of Ebola hemorrhagic fever in West Africa reminded us of how interconnected the world is and how vulnerable we can be to the spread of virulent diseases. Science, however, gives us powerful tools for gaining insight into how pathogens operate and, consequently, how to design strategies to defeat them. Here we report on researchers from UC San Francisco who used protein crystallography at the ALS

  13. Shutting Out Ebola and Other Viruses

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Shutting Out Ebola and Other Viruses Print Throughout the summer and fall of 2014, a tragic outbreak of Ebola hemorrhagic fever in West Africa reminded us of how interconnected the world is and how vulnerable we can be to the spread of virulent diseases. Science, however, gives us powerful tools for gaining insight into how pathogens operate and, consequently, how to design strategies to defeat them. Here we report on researchers from UC San Francisco who used protein crystallography at the ALS

  14. Structure of the Triatoma virus capsid

    SciTech Connect (OSTI)

    Squires, Galle; Pous, Joan; Agirre, Jon; Rozas-Dennis, Gabriela S.; Costabel, Marcelo D.; Marti, Gerardo A.; Navaza, Jorge; Bressanelli, Stphane; Gurin, Diego M. A.; Rey, Felix A.

    2013-06-01

    The crystallographic structure of TrV shows specific morphological and functional features that clearly distinguish it from the type species of the Cripavirus genus, CrPV. The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.

  15. Immobilization and One-Dimensional Arrangement of Virus Capsids with

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Nanoscale Precision Using DNA Origami Immobilization and One-Dimensional Arrangement of Virus Capsids with Nanoscale Precision Using DNA Origami Authors: Stephanopoulos, N., Liu, M., Tong, G., Li, Z., Liu, Y., Yan, H., and Francis, M. Title: Immobilization and One-Dimensional Arrangement of Virus Capsids with Nanoscale Precision Using DNA Origami Source: Nano Letters Year: 2010 Volume: 10 Pages: 2714-2720 ABSTRACT: DNA origami was used as a scaffold to arrange spherical virus capsids into

  16. This is a paper model of the MS2 virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    a paper model of the MS2 virus. MS2 is a nanoscale virus that lives in the human gut. It is benign and doesn't interfere with us. A virus, it attaches to a host cell that it identifies using protein markers on its exterior. Once attached, it injects its RNA genetic material into the cell. This material then co-opts the cell's metabolism to produce copies of the virus, which the cell releases back into the organism's tissues. Researchers have found that this mechanism has potential as a treatment

  17. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Immortality is not a good thing for cells, and in fact, cells will destroy themselves in a process called apoptosis when they are a danger to other cells. For instance, when a cell is infected by a virus it becomes an unwilling factory for the virus, which uses the cell machinery to produce ever more copies of itself. Eventually, if the cell doesn't die, it will spew all those new viruses into the bloodstream. The process of

  18. HIV virus spread and evolution studied through computer modeling

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and the actual, rapid evolution of the virus (phylogenetics) within each patient's body. "We have developed novel ways of estimating epidemics dynamics such as who infected...

  19. Serial femtosecond X-ray diffraction of enveloped virus microcrystals

    SciTech Connect (OSTI)

    Lawrence, Robert M.; Conrad, Chelsie E.; Zatsepin, Nadia A.; Grant, Thomas D.; Liu, Haiguang; James, Daniel; Nelson, Garrett; Subramanian, Ganesh; Aquila, Andrew; Hunter, Mark S.; Liang, Mengning; Boutet, Sbastien; Coe, Jesse; Spence, John C. H.; Weierstall, Uwe; Liu, Wei; Fromme, Petra; Cherezov, Vadim; Hogue, Brenda G.

    2015-08-20

    Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ~700 diameter. Microcrystals delivered in viscous agarose medium diffracted to ~40 resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is a pertinent step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

  20. Genomics-enabled sensor platform for rapid detection of viruses...

    Office of Scientific and Technical Information (OSTI)

    platforms for preclinical and field testing that utilize the assays developed in goal 1. We generated and characterized suitable primersmore for West Nile Virus RNA detection. ...

  1. Structural Rearrangement in Ebola Virus Protein VP40 Creates...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    lab revealed how the filaments undergo electrostatically driven rearrangements and polymerization to build and bud Ebola virus virions. Atomic models built from their structures...

  2. Genomics-enabled sensor platform for rapid detection of viruses...

    Office of Scientific and Technical Information (OSTI)

    platforms for preclinical and field testing that utilize the assays developed in goal 1. We generated and characterized suitable primers more for West Nile Virus RNA detection. ...

  3. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Immortality is not a good thing for cells, and in fact, cells will destroy themselves in a process called apoptosis when they are a danger to other cells. For instance, when a cell is infected by a virus it becomes an unwilling factory for the virus, which uses the cell machinery to produce ever more copies of itself. Eventually, if the cell doesn't die, it will spew all those new viruses into the bloodstream. The process of

  4. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Immortality is not a good thing for cells, and in fact, cells will destroy themselves in a process called apoptosis when they are a danger to other cells. For instance, when a cell is infected by a virus it becomes an unwilling factory for the virus, which uses the cell machinery to produce ever more copies of itself. Eventually, if the cell doesn't die, it will spew all those new viruses into the bloodstream. The process of

  5. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Immortality is not a good thing for cells, and in fact, cells will destroy themselves in a process called apoptosis when they are a danger to other cells. For instance, when a cell is infected by a virus it becomes an unwilling factory for the virus, which uses the cell machinery to produce ever more copies of itself. Eventually, if the cell doesn't die, it will spew all those new viruses into the bloodstream. The process of

  6. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Wednesday, 03 December 2014 00:00 Immortality is not a good thing for cells, and in fact, cells will destroy themselves in a process called apoptosis when they are a danger to other cells. For instance, when a cell is infected by a virus it becomes an unwilling factory for the virus, which uses the cell machinery to produce ever more copies of itself. Eventually, if

  7. Serial femtosecond X-ray diffraction of enveloped virus microcrystals

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lawrence, Robert M.; Conrad, Chelsie E.; Zatsepin, Nadia A.; Grant, Thomas D.; Liu, Haiguang; James, Daniel; Nelson, Garrett; Subramanian, Ganesh; Aquila, Andrew; Hunter, Mark S.; et al

    2015-08-20

    Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ~700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ~40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is a pertinent step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

  8. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function....

  9. Structural Basis of Pre-existing Immunity to the 2009 H1N1 Pandemic

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Influenza Virus Structural Basis of Pre-existing Immunity to the 2009 H1N1 Pandemic Influenza Virus The emergence of the 2009 H1N1 influenza pandemic, also known as the "swine flu", marks the first human flu pandemic in 40 years and has caused significant human infection and mortality globally (1). The emergence of the 2009 H1N1 flu marks the first time that an influenza pandemic was triggered by a virus carrying the same hemagglutinin (HA) subtype as circulating seasonal strains.

  10. Tobacco mosaic virus: A biological building block for micro/nano...

    Office of Scientific and Technical Information (OSTI)

    Tobacco mosaic virus: A biological building block for micronanobio systems Citation Details In-Document Search Title: Tobacco mosaic virus: A biological building block for micro...

  11. Chimeric human parainfluenza virus bearing the Ebola virus glycoprotein as the sole surface protein is immunogenic and highly protective against Ebola virus challenge

    SciTech Connect (OSTI)

    Bukreyev, Alexander Marzi, Andrea; Feldmann, Friederike; Zhang Liqun; Dorward, David W.; Pickles, Raymond J.; Feldmann, Heinz; Collins, Peter L.

    2009-01-20

    We generated a new live-attenuated vaccine against Ebola virus (EBOV) based on a chimeric virus HPIV3/{delta}F-HN/EboGP that contains the EBOV glycoprotein (GP) as the sole transmembrane envelope protein combined with the internal proteins of human parainfluenza virus type 3 (HPIV3). Electron microscopy analysis of the virus particles showed that they have an envelope and surface spikes resembling those of EBOV and a particle size and shape resembling those of HPIV3. When HPIV3/{delta}F-HN/EboGP was inoculated via apical surface of an in vitro model of human ciliated airway epithelium, the virus was released from the apical surface; when applied to basolateral surface, the virus infected basolateral cells but did not spread through the tissue. Following intranasal (IN) inoculation of guinea pigs, scattered infected cells were detected in the lungs by immunohistochemistry, but infectious HPIV3/{delta}F-HN/EboGP could not be recovered from the lungs, blood, or other tissues. Despite the attenuation, the virus was highly immunogenic, and a single IN dose completely protected the animals against a highly lethal intraperitoneal challenge of guinea pig-adapted EBOV.

  12. A replication-deficient rabies virus vaccine expressing Ebola virus glycoprotein is highly attenuated for neurovirulence

    SciTech Connect (OSTI)

    Papaneri, Amy B.; Wirblich, Christoph; Cann, Jennifer A.; Cooper, Kurt; Jahrling, Peter B.; Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick MD, 21702 ; Schnell, Matthias J.; Blaney, Joseph E.

    2012-12-05

    We are developing inactivated and live-attenuated rabies virus (RABV) vaccines expressing Ebola virus (EBOV) glycoprotein for use in humans and endangered wildlife, respectively. Here, we further characterize the pathogenesis of the live-attenuated RABV/EBOV vaccine candidates in mice in an effort to define their growth properties and potential for safety. RABV vaccines expressing GP (RV-GP) or a replication-deficient derivative with a deletion of the RABV G gene (RV{Delta}G-GP) are both avirulent after intracerebral inoculation of adult mice. Furthermore, RV{Delta}G-GP is completely avirulent upon intracerebral inoculation of suckling mice unlike parental RABV vaccine or RV-GP. Analysis of RV{Delta}G-GP in the brain by quantitative PCR, determination of virus titer, and immunohistochemistry indicated greatly restricted virus replication. In summary, our findings indicate that RV-GP retains the attenuation phenotype of the live-attenuated RABV vaccine, and RV{Delta}G-GP would appear to be an even safer alternative for use in wildlife or consideration for human use.

  13. Iowa State University | OSTI, US Dept of Energy, Office of Scientific...

    Office of Scientific and Technical Information (OSTI)

    Physicist developing, improving designer optical materials Chemists discover proton mechanism used by flu virus to infect cells ISU, Ames Lab's Bryden & McCorkle win 2010 R&D 100 ...

  14. Structural basis for the antibody neutralization of Herpes simplex virus

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Structural basis for the antibody neutralization of Herpes simplex virus Citation Details In-Document Search Title: Structural basis for the antibody neutralization of Herpes simplex virus The gD-E317-Fab complex crystal revealed the conformational epitope of human mAb E317 on HSV gD, providing a molecular basis for understanding the viral neutralization mechanism. Glycoprotein D (gD) of Herpes simplex virus (HSV) binds to a host cell surface receptor,

  15. Virus Assemblies as Templates for Nanocircuits

    SciTech Connect (OSTI)

    James N Culver; Michael T Harris

    2011-08-31

    The goals of this project were directed at the identification and characterization of bio-mineralization processes and patterning methods for the development of nano scale materials and structures with novel energy and conductive traits. This project utilized a simple plant virus as a model template to investigate methods to attach and coat metals and other inorganic compounds onto biologically based nanotemplates. Accomplishments include: the development of robust biological nanotemplates with enhanced inorganic coating activities; novel coating strategies that allow for the deposition of a continuous inorganic layer onto a bio-nanotemplate even in the absence of a reducing agent; three-dimensional patterning methods for the assemble of nano-featured high aspect ratio surfaces and the demonstrated use of these surfaces in enhancing battery and energy storage applications. Combined results from this project have significantly advanced our understanding and ability to utilize the unique self-assembly properties of biologically based molecules to produce novel materials at the nanoscale level.

  16. Nanomachines: How Viruses Work, and How We Can Stop Them

    ScienceCinema (OSTI)

    Carolyn Bertozzi

    2010-01-08

    Nature's Nasty Nanomachines: How Viruses Work, and How We Can Stop Them. Carolyn Bertozzi, director of Berkeley Lab's Molecular Foundry, discusses this topic at a Feb. 21, 2009 Nano*High talk.

  17. Structure of the Ebola Virus Glycoprotein Bound to an Antibody...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor Print Ebolavirus, one of two members of the family of filoviruses, causes a severe hemorrhagic...

  18. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Designer Proteins Target Epstein-Barr-Virus-Associated Cancer Print Immortality is not a good thing for cells, and in fact, cells will destroy themselves in a process called...

  19. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Functions of Ebola Virus Print Friday, 13 June 2014 10:25 A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function....

  20. Multidisciplinary team aids understanding of Hepatitis C virus...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    this drug could cause such a rapid drop in the amount of virus in an infected person's blood could greatly enhance the ability to design optimal drug therapies and ultimately cure...

  1. Human immunodeficiency virus type 1 clade M mosaic gag polypeptides

    Office of Scientific and Technical Information (OSTI)

    (Patent) | SciTech Connect Patent: Human immunodeficiency virus type 1 clade M mosaic gag polypeptides Citation Details In-Document Search Title: Human immunodeficiency virus type 1 clade M mosaic gag polypeptides The present invention relates to mosaic HIV-1 group M Gag sequences and to a composition comprising same. Authors: Korber, Bette T ; Perkins, Simon ; Bhattacharya, Tanmoy ; Fischer, William M ; Theiler, James ; Letvin, Norman ; Haynes, Barton F ; Hahn, Beatrice H ; Yusim, Karina ;

  2. Solid flexible electrochemical supercapacitor using Tobacco mosaic virus

    Office of Scientific and Technical Information (OSTI)

    nanostructures and ALD ruthenium oxide (Journal Article) | SciTech Connect Solid flexible electrochemical supercapacitor using Tobacco mosaic virus nanostructures and ALD ruthenium oxide Citation Details In-Document Search Title: Solid flexible electrochemical supercapacitor using Tobacco mosaic virus nanostructures and ALD ruthenium oxide Authors: Gnerlich, Markus ; Pomerantseva, Ekaterina ; Gregorczyk, Keith ; Ketchum, D ; Rubloff, Gary W ; Ghodssi, Reza Publication Date: 2013-10-24 OSTI

  3. Structure of the Newcastle disease virus hemagglutinin-neuraminidase (HN)

    Office of Scientific and Technical Information (OSTI)

    ectodomain reveals a four-helix bundle stalk (Journal Article) | SciTech Connect of the Newcastle disease virus hemagglutinin-neuraminidase (HN) ectodomain reveals a four-helix bundle stalk Citation Details In-Document Search Title: Structure of the Newcastle disease virus hemagglutinin-neuraminidase (HN) ectodomain reveals a four-helix bundle stalk The paramyxovirus hemagglutinin-neuraminidase (HN) protein plays multiple roles in viral entry and egress, including binding to sialic acid

  4. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALS Capabilities Reveal Multiple Functions of Ebola Virus ALS Capabilities Reveal Multiple Functions of Ebola Virus Print Friday, 13 June 2014 10:25 A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the

  5. High molecular weight polysaccharide that binds and inhibits virus

    DOE Patents [OSTI]

    Konowalchuk, Thomas W

    2014-01-14

    This invention provides a high molecular weight polysaccharide capable of binding to and inhibiting virus and related pharmaceutical formulations and methods on inhibiting viral infectivity and/or pathogenicity, as well as immunogenic compositions. The invention further methods of inhibiting the growth of cancer cells and of ameliorating a symptom of aging. Additionally, the invention provides methods of detecting and/or quantifying and/or isolating viruses.

  6. Dengue Virus Infection Perturbs Lipid Homeostasis in Infected Mosquito Cells

    SciTech Connect (OSTI)

    Perera, Rushika M.; Riley, Catherine; Isaac, Georgis; Hopf- Jannasch, Amber; Moore, Ronald J.; Weitz, Karl K.; Pasa-Tolic, Ljiljana; Metz, Thomas O.; Adamec, Jiri; Kuhn, Richard J.

    2012-03-22

    Dengue virus causes {approx}50-100 million infections per year and thus is considered one of the most aggressive arthropod-borne human pathogen worldwide. During its replication, dengue virus induces dramatic alterations in the intracellular membranes of infected cells. This phenomenon is observed both in human and vector-derived cells. Using high-resolution mass spectrometry of mosquito cells, we show that this membrane remodeling is directly linked to a unique lipid repertoire induced by dengue virus infection. Specifically, 15% of the metabolites detected were significantly different between DENV infected and uninfected cells while 85% of the metabolites detected were significantly different in isolated replication complex membranes. Furthermore, we demonstrate that intracellular lipid redistribution induced by the inhibition of fatty acid synthase, the rate-limiting enzyme in lipid biosynthesis, is sufficient for cell survival but is inhibitory to dengue virus replication. Lipids that have the capacity to destabilize and change the curvature of membranes as well as lipids that change the permeability of membranes are enriched in dengue virus infected cells. Several sphingolipids and other bioactive signaling molecules that are involved in controlling membrane fusion, fission, and trafficking as well as molecules that influence cytoskeletal reorganization are also up regulated during dengue infection. These observations shed light on the emerging role of lipids in shaping the membrane and protein environments during viral infections and suggest membrane-organizing principles that may influence virus-induced intracellular membrane architecture.

  7. Enteric viruses in a mangrove lagoon, survival and shellfish incidence

    SciTech Connect (OSTI)

    Lopez de Cardona, I.; Bermudez, M.; Billmire, E.; Hazen, T.C.

    1988-12-31

    Mangrove oysters (Crassostrea rhizophorae) were screened for enteric viruses. For 18 months oysters were collected from Cano Boqueron, a tropical mangrove lagoon on the southwest coast of Puerto Rico. This popular tourist resort has two primary sewage treatment plants which service 158 single family cabanas. In spite of the heavy seasonal input of sewage to Cano Boqueron and high densities of fecal coliform bacteria, enteric viruses were not detected in shellfish meat. Because no viruses were detected in the oysters, a virus survival study was performed. Poliovirus type 1 was placed in diffusion chambers in situ at two sites in Cano Boqueron. More than 95% of the poliovirus inactivation occurred within 24 h. Virus inactivation was significantly different by site, indicating different inactivation rates within the lagoon. Chamber studies done simultaneously with Escherichia coli did not reveal differences between sites. It is suggested that the sewage effluent had an antiviral effect in the absence of an antibacterial effect. This study demonstrates the importance for establishing microbial contamination standards for shellfish growing waters in the tropics based upon in situ studies with tropical species, e.g. mangrove oyster.

  8. Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutini...

    Office of Scientific and Technical Information (OSTI)

    H1N1 Influenza Virus Hemagglutinin Receptor Binding Site Citation Details In-Document Search Title: Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin ...

  9. FLU5A425 | netl.doe.gov

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    REACTOR EXPERIMENT USED NUCLEAR FUEL (Technical Report) | SciTech Connect FLOWSHEET EVALUATION FOR THE DISSOLVING AND NEUTRALIZATION OF SODIUM REACTOR EXPERIMENT USED NUCLEAR FUEL Citation Details In-Document Search Title: FLOWSHEET EVALUATION FOR THE DISSOLVING AND NEUTRALIZATION OF SODIUM REACTOR EXPERIMENT USED NUCLEAR FUEL This report includes the literature review, hydrogen off-gas calculations, and hydrogen generation tests to determine that H-Canyon can safely dissolve the Sodium

  10. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Publication about this research: J. Stevens, O. Blixt, T.M. Tumpey, J.K. Taubenberger, J.C. Paulson, and I.A. Wilson, "Structure and receptor specificity of the hemagglutinin from ...

  11. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    SciTech Connect Other: Structure and Function of Microbial Metal-Reduction Proteins Citation Details In-Document Search Title: Structure and Function of Microbial Metal-Reduction Proteins In this project, we proposed (i) identification of metal-reduction genes, (ii) development of new threading techniques and (iii) fold recognition and structure prediction of metal-reduction proteins. However, due to the reduction of the budget, we revised our plan to focus on two specific aims of (i)

  12. February most likely month for flu season to peak

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    that Wikipedia article access logs are shown to highly correlate with historical influenza-like illness (ILI) records and allow for accurate prediction of ILI data several...

  13. Fast pandemic detection tool ready to fight flu

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    biological pathogens that could give rise to potentially deadly pandemics such as Influenza A (H1N1). June 9, 2009 Los Alamos National Laboratory sits on top of a once-remote...

  14. Pandemic Flu Planning | Y-12 National Security Complex

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    on employee safety and communications. History of pandemics In 1918 and 1919, an Influenza Pandemic occurred in three waves in the United States. Learn more. Resources you can...

  15. Point-of-Care Flu Diagnosis | GE Global Research

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Advanced Research Projects Agency (DARPA) to develop a breakthrough medical device ... The nearly 5.8 million in funding from DARPA for the project will result in the ...

  16. ORISE: Pandemic Flu Toolkits | How ORISE is Making a Difference

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    workshops that have been presented to the Asia-Pacific Economic Cooperation (APEC) and other nations around the world. By developing training toolkits and providing...

  17. Development of simulation tools for virus shell assembly. Final report

    SciTech Connect (OSTI)

    Berger, Bonnie

    2001-01-05

    Prof. Berger's major areas of research have been in applying computational and mathematical techniques to problems in biology, and more specifically to problems in protein folding and genomics. Significant progress has been made in the following areas relating to virus shell assembly: development has been progressing on a second-generation self-assembly simulator which provides a more versatile and physically realistic model of assembly; simulations are being developed and applied to a variety of problems in virus assembly; and collaborative efforts have continued with experimental biologists to verify and inspire the local rules theory and the simulator. The group has also worked on applications of the techniques developed here to other self-assembling structures in the material and biological sciences. Some of this work has been conducted in conjunction with Dr. Sorin Istrail when he was at Sandia National Labs.

  18. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALS Capabilities Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the protein. Recently, researchers used beamline capabilities at the ALS to demonstrate that a

  19. HIV virus spread and evolution studied through computer modeling

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    HIV and evolution studied through computer modeling HIV virus spread and evolution studied through computer modeling This approach distinguishes between susceptible and infected individuals to capture the full infection history, including contact tracing data for infected individuals. November 19, 2013 Scanning electron micrograph of HIV-1 budding (in green) from cultured lymphocytes. The image has been colored to highlight important features. Scanning electron micrograph of HIV-1 budding (in

  20. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALS Capabilities Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the protein. Recently, researchers used beamline capabilities at the ALS to demonstrate that a

  1. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALS Capabilities Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the protein. Recently, researchers used beamline capabilities at the ALS to demonstrate that a

  2. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALS Capabilities Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the protein. Recently, researchers used beamline capabilities at the ALS to demonstrate that a

  3. Structural Rearrangement in Ebola Virus Protein VP40 Creates Multiple

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Functions | Stanford Synchrotron Radiation Lightsource Structural Rearrangement in Ebola Virus Protein VP40 Creates Multiple Functions Monday, March 31, 2014 Figure 1. Three structures of VP40. Top, a butterfly-shaped dimer structure critical for membrane trafficking. Middle, a rearranged hexameric structure essential for building and releasing nascent virions. Bottom, an RNA-binding octameric ring that controls transcription in infected cells. As x-ray crystallographers, we often assume

  4. Virus-based Piezoelectric Energy Generation - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Energy Storage Energy Storage Electricity Transmission Electricity Transmission Advanced Materials Advanced Materials Find More Like This Return to Search Virus-based Piezoelectric Energy Generation Lawrence Berkeley National Laboratory Contact LBL About This Technology Publications: PDF Document Publication Bacteriophage_Commercial Analysis_EERE_20130521 ps.pdf (1,100 KB) Technology Marketing Summary Researchers at Berkeley Lab have demonstrated that the piezoelectric and liquid-crystalline

  5. West Nile virus isolated from Virginia opossum (Didelphis virginiana) in Northwest Missouri 2012

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bosco-Lauth, Angela; Harmon, Jessica; Lash, R. Ryan; Weiss, Sonja; Langevin, Stanley; Savage, Harry; Marvin S. Godsey, Jr.; Burkhalter, Kristen; Root, J. Jeffrey; Gidlewski, Thomas; et al

    2014-12-01

    We describe the isolation of West Nile virus (WNV; Flaviviridae, flavivirus) from blood of a Virginia opossum (Didelphis virginiana) collected in northwestern Missouri, USA in August 2012. Furthermore, sequencing determined that the virus was related to lineage 1a WNV02 strains. We discuss the role of wildlife in WNV disease epidemiology.

  6. Venezuelan equine encephalitis virus entry mechanism requires late endosome formation and resists cell membrane cholesterol depletion

    SciTech Connect (OSTI)

    Kolokoltsov, Andrey A.; Fleming, Elisa H.; Davey, Robert A. . E-mail: radavey@utmb.edu

    2006-04-10

    Virus envelope proteins determine receptor utilization and host range. The choice of receptor not only permits specific targeting of cells that express it, but also directs the virus into specific endosomal trafficking pathways. Disrupting trafficking can result in loss of virus infectivity due to redirection of virions to non-productive pathways. Identification of the pathway or pathways used by a virus is, thus, important in understanding virus pathogenesis mechanisms and for developing new treatment strategies. Most of our understanding of alphavirus entry has focused on the Old World alphaviruses, such as Sindbis and Semliki Forest virus. In comparison, very little is known about the entry route taken by more pathogenic New World alphaviruses. Here, we use a novel contents mixing assay to identify the cellular requirements for entry of a New World alphavirus, Venezuelan equine encephalitis virus (VEEV). Expression of dominant negative forms of key endosomal trafficking genes shows that VEEV must access clathrin-dependent endocytic vesicles for membrane fusion to occur. Unexpectedly, the exit point is different from Old World alphaviruses that leave from early endosomes. Instead, VEEV also requires functional late endosomes. Furthermore, unlike the Old World viruses, VEEV entry is insensitive to cholesterol sequestration from cell membranes and may reflect a need to access an endocytic compartment that lacks cholesterol. This indicates fundamental differences in the entry route taken by VEEV compared to Old World alphaviruses.

  7. Inhibition of lytic infection of pseudorabies virus by arginine depletion

    SciTech Connect (OSTI)

    Wang, H.-C. [Department of Veterinary Medicine, College of Veterinary Medicine, National Chung-Hsing University, Taichung 402, Taiwan (China); Kao, Y.-C. [Department of Veterinary Medicine, College of Veterinary Medicine, National Chung-Hsing University, Taichung 402, Taiwan (China); Chang, T-J. [Department of Veterinary Medicine, College of Veterinary Medicine, National Chung-Hsing University, Taichung 402, Taiwan (China); Wong, M.-L. [Department of Veterinary Medicine, College of Veterinary Medicine, National Chung-Hsing University, Taichung 402, Taiwan (China)]. E-mail: mlwong@dragon.nchu.edu.tw

    2005-08-26

    Pseudorabies virus (PRV) is a member of Alphahepesviruses; it is an enveloped virus with a double-stranded DNA genome. Polyamines (such as spermine and spermidine) are ubiquitous in animal cells and participate in cellular proliferation and differentiation. Previous results of our laboratory showed that the PRV can accomplish lytic infection either in the presence of exogenous spermine (or spermidine) or depletion of cellular polyamines. The amino acid arginine is a precursor of polyamine biosynthesis. In this work, we investigated the role of arginine in PRV infection. It was found that the plaque formation of PRV was inhibited by arginase (enzyme catalyzing the conversion of arginine into ornithine and urea) treatment whereas this inhibition can be reversed by exogenous arginine, suggesting that arginine is essential for PRV proliferation. Western blotting was conducted to study the effect of arginine depletion on the levels of structural proteins of PRV in virus-infected cells. Four PRV structural proteins (gB, gE, UL47, and UL48) were chosen for examination, and results revealed that the levels of viral proteins were obviously reduced in long time arginase treatment. However, the overall protein synthesis machinery was apparently not influenced by arginase treatment either in mock or PRV-infected cells. Analyzing with native gel, we found that arginase treatment affected the mobility of PRV structural proteins, suggesting the conformational change of viral proteins by arginine depletion. Heat shock proteins, acting as molecular chaperons, participate in protein folding and translocation. Our results demonstrated that long time arginase treatment could reduce the expression of cellular heat shock proteins 70 (hsc70 and hsp70), and transcriptional suppression of heat shock protein 70 gene promoter was one of the mechanisms involved in this reduced expression.

  8. LINGUISTIC ANALYSIS OF THE NUCLEOPROTEIN GENE OF INFLUENZA A VIRUS

    SciTech Connect (OSTI)

    A. SKOURIKHINE; T. BURR

    2000-05-01

    We applied linguistic analysis approach, specifically N-grams, to classify nucleotide and amino acids sequences of nucleoprotein (NP) gene of the Influenza A virus isolated from a range of hosts and geographic regions. We considered letter frequency (1-grams), letter pairs frequency (2-grams) and triplets' frequency (3-grams). Classification trees based on 1,2,3-grams variables were constructed for the same NP nucleotide and amino acids strains and their classification efficiency were compared with the clustering obtained using phylogenetic analysis. The results have shown that disregarding positional information for a NP gene can provide the same level of recognition accuracy like alternative more complex classification techniques.

  9. Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus

    SciTech Connect (OSTI)

    Zhou, Dongwen; Chung, Suhman; Miller, Maria; Le Grice, Stuart F.J.; Wlodawer, Alexander

    2012-06-19

    The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site {alpha}-hydroxytropolone inhibitor. Enzymatic assays showed that the intact RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with {beta}-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.

  10. Non-coding RNAs and heme oxygenase-1 in vaccinia virus infection

    SciTech Connect (OSTI)

    Meseda, Clement A.; Srinivasan, Kumar; Wise, Jasen; Catalano, Jennifer; Yamada, Kenneth M.; Dhawan, Subhash

    2014-11-07

    Highlights: Heme oxygenase-1 (HO-1) induction inhibited vaccinia virus infection of macrophages. Reduced infectivity inversely correlated with increased expression of non-coding RNAs. The regulation of HO-1 and ncRNAs suggests a novel host defense response against vaccinia virus infection. - Abstract: Small nuclear RNAs (snRNAs) are <200 nucleotide non-coding uridylate-rich RNAs. Although the functions of many snRNAs remain undetermined, a population of snRNAs is produced during the early phase of infection of cells by vaccinia virus. In the present study, we demonstrate a direct correlation between expression of the cytoprotective enzyme heme oxygenase-1 (HO-1), suppression of selective snRNA expression, and inhibition of vaccinia virus infection of macrophages. Hemin induced HO-1 expression, completely reversed virus-induced host snRNA expression, and suppressed vaccinia virus infection. This involvement of specific virus-induced snRNAs and associated gene clusters suggests a novel HO-1-dependent host-defense pathway in poxvirus infection.

  11. Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Survivor Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor Print Ebolavirus, one of two members of the family of filoviruses, causes a severe hemorrhagic fever with 50-90% human mortality. That no vaccines or treatments are yet available combined with the frequent re-emergence of the virus, its high prevalence among wildlife, and ease of importation of the virus make it a significant public health concern. A team of researchers from the Scripps Research

  12. Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Survivor Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor Print Ebolavirus, one of two members of the family of filoviruses, causes a severe hemorrhagic fever with 50-90% human mortality. That no vaccines or treatments are yet available combined with the frequent re-emergence of the virus, its high prevalence among wildlife, and ease of importation of the virus make it a significant public health concern. A team of researchers from the Scripps Research

  13. Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Survivor Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor Print Ebolavirus, one of two members of the family of filoviruses, causes a severe hemorrhagic fever with 50-90% human mortality. That no vaccines or treatments are yet available combined with the frequent re-emergence of the virus, its high prevalence among wildlife, and ease of importation of the virus make it a significant public health concern. A team of researchers from the Scripps Research

  14. Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Survivor Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor Print Ebolavirus, one of two members of the family of filoviruses, causes a severe hemorrhagic fever with 50-90% human mortality. That no vaccines or treatments are yet available combined with the frequent re-emergence of the virus, its high prevalence among wildlife, and ease of importation of the virus make it a significant public health concern. A team of researchers from the Scripps Research

  15. Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Survivor Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor Print Wednesday, 26 November 2008 00:00 Ebolavirus, one of two members of the family of filoviruses, causes a severe hemorrhagic fever with 50-90% human mortality. That no vaccines or treatments are yet available combined with the frequent re-emergence of the virus, its high prevalence among wildlife, and ease of

  16. Genomics-enabled sensor platform for rapid detection of viruses related to

    Office of Scientific and Technical Information (OSTI)

    disease outbreak. (Technical Report) | SciTech Connect SciTech Connect Search Results Technical Report: Genomics-enabled sensor platform for rapid detection of viruses related to disease outbreak. Citation Details In-Document Search Title: Genomics-enabled sensor platform for rapid detection of viruses related to disease outbreak. Bioweapons and emerging infectious diseases pose growing threats to our national security. Both natural disease outbreak and outbreaks due to a bioterrorist attack

  17. Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin

    Office of Scientific and Technical Information (OSTI)

    Receptor Binding Site (Journal Article) | SciTech Connect Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin Receptor Binding Site Citation Details In-Document Search Title: Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin Receptor Binding Site Authors: Hong, Minsun ; Lee, Peter S. ; Hoffman, Ryan M.B. ; Zhu, Xueyong ; Krause, Jens C. ; Laursen, Nick S. ; Yoon, Sung-il ; Song, Langzhou ; Tussey, Lynda ; Crowe, Jr., James E. ; Ward, Andrew B. ;

  18. Tobacco mosaic virus: A biological building block for micro/nano/bio

    Office of Scientific and Technical Information (OSTI)

    systems (Journal Article) | SciTech Connect Tobacco mosaic virus: A biological building block for micro/nano/bio systems Citation Details In-Document Search Title: Tobacco mosaic virus: A biological building block for micro/nano/bio systems Authors: Fan, Xiao Z ; Pomerantseva, Ekaterina ; Gnerlich, Markus ; Brown, Adam ; Gerasopoulos, K ; McCarthy, M ; Culver, James ; Ghodssi, Reza Publication Date: 2013-01-01 OSTI Identifier: 1160750 DOE Contract Number: SC0001160 Resource Type: Journal

  19. Human monoclonal antibodies derived from a patient infected with 2009 pandemic influenza A virus broadly cross-neutralize group 1 influenza viruses

    SciTech Connect (OSTI)

    Pan, Yang; Sasaki, Tadahiro; Du, Anariwa; and others

    2014-07-18

    Highlights: Influenza infection can elicit heterosubtypic antibodies to group 1 influenza virus. Three human monoclonal antibodies were generated from an H1N1-infected patient. The antibodies predominantly recognized ?-helical stem of viral hemagglutinin (HA). The antibodies inhibited HA structural activation during the fusion process. The antibodies are potential candidates for future antibody therapy to influenza. - Abstract: Influenza viruses are a continuous threat to human public health because of their ability to evolve rapidly through genetic drift and reassortment. Three human monoclonal antibodies (HuMAbs) were generated in this study, 1H11, 2H5 and 5G2, and they cross-neutralize a diverse range of group 1 influenza A viruses, including seasonal H1N1, 2009 pandemic H1N1 (H1N1pdm) and avian H5N1 and H9N2. The three HuMAbs were prepared by fusing peripheral blood lymphocytes from an H1N1pdm-infected patient with a newly developed fusion partner cell line, SPYMEG. All the HuMAbs had little hemagglutination inhibition activity but had strong membrane-fusion inhibition activity against influenza viruses. A protease digestion assay showed the HuMAbs targeted commonly a short ?-helix region in the stalk of the hemagglutinin. Furthermore, Ile45Phe and Glu47Gly double substitutions in the ?-helix region made the HA unrecognizable by the HuMAbs. These two amino acid residues are highly conserved in the HAs of H1N1, H5N1 and H9N2 viruses. The HuMAbs reported here may be potential candidates for the development of therapeutic antibodies against group 1 influenza viruses.

  20. Chimeric SV40 virus-like particles induce specific cytotoxicity and protective immunity against influenza A virus without the need of adjuvants

    SciTech Connect (OSTI)

    Kawano, Masaaki; Morikawa, Katsuma; Suda, Tatsuya; Ohno, Naohito; Matsushita, Sho; Akatsuka, Toshitaka; Handa, Hiroshi; Matsui, Masanori

    2014-01-05

    Virus-like particles (VLPs) are a promising vaccine platform due to the safety and efficiency. However, it is still unclear whether polyomavirus-based VLPs are useful for this purpose. Here, we attempted to evaluate the potential of polyomavirus VLPs for the antiviral vaccine using simian virus 40 (SV40). We constructed chimeric SV40-VLPs carrying an HLA-A{sup ⁎}02:01-restricted, cytotoxic T lymphocyte (CTL) epitope derived from influenza A virus. HLA-A{sup ⁎}02:01-transgenic mice were then immunized with the chimeric SV40-VLPs. The chimeric SV40-VLPs effectively induced influenza-specific CTLs and heterosubtypic protection against influenza A viruses without the need of adjuvants. Because DNase I treatment of the chimeric SV40-VLPs did not disrupt CTL induction, the intrinsic adjuvant property may not result from DNA contaminants in the VLP preparation. In addition, immunization with the chimeric SV40-VLPs generated long-lasting memory CTLs. We here propose that the chimeric SV40-VLPs harboring an epitope may be a promising CTL-based vaccine platform with self-adjuvant properties. - Highlights: • We constructed chimeric SV40-VLPs carrying an influenza virus-derived CTL epitope. • Chimeric SV40-VLPs induce influenza-specific CTLs in mice without adjuvants. • Chimeric SV40-VLPs induce heterosubtypic protection against influenza A viruses. • Chimeric SV40-VLPs induce long-lasting memory CTLs. • Chimeric SV40-VLPs is a promising vaccine platform with self-adjuvant properties.

  1. ARM - Field Campaign - Columbia Basin Wind Energy Study

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    govCampaignsColumbia Basin Wind Energy Study Campaign Links Outsmarting the Wind -- U.S. News Science Old meteorological techniques used in new wind farm study -- EcoSeed ARM Data...

  2. Alteration of cell cycle progression by Sindbis virus infection

    SciTech Connect (OSTI)

    Yi, Ruirong; Saito, Kengo; Isegawa, Naohisa; Shirasawa, Hiroshi

    2015-07-10

    We examined the impact of Sindbis virus (SINV) infection on cell cycle progression in a cancer cell line, HeLa, and a non-cancerous cell line, Vero. Cell cycle analyses showed that SINV infection is able to alter the cell cycle progression in both HeLa and Vero cells, but differently, especially during the early stage of infection. SINV infection affected the expression of several cell cycle regulators (CDK4, CDK6, cyclin E, p21, cyclin A and cyclin B) in HeLa cells and caused HeLa cells to accumulate in S phase during the early stage of infection. Monitoring SINV replication in HeLa and Vero cells expressing cell cycle indicators revealed that SINV which infected HeLa cells during G{sub 1} phase preferred to proliferate during S/G{sub 2} phase, and the average time interval for viral replication was significantly shorter in both HeLa and Vero cells infected during G{sub 1} phase than in cells infected during S/G{sub 2} phase. - Highlights: • SINV infection was able to alter the cell cycle progression of infected cancer cells. • SINV infection can affect the expression of cell cycle regulators. • SINV infection exhibited a preference for the timing of viral replication among the cell cycle phases.

  3. Crystal Structure of a Virus-Encoded Putative Glycosyltransferase

    SciTech Connect (OSTI)

    Xiang, Ye; Baxa, Ulrich; Zhang, Ying; Steven, Alasdair C.; Lewis, Gentry L.; Van Etten, James L.; Rossmann, Michael G.

    2010-11-22

    The chloroviruses (family Phycodnaviridae), unlike most viruses, encode some, if not most, of the enzymes involved in the glycosylation of their structural proteins. Annotation of the gene product B736L from chlorovirus NY-2A suggests that it is a glycosyltransferase. The structure of the recombinantly expressed B736L protein was determined by X-ray crystallography to 2.3-{angstrom} resolution, and the protein was shown to have two nucleotide-binding folds like other glycosyltransferase type B enzymes. This is the second structure of a chlorovirus-encoded glycosyltransferase and the first structure of a chlorovirus type B enzyme to be determined. B736L is a retaining enzyme and belongs to glycosyltransferase family 4. The donor substrate was identified as GDP-mannose by isothermal titration calorimetry and was shown to bind into the cleft between the two domains in the protein. The active form of the enzyme is probably a dimer in which the active centers are separated by about 40 {angstrom}.

  4. Adaptive immunity and histopathology in frog virus 3-infected Xenopus

    SciTech Connect (OSTI)

    Robert, Jacques . E-mail: robert@mail.rochester.edu; Morales, Heidi; Buck, Wayne; Cohen, Nicholas; Marr, Shauna; Gantress, Jennifer

    2005-02-20

    Xenopus has been used as an experimental model to evaluate the contribution of adaptive cellular immunity in amphibian host susceptibility to the emerging ranavirus FV3. Conventional histology and immunohistochemistry reveal that FV3 has a strong tropism for the proximal tubular epithelium of the kidney and is rarely disseminated elsewhere in Xenopus hosts unless their immune defenses are impaired or developmentally immature as in larvae. In such cases, virus is found widespread in most tissues. Adults, immunocompromised by depletion of CD8{sup +} T cells or by sub-lethal {gamma}-irradiation, show increased susceptibility to FV3 infection. Larvae and irradiated (but not normal) adults can be cross-infected through water by infected adult conspecifics (irradiated or not). The natural MHC class I deficiency and the absence of effect of anti-CD8 treatment on both larval CD8{sup +} T cells and larval susceptibility to FV3 are consistent with an inefficient CD8{sup +} T cell effector function during this developmental period.

  5. Selective destruction of cells infected with human immunodeficiency virus

    DOE Patents [OSTI]

    Keener, William K.; Ward, Thomas E.

    2003-09-30

    Compositions and methods for selectively killing a cell containing a viral protease are disclosed. The composition is a variant of a protein synthesis inactivating toxin wherein a viral protease cleavage site is interposed between the A and B chains. The variant of the type II ribosome-inactivating protein is activated by digestion of the viral protease cleavage site by the specific viral protease. The activated ribosome-inactivating protein then kills the cell by inactivating cellular ribosomes. A preferred embodiment of the invention is specific for human immunodeficiency virus (HIV) and uses ricin as the ribosome-inactivating protein. In another preferred embodiment of the invention, the variant of the ribosome-inactivating protein is modified by attachment of one or more hydrophobic agents. The hydrophobic agent facilitates entry of the variant of the ribosome-inactivating protein into cells and can lead to incorporation of the ribosome-inactivating protein into viral particles. Still another preferred embodiment of the invention includes a targeting moiety attached to the variants of the ribosome-inactivating protein to target the agent to HIV infectable cells.

  6. Selective Destruction Of Cells Infected With The Human Immunodeficiency Virus

    DOE Patents [OSTI]

    Keener, William K.; Ward, Thomas E.

    2006-03-28

    Compositions and methods for selectively killing a cell containing a viral protease are disclosed. The composition is a varient of a protein synthesis inactivating toxin wherein a viral protease cleavage site is interposed between the A and B chains. The variant of the type II ribosome-inactivating protein is activated by digestion of the viral protease cleavage site by the specific viral protease. The activated ribosome-inactivating protein then kills the cell by inactivating cellular ribosomes. A preferred embodiment of the invention is specific for human immunodeficiency virus (HIV) and uses ricin as the ribosome-inactivating protein. In another preferred embodiment of the invention, the variant of the ribosome-inactivating protein is modified by attachment of one or more hydrophobic agents. The hydrophobic agent facilitates entry of the variant of the ribosome-inactivating protein into cells and can lead to incorporation of the ribosome-inactivating protein into viral particles. Still another preferred embodiment of the invention includes a targeting moiety attached to the variants of the ribosome-inactivating protein to target the agent to HIV infectable cells.

  7. Characterization of genetic variability of Venezuelan equine encephalitis viruses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gardner, Shea N.; McLoughlin, Kevin; Be, Nicholas A.; Allen, Jonathan; Weaver, Scott C.; Forrester, Naomi; Guerbois, Mathilde; Jaing, Crystal

    2016-04-07

    Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne alphavirus that has caused large outbreaks of severe illness in both horses and humans. New approaches are needed to rapidly infer the origin of a newly discovered VEEV strain, estimate its equine amplification and resultant epidemic potential, and predict human virulence phenotype. We performed whole genome single nucleotide polymorphism (SNP) analysis of all available VEE antigenic complex genomes, verified that a SNP-based phylogeny accurately captured the features of a phylogenetic tree based on multiple sequence alignment, and developed a high resolution genome-wide SNP microarray. We used the microarray to analyze a broadmore » panel of VEEV isolates, found excellent concordance between array- and sequence-based SNP calls, genotyped unsequenced isolates, and placed them on a phylogeny with sequenced genomes. The microarray successfully genotyped VEEV directly from tissue samples of an infected mouse, bypassing the need for viral isolation, culture and genomic sequencing. Lastly, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype.« less

  8. P1-Substituted Symmetry-Based Human Immunodeficiency Virus Protease Inhibitors with Potent Antiviral Activity against Drug-Resistant Viruses

    SciTech Connect (OSTI)

    DeGoey, David A.; Grampovnik, David J.; Chen, Hui-Ju; Flosi, William J.; Klein, Larry L.; Dekhtyar, Tatyana; Stoll, Vincent; Mamo, Mulugeta; Molla, Akhteruzzaman; Kempf, Dale J.

    2013-03-07

    Because there is currently no cure for HIV infection, patients must remain on long-term drug therapy, leading to concerns over potential drug side effects and the emergence of drug resistance. For this reason, new and safe antiretroviral agents with improved potency against drug-resistant strains of HIV are needed. A series of HIV protease inhibitors (PIs) with potent activity against both wild-type (WT) virus and drug-resistant strains of HIV was designed and synthesized. The incorporation of substituents with hydrogen bond donor and acceptor groups at the P1 position of our symmetry-based inhibitor series resulted in significant potency improvements against the resistant mutants. By this approach, several compounds, such as 13, 24, and 29, were identified that demonstrated similar or improved potencies compared to 1 against highly mutated strains of HIV derived from patients who previously failed HIV PI therapy. Overall, compound 13 demonstrated the best balance of potency against drug resistant strains of HIV and oral bioavailability in pharmacokinetic studies. X-ray analysis of an HIV PI with an improved resistance profile bound to WT HIV protease is also reported.

  9. West Nile virus isolated from Virginia opossum (Didelphis virginiana) in Northwest Missouri 2012

    SciTech Connect (OSTI)

    Bosco-Lauth, Angela; Harmon, Jessica; Lash, R. Ryan; Weiss, Sonja; Langevin, Stanley; Savage, Harry; Marvin S. Godsey, Jr.; Burkhalter, Kristen; Root, J. Jeffrey; Gidlewski, Thomas; Nicholson, William; Brault, Aaron C.; Komar, Nicholas

    2014-12-01

    We describe the isolation of West Nile virus (WNV; Flaviviridae, flavivirus) from blood of a Virginia opossum (Didelphis virginiana) collected in northwestern Missouri, USA in August 2012. Furthermore, sequencing determined that the virus was related to lineage 1a WNV02 strains. We discuss the role of wildlife in WNV disease epidemiology.

  10. Rapid detection of Ebola virus with a reagent-free, point-of-care biosensor

    SciTech Connect (OSTI)

    Baca, Justin T.; Severns, Virginia; Lovato, Debbie; Branch, Darren W.; Larson, Richard S.

    2015-04-14

    Surface acoustic wave (SAW) sensors can rapidly detect Ebola antigens at the point-of-care without the need for added reagents, sample processing, or specialized personnel. This preliminary study demonstrates SAW biosensor detection of the Ebola virus in a concentration-dependent manner. The detection limit with this methodology is below the average level of viremia detected on the first day of symptoms by PCR. We observe a log-linear sensor response for highly fragmented Ebola viral particles, with a detection limit corresponding to 1.9 × 10⁴ PFU/mL prior to virus inactivation. We predict greatly improved sensitivity for intact, infectious Ebola virus. This point-of-care methodology has the potential to detect Ebola viremia prior to symptom onset, greatly enabling infection control and rapid treatment. This biosensor platform is powered by disposable AA batteries and can be rapidly adapted to detect other emerging diseases in austere conditions.

  11. Rapid detection of Ebola virus with a reagent-free, point-of-care biosensor

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Baca, Justin T.; Severns, Virginia; Lovato, Debbie; Branch, Darren W.; Larson, Richard S.

    2015-04-14

    Surface acoustic wave (SAW) sensors can rapidly detect Ebola antigens at the point-of-care without the need for added reagents, sample processing, or specialized personnel. This preliminary study demonstrates SAW biosensor detection of the Ebola virus in a concentration-dependent manner. The detection limit with this methodology is below the average level of viremia detected on the first day of symptoms by PCR. We observe a log-linear sensor response for highly fragmented Ebola viral particles, with a detection limit corresponding to 1.9 × 10⁴ PFU/mL prior to virus inactivation. We predict greatly improved sensitivity for intact, infectious Ebola virus. This point-of-care methodologymore » has the potential to detect Ebola viremia prior to symptom onset, greatly enabling infection control and rapid treatment. This biosensor platform is powered by disposable AA batteries and can be rapidly adapted to detect other emerging diseases in austere conditions.« less

  12. Three dimensional colorimetric assay assemblies

    DOE Patents [OSTI]

    Charych, Deborah; Reichart, Anke

    2000-01-01

    A direct assay is described using novel three-dimensional polymeric assemblies which change from a blue to red color when exposed to an analyte, in one case a flu virus. The assemblies are typically in the form of liposomes which can be maintained in a suspension, and show great intensity in their color changes. Their method of production is also described.

  13. Apple latent spherical virus vectors for reliable and effective virus-induced gene silencing among a broad range of plants including tobacco, tomato, Arabidopsis thaliana, cucurbits, and legumes

    SciTech Connect (OSTI)

    Igarashi, Aki; Yamagata, Kousuke; Sugai, Tomokazu; Takahashi, Yukari; Sugawara, Emiko; Tamura, Akihiro; Yaegashi, Hajime; Yamagishi, Noriko; Takahashi, Tsubasa; Isogai, Masamichi; Takahashi, Hideki; Yoshikawa, Nobuyuki

    2009-04-10

    Apple latent spherical virus (ALSV) vectors were evaluated for virus-induced gene silencing (VIGS) of endogenous genes among a broad range of plant species. ALSV vectors carrying partial sequences of a subunit of magnesium chelatase (SU) and phytoene desaturase (PDS) genes induced highly uniform knockout phenotypes typical of SU and PDS inhibition on model plants such as tobacco and Arabidopsis thaliana, and economically important crops such as tomato, legume, and cucurbit species. The silencing phenotypes persisted throughout plant growth in these plants. In addition, ALSV vectors could be successfully used to silence a meristem gene, proliferating cell nuclear antigen and disease resistant N gene in tobacco and RCY1 gene in A. thaliana. As ALSV infects most host plants symptomlessly and effectively induces stable VIGS for long periods, the ALSV vector is a valuable tool to determine the functions of interested genes among a broad range of plant species.

  14. Lung Irradiation Increases Mortality After Influenza A Virus Challenge Occurring Late After Exposure

    SciTech Connect (OSTI)

    Manning, Casey M.; Johnston, Carl J.; Department of Pediatrics, University of Rochester Medical Center, Rochester, New York ; Reed, Christina K.; Lawrence, B. Paige; Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York ; Williams, Jacqueline P.; Finkelstein, Jacob N.

    2013-05-01

    Purpose: To address whether irradiation-induced changes in the lung environment alter responses to a viral challenge delivered late after exposure but before the appearance of late lung radiation injury. Methods and Materials: C57BL/6J mice received either lung alone or combined lung and whole-body irradiation (0-15 Gy). At 10 weeks after irradiation, animals were infected with 120 HAU influenza virus strain A/HKx31. Innate and adaptive immune cell recruitment was determined using flow cytometry. Cytokine and chemokine production and protein leakage into the lung after infection were assessed. Results: Prior irradiation led to a dose-dependent failure to regain body weight after infection and exacerbated mortality, but it did not affect virus-specific immune responses or virus clearance. Surviving irradiated animals displayed a persistent increase in total protein in bronchoalveolar lavage fluid and edema. Conclusions: Lung irradiation increased susceptibility to death after infection with influenza virus and impaired the ability to complete recovery. This altered response does not seem to be due to a radiation effect on the immune response, but it may possibly be an effect on epithelial repair.

  15. A C. elegans-based foam for rapid on-site detection of residual live virus.

    SciTech Connect (OSTI)

    Negrete, Oscar A.; Branda, Catherine; Hardesty, Jasper O. E.; Tucker, Mark David; Kaiser, Julia N.; Kozina, Carol L.; Chirica, Gabriela S.

    2012-02-01

    In the response to and recovery from a critical homeland security event involving deliberate or accidental release of biological agents, initial decontamination efforts are necessarily followed by tests for the presence of residual live virus or bacteria. Such 'clearance sampling' should be rapid and accurate, to inform decision makers as they take appropriate action to ensure the safety of the public and of operational personnel. However, the current protocol for clearance sampling is extremely time-intensive and costly, and requires significant amounts of laboratory space and capacity. Detection of residual live virus is particularly problematic and time-consuming, as it requires evaluation of replication potential within a eukaryotic host such as chicken embryos. The intention of this project was to develop a new method for clearance sampling, by leveraging Sandia's expertise in the biological and material sciences in order to create a C. elegans-based foam that could be applied directly to the entire contaminated area for quick and accurate detection of any and all residual live virus by means of a fluorescent signal. Such a novel technology for rapid, on-site detection of live virus would greatly interest the DHS, DoD, and EPA, and hold broad commercial potential, especially with regard to the transportation industry.

  16. Structure of the Newcastle disease virus F protein in the post-fusion conformation

    SciTech Connect (OSTI)

    Swanson, Kurt; Wen, Xiaolin; Leser, George P.; Paterson, Reay G.; Lamb, Robert A.; Jardetzky, Theodore S. (Stanford-MED); (NWU); (HHMI)

    2010-11-17

    The paramyxovirus F protein is a class I viral membrane fusion protein which undergoes a significant refolding transition during virus entry. Previous studies of the Newcastle disease virus, human parainfluenza virus 3 and parainfluenza virus 5 F proteins revealed differences in the pre- and post-fusion structures. The NDV Queensland (Q) F structure lacked structural elements observed in the other two structures, which are key to the refolding and fusogenic activity of F. Here we present the NDV Australia-Victoria (AV) F protein post-fusion structure and provide EM evidence for its folding to a pre-fusion form. The NDV AV F structure contains heptad repeat elements missing in the previous NDV Q F structure, forming a post-fusion six-helix bundle (6HB) similar to the post-fusion hPIV3 F structure. Electrostatic and temperature factor analysis of the F structures points to regions of these proteins that may be functionally important in their membrane fusion activity.

  17. Identification of full-length transmitted/founder viruses and their progeny in primary HIV-1 infection

    SciTech Connect (OSTI)

    Korber, Bette; Hraber, Peter; Giorgi, Elena; Bhattacharya, T

    2009-01-01

    Identification of transmitted/founder virus genomes and their progeny by is a novel strategy for probing the molecular basis of HIV-1 transmission and for evaluating the genetic imprint of viral and host factors that act to constrain or facilitate virus replication. Here, we show in a cohort of twelve acutely infected subjects (9 clade B; 3 clade C), that complete genomic sequences of transmitted/founder viruses could be inferred using single genome amplification of plasma viral RNA, direct amplicon sequencing, and a model of random virus evolution. This allowed for the precise identification, chemical synthesis, molecular cloning, and biological analysis of those viruses actually responsible for productive clinical infection and for a comprehensive mapping of sequential viral genomes and proteomes for mutations that are necessary or incidental to the establishment of HIV-1 persistence. Transmitted/founder viruses were CD4 and CCR5 tropic, replicated preferentially in activated primary T-Iymphocytes but not monocyte-derived macrophages, and were effectively shielded from most heterologous or broadly neutralizing antibodies. By 3 months of infection, the evolving viral quasispecies in three subjects showed mutational fixation at only 2-5 discreet genomic loci. By 6-12 months, mutational fixation was evident at 18-27 genomic loci. Some, but not all, of these mutations were attributable to virus escape from cytotoxic Tlymphocytes or neutralizing antibodies, suggesting that other viral or host factors may influence early HIV -1 fitness.

  18. Surveillance for Western equine encephalitis St. Louis encephalitis and West Nile viruses using reverse transcription loop-mediated isothermal amplification

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Meagher, Robert J.; Ball, Cameron Scott; Langevin, Stanley A.; Fang, Ying; Wheeler, Sarah S.; Coffey, Lark L.

    2016-01-25

    In this study, collection of mosquitoes and testing for vector-borne viruses is a key surveillance activity that directly influences the vector control efforts of public health agencies, including determining when and where to apply insecticides. Vector control districts in California routinely monitor for three human pathogenic viruses including West Nile virus (WNV), Western equine encephalitis virus (WEEV), and St. Louis encephalitis virus (SLEV). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) offers highly sensitive and specific detection of these three viruses in a single multiplex reaction, but this technique requires costly, specialized equipment that is generally only available in centralized publicmore » health laboratories. We report the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect WNV, WEEV, and SLEV RNA extracted from pooled mosquito samples collected in California, including novel primer sets for specific detection of WEEV and SLEV, targeting the nonstructural protein 4 (nsP4) gene of WEEV and the 3’ untranslated region (3’-UTR) of SLEV. Our WEEV and SLEV RT-LAMP primers allowed detection of <0.1 PFU/reaction of their respective targets in <30 minutes, and exhibited high specificity without cross reactivity when tested against a panel of alphaviruses and flaviviruses. Furthermore, the SLEV primers do not cross-react with WNV, despite both viruses being closely related members of the Japanese encephalitis virus complex. The SLEV and WEEV primers can also be combined in a single RT-LAMP reaction, with discrimination between amplicons by melt curve analysis. Although RT-qPCR is approximately one order of magnitude more sensitive than RT-LAMP for all three targets, the RT-LAMP technique is less instrumentally intensive than RT-qPCR and provides a more cost-effective method of vector-borne virus surveillance.« less

  19. Ocean Viruses: Tiny entities with Global Impacts ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Sullivan, Matthew B [University of Arizona

    2013-01-15

    Matt Sullivan from the University of Arizona on "Ocean Viruses: Tiny Entities with Global Impacts" at the 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif.

  20. Ocean Viruses: Tiny entities with Global Impacts ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Sullivan, Matthew B [University of Arizona] [University of Arizona

    2012-03-22

    Matt Sullivan from the University of Arizona on "Ocean Viruses: Tiny Entities with Global Impacts" at the 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif.

  1. DOE Grant DEFG02-95ER25253 Final Report Development of Simulation Tools for Virus Shell Assembly

    Office of Scientific and Technical Information (OSTI)

    i . ? 1 r DOE Grant DEFG02-95ER25253 Final Report Development of Simulation Tools for Virus Shell Assembly Bonnie Berger Introduction Prof. Berger's major areas of research have been in applying computational and mathematical tech- niques to problems in biology, and more specifically to problems in protein folding and genomics. Significant progress has been made in the following areas relating to virus shell assembly: develop- ment has been progressing on a second-generation self-assembly

  2. Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Moody, M.  Anthony; Gao, Feng; Gurley, Thaddeus  C.; Amos, Joshua  D.; Kumar, Amit; Hora, Bhavna; Marshall, Dawn  J.; Whitesides, John  F.; Xia, Shi-Mao; Parks, Robert; et al

    2015-09-09

    The third variable (V3) loop and the CD4 binding site (CD4bs) of the viral envelope are frequently targeted by neutralizing antibodies (nAbs) in HIV-1-infected individuals. In chronic infection, virus escape mutants repopulate the plasma and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize, but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tiermore » 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.« less

  3. Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses

    SciTech Connect (OSTI)

    Moody, M.  Anthony; Gao, Feng; Gurley, Thaddeus  C.; Amos, Joshua  D.; Kumar, Amit; Hora, Bhavna; Marshall, Dawn  J.; Whitesides, John  F.; Xia, Shi-Mao; Parks, Robert; Lloyd, Krissey  E.; Hwang, Kwan-Ki; Lu, Xiaozhi; Bonsignori, Mattia; Finzi, Andrés; Vandergrift, Nathan  A.; Alam, S.  Munir; Ferrari, Guido; Shen, Xiaoying; Tomaras, Georgia  D.; Kamanga, Gift; Cohen, Myron  S.; Sam, Noel  E.; Kapiga, Saidi; Gray, Elin S.; Tumba, Nancy  L.; Morris, Lynn; Zolla-Pazner, Susan; Gorny, Miroslaw  K.; Mascola, John  R.; Hahn, Beatrice H.; Shaw, George  M.; Sodroski, Joseph  G.; Liao, Hua-Xin; Montefiori, David C.; Hraber, Peter T.; Korber, Bette T.; Haynes, Barton F.

    2015-09-09

    The third variable (V3) loop and the CD4 binding site (CD4bs) of the viral envelope are frequently targeted by neutralizing antibodies (nAbs) in HIV-1-infected individuals. In chronic infection, virus escape mutants repopulate the plasma and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize, but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tier 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.

  4. Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients

    SciTech Connect (OSTI)

    Yue, Ling; Pfafferott, Katja J.; Baalwa, Joshua; Conrod, Karen; Dong, Catherine C.; Chui, Cecilia; Rong, Rong; Claiborne, Daniel T.; Prince, Jessica L.; Tang, Jianming; Ribeiro, Ruy M.; Cormier, Emmanuel; Hahn, Beatrice H.; Perelson, Alan S.; Shaw, George M.; Karita, Etienne; Gilmour, Jill; Goepfert, Paul; Derdeyn, Cynthia A.; Allen, Susan A.; Borrow, Persephone; Hunter, Eric; Douek, Daniel C.

    2015-01-08

    Control of virus replication in HIV-1 infection is critical to delaying disease progression. While cellular immune responses are a key determinant of control, relatively little is known about the contribution of the infecting virus to this process. To gain insight into this interplay between virus and host in viral control, we conducted a detailed analysis of two heterosexual HIV-1 subtype A transmission pairs in which female recipients sharing three HLA class I alleles exhibited contrasting clinical outcomes: R880F controlled virus replication while R463F experienced high viral loads and rapid disease progression. Near full-length single genome amplification defined the infecting transmitted/founder (T/F) virus proteome and subsequent sequence evolution over the first year of infection for both acutely infected recipients. T/F virus replicative capacities were compared in vitro, while the development of the earliest cellular immune response was defined using autologous virus sequence-based peptides. The R880F T/F virus replicated significantly slower in vitro than that transmitted to R463F. While neutralizing antibody responses were similar in both subjects, during acute infection R880F mounted a broad T cell response, the most dominant components of which targeted epitopes from which escape was limited. In contrast, the primary HIV-specific T cell response in R463F was focused on just two epitopes, one of which rapidly escaped. This comprehensive study highlights both the importance of the contribution of the lower replication capacity of the transmitted/founder virus and an associated induction of a broad primary HIV-specific T cell response, which was not undermined by rapid epitope escape, to long-term viral control in HIV-1 infection. It underscores the importance of the earliest CD8 T cell response targeting regions of the virus proteome that cannot mutate without a high fitness cost, further emphasizing the need for vaccines that elicit a breadth of T cell responses to conserved viral epitopes.

  5. Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Yue, Ling; Pfafferott, Katja J.; Baalwa, Joshua; Conrod, Karen; Dong, Catherine C.; Chui, Cecilia; Rong, Rong; Claiborne, Daniel T.; Prince, Jessica L.; Tang, Jianming; et al

    2015-01-08

    Control of virus replication in HIV-1 infection is critical to delaying disease progression. While cellular immune responses are a key determinant of control, relatively little is known about the contribution of the infecting virus to this process. To gain insight into this interplay between virus and host in viral control, we conducted a detailed analysis of two heterosexual HIV-1 subtype A transmission pairs in which female recipients sharing three HLA class I alleles exhibited contrasting clinical outcomes: R880F controlled virus replication while R463F experienced high viral loads and rapid disease progression. Near full-length single genome amplification defined the infecting transmitted/foundermore » (T/F) virus proteome and subsequent sequence evolution over the first year of infection for both acutely infected recipients. T/F virus replicative capacities were compared in vitro, while the development of the earliest cellular immune response was defined using autologous virus sequence-based peptides. The R880F T/F virus replicated significantly slower in vitro than that transmitted to R463F. While neutralizing antibody responses were similar in both subjects, during acute infection R880F mounted a broad T cell response, the most dominant components of which targeted epitopes from which escape was limited. In contrast, the primary HIV-specific T cell response in R463F was focused on just two epitopes, one of which rapidly escaped. This comprehensive study highlights both the importance of the contribution of the lower replication capacity of the transmitted/founder virus and an associated induction of a broad primary HIV-specific T cell response, which was not undermined by rapid epitope escape, to long-term viral control in HIV-1 infection. It underscores the importance of the earliest CD8 T cell response targeting regions of the virus proteome that cannot mutate without a high fitness cost, further emphasizing the need for vaccines that elicit a breadth of T cell responses to conserved viral epitopes.« less

  6. Recombination enhances HIV-1 envelope diversity by facilitating the survival of latent genomic fragments in the plasma virus population

    SciTech Connect (OSTI)

    Immonen, Taina T.; Conway, Jessica M.; Romero-Severson, Ethan O.; Perelson, Alan S.; Leitner, Thomas; Kouyos, Roger Dimitri

    2015-12-22

    HIV-1 is subject to immune pressure exerted by the host, giving variants that escape the immune response an advantage. Virus released from activated latent cells competes against variants that have continually evolved and adapted to host immune pressure. Nevertheless, there is increasing evidence that virus displaying a signal of latency survives in patient plasma despite having reduced fitness due to long-term immune memory. We investigated the survival of virus with latent envelope genomic fragments by simulating within-host HIV-1 sequence evolution and the cycling of viral lineages in and out of the latent reservoir. Our model incorporates a detailed mutation process including nucleotide substitution, recombination, latent reservoir dynamics, diversifying selection pressure driven by the immune response, and purifying selection pressure asserted by deleterious mutations. We evaluated the ability of our model to capture sequence evolution in vivo by comparing our simulated sequences to HIV-1 envelope sequence data from 16 HIV-infected untreated patients. Empirical sequence divergence and diversity measures were qualitatively and quantitatively similar to those of our simulated HIV-1 populations, suggesting that our model invokes realistic trends of HIV-1 genetic evolution. Moreover, reconstructed phylogenies of simulated and patient HIV-1 populations showed similar topological structures. Our simulation results suggest that recombination is a key mechanism facilitating the persistence of virus with latent envelope genomic fragments in the productively infected cell population. Recombination increased the survival probability of latent virus forms approximately 13-fold. Prevalence of virus with latent fragments in productively infected cells was observed in only 2% of simulations when we ignored recombination, while the proportion increased to 27% of simulations when we allowed recombination. We also found that the selection pressures exerted by different fitness landscapes influenced the shape of phylogenies, diversity trends, and survival of virus with latent genomic fragments. Furthermore, our model predicts that the persistence of latent genomic fragments from multiple different ancestral origins increases sequence diversity in plasma for reasonable fitness landscapes.

  7. Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein-?RNA complex

    SciTech Connect (OSTI)

    Alayyoubi, Maher; Leser, George P.; Kors, Christopher A.; Lamb, Robert A.

    2015-04-07

    Parainfluenza virus 5 (PIV5) is a member of the Paramyxoviridae family of membrane-enveloped viruses with a negative-sense RNA genome that is packaged and protected by long filamentous nucleocapsid-helix structures (RNPs). These RNPs, consisting of ~2,600 protomers of nucleocapsid (N) protein, form the template for viral transcription and replication. We have determined the 3D X-ray crystal structure of the nucleoprotein (N)-RNA complex from PIV5 to 3.11- resolution. The structure reveals a 13-mer nucleocapsid ring whose diameter, cavity, and pitch/height dimensions agree with EM data from early studies on the Paramyxovirinae subfamily of native RNPs, indicating that it closely represents one-turn in the building block of the RNP helices. The PIV5-N nucleocapsid ring encapsidates a nuclease resistant 78-nt RNA strand in its positively charged groove formed between the N-terminal (NTD) and C-terminal (CTD) domains of its successive N protomers. Six nucleotides precisely are associated with each N protomer, with alternating three-base-in three-base-out conformation. The binding of six nucleotides per protomer is consistent with the "rule of six" that governs the genome packaging of the Paramyxovirinae subfamily of viruses. PIV5-N protomer subdomains are very similar in structure to the previously solved Nipah-N structure, but with a difference in the angle between NTD/CTD at the RNA hinge region. Based on the Nipah-N structure we modeled a PIV5-N open conformation in which the CTD rotates away from the RNA strand into the inner spacious nucleocapsid-ring cavity. This rotation would expose the RNA for the viral polymerase activity without major disruption of the nucleocapsid structure.

  8. Dynamics of lipid droplets induced by the hepatitis C virus core protein

    SciTech Connect (OSTI)

    Lyn, Rodney K.; Department of Chemistry, University of Ottawa, Ottawa ; Kennedy, David C.; Stolow, Albert; Ridsdale, Andrew; Pezacki, John Paul

    2010-09-03

    Research highlights: {yields} Hepatitis C virus uses lipid droplets (LD) onto which HCV core proteins bind. {yields} HCV core proteins on LDs facilitate viral particle assembly. {yields} We used a novel combination of CARS, two-photon fluorescence, and DIC microscopies. {yields} Particle tracking experiments show that core slowly affects LD localization. {yields} Particle tracking measured the change in speed and directionality of LD movement. -- Abstract: The hepatitis C virus (HCV) is a global health problem, with limited treatment options and no vaccine available. HCV uses components of the host cell to proliferate, including lipid droplets (LD) onto which HCV core proteins bind and facilitate viral particle assembly. We have measured the dynamics of HCV core protein-mediated changes in LDs and rates of LD movement on microtubules using a combination of coherent anti-Stokes Raman scattering (CARS), two-photon fluorescence (TPF), and differential interference contrast (DIC) microscopies. Results show that the HCV core protein induces rapid increases in LD size. Particle tracking experiments show that HCV core protein slowly affects LD localization by controlling the directionality of LD movement on microtubules. These dynamic processes ultimately aid HCV in propagating and the molecules and interactions involved represent novel targets for potential therapeutic intervention.

  9. Improving Anti-Influenza Medications

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Improving Anti-Influenza Medications Improving Anti-Influenza Medications Print Monday, 07 March 2016 16:16 The annual flu epidemics caused by influenza viruses, especially the influenza A virus, affect about 10-20% of the world's population each season. This highly contagious illness can trigger serious complications and can still lead at times to death, even today. Scientists have been working for a while with the M2 proton channel from the influenza A virus, which is one of nature's smallest

  10. Recombination enhances HIV-1 envelope diversity by facilitating the survival of latent genomic fragments in the plasma virus population

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Immonen, Taina T.; Conway, Jessica M.; Romero-Severson, Ethan O.; Perelson, Alan S.; Leitner, Thomas; Kouyos, Roger Dimitri

    2015-12-22

    HIV-1 is subject to immune pressure exerted by the host, giving variants that escape the immune response an advantage. Virus released from activated latent cells competes against variants that have continually evolved and adapted to host immune pressure. Nevertheless, there is increasing evidence that virus displaying a signal of latency survives in patient plasma despite having reduced fitness due to long-term immune memory. We investigated the survival of virus with latent envelope genomic fragments by simulating within-host HIV-1 sequence evolution and the cycling of viral lineages in and out of the latent reservoir. Our model incorporates a detailed mutation processmore » including nucleotide substitution, recombination, latent reservoir dynamics, diversifying selection pressure driven by the immune response, and purifying selection pressure asserted by deleterious mutations. We evaluated the ability of our model to capture sequence evolution in vivo by comparing our simulated sequences to HIV-1 envelope sequence data from 16 HIV-infected untreated patients. Empirical sequence divergence and diversity measures were qualitatively and quantitatively similar to those of our simulated HIV-1 populations, suggesting that our model invokes realistic trends of HIV-1 genetic evolution. Moreover, reconstructed phylogenies of simulated and patient HIV-1 populations showed similar topological structures. Our simulation results suggest that recombination is a key mechanism facilitating the persistence of virus with latent envelope genomic fragments in the productively infected cell population. Recombination increased the survival probability of latent virus forms approximately 13-fold. Prevalence of virus with latent fragments in productively infected cells was observed in only 2% of simulations when we ignored recombination, while the proportion increased to 27% of simulations when we allowed recombination. We also found that the selection pressures exerted by different fitness landscapes influenced the shape of phylogenies, diversity trends, and survival of virus with latent genomic fragments. Furthermore, our model predicts that the persistence of latent genomic fragments from multiple different ancestral origins increases sequence diversity in plasma for reasonable fitness landscapes.« less

  11. Synergized resmethrin and corticosterone alter the chicken's response to west nile virus

    SciTech Connect (OSTI)

    Jankowski, Mark David; Franson, J Christian; Mostl, Erich; Porter, Warren P; Hofmeister, Erik K

    2009-01-01

    Debate concerning arbovirus control strategies remains contentious because concern regarding the relative risk of viral infection and environmental toxicant exposure is high but inadequately characterized. Taking this into account, mosquito control agencies employ aerial insecticides only after arbovirus surveillance data indicate high local mosquito-infection-rates. Successfully mitigating the risk of adult-mosquito-control insecticides ('adulticides') to non-target species such as humans, domestic animals, fish, beneficial insects and wildlife, while increasing their efficacy to reduce arbovirus outbreak intensity requires targeted scientific data from animal toxicity studies and environmental monitoring activities. Wild birds are an important reservoir host for WNv and are potentially exposed to insecticides used for mosquito control. However, no risk assessments have evaluated whether insecticides augment or extend the potential transmissibility of West Nile virus (WNv) in birds. In order to augment existing resmethrin risk assessments, we aimed to determine whether synergized resmethrin (SR) may cause chickens to develop an elevated or extended WN viremia and if subacute stress may affect its immunotoxicity. We distributed 40 chickens into four groups then exposed them prior to and during WNv infection with SR (50 {mu}g/l resmethrin + 150 {mu}g/l piperonyl butoxide) and/or 20 mg/I corticosterone (CORT) in their drinking-water. Corticosterone was given for 10 continuous days and SR was given for 3 alternate days starting the 3rd day of CORT exposure, then chickens were subcutaneously inoculated with WNv on the 5th day of CORT treatment. Compared to controls, CORT treatment extended and elevated viremia, enhanced WNv-specific antibody and increased the percentage of birds that shed oral virus, whereas SR treatment extended viremia, depressed WNv-specific IgG, and increased the percentage of CORT-treated birds that shed oral virus. Corticosterone and SR independently and interactively altered immunity to WNv in chickens. Further characterization of how variations in SR-exposure to and CORT levels in chickens and wild birds relate to laboratory WNv-infection trials is warranted in order to place these findings into an epidemiological context.

  12. Improving the Capacity of Sodium Ion Battery Using a Virus-Templated Nanostructured Composite Cathode

    SciTech Connect (OSTI)

    Moradi, M; Li, Z; Qi, JF; Xing, WT; Xiang, K; Chiang, YM; Belcher, AM

    2015-05-01

    In this work we investigated an energy-efficient biotemplated route to synthesize nanostructured FePO4 for sodium-based batteries. Self-assembled M13 viruses and single wall carbon nanotubes (SWCNTs) have been used as a template to grow amorphous FePO4 nanoparticles at room temperature (the active composite is denoted as Bio-FePO4-CNT) to enhance the electronic conductivity of the active material. Preliminary tests demonstrate a discharge capacity as high as 166 mAh/g at C/10 rate, corresponding to composition Na0.9FePO4, which along with higher C-rate tests show this material to have the highest capacity and power performance reported for amorphous FePO4 electrodes to date.

  13. Relative concordance of human immunodeficiency virus oligomeric and monomeric envelope in CCR5 coreceptor usage

    SciTech Connect (OSTI)

    Teeravechyan, Samaporn; Suphaphiphat, Pirada; Essex, Max; Lee, Tun-Hou

    2008-01-20

    A major difference between binding and fusion assays commonly used to study the human immunodeficiency virus (HIV) envelope is the use of monomeric envelope for the former assay and oligomeric envelope for the latter. Due to discrepancies in their readouts for some mutants, envelope regions involved in CCR5 coreceptor usage were systematically studied to determine whether the discordance is due to inherent differences between the two assays or whether it genuinely reflects functional differences at each entry step. By adding the binding inhibitor TAK-779 to delay coreceptor binding kinetics in the fusion assay, the readouts were found comparable between the assays for the mutants analysed in this study. Our finding indicates that monomeric binding reflects oligomeric envelope-CCR5 interaction, thus discordant results between binding and fusion assays do not necessarily indicate differences in coreceptor usage by oligomeric envelope and monomeric gp120.

  14. Cell cycle regulation of human immunodeficiency virus type 1 integration in T cells: antagonistic effects of nuclear envelope breakdown and chromatin condensation

    SciTech Connect (OSTI)

    Mannioui, Abdelkrim . E-mail: karim.mannioui@chu-stlouis.fr; Schiffer, Cecile . E-mail: cecile.schiffer@voila.fr; Felix, Nathalie . E-mail: nathalie.felix@chu-stlouis.fr

    2004-11-10

    We examined the influence of mitosis on the kinetics of human immunodeficiency virus type 1 integration in T cells. Single-round infection of cells arrested in G1b or allowed to synchronously proceed through division showed that mitosis delays virus integration until 18-24 h postinfection, whereas integration reaches maximum levels by 15 h in G1b-arrested cells. Subcellular fractionation of metaphase-arrested cells indicated that, while nuclear envelope disassembly facilitates docking of viral DNA to chromatin, chromosome condensation directly antagonizes and therefore delays integration. As a result of the balance between the two effects, virus integration efficiency is eventually up to threefold greater in dividing cells. At the single-cell level, using a green fluorescent protein-expressing reporter virus, we found that passage through mitosis leads to prominent asymmetric segregation of the viral genome in daughter cells without interfering with provirus expression.

  15. Iran Deal @ PPPL.key

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Technical Information Iowa State University Spotlights Home DOE Applauds ISU Science and Technical Programs Ames Laboratory is a DOE National Laboratory operated under contract by Iowa State University Physicist developing, improving designer optical materials Chemists discover proton mechanism used by flu virus to infect cells ISU, Ames Lab's Bryden & McCorkle win 2010 R&D 100 Award New tool for cell research may help unravel secrets of disease Beardshear Hall ISU's vision is to

  16. Towards understanding of Nipah virus attachment protein assembly and the role of protein affinity and crowding for membrane curvature events.

    SciTech Connect (OSTI)

    Stachowiak, Jeanne C.; Hayden, Carl C.; Negrete, Oscar A.; Davis, Ryan Wesley; Sasaki, Darryl Yoshio

    2013-10-01

    Pathogenic viruses are a primary threat to our national security and to the health and economy of our world. Effective defense strategies to combat viral infection and spread require the development of understanding of the mechanisms that these pathogens use to invade the host cell. We present in this report results of our research into viral particle recognition and fusion to cell membranes and the role that protein affinity and confinement in lipid domains plays in membrane curvature in cellular fusion and fission events. Herein, we describe 1) the assembly of the G attachment protein of Nipah virus using point mutation studies to define its role in viral particle fusion to the cell membrane, 2) how lateral pressure of membrane bound proteins induce curvature in model membrane systems, and 3) the role of membrane curvature in the selective partitioning of molecular receptors and specific affinity of associated proteins.

  17. Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B)

    SciTech Connect (OSTI)

    Lerch, Thomas F.; Chapman, Michael S.

    2012-02-05

    Adeno-associated virus is a promising vector for gene therapy. In the current study, the binding site on AAV serotype 3B for the heparan sulfate proteoglycan (HSPG) receptor has been characterized. X-ray diffraction identified a disaccharide binding site at the most positively charged region on the virus surface. The contributions of basic amino acids at this and other sites were characterized using site-directed mutagenesis. Both heparin and cell binding are correlated to positive charge at the disaccharide binding site, and transduction is significantly decreased in AAV-3B vectors mutated at this site to reduce heparin binding. While the receptor attachment sites of AAV-3B and AAV-2 are both in the general vicinity of the viral spikes, the exact amino acids that participate in electrostatic interactions are distinct. Diversity in the mechanisms of cell attachment by AAV serotypes will be an important consideration for the rational design of improved gene therapy vectors.

  18. Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B)

    SciTech Connect (OSTI)

    Lerch, Thomas F.; Chapman, Michael S.

    2012-05-24

    Adeno-associated virus is a promising vector for gene therapy. In the current study, the binding site on AAV serotype 3B for the heparan sulfate proteoglycan (HSPG) receptor has been characterized. X-ray diffraction identified a disaccharide binding site at the most positively charged region on the virus surface. The contributions of basic amino acids at this and other sites were characterized using site-directed mutagenesis. Both heparin and cell binding are correlated to positive charge at the disaccharide binding site, and transduction is significantly decreased in AAV-3B vectors mutated at this site to reduce heparin binding. While the receptor attachment sites of AAV-3B and AAV-2 are both in the general vicinity of the viral spikes, the exact amino acids that participate in electrostatic interactions are distinct. Diversity in the mechanisms of cell attachment by AAV serotypes will be an important consideration for the rational design of improved gene therapy vectors.

  19. Development and Characterization of A Multiplexed RT-PCR Species Specific Assay for Bovine and one for Porcine Foot-and-Mouth Disease Virus Rule-Out

    SciTech Connect (OSTI)

    Smith, S M; Danganan, L; Tammero, L; Vitalis, B; Lenhoff, R; Naraghi-arani, P; Hindson, B

    2007-08-06

    Lawrence Livermore National Laboratory (LLNL), in collaboration with the Department of Homeland Security (DHS) and the United States Department of Agriculture (USDA), Animal and Plant Health Inspection Services (APHIS) has developed candidate multiplexed assays that may potentially be used within the National Animal Health Laboratory Network (NAHLN), the National Veterinary Services Laboratory (Ames, Iowa) and the Plum Island Animal Disease Center (PIADC). This effort has the ability to improve our nation's capability to discriminate between foreign animal diseases and those that are endemic using a single assay, thereby increasing our ability to protect food and agricultural resources with a diagnostic test which could enhance the nation's capabilities for early detection of a foreign animal disease. In FY2005 with funding from the DHS, LLNL developed the first version (Version 1.0) of a multiplexed (MUX) nucleic-acid-based RT-PCR assay that included signatures for foot-and-mouth disease virus (FMDV) detection with rule-out tests for two other foreign animal diseases (FADs) of swine, Vesicular Exanthema of Swine (VESV) and Swine Vesicular Disease Virus (SVDV), and four other domestic viral diseases Bovine Viral Diarrhea Virus (BVDV), Bovine Herpes Virus 1 (BHV-1), Bluetongue virus (BTV) and Parapox virus complex (which includes Bovine Papular Stomatitis Virus [BPSV], Orf of sheep, and Pseudocowpox). In FY06, LLNL has developed Bovine and Porcine species-specific panel which included existing signatures from Version 1.0 panel as well as new signatures. The MUX RT-PCR porcine assay for detection of FMDV includes the FADs, VESV and SVD in addition to vesicular stomatitis virus (VSV) and porcine reproductive and respiratory syndrome (PRRS). LLNL has also developed a MUX RT-PCR bovine assay for detection of FMDV with rule out tests for the two bovine FADs malignant catarrhal fever (MCF), rinderpest virus (RPV) and the domestic diseases vesicular stomatitis virus (VSV), bovine viral diarrhea virus (BVDV), infectious bovine rhinotracheitus virus (BHV-1), bluetongue virus (BTV), and the Parapox viruses (which are of two bovine types) bovine papular stomatitis virus (BPSV) and psuedocowpox (PCP). A timeline for this development is presented in Table 1. The development of the Version 1.0 panel for FMDV rule-out and the most current efforts aimed to designed species specific panels has spanned over 2 1/2 years with multiple collaborative partnerships. This document provides a summary of the development, testing and performance data at OIE Stage 1 Feasibility into Stage 2 Assay Development and Standardization1 (see Table 2), gathered as of June 30th, 2007 for the porcine and bovine MUX assay panels. We present an overview of the identification and selection of candidate genetic signatures, the assay development process, and preliminary performance data for each of the individual signatures as characterized in the multiplexed format for the porcine and bovine panels. The Stage 1 Feasibility data of the multiplexed panels is presented in this report also includes relevant data acquired from the Version 1.0 panel as supporting information where appropriate. In contrast to last years effort, the development of the bovine and porcine panels is pending additional work to complete analytical characterization of FMDV, VESV, SVD, RPV and MCF. The signature screening process and final panel composition impacts this effort. The unique challenge presented this year was having strict predecessor limitations in completing characterization, where efforts at LLNL must precede efforts at PIADC, such challenges were alleviated in the 2006 reporting by having characterization data from the interlaboratory comparison and at Plum Island under AgDDAP project. We will present an addendum at a later date with additional data on the characterization of the porcine and bovine multiplex assays when that data is available. As a summary report, this document does not provide the details of signature generation, evaluation, and testing, nor does it provide spec

  20. Characterization of Coffee ringspot virus-Lavras: A model for an emerging threat to coffee production and quality

    SciTech Connect (OSTI)

    Ramalho, T.O.; Figueira, A.R.; Sotero, A.J.; Wang, R.; Geraldino Duarte, P.S.; Farman, M.; Goodin, M.M.

    2014-09-15

    The emergence of viruses in Coffee (Coffea arabica and Coffea canephora), the most widely traded agricultural commodity in the world, is of critical concern. The RNA1 (6552 nt) of Coffee ringspot virus is organized into five open reading frames (ORFs) capable of encoding the viral nucleocapsid (ORF1p), phosphoprotein (ORF2p), putative cell-to-cell movement protein (ORF3p), matrix protein (ORF4p) and glycoprotein (ORF5p). Each ORF is separated by a conserved intergenic junction. RNA2 (5945 nt), which completes the bipartite genome, encodes a single protein (ORF6p) with homology to RNA-dependent RNA polymerases. Phylogenetic analysis of L protein sequences firmly establishes CoRSV as a member of the recently proposed Dichorhavirus genus. Predictive algorithms, in planta protein expression, and a yeast-based nuclear import assay were used to determine the nucleophillic character of five CoRSV proteins. Finally, the temperature-dependent ability of CoRSV to establish systemic infections in an initially local lesion host was quantified. - Highlights: • We report genome sequence determination for Coffee ringspot virus (CoRSV). • CoRSV should be considered a member of the proposed Dichorhavirus genus. • We report temperature-dependent systemic infection of an initially local lesion host. • We report in planta protein and localization data for five CoRSV proteins. • In silico predictions of the CoRSV proteins were validated using in vivo assays.

  1. The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex

    SciTech Connect (OSTI)

    Blanc, Guillaume; Duncan, Garry A.; Agarakova, Irina; Borodovsky, Mark; Gurnon, James; Kuo, Alan; Lindquist, Erika; Lucas, Susan; Pangailinan, Jasmyn; Polle, Juergen; Salamov, Asaf; Terry, Astrid; Yamada, Takashi; Dunigan, David D.; Grigoriev, Igor V.; Claverie, Jean-Michel; Etten, James L. Van

    2010-05-06

    Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes.

  2. Structure of unliganded HSV gD reveals a mechanism for receptor-mediated activation of virus entry

    SciTech Connect (OSTI)

    Krummenacher, Claude; Supekar, Vinit M.; Whitbeck, J. Charles; Lazear, Eric; Connolly, Sarah A.; Eisenberg, Roselyn J.; Cohen, Gary H.; Wiley, Don C.; Carfi, Andrea

    2010-07-19

    Herpes simplex virus (HSV) entry into cells requires binding of the envelope glycoprotein D (gD) to one of several cell surface receptors. The 50 C-terminal residues of the gD ectodomain are essential for virus entry, but not for receptor binding. We have determined the structure of an unliganded gD molecule that includes these C-terminal residues. The structure reveals that the C-terminus is anchored near the N-terminal region and masks receptor-binding sites. Locking the C-terminus in the position observed in the crystals by an intramolecular disulfide bond abolished receptor binding and virus entry, demonstrating that this region of gD moves upon receptor binding. Similarly, a point mutant that would destabilize the C-terminus structure was nonfunctional for entry, despite increased affinity for receptors. We propose that a controlled displacement of the gD C-terminus upon receptor binding is an essential feature of HSV entry, ensuring the timely activation of membrane fusion.

  3. Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20

    SciTech Connect (OSTI)

    McCraw, Dustin M.; O' Donnell, Jason K.; Taylor, Kenneth A.; Stagg, Scott M.; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306 ; Chapman, Michael S.

    2012-09-15

    The use of adeno-associated virus (AAV) as a gene therapy vector is limited by the host neutralizing immune response. The cryo-electron microscopy (EM) structure at 8.5 A resolution is determined for a complex of AAV-2 with the Fab' fragment of monoclonal antibody (MAb) A20, the most extensively characterized AAV MAb. The binding footprint is determined through fitting the cryo-EM reconstruction with a homology model following sequencing of the variable domain, and provides a structural basis for integrating diverse prior epitope mappings. The footprint extends from the previously implicated plateau to the side of the spike, and into the conserved canyon, covering a larger area than anticipated. Comparison with structures of binding and non-binding serotypes indicates that recognition depends on a combination of subtle serotype-specific features. Separation of the neutralizing epitope from the heparan sulfate cell attachment site encourages attempts to develop immune-resistant vectors that can still bind to target cells.

  4. Human borna disease virus infection impacts host proteome and histone lysine acetylation in human oligodendroglia cells

    SciTech Connect (OSTI)

    Liu, Xia; Zhao, Libo; Yang, Yongtao; Bode, Liv; Huang, Hua; Liu, Chengyu; Huang, Rongzhong; Zhang, Liang; and others

    2014-09-15

    Background: Borna disease virus (BDV) replicates in the nucleus and establishes persistent infections in mammalian hosts. A human BDV strain was used to address the first time, how BDV infection impacts the proteome and histone lysine acetylation (Kac) of human oligodendroglial (OL) cells, thus allowing a better understanding of infection-driven pathophysiology in vitro. Methods: Proteome and histone lysine acetylation were profiled through stable isotope labeling for cell culture (SILAC)-based quantitative proteomics. The quantifiable proteome was annotated using bioinformatics. Histone acetylation changes were validated by biochemistry assays. Results: Post BDV infection, 4383 quantifiable differential proteins were identified and functionally annotated to metabolism pathways, immune response, DNA replication, DNA repair, and transcriptional regulation. Sixteen of the thirty identified Kac sites in core histones presented altered acetylation levels post infection. Conclusions: BDV infection using a human strain impacted the whole proteome and histone lysine acetylation in OL cells. - Highlights: • A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells). • This study is the first to reveal the host proteomic and histone Kac profiles in BDV-infected OL cells. • BDV infection affected the expression of many transcription factors and several HATs and HDACs.

  5. Molecular basis of endosomal-membrane association for the dengue virus envelope protein

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Rogers, David M.; Kent, Michael S.; Rempe, Susan B.

    2015-01-02

    Dengue virus is coated by an icosahedral shell of 90 envelope protein dimers that convert to trimers at low pH and promote fusion of its membrane with the membrane of the host endosome. We provide the first estimates for the free energy barrier and minimum for two key steps in this process: host membrane bending and protein–membrane binding. Both are studied using complementary membrane elastic, continuum electrostatics and all-atom molecular dynamics simulations. The predicted host membrane bending required to form an initial fusion stalk presents a 22–30 kcal/mol free energy barrier according to a constrained membrane elastic model. Combined continuummore »and molecular dynamics results predict a 15 kcal/mol free energy decrease on binding of each trimer of dengue envelope protein to a membrane with 30% anionic phosphatidylglycerol lipid. The bending cost depends on the preferred curvature of the lipids composing the host membrane leaflets, while the free energy gained for protein binding depends on the surface charge density of the host membrane. The fusion loop of the envelope protein inserts exactly at the level of the interface between the membrane's hydrophobic and head-group regions. As a result, the methods used in this work provide a means for further characterization of the structures and free energies of protein-assisted membrane fusion.« less

  6. Primary Radiation Therapy for Head-and-Neck Cancer in the Setting of Human Immunodeficiency Virus

    SciTech Connect (OSTI)

    Klein, Emily A.; Guiou, Michael; Farwell, D. Gregory; Luu, Quang; Lau, Derick H.; Stuart, Kerri; Vaughan, Andrew; Vijayakumar, Srinivasan; Chen, Allen M.

    2011-01-01

    Purpose: To analyze outcomes after radiation therapy for head-and-neck cancer among a cohort of patients with human immunodeficiency virus (HIV). Methods and Materials: The medical records of 12 patients with serologic evidence of HIV who subsequently underwent radiation therapy to a median dose of 68 Gy (range, 64-72 Gy) for newly diagnosed squamous cell carcinoma of the head and neck were reviewed. Six patients (50%) received concurrent chemotherapy. Intensity-modulated radiotherapy was used in 6 cases (50%). All patients had a Karnofsky performance status of 80 or 90. Nine patients (75%) were receiving antiretroviral therapies at the time of treatment, and the median CD4 count was 460 (range, 266-800). Toxicity was graded according to the Radiation Therapy Oncology Group / European Organization for the Treatment of Cancer toxicity criteria. Results: The 3-year estimates of overall survival and local-regional control were 78% and 92%, respectively. Acute Grade 3+ toxicity occurred in 7 patients (58%), the most common being confluent mucositis (5 patients) and moist skin desquamation (4 patients). Two patients experienced greater than 10% weight loss, and none experienced more than 15% weight loss from baseline. Five patients (42%) experienced treatment breaks in excess of 10 cumulative days, although none required hospitalization. There were no treatment-related fatalities. Conclusions: Radiation therapy for head-and-neck cancer seems to be relatively well tolerated among appropriately selected patients with HIV. The observed rates of toxicity were comparable to historical controls without HIV.

  7. Rational design and adaptive management of combination therapies for Hepatitis C virus infection

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ke, Ruian; Loverdo, Claude; Qi, Hangfei; Sun, Ren; Lloyd-Smith, James O.; Kouyos, Roger Dimitri

    2015-06-30

    Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV) have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensatemore » when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design.« less

  8. Molecular basis of endosomal-membrane association for the dengue virus envelope protein

    SciTech Connect (OSTI)

    Rogers, David M.; Kent, Michael S.; Rempe, Susan B.

    2015-01-02

    Dengue virus is coated by an icosahedral shell of 90 envelope protein dimers that convert to trimers at low pH and promote fusion of its membrane with the membrane of the host endosome. We provide the first estimates for the free energy barrier and minimum for two key steps in this process: host membrane bending and protein–membrane binding. Both are studied using complementary membrane elastic, continuum electrostatics and all-atom molecular dynamics simulations. The predicted host membrane bending required to form an initial fusion stalk presents a 22–30 kcal/mol free energy barrier according to a constrained membrane elastic model. Combined continuum and molecular dynamics results predict a 15 kcal/mol free energy decrease on binding of each trimer of dengue envelope protein to a membrane with 30% anionic phosphatidylglycerol lipid. The bending cost depends on the preferred curvature of the lipids composing the host membrane leaflets, while the free energy gained for protein binding depends on the surface charge density of the host membrane. The fusion loop of the envelope protein inserts exactly at the level of the interface between the membrane's hydrophobic and head-group regions. As a result, the methods used in this work provide a means for further characterization of the structures and free energies of protein-assisted membrane fusion.

  9. Rational design and adaptive management of combination therapies for Hepatitis C virus infection

    SciTech Connect (OSTI)

    Ke, Ruian; Loverdo, Claude; Qi, Hangfei; Sun, Ren; Lloyd-Smith, James O.; Kouyos, Roger Dimitri

    2015-06-30

    Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV) have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensate when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design.

  10. Human immunodeficiency virus contains an epitope immunoreactive with thymosin. cap alpha. /sub 1/ and the 30-amino acid synthetic p17 group-specific antigen peptide HGP-30

    SciTech Connect (OSTI)

    Naylor, P.H.; Naylor, C.W.; Badamchian, M.; Wada, S.; Goldstein, A.L.; Wang, S.S.; Sun, D.K.; Thornton, A.H.; Sarin, P.S.

    1987-05-01

    The authors have reported that an antiserum prepared against thymosin ..cap alpha../sub 1/ (which shares a region of homology with the p17 protein of the acquired immunodeficiency syndrome (AIDS)-associated human immunodeficiency virus) effectively neutralized the AIDs virus and prevented its replication in H9 cells. Using HPLC and immunoblot analysis, they have identified from a clone B, type III human T-lymphotropic virus (HTLV-IIIB) extracts a protein with a molecular weight of 17,000 that is immunoreactive with thymosin ..cap alpha../sub 1/. In contrast, no immunoreactivity was found in retroviral extracts from a number of nonhuman species including feline, bovine, simian, gibbon, and murine retroviruses. Heterologous antiserum prepared against a 30-amino acid synthetic peptide analogue (HGP-30) does not cross-react with thymosin ..cap alpha../sub 1/ but does react specifically with the p17 protein of the AIDS virus in a manner identical to that seen with an HTLV-IIIB p17-specific monoclonal antibody. The demonstration that this synthetic analogue is immunogenic and that antibodies to HGP-30 cross-react not only with synthetic peptide but also with the HTLV-IIIB p17 viral protein provides an additional, and potentially more specific, candidate for development of a synthetic peptide vaccine for AIDS. In addition, the p17 synthetic peptide (HGP-3) may prove to be useful in a diagnostic assay for the detection of AIDS virus infection in seronegative individuals.

  11. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This alsomore » represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.« less

  12. Both core and F proteins of hepatitis C virus could enhance cell proliferation in transgenic mice

    SciTech Connect (OSTI)

    Hu, Wen-Ta; Li, Hui-Chun; Lee, Shen-Kao; Ma, Hsin-Chieh; Yang, Chee-Hing; Chen, Hung-Ling; Lo, Shih-Yen; Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan

    2013-05-24

    Highlights: HCV core and F proteins could induce hepatocyte proliferation in the transgenic mice. ?-Catenin signaling pathway was activated by core protein in the transgenic mice. ?-Catenin signaling pathway was activated by myc-F protein in the transgenic mice. Expression of SMA protein was enhanced by core but not myc-F protein. -- Abstract: The role of the protein encoded by the alternative open reading frame (ARF/F/core+1) of the Hepatitis C virus (HCV) genome in viral pathogenesis remains unknown. The different forms of ARF/F/core+1 protein were labile in cultured cells, a myc-tag fused at the N-terminus of the F protein made it more stable. To determine the role of core and F proteins in HCV pathogenesis, transgenic mice with either protein expression under the control of Albumin promoter were generated. Expression of core protein and F protein with myc tag (myc-F) could be detected by Western blotting analysis in the livers of these mice. The ratio of liver to body weight is increased for both core and myc-F transgenic mice compared to that of wild type mice. Indeed, the proliferating cell nuclear antigen protein, a proliferation marker, was up-regulated in the transgenic mice with core or myc-F protein. Further analyses by microarray and Western blotting suggested that ?-catenin signaling pathway was activated by either core or myc-F protein in the transgenic mice. These transgenic mice were further treated with either Diethynitrosamine (a tumor initiator) or Phenobarbital (a tumor promoter). Phenobarbital but not Diethynitrosamine treatment could increase the liver/body weight ratio of these mice. However, no tumor formation was observed in these mice. In conclusion, HCV core and myc-F proteins could induce hepatocyte proliferation in the transgenic mice possibly through ?-catenin signaling pathway.

  13. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    SciTech Connect (OSTI)

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This also represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.

  14. Inhibition of hepatitis B virus (HBV) by LNA-mediated nuclear interference with HBV DNA transcription

    SciTech Connect (OSTI)

    Sun, Zhen; Department of Biochemistry and Molecular Biology, Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 ; Xiang, Wenqing; Guo, Yajuan; Chen, Zhi; Liu, Wei; Lu, Daru

    2011-06-10

    Highlights: {yields} LNA-modified oligonucleotides can pass through the plasma membrane of cultured cells even without using transfection machinery. {yields} LNA-modified oligonucleotides passed efficiently across the cell membrane, and lipid-coating facilitated translocation from the cytoplasm to the nucleus. {yields} LNA-oligonucleotide designed to target nuclear HBV DNA efficiently suppresses HBV replication and transcription in cultured hepatic cells. -- Abstract: Silencing target genes with small regulatory RNAs is widely used to investigate gene function and therapeutic drug development. Recently, triplex-based approaches have provided another attractive means to achieve targeted gene regulation and gene manipulation at the molecular and cellular levels. Nuclear entry of oligonucleotides and enhancement of their affinity to the DNA targets are key points of such approaches. In this study, we developed lipid-based transport of a locked-nucleic-acid (LNA)-modified oligonucleotide for hepatitis B virus (HBV) DNA interference in human hepatocytes expressing HBV genomic DNA. In these cells, the LNA-modified oligonucleotides passed efficiently across the cell membrane, and lipid-coating facilitated translocation from the cytoplasm to the nucleus. The oligonucleotide specifically targeting HBV DNA clearly interfered with HBV DNA transcription as shown by a block in pregenomic RNA (pgRNA) production. The HBV DNA-targeted oligonucleotide suppressed HBV DNA replication and HBV protein production more efficiently than small interfering RNAs directed to the pgRNA. These results demonstrate that fusion with lipid can carry LNA-modified oligonucleotides to the nucleus where they regulate gene expression. Interfering with HBV DNA transcription by LNA-modified oligonucleotides has strong potential as a new strategy for HBV inhibition.

  15. The Role of a Host Protein (TIP) in the Resistance Response of Arabidopsis to Turnip Crinkle Virus Infection.

    SciTech Connect (OSTI)

    T. Jack Morris, School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118

    2008-10-20

    Our research on Turnip crinkle virus (TCV) has shown that the viral capsid protein (CP) is both a virulence factor as well as the elicitor of a hypersensitive resistance response (HR) to the virus in Arabidopsis. Initially, we identified a protein from Arabidopsis that specifically interacted with the viral CP using a yeast two-hybrid screen. This protein, designated TIP for TCV-Interacting Protein, is a member of the NAC family of plant transcription factors implicated in the regulation of development and senescence. When TCV CP was mutated to eliminate its ability to interact with TIP, the corresponding virus mutants broke the HR-mediated resistance conferred by the HRT resistance (R) gene in Arabidopsis ecotype Dijon (Di)-17. This result suggested that TIP is a component of the signal transduction pathway that leads to the genetically specified TCV resistance. We next confirmed that TIP and the viral CP interact in plant cells and that this interaction prevents nuclear localization of this transcription factor. We demonstrated that TCV CP suppresses post-transcriptional gene silencing (PTGS), a newly discovered RNA-mediated defense system in plants. Together these results suggest that the CP is a virulence factor that could well be functioning through its interaction with TIP. We have proposed a model involving the role of TIP and CP in triggering HR mediated plant defense that fits with the current thinking about how gene-for-gene resistance may function. A unique component of our system is the opportunity to link R-gene function with the newly discovered RNA silencing pathway that is not only a potent defense against viral pathogens, but also regulates early development in plants. In the current funding period we made several significant findings: First, we completed an array analysis comparing gene expression in Arabidopsis infected with TCV and a mutant virus unable to bind TIP. Second, we produced transgenic lines that over-express and inducibly under-express TIP. These accomplishments now form the basis for our continued effort towards providing a complete understanding of molecular events leading to susceptible and resistant interactions between TCV and Arabidopsis plants. Our data strongly suggest that TIP is involved in activating the SA-mediated defense pathway and that TCV CP acts to repress this role of TIP.

  16. Release of the herpes simplex virus 1 protease by self cleavage is required for proper conformation of the portal vertex

    SciTech Connect (OSTI)

    Yang, Kui; Wills, Elizabeth G.; Baines, Joel D.

    2012-07-20

    We identify an NLS within herpes simplex virus scaffold proteins that is required for optimal nuclear import of these proteins into infected or uninfected nuclei, and is sufficient to mediate nuclear import of GFP. A virus lacking this NLS replicated to titers reduced by 1000-fold, but was able to make capsids containing both scaffold and portal proteins suggesting that other functions can complement the NLS in infected cells. We also show that Vp22a, the major scaffold protein, is sufficient to mediate the incorporation of portal protein into capsids, whereas proper portal immunoreactivity in the capsid requires the larger scaffold protein pU{sub L}26. Finally, capsid angularization in infected cells did not require the HSV-1 protease unless full length pU{sub L}26 was expressed. These data suggest that the HSV-1 portal undergoes conformational changes during capsid maturation, and reveal that full length pU{sub L}26 is required for this conformational change.

  17. Activation/proliferation and apoptosis of bystander goat lymphocytes induced by a macrophage-tropic chimeric caprine arthritis encephalitis virus expressing SIV Nef

    SciTech Connect (OSTI)

    Bouzar, Baya Amel; Rea, Angela; Hoc-Villet, Stephanie; Garnier, Celine; Guiguen, Francois; Jin Yuhuai; Narayan, Opendra; Chebloune, Yahia . E-mail: ychebloune@kumc.edu

    2007-08-01

    Caprine arthritis encephalitis virus (CAEV) is the natural lentivirus of goats, well known for its tropism for macrophages and its inability to cause infection in lymphocytes. The viral genome lacks nef, tat, vpu and vpx coding sequences. To test the hypothesis that when nef is expressed by the viral genome, the virus became toxic for lymphocytes during replication in macrophages, we inserted the SIVsmm PBj14 nef coding sequences into the genome of CAEV thereby generating CAEV-nef. This recombinant virus is not infectious for lymphocytes but is fully replication competent in goat macrophages in which it constitutively expresses the SIV Nef. We found that goat lymphocytes cocultured with CAEV-nef-infected macrophages became activated, showing increased expression of the interleukin-2 receptor (IL-2R). Activation correlated with increased proliferation of the cells. Interestingly, a dual effect in terms of apoptosis regulation was observed in exposed goat lymphocytes. Nef was found first to induce a protection of lymphocytes from apoptosis during the first few days following exposure to infected macrophages, but later it induced increased apoptosis in the activated lymphocytes. This new recombinant virus provides a model to study the functions of Nef in the context of infection of macrophages, but in absence of infection of T lymphocytes and brings new insights into the biological effects of Nef on lymphocytes.

  18. A human monoclonal antibody derived from a vaccinated volunteer recognizes heterosubtypically a novel epitope on the hemagglutinin globular head of H1 and H9 influenza A viruses

    SciTech Connect (OSTI)

    Boonsathorn, Naphatsawan; Panthong, Sumolrat; Chittaganpitch, Malinee; Phuygun, Siripaporn; Waicharoen, Sunthareeya; Prachasupap, Apichai; Yasugi, Mayo; Ono, Ken-ichiro; and others

    2014-09-26

    Highlights: A human monoclonal antibody against influenza virus was produced from a volunteer. The antibody was generated from the PBMCs of the volunteer using the fusion method. The antibody neutralized heterosubtypically group 1 influenza A viruses (H1 and H9). The antibody targeted a novel epitope in globular head region of the hemagglutinin. Sequences of the identified epitope are highly conserved among H1 and H9 subtypes. - Abstract: Most neutralizing antibodies elicited during influenza virus infection or by vaccination have a narrow spectrum because they usually target variable epitopes in the globular head region of hemagglutinin (HA). In this study, we describe a human monoclonal antibody (HuMAb), 5D7, that was prepared from the peripheral blood lymphocytes of a vaccinated volunteer using the fusion method. The HuMAb heterosubtypically neutralizes group 1 influenza A viruses, including seasonal H1N1, 2009 pandemic H1N1 (H1N1pdm) and avian H9N2, with a strong hemagglutinin inhibition activity. Selection of an escape mutant showed that the HuMAb targets a novel conformational epitope that is located in the HA head region but is distinct from the receptor binding site. Furthermore, Phe114Ile substitution in the epitope made the HA unrecognizable by the HuMAb. Amino acid residues in the predicted epitope region are also highly conserved in the HAs of H1N1 and H9N2. The HuMAb reported here may be a potential candidate for the development of therapeutic/prophylactic antibodies against H1 and H9 influenza viruses.

  19. An intrinsically disordered peptide from Ebola virus VP35 controls viral RNA synthesis by modulating nucleoprotein-RNA interactions

    SciTech Connect (OSTI)

    Leung, Daisy  W.; Borek, Dominika; Luthra, Priya; Binning, Jennifer  M.; Anantpadma, Manu; Liu, Gai; Harvey, Ian B.; Su, Zhaoming; Endlich-Frazier, Ariel; Pan, Juanli; Shabman, Reed  S.; Chiu, Wah; Davey, Robert  A.; Otwinowski, Zbyszek; Basler, Christopher  F.; Amarasinghe, Gaya  K.

    2015-04-01

    During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.

  20. Human non-neutralizing HIV-1 envelope monoclonal antibodies limit the number of founder viruses during SHIV mucosal infection in rhesus macaques

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Santra, Sampa; Tomaras, Georgia D.; Warrier, Ranjit; Nicely, Nathan I.; Liao, Hua -Xin; Pollara, Justin; Liu, Pinghuang; Alam, S. Munir; Zhang, Ruijun; Cocklin, Sarah L.; et al

    2015-08-03

    HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4⁺ T cells. Although broadly neutralizing antibodies (bnAbs) are the type of HIV-1 antibodies that are most likely protective, they are not induced with current vaccine candidates. In contrast, antibodies that do not neutralize primary HIV-1 strains in the TZM-bl infection assay are readily induced by current vaccine candidates and have also been implicated as secondary correlates of decreased HIV-1 risk in the RV144 vaccine efficacy trial. Here, we have studied the capacity of anti-Env monoclonal antibodies (mAbs) against either the immunodominant regionmore » of gp41 (7B2 IgG1), the first constant region of gp120 (A32 IgG1), or the third variable loop (V3) of gp120 (CH22 IgG1) to modulate in vivo rectal mucosal transmission of a high-dose simian-human immunodeficiency virus (SHIV-BaL) in rhesus macaques. 7B2 IgG1 or A32 IgG1, each containing mutations to enhance Fc function, was administered passively to rhesus macaques but afforded no protection against productive clinical infection while the positive control antibody CH22 IgG1 prevented infection in 4 of 6 animals. Enumeration of transmitted/founder (T/F) viruses revealed that passive infusion of each of the three antibodies significantly reduced the number of T/F genomes. Some antibodies that bind HIV-1 Env but fail to neutralize virus in traditional neutralization assays may limit the number of T/F viruses involved in transmission without leading to enhancement of viral infection. For one of these mAbs, gp41 mAb 7B2, we provide the first co-crystal structure in complex with a common cyclical loop motif demonstrated to be critical for infection by other retroviruses.« less

  1. Human non-neutralizing HIV-1 envelope monoclonal antibodies limit the number of founder viruses during SHIV mucosal infection in rhesus macaques

    SciTech Connect (OSTI)

    Santra, Sampa; Tomaras, Georgia D.; Warrier, Ranjit; Nicely, Nathan I.; Liao, Hua -Xin; Pollara, Justin; Liu, Pinghuang; Alam, S. Munir; Zhang, Ruijun; Cocklin, Sarah L.; Shen, Xiaoying; Duffy, Ryan; Xia, Shi -Mao; Schutte, Robert J.; Pemble IV, Charles W.; Dennison, S. Moses; Li, Hui; Chao, Andrew; Vidnovic, Kora; Evans, Abbey; Klein, Katja; Kumar, Amit; Robinson, James; Landucci, Gary; Forthal, Donald N.; Montefiori, David C.; Kaewkungwal, Jaranit; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Rerks-Ngarm, Supachai; Robb, Merlin L.; Michael, Nelson L.; Kim, Jerome H.; Soderberg, Kelly A.; Giorgi, Elena E.; Blair, Lily; Korber, Bette T.; Moog, Christiane; Shattock, Robin J.; Letvin, Norman L.; Schmitz, Joern E.; Moody, M. A.; Gao, Feng; Ferrari, Guido; Shaw, George M.; Haynes, Barton F.; Douek, Daniel C.

    2015-08-03

    HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4⁺ T cells. Although broadly neutralizing antibodies (bnAbs) are the type of HIV-1 antibodies that are most likely protective, they are not induced with current vaccine candidates. In contrast, antibodies that do not neutralize primary HIV-1 strains in the TZM-bl infection assay are readily induced by current vaccine candidates and have also been implicated as secondary correlates of decreased HIV-1 risk in the RV144 vaccine efficacy trial. Here, we have studied the capacity of anti-Env monoclonal antibodies (mAbs) against either the immunodominant region of gp41 (7B2 IgG1), the first constant region of gp120 (A32 IgG1), or the third variable loop (V3) of gp120 (CH22 IgG1) to modulate in vivo rectal mucosal transmission of a high-dose simian-human immunodeficiency virus (SHIV-BaL) in rhesus macaques. 7B2 IgG1 or A32 IgG1, each containing mutations to enhance Fc function, was administered passively to rhesus macaques but afforded no protection against productive clinical infection while the positive control antibody CH22 IgG1 prevented infection in 4 of 6 animals. Enumeration of transmitted/founder (T/F) viruses revealed that passive infusion of each of the three antibodies significantly reduced the number of T/F genomes. Some antibodies that bind HIV-1 Env but fail to neutralize virus in traditional neutralization assays may limit the number of T/F viruses involved in transmission without leading to enhancement of viral infection. For one of these mAbs, gp41 mAb 7B2, we provide the first co-crystal structure in complex with a common cyclical loop motif demonstrated to be critical for infection by other retroviruses.

  2. Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor, P

    SciTech Connect (OSTI)

    Green, Todd J.; Luo, Ming

    2009-10-05

    The negative-strand RNA viruses (NSRVs) are unique because their nucleocapsid, not the naked RNA, is the active template for transcription and replication. The viral polymerase of nonsegmented NSRVs contains a large polymerase catalytic subunit (L) and a nonenzymatic cofactor, the phosphoprotein (P). Insight into how P delivers the polymerase complex to the nucleocapsid has long been pursued by reverse genetics and biochemical approaches. Here, we present the X-ray crystal structure of the C-terminal domain of P of vesicular stomatitis virus, a prototypic nonsegmented NSRV, bound to nucleocapsid-like particles. P binds primarily to the C-terminal lobe of 2 adjacent N proteins within the nucleocapsid. This binding mode is exclusive to the nucleocapsid, not the nucleocapsid (N) protein in other existing forms. Localization of phosphorylation sites within P and their proximity to the RNA cavity give insight into how the L protein might be oriented to access the RNA template.

  3. Development and Characterization of a Multiplexed RT-PCR Species Specific Assay for Bovine and one for Porcine Foot-and-Mouth Disease Virus Rule-Out Supplemental Materials

    SciTech Connect (OSTI)

    Smith, S; Danganan, L; Tammero, L; Lenhoff, R; Naraghi-arani, P; Hindson, B

    2007-08-06

    Lawrence Livermore National Laboratory (LLNL), in collaboration with the Department of Homeland Security (DHS) and the United States Department of Agriculture (USDA), Animal and Plant Health Inspection Services (APHIS) has developed advanced rapid diagnostics that may be used within the National Animal Health Laboratory Network (NAHLN), the National Veterinary Services Laboratory (Ames, Iowa) and the Plum Island Animal Disease Center (PIADC). This effort has the potential to improve our nation's ability to discriminate between foreign animal diseases and those that are endemic using a single assay, thereby increasing our ability to protect animal populations of high economic importance in the United States. Under 2005 DHS funding we have developed multiplexed (MUX) nucleic-acid-based PCR assays that combine foot-and-mouth disease virus (FMDV) detection with rule-out tests for two other foreign animal diseases Vesicular Exanthema of Swine (VESV) and Swine Vesicular Disease (SVD) and four other domestic viral diseases Bovine Viral Diarrhea Virus (BVDV), Bovine Herpes Virus 1 (BHV-1 or Infectious Bovine Rhinotracheitus IBR), Bluetongue virus (BTV) and Parapox virus complex (which includes Bovine Papular Stomatitis Virus BPSV, Orf of sheep, and Pseudocowpox). Under 2006 funding we have developed a Multiplexed PCR [MUX] porcine assay for detection of FMDV with rule out tests for VESV and SVD foreign animal diseases in addition to one other domestic vesicular animal disease vesicular stomatitis virus (VSV) and one domestic animal disease of swine porcine reproductive and respiratory syndrome (PRRS). We have also developed a MUX bovine assay for detection of FMDV with rule out tests for the two bovine foreign animal diseases malignant catarrhal fever (MCF), rinderpest virus (RPV) and the domestic diseases vesicular stomatitis virus (VSV), bovine viral diarrhea virus (BVDV), infectious bovine rhinotracheitus virus (BHV-1), bluetongue virus (BTV), and the Parapox viruses which are of two bovine types bovine papular stomatitis virus (BPSV) and psuedocowpox (PCP). This document provides details of signature generation, evaluation, and testing, as well as the specific methods and materials used. A condensed summary of the development, testing and performance of the multiplexed assay panel was presented in a 126 page separate document, entitled 'Development and Characterization of A Multiplexed RT-PCR Species Specific Assay for Bovine and one for Porcine Foot-and-Mouth Disease Virus Rule-Out'. This supplemental document provides additional details of large amount of data collected for signature generation, evaluation, and testing, as well as the specific methods and materials used for all steps in the assay development and utilization processes. In contrast to last years effort, the development of the bovine and porcine panels is pending additional work to complete analytical characterization of FMDV, VESV, VSV, SVD, RPV and MCF. The signature screening process and final panel composition impacts this effort. The unique challenge presented this year was having strict predecessor limitations in completing characterization, where efforts at LLNL must preceed efforts at PIADC, such challenges were alleviated in the 2006 reporting by having characterization data from the interlaboratory comparison and at Plum Island under AgDDAP project. We will present an addendum at a later date with additional data on the characterization of the porcine and bovine multiplex assays when that data is available.

  4. An intrinsically disordered peptide from Ebola virus VP35 controls viral RNA synthesis by modulating nucleoprotein-RNA interactions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Leung, Daisy  W.; Borek, Dominika; Luthra, Priya; Binning, Jennifer  M.; Anantpadma, Manu; Liu, Gai; Harvey, Ian B.; Su, Zhaoming; Endlich-Frazier, Ariel; Pan, Juanli; et al

    2015-04-01

    During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludesmore » a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.« less

  5. Palmitoylation of the feline immunodeficiency virus envelope glycoprotein and its effect on fusion activity and envelope incorporation into virions

    SciTech Connect (OSTI)

    Gonzalez, Silvia A.; Paladino, Monica G.; Affranchino, Jose L.

    2012-06-20

    The feline immunodeficiency virus (FIV) envelope glycoprotein (Env) possesses a short cytoplasmic domain of 53 amino acids containing four highly conserved cysteines at Env positions 804, 811, 815 and 848. Since palmitoylation of transmembrane proteins occurs at or near the membrane anchor, we investigated whether cysteines 804, 811 and 815 are acylated and analyzed the relevance of these residues for Env functions. Replacement of cysteines 804, 811 and 815 individually or in combination by serine residues resulted in Env glycoproteins that were efficiently expressed and processed. However, mutations C804S and C811S reduced Env fusogenicity by 93% and 84%, respectively, compared with wild-type Env. By contrast, mutant C815S exhibited a fusogenic capacity representing 50% of the wild-type value. Remarkably, the double mutation C804S/C811S abrogated both Env fusion activity and Env incorporation into virions. Finally, by means of Click chemistry assays we demonstrated that the four FIV Env cytoplasmic cysteines are palmitoylated.

  6. Molecular Foundry

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NEWS ARCHIVE < News and Highlights Research Performed by Foundry Industrial Users Honored by Nanotechnology Journal User work on printable photonics was selected as a Highlight of the Year by Nanotechnology in the area of "patterning and nano fabrication". [MORE] Outsmarting Thermodynamics in Self-assembly of Nanostructures Foundry user - and Materials Sciences Division Director - reports method for symmetry-breaking in feedback-driven self-assembly of optical metamaterials. [MORE]

  7. News Item

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Outsmarting Thermodynamics in Self-assembly of Nanostructures If you can uniformly break the symmetry of nanorod pairs in a colloidal solution, you're one step closer to achieving new and exciting metamaterial properties. The development of an innovative self-assembly route could surpass the conventional thermodynamic limit in chemical synthetic systems and lead to the production of nanostructures that have historically been considered impossible to assemble. But traditional thermodynamic-driven

  8. NREL: Photovoltaics Research - News Release Archives

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 December 28, 2012 Award-Winning PV Cell Pushes Efficiency Higher NREL and Solar Junction outsmart the solar spectrum and set a world record with a 44%-efficient solar cell. December 4, 2012 NREL Teams with Berkeley Lab to Analyze Solar Pricing Trends and Benchmark "Soft" Costs for PV Systems The U.S. Department of Energy's (DOE)'s National Renewable Energy Laboratory (NREL) and Lawrence Berkeley National Laboratory (LBL) jointly released two reports examining solar photovoltaic (PV)

  9. NREL: Solar Research - News Release Archives

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 December 28, 2012 Award-Winning PV Cell Pushes Efficiency Higher NREL and Solar Junction outsmart the solar spectrum and set a world record with a 44%-efficient solar cell. December 4, 2012 NREL Teams with Berkeley Lab to Analyze Solar Pricing Trends and Benchmark "Soft" Costs for PV Systems The U.S. Department of Energy's (DOE)'s National Renewable Energy Laboratory (NREL) and Lawrence Berkeley National Laboratory (LBL) jointly released two reports examining solar photovoltaic (PV)

  10. Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function

    SciTech Connect (OSTI)

    Polonskaya, Zhanna; Benham, Craig J.; Hearing, Janet . E-mail: jhearing@ms.cc.sunysb.edu

    2004-10-25

    The minimal replicator of the Epstein-Barr virus (EBV) latent cycle origin of DNA replication oriP is composed of two binding sites for the Epstein-Barr virus nuclear antigen-1 (EBNA-1) and flanking inverted repeats that bind the telomere repeat binding factor TRF2. Although not required for minimal replicator activity, additional binding sites for EBNA-1 and TRF2 and one or more auxiliary elements located to the right of the EBNA-1/TRF2 sites are required for the efficient replication of oriP plasmids. Another region of oriP that is predicted to be destabilized by DNA supercoiling is shown here to be an important functional component of oriP. The ability of DNA fragments of unrelated sequence and possessing supercoiled-induced DNA duplex destabilized (SIDD) structures, but not fragments characterized by helically stable DNA, to substitute for this component of oriP demonstrates a role for the SIDD region in the initiation of oriP-plasmid DNA replication.

  11. Joint environmental assessment 1997--2001 of the California Department of Food and Agriculture Curly Top Virus Control Program for Bureau of Land Management and Department of Energy

    SciTech Connect (OSTI)

    1997-03-01

    The DOE, Naval Petroleum reserves in California (NPRC), proposes to sign an Amendment to the Cooperative Agreement and Supplement with the California Department of Food and Agriculture (CDFA) to extend the term of the Curly Top Virus Control Program (CTVCP) in California. This program involves Malathion spraying on NPRC lands to control the beet leafhopper, over a five year period from 1997 through 2001. It is expected that approximately 330 acres on Naval Petroleum Reserve Number 1 (NPR-1) and approximately 9,603 acres on Naval Petroleum Reserve Number 2 (NPR-2) will be treated with Malathion annually by CDFA during the course of this program. The actual acreage subject to treatment can vary from year to year. Pursuant to the requirements of the National Environmental Policy Act of 1969 (NEPA), as amended, the potential impacts of the proposed action were analyzed in a Joint Environmental Assessment (DOE/EA-1011) with the US Department of Interior, Bureau of Land Management (BLM) acting as lead agency, in consultation with the CDFA, and the DOE acting as a cooperating agency. Based on the analysis in the EA, DOE has determined that the conduct of the Curly Top Virus Control Program in California is not a major Federal action significantly affecting the quality of the human environment, within the meaning of the NEPA. Therefore, the preparation of an Environmental Impact Statement is not required and DOE is consequently issuing a FONSI.

  12. Overexpression of the human BCL-2 gene product results in growth enhancement of Epstein-Barr virus-immortalized B cells

    SciTech Connect (OSTI)

    Tsujimoto, Yoshihide (Wistar Institute of Anatomy and Biology, Philadelphia, PA (USA))

    1989-03-01

    The biological activity of the human BCL-2 gene product was analyzed in an Epstein-Barr virus (EBV)-infected human lymphoblastoid B-cell line transfected with BCL-2 sequences driven by the simian virus 40 promoter and enhancer. Overproduction of the BCL-2 protein conferred a selective growth advantage to the EBV-infected B cells as compared with control transfectants in low-serum medium and also after seeding at limiting dilution but did not render the cells tumorigenic in athymic nude mice. This growth enhancement was also seen in cells transfected with the BCL-2 gene with its own promoter juxtaposed to the immunoglobulin heavy chain gene enhancer, which represents the translocated form of the BCL-2 gene observed in follicular lymphomas with the t(14;18) translocation. The growth advantage of EBV-infected B cells overproducing the BCL-2 protein is neither due to the enhanced growth factor production nor due to an enhanced sensitivity of the BCL-2 transfectants to interleukins 1 or 6, although both lymphokines are known to stimulate proliferation of EBV-infected B-cell lines. The growth advantage of EBV-infected B-cell lines. The growth advantage of EBV-infected B cells by overproduction of the BCL-2 protein suggests the direct involvement of the BCL-2 gene product in the pathogenesis of follicular lymphoma.

  13. In vivo subcellular localization of Mal de Rio Cuarto virus (MRCV) non-structural proteins in insect cells reveals their putative functions

    SciTech Connect (OSTI)

    Maroniche, Guillermo A.; Mongelli, Vanesa C.; Llauger, Gabriela; Alfonso, Victoria; Taboga, Oscar

    2012-09-01

    The in vivo subcellular localization of Mal de Rio Cuarto virus (MRCV, Fijivirus, Reoviridae) non-structural proteins fused to GFP was analyzed by confocal microscopy. P5-1 showed a cytoplasmic vesicular-like distribution that was lost upon deleting its PDZ binding TKF motif, suggesting that P5-1 interacts with cellular PDZ proteins. P5-2 located at the nucleus and its nuclear import was affected by the deletion of its basic C-termini. P7-1 and P7-2 also entered the nucleus and therefore, along with P5-2, could function as regulators of host gene expression. P6 located in the cytoplasm and in perinuclear cloud-like inclusions, was driven to P9-1 viroplasm-like structures and co-localized with P7-2, P10 and {alpha}-tubulin, suggesting its involvement in viroplasm formation and viral intracellular movement. Finally, P9-2 was N-glycosylated and located at the plasma membrane in association with filopodia-like protrusions containing actin, suggesting a possible role in virus cell-to-cell movement and spread.

  14. Non-destructive observation of intact bacteria and viruses in water by the highly sensitive frequency transmission electric-field method based on SEM

    SciTech Connect (OSTI)

    Ogura, Toshihiko

    2014-08-08

    Highlights: We developed a high-sensitive frequency transmission electric-field (FTE) system. The output signal was highly enhanced by applying voltage to a metal layer on SiN. The spatial resolution of new FTE method is 41 nm. New FTE system enables observation of the intact bacteria and virus in water. - Abstract: The high-resolution structural analysis of biological specimens by scanning electron microscopy (SEM) presents several advantages. Until now, wet bacterial specimens have been examined using atmospheric sample holders. However, images of unstained specimens in water using these holders exhibit very poor contrast and heavy radiation damage. Recently, we developed the frequency transmission electric-field (FTE) method, which facilitates the SEM observation of biological specimens in water without radiation damage. However, the signal detection system presents low sensitivity. Therefore, a high EB current is required to generate clear images, and thus reducing spatial resolution and inducing thermal damage to the samples. Here a high-sensitivity detection system is developed for the FTE method, which enhances the output signal amplitude by hundredfold. The detection signal was highly enhanced when voltage was applied to the metal layer on silicon nitride thin film. This enhancement reduced the EB current and improved the spatial resolution as well as the signal-to-noise ratio. The spatial resolution of a high-sensitive FTE system is 41 nm, which is considerably higher than previous FTE system. New FTE system can easily be utilised to examine various unstained biological specimens in water, such as living bacteria and viruses.

  15. Heme oxygenase-1 induction alters chemokine regulation and ameliorates human immunodeficiency virus-type-1 infection in lipopolysaccharide-stimulated macrophages

    SciTech Connect (OSTI)

    Zhou, Zhao-Hua; Kumari, Namita; Nekhai, Sergei; Clouse, Kathleen A.; Wahl, Larry M.; Yamada, Kenneth M.; Dhawan, Subhash

    2013-06-07

    Highlights: Lipopolysaccharide stimulation of heme oxygenase-1 (HO-1) ameliorated HIV-1 infection of primary human macrophages. The partial protection by HO-1 against HIV infection was associated with induction of chemokines such as MIP1? and MIP1?. This mechanism explains lipopolysaccharide-stimulated HO-1-mediated inhibition of HIV-1 infection of macrophages. -- Abstract: We have elucidated a putative mechanism for the host resistance against HIV-1 infection of primary human monocyte-derived macrophages (MDM) stimulated with lipopolysaccharide (LPS). We show that LPS-activated MDM both inhibited HIV-1 entry into the cells and were refractory to post-entry productive viral replication. LPS-treated cells were virtually negative for mature virions as revealed by transmission electron microscopy. LPS activation of MDM markedly enhanced the expression of heme oxygenase-1 (HO-1), a potent inducible cytoprotective enzyme. Increased HO-1 expression was accompanied by elevated production of macrophage inflammatory chemokines (MIP1? and MIP1?) by LPS-activated MDM, significantly decreased surface chemokine receptor-5 (CCR-5) expression, and substantially reduced virus replication. Treatment of cells with HO-1 inhibitor SnPP IX (tin protoporphyrin IX) attenuated the LPS-mediated responses, HIV-1 replication and secretion of MIP1?, MIP1?, and LD78? chemokines with little change in surface CCR-5 expression. These results identify a novel role for HO-1 in the modulation of host immune response against HIV infection of MDM.

  16. The tale of a modern animal plague: Tracing the evolutionary history and determining the time-scale for foot and mouth disease virus

    SciTech Connect (OSTI)

    Tully, Damien C. Fares, Mario A.

    2008-12-20

    Despite significant advances made in the understanding of its epidemiology, foot and mouth disease virus (FMDV) is among the most unexpected agricultural devastating plagues. While the disease manifests itself as seven immunologically distinct strains their origin, population dynamics, migration patterns and divergence times remain unknown. Herein we have assembled a comprehensive data set of gene sequences representing the global diversity of the disease and inferred the time-scale and evolutionary history for FMDV. Serotype-specific rates of evolution and divergence times were estimated using a Bayesian coalescent framework. We report that an ancient precursor FMDV gave rise to two major diversification events spanning a relatively short interval of time. This radiation event is estimated to have taken place towards the end of the 17th and the beginning of the 18th century giving us the present circulating Euro-Asiatic and South African viral strains. Furthermore our results hint that Europe acted as a possible hub for the disease from where it successfully dispersed elsewhere via exploration and trading routes.

  17. Structural Analysis of a Viral Ovarian Tumor Domain Protease from the Crimean-Congo Hemorrhagic Fever Virus in Complex with Covalently Bonded Ubiquitin

    SciTech Connect (OSTI)

    Capodagli, Glenn C.; McKercher, Marissa A.; Baker, Erica A.; Masters, Emily M.; Brunzelle, Joseph S.; Pegan, Scott D.

    2014-10-02

    Crimean-Congo hemorrhagic fever (CCHF) virus is a tick-borne, negative-sense, single-stranded RNA [ssRNA(-)] nairovirus that produces fever, prostration, and severe hemorrhages in humans. With fatality rates for CCHF ranging up to 70% based on several factors, CCHF is considered a dangerous emerging disease. Originally identified in the former Soviet Union and the Congo, CCHF has rapidly spread across large sections of Europe, Asia, and Africa. Recent reports have identified a viral homologue of the ovarian tumor protease superfamily (vOTU) within its L protein. This protease has subsequently been implicated in downregulation of the type I interferon immune response through cleavage of posttranslational modifying proteins ubiquitin (Ub) and the Ub-like interferon-simulated gene 15 (ISG15). Additionally, homologues of vOTU have been suggested to perform similar roles in the positive-sense, single-stranded RNA [ssRNA(+)] arteriviruses. By utilizing X-ray crystallographic techniques, the structure of vOTU covalently bound to ubiquitin propylamine, a suicide substrate of the enzyme, was elucidated to 1.7 {angstrom}, revealing unique structural elements that define this new subclass of the OTU superfamily. In addition, kinetic studies were carried out with aminomethylcoumarin (AMC) conjugates of monomeric Ub, ISG15, and NEDD8 (neural precursor cell expressed, developmentally downregulated 8) substrates in order to provide quantitative insights into vOTU's preference for Ub and Ub-like substrates.

  18. Flow cytometric detection of human immunodeficiency virus type 1 proviral DNA by the polymerase chain reaction incorporating digoxigenin- or fluorescein-labeled dUTP

    SciTech Connect (OSTI)

    Yang, Gang; Olson, J.C.; Pu, R.; Vyas, G.N.

    1995-10-01

    Serological assays are routinely used in the laboratory diagnosis of human immunodeficiency virus type-1 (HrV-1) infection, but the polymerase chain reaction (PCR) is ultimately the most sensitive and direct method for establishing definitive diagnosis. As an alternative to the conventional radioactive PCR procedure we have developed and evaluated a pair of rapid nonradioisotopic flow cytometric detection methods. Using heminested PCR we directly incorporated fluorescein-12-dUTP (fluo-dUTP) or digoxigenin-11-dUTP (dig-dUTP) into the PCR-amplicons. The labeled amplicons were hybridized with biotinylated antisense and sense probes, followed by capture of the hybrid DNA using streptavidin-coated beads which were finally analyzed in a flow cytometer by (1) direct detection of the fluorescence intensity of the amplicons incorporating fluo-dUTP and (2) immunodetection of the amplicons incorporating dig-dUTP by anti-digoxigenin IgG labeled with fluorescein isothiocyanate (FITC). Although both assays were functionally comparable with radiolabeled probe in reliably detecting as low as five copies of HIV-1 proviral DNA sequences, the immunodetection of dig-dUTP consistently yielded higher mean channel fluorescence and gave a stable signal over an extended period of 12-14 weeks. In testing a panel of 20 pedigreed PBMC specimens from blood donors with or without HIV-1 infection, the results of both flow cytometric assays were identical with those of the conventional radioactive procedure. Therefore, we conclude that the dig-dUTP incorporation in amplicons, hybridization with a pair of sense-antisense biotinylated probes and immunodetection of hybrids by flow cytometric analyses is the nonisotopic method of choice for PCR-diagnosis of HIV-1 infection. 21 refs., 2 figs., 4 tabs.

  19. Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion

    SciTech Connect (OSTI)

    Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.; Yuan, Ping; Jardetzky, Theodore S.; Lamb, Robert A.

    2014-10-02

    Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 {angstrom}, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.

  20. Metronomic Adjuvant Chemotherapy Improves Treatment Outcome in Nasopharyngeal Carcinoma Patients With Postradiation Persistently Detectable Plasma Epstein-Barr Virus Deoxyribonucleic Acid

    SciTech Connect (OSTI)

    Twu, Chih-Wen; Wang, Wen-Yi; Chen, Chien-Chih; Liang, Kai-Li; Jiang, Rong-San; Wu, Ching-Te; Shih, Yi-Ting; Lin, Po-Ju; Liu, Yi-Chun; Lin, Jin-Ching

    2014-05-01

    Purpose: To investigate the effects of adjuvant chemotherapy in nasopharyngeal carcinoma (NPC) patients with persistently detectable plasma Epstein-Barr virus DNA (pEBV DNA) after curative radiation therapy plus induction/concurrent chemotherapy. Methods and Materials: The study population consisted of 625 NPC patients with available pEBV DNA levels before and after treatment. Eighty-five patients with persistently detectable pEBV DNA after 1 week of completing radiation therapy were eligible for this retrospective study. Of the 85 patients, 33 were administered adjuvant chemotherapy consisting of oral tegafur-uracil (2 capsules twice daily) for 12 months with (n=4) or without (n=29) preceding intravenous chemotherapy of mitomycin-C, epirubicin, and cisplatin. The remaining 52 patients who did not receive adjuvant chemotherapy served as the control group. Results: Baseline patient characteristics at diagnosis (age, sex, pathologic type, performance status, T classification, N classification, and overall stage), as well as previous treatment modality, were comparable in both arms. After a median follow-up of 70 months for surviving patients, 45.5% (15 of 33 patients) with adjuvant chemotherapy and 71.2% (37 of 52 patients) without adjuvant chemotherapy experienced tumor relapses (P=.0323). There were a significant reduction in distant failure (P=.0034) but not in local or regional recurrence. The 5-year overall survival rate was 71.6% for patients with adjuvant chemotherapy and 28.7% for patients without adjuvant chemotherapy (hazard ratio 0.27; 95% confidence interval 0.17-0.55; P<.0001). Conclusions: Our retrospective data showed that adjuvant chemotherapy can reduce distant failure and improve overall survival in NPC patients with persistently detectable pEBV DNA after curative radiation therapy plus induction/concurrent chemotherapy.

  1. Glycoprotein 5 of porcine reproductive and respiratory syndrome virus strain SD16 inhibits viral replication and causes G2/M cell cycle arrest, but does not induce cellular apoptosis in Marc-145 cells

    SciTech Connect (OSTI)

    Mu, Yang; Li, Liangliang; Zhang, Beibei; Huang, Baicheng; Gao, Jiming; and others

    2015-10-15

    Cell apoptosis is common after infection with porcine reproductive and respiratory syndrome virus (PRRSV). PRRSV GP5 has been reported to induce cell apoptosis. To further understand the role of GP5 in PRRSV induced cell apoptosis, we established Marc-145 cell lines stably expressing full-length GP5, GP5{sup Δ84-96} (aa 84-96 deletion), and GP5{sup Δ97-119} (aa 97-119 deletion). Cell proliferation, cell cycle progression, cell apoptosis and virus replication in these cell lines were evaluated. Neither truncated nor full-length GP5 induced cell apoptosis in Marc-145 cells. However, GP5{sup Δ97-119}, but not full-length or GP5{sup Δ84-96}, induced a cell cycle arrest at the G2/M phase resulting in a reduction in the growth of Marc-145 cells. Additionally, GP5{sup Δ84-96} inhibited the replication of PRRSV in Marc-145 cells through induction of IFN-β. These findings suggest that PRRSV GP5 is not responsible for inducing cell apoptosis in Marc-145 cells under these experimental conditions; however it has other important roles in virus/host cell biology. - Highlights: • Marc-145 cell lines stable expression PRRSV GP5 or truncated GP5 were constructed. • GP5{sup Δ97-119} expression in Marc-145 cell induced cell cycle arrest at G2/M phase. • Expression of GP5 and truncated GP5 could not induce Marc-145 cells apoptosis. • PRRSV replication in Marc-145-GP5{sup Δ84-96} was significantly inhibited.

  2. High-Sensitivity C-Reactive Protein Complements Plasma Epstein-Barr Virus Deoxyribonucleic Acid Prognostication in Nasopharyngeal Carcinoma: A Large-Scale Retrospective and Prospective Cohort Study

    SciTech Connect (OSTI)

    Tang, Lin-Quan; Li, Chao-Feng; Chen, Qiu-Yan; Zhang, Lu; Lai, Xiao-Ping; He, Yun; Xu, Yun-Xiu-Xiu; Hu, Dong-Peng; Wen, Shi-Hua; Peng, Yu-Tuan; Chen, Wen-Hui; Liu, Huai; Guo, Shan-Shan; Liu, Li-Ting; Li, Jing; Zhang, Jing-Ping; and others

    2015-02-01

    Purpose: To evaluate the effects of combining the assessment of circulating high-sensitivity C-reactive protein (hs-CRP) with that of Epstein-Barr virus DNA (EBV DNA) in the pretherapy prognostication of nasopharyngeal carcinoma (NPC). Patients and Methods: Three independent cohorts of NPC patients (training set of n=3113, internal validation set of n=1556, and prospective validation set of n=1668) were studied. Determinants of disease-free survival, distant metastasis–free survival, and overall survival were assessed by multivariate analysis. Hazard ratios and survival probabilities of the patient groups, segregated by clinical stage (T1-2N0-1M0, T3-4N0-1M0, T1-2N2-3M0, and T3-4N2-3M0) and EBV DNA load (low or high) alone, and also according to hs-CRP level (low or high), were compared. Results: Elevated hs-CRP and EBV DNA levels were significantly correlated with poor disease-free survival, distant metastasis–free survival, and overall survival in both the training and validation sets. Associations were similar and remained significant after excluding patients with cardiovascular disease, diabetes, and chronic hepatitis B. Patients with advanced-stage disease were segregated by high EBV DNA levels and high hs-CRP level into a poorest-risk group, and participants with either high EBV DNA but low hs-CRP level or high hs-CRP but low EBV DNA values had poorer survival compared with the bottom values for both biomarkers. These findings demonstrate a significant improvement in the prognostic ability of conventional advanced NPC staging. Conclusion: Baseline plasma EBV DNA and serum hs-CRP levels were significantly correlated with survival in NPC patients. The combined interpretation of EBV DNA with hs-CRP levels led to refinement of the risks for the patient subsets, with improved risk discrimination in patients with advanced-stage disease.

  3. 2010 | U.S. DOE Office of Science (SC)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    0 News News Home Featured Articles 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 Science Headlines Science Highlights Presentations & Testimony News Archives Communications and Public Affairs Contact Information Office of Science U.S. Department of Energy 1000 Independence Ave., SW Washington, DC 20585 P: (202) 586-5430 Featured Articles 2010 Print Text Size: A A A FeedbackShare Page A line of windmills in the sunset 12.27.10From the Labs Outsmarting the Wind External link

  4. Zika Virus Disease and Prevention

    Office of Environmental Management (EM)

    Department of Energy ZERH Webinar: Successful Strategies for the Housing Innovation Awards ZERH Webinar: Successful Strategies for the Housing Innovation Awards Since 2013, DOE has recognized 70 Housing Innovation Award winners and 13 Grand Award winners for innovative DOE Zero Energy Ready Homes. The 2016 Housing Innovation Awards applications will open May 1, 2016. Take this opportunity to learn the step-by-step process to apply for a 2016 Housing Innovation Award. DOE Zero Energy Ready

  5. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    forecast calls for flu January 15, 2016 The forecast calls for flu Beyond the familiar flu, infectious-and preventable-diseases such as HIV and measles kill millions around the world. Forecasting their impact would enable the public health community to take steps to spare the public the grief and economic impact of an epidemic. Yet the science of predicting infectious diseases lags far behind a similarly complex field, weather forecasting. It too is marked by huge unknowns but has steadily

  6. Activated Carbon Injection

    SciTech Connect (OSTI)

    2014-07-16

    History of the Clean Air Act and how the injection of carbon into a coal power plant's flu smoke can reduce the amount of mercury in the smoke.

  7. ALSNews Vol. 338

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to the future of scientific research. Read more... Toward Design of a Universal Flu Vaccine Scientists have determined the structures of antibodies that protect against broad...

  8. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    can say this because of the model they have constructed. Using historical data, a mathematical representation of how flu spreads through a population, and data for the current...

  9. ORISE: Process and Program Evaluation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    (measles, mumps and rubella) vaccine Immunization of health care workers against 2009 influenza A (H1N1) Vaccination of CDC employees against seasonal flu Factors influencing...

  10. Activated Carbon Injection

    ScienceCinema (OSTI)

    None

    2014-07-22

    History of the Clean Air Act and how the injection of carbon into a coal power plant's flu smoke can reduce the amount of mercury in the smoke.

  11. 1663 March 2013

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Spotlights Safer nuclear power Alternative fuel rod cladding materials make a Fukushima-type explosion much less likely Preventing a pandemic Simulations of a flu pandemic ...

  12. Smarter Drugs: How Protein Crystallography Revolutionizes Drug Design

    SciTech Connect (OSTI)

    Smith, Clyde

    2005-04-26

    According to Smith, protein crystallography allows scientists to design drugs in a much more efficient way than the standard methods traditionally used by large drug companies, which can cost close to a billion dollars and take 10 to 15 years. 'A lot of the work can be compressed down,' Smith said. Protein crystallography enables researchers to learn the structure of molecules involved in disease and health. Seeing the loops, folds and placement of atoms in anything from a virus to a healthy cell membrane gives important information about how these things work - and how to encourage, sidestep or stop their functions. Drug design can be much faster when the relationship between structure and function tells you what area of a molecule to target. Smith will use a timeline to illustrate the traditional methods of drug development and the new ways it can be done now. 'It is very exciting work. There have been some failures, but many successes too.' A new drug to combat the flu was developed in a year or so. Smith will tell us how. He will also highlight drugs developed to combat HIV, Tuberculosis, hypertension and Anthrax.

  13. Site Index - HPMC Occupational Health Services

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Flu Prevention Hand Washing Healthy Sleep Heat Stress Radon Signs of a Heart Attack "Cough CPR:" Urban Myth Signs of a Stroke Coping with Stress & Change Skin Cancer Awareness...

  14. Welcome to Stanford Synchrotron Radiation Lightsource | Stanford...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    SSRL Science in SLAC Today Q&A: Biologist Describes Milestone toward a Universal Flu Vaccine SSRL Upgrades, Adds Equipment for Next Round of Experiments X-ray Microscope Reveals...

  15. Science Summary

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    H1N1 Flu Links Scientific Highlight Wilson Lab Scripps Press Release Scripps ... A group of researchers led by Prof. Ian Wilson of The Scripps Research Institute has found ...

  16. ORISE: H1N1 Media Analysis | How ORISE is Making a Difference

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    H1N1 map This map represents the geographic origin or location of daily news articles related to H1N1 flu. The map is generated out of ORISE's Auto-INFORM database, which...

  17. 2014 - 09 | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Appraisal Process Begins Today, 9292014 Mon, 09292014 - 2:02pm Occupational Medicine Offers Staff Flu Vaccines by Appointment Thu, 09252014 - 7:45am 12 GeV CEBAF...

  18. Inspection Report: IG-0784 | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    December 19, 2007 The Department of Energy's Pandemic Influenza Planning According to the ... of its workforce, could become sick from a mutated avian influenza (bird flu) H5N1 strain. ...

  19. Zika Virus Disease and Prevention Presentation | Department of Energy

    Office of Environmental Management (EM)

    Research & Development » Workforce Development and Education Workforce Development and Education Continued growth in the U.S. wind industry requires trained and qualified workers to manufacture, construct, operate, and maintain wind turbines. Additionally, the nation will continue to need skilled scientists and engineers who can develop the next generation of wind power technologies. The National Skills Assessment of the U.S. Wind Industry in 2012 provides the first comprehensive overview

  20. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    analysis. A small number of the top proteins were expressed and purified from E. coli, and further binding tests selected two proteins that bound to BHRF1 with acceptable...

  1. Immunogenic compositions comprising human immunodeficiency virus (HIV) mosaic Nef proteins

    DOE Patents [OSTI]

    Korber, Bette T.; Perkins, Simon; Bhattacharya, Tanmoy; Fischer, William M.; Theiler, James; Letvin, Norman; Haynes, Barton F.; Hahn, Beatrice H.; Yusim, Karina; Kuiken, Carla

    2012-02-21

    The present invention relates to mosaic clade M HIV-1 Nef polypeptides and to compositions comprising same. The polypeptides of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

  2. Structure of the Ebola virus glycoprotein bound to an antibody...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    a heavily glycosylated, unstructured mucin-like domain. GP was known to be cleaved by cathepsin proteases as an essential step in entry, but the precise site or role of cleavage...

  3. Human immunodeficiency virus type 1 clade M mosaic gag polypeptides

    DOE Patents [OSTI]

    Korber, Bette T; Perkins, Simon; Bhattacharya, Tanmoy; Fischer, William M; Theiler, James; Letvin, Norman; Haynes, Barton F; Hahn, Beatrice H; Yusim, Karina; Kuiken, Carla

    2015-04-21

    The present invention relates to mosaic HIV-1 group M Gag sequences and to a composition comprising same.

  4. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    up the question of whether there are other transformers or morpheeins that exist in biology and may even be linked to human disease. Research conducted by: Z.A. Bornholdt,...

  5. Mosaic protein and nucleic acid vaccines against hepatitis C virus

    DOE Patents [OSTI]

    Yusim, Karina; Korber, Bette T. M.; Kuiken, Carla L.; Fischer, William M.

    2013-06-11

    The invention relates to immunogenic compositions useful as HCV vaccines. Provided are HCV mosaic polypeptide and nucleic acid compositions which provide higher levels of T-cell epitope coverage while minimizing the occurrence of unnatural and rare epitopes compared to natural HCV polypeptides and consensus HCV sequences.

  6. Human immunodeficiency virus type 1 clade M mosaic gag polypeptides...

    Office of Scientific and Technical Information (OSTI)

    Sponsoring Org: USDOE Country of Publication: United States Language: English Subject: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES Word Cloud More Like This Full Text ...

  7. Genomics-enabled sensor platform for rapid detection of viruses...

    Office of Scientific and Technical Information (OSTI)

    ; Pfeifer, Kent Bryant ; Branch, Darren W. ; Wheeler, David Roger ; Polsky, Ronen ; Lopez, DeAnna M. ; Ebel, Gregory D. 1 ; Prasad, Abhishek N. 1 ; Brozik, James A. 2 ; ...

  8. Designer Proteins Target Epstein-Barr-Virus-Associated Cancer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The crystal structure of Epstein-Barr Viral BHRF1 (black) bound to a designed protein ... The study shows not just how to help defeat EBV, but also opens up a whole new way to ...

  9. ALS Capabilities Reveal Multiple Functions of Ebola Virus

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Society for the Promotion of Science, and the Japan Ministry of Education, Culture, Sports, Science, and Technology. Operation of the ALS is supported by the U.S. Department of...

  10. Text and Structural Data Mining of Influenza Mentions in Web and Social Media

    SciTech Connect (OSTI)

    Corley, Courtney D.; Cook, Diane; Mikler, Armin R.; Singh, Karan P.

    2010-02-22

    Text and structural data mining of Web and social media (WSM) provides a novel disease surveillance resource and can identify online communities for targeted public health communications (PHC) to assure wide dissemination of pertinent information. WSM that mention influenza are harvested over a 24-week period, 5-October-2008 to 21-March-2009. Link analysis reveals communities for targeted PHC. Text mining is shown to identify trends in flu posts that correlate to real-world influenza-like-illness patient report data. We also bring to bear a graph-based data mining technique to detect anomalies among flu blogs connected by publisher type, links, and user-tags.

  11. Nucleic acids encoding mosaic clade M human immunodeficiency virus type 1 (HIV-1) envelope immunogens

    DOE Patents [OSTI]

    Korber, Bette T; Fischer, William; Liao, Hua-Xin; Haynes, Barton F; Letvin, Norman; Hahn, Beatrice H

    2015-04-21

    The present invention relates to nucleic acids encoding mosaic clade M HIV-1 Env polypeptides and to compositions and vectors comprising same. The nucleic acids of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

  12. Mosaic clade M human immunodeficiency virus type 1 (HIV-1) envelope immunogens

    DOE Patents [OSTI]

    Korber, Bette T.; Fischer, William; Liao, Hua-Xin; Haynes, Barton F.; Letvin, Norman; Hahn; Beatrice H.

    2011-05-31

    The present invention relates to mosaic clade M HIV-1 Env polypeptides and to compositions comprising same. The polypeptides of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

  13. Nucleic acids encoding modified human immunodeficiency virus type 1 (HIV-1) group M consensus envelope glycoproteins

    DOE Patents [OSTI]

    Haynes, Barton F.; Gao, Feng; Korber, Bette T.; Hahn, Beatrice H.; Shaw, George M.; Kothe, Denise; Li, Ying Ying; Decker, Julie; Liao, Hua-Xin

    2011-12-06

    The present invention relates, in general, to an immunogen and, in particular, to an immunogen for inducing antibodies that neutralizes a wide spectrum of HIV primary isolates and/or to an immunogen that induces a T cell immune response. The invention also relates to a method of inducing anti-HIV antibodies, and/or to a method of inducing a T cell immune response, using such an immunogen. The invention further relates to nucleic acid sequences encoding the present immunogens.

  14. Viruses in laboratory-reared cactus moth, Cactoblastis cactorum (Lepidoptera: Pyralidae)

    SciTech Connect (OSTI)

    Marti, O.G.; Myers, R.E.; Carpenter, J.E.; Styer, E.L.

    2007-03-15

    The cactus moth, Cactoblastis cactorum (Lepidoptera: Pyralidae: Phycitinae), is a non-native species threatening a variety of native cacti, particularly endangered species of Opuntia (Zimmerman et al. 2001), on the coast of the Gulf of Mexico. Cactoblastis cactorum populations have expanded from Florida northward along the Atlantic coast as far as Charleston, SC, and westward along the Gulf of Mexico to Dauphin Island, south of Mobile, AL. It is feared that further movement to the west will allow C. cactorum to enter the US desert Southwest and Mexico, particularly the latter. Numerous cactus species, especially those of the genera Opuntia and Nopalea, are native to the U.S. and Mexico. Local economies based on agricultural and horticultural uses of cacti could be devastated by C. cactorum (Vigueras and Portillo 2001). A bi-national control program between the US and Mexico is being developed, utilizing the sterile insect technique (SIT). In the SIT program, newly emerged moths are irradiated with a {sup 60}Co source and released to mate with wild individuals. The radiation dose completely sterilizes the females and partially sterilizes the males. When irradiated males mate with wild females, the F1 progeny of these matings are sterile. In order for the SIT program to succeed, large numbers of moths must be reared from egg to adult on artificial diet in a quarantined rearing facility (Carpenter et al. 2001). Irradiated insects must then be released in large numbers at the leading edge of the invasive population and at times which coincide with the presence of wild individuals available for mating. Mortality from disease in the rearing colony disrupts the SIT program by reducing the numbers of insects available for release.

  15. Analysis of phases in the structure determination of an icosahedral virus

    SciTech Connect (OSTI)

    Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G.

    2012-03-15

    The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or {pi}. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed.

  16. Discovery of Disease Co-occurrence Patterns from Electronic Healthcare Reimbursement Claims Data

    SciTech Connect (OSTI)

    Ramanathan, Arvind; Pullum, Laura L; Hobson, Tanner C; Quinn, Shannon; Chennubhotla, Chakra; Valkova, Silvia

    2014-01-01

    Effective public health surveillance is important for national secu- rity. With novel emerging infectious diseases being reported across different parts of the world, there is a need to build effective bio- surveillance systems that can track, monitor and report such events in a timely manner. Additionally, there is a need to identify sus- ceptible geographic regions/populations where these diseases may have a significant impact and design preemptive strategies to tackle them. With the digitization of health related information through electronic health records (EHR) and electronic healthcare claim re- imbursements (eHCR), there is a tremendous opportunity to ex- ploit these datasets for public health surveillance. In this paper, we present our analysis on the use of eHCR data for bio-surveillance by studying the 2009-2010 H1N1 pandemic flu season. We present a novel approach to extract spatial and temporal patterns of flu in- cidence across the United States (US) from eHCRs and find that a small, but distinct set of break-out patterns govern the flu and asthma incidence rates across the entire country. Further, we ob- serve a distinct temporal lag in the onset of flu when compared to asthma across geographic regions in the US. The patterns extracted from the data collectively indicate how these break-out patterns are coupled, even though the flu represents an infectious disease whereas asthma represents a typical chronic condition. Taken to- gether, our approach demonstrates how mining eHCRs can provide novel insights in tackling public health concerns.

  17. SSRL HEADLINES April 2009

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    0 April, 2009 __________________________________________________________________________ Contents of this Issue: User Safety Update Caution Advised Regarding Swine Flu Outbreak Science Highlight - Novel Mechanism for DNA Biosynthesis in Organisms with Gene thyX could Lead to Better Antibiotics Science Highlight - Finding the Crystal Structure of P-gp: A Protein that Makes Cancer Cells Resistant to Chemotherapy Science Highlight - A New Way to Limit Damaging Production of Nitric Oxide From the

  18. News Item

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4, 2014 Time: 11:00 am Speaker: Dr. David Baker, University of Washington Title: Design of Protein Structures, Functions and Assemblies Location: 67-3111 Chemla Room Hosted by Ron Zuckermann Abstract: I will describe recent advances in computational protein design which allow the generation of new protein structures and functions. I will describe the use of these methods to design ultra-stable idealized proteins, flu neutralizing proteins, high affinity ligand binding proteins, and self

  19. The effects of 5-fluorouracil and doxorubicin on expression of human immunodeficiency virus type 1 long terminal repeat

    SciTech Connect (OSTI)

    Panozzo, J.; Akan, E.; Griffiths, T.D.; Woloschak, G.E.

    1996-03-01

    Previous work by many groups has documented induction of the HIV-LTR following exposure of cells to ultraviolet light and other DNA damaging agents. Our experiments set out to determine the relative activation or repression of the HIV-LTR in response to two classes of chemotherapeutic agents: Doxorubicin is a DNA-damage inducing agent, and 5-fluorouracil has an antimetabolic mode of action. Using HeLa cells stably transfected with a construct in which HIV-LTR drives expression of the chloramphenicol acetyl transferase reporter gene, we demonstrated an up to 10-fold induction following doxorubicin treatment in 24 h post-treatment. This induction was repressed by treatment with salicylic acid, suggesting a role for prostaglandin/cyclo-oxygenase pathways and/or NFKB in the inductive response. Induction by 5-fluorouracil, in contrast, was more modest (two-fold at most) though it was consistently elevated over controls.

  20. Structure of a bacterial virus DNA-injection protein complex reveals a decameric assembly with a constricted molecular channel

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhao, Haiyan; Speir, Jeffrey A.; Matsui, Tsutomu; Lin, Zihan; Liang, Lingfei; Lynn, Anna Y.; Varnado, Brittany; Weiss, Thomas M.; Tang, Liang; Schuch, Raymond

    2016-02-16

    The multi-layered cell envelope structure of Gram-negative bacteria represents significant physical and chemical barriers for short-tailed phages to inject phage DNA into the host cytoplasm. Here we show that a DNA-injection protein of bacteriophage Sf6, gp12, forms a 465-kDa, decameric assembly in vitro. The electron microscopic structure of the gp12 assembly shows a ~150-Å, mushroom-like architecture consisting of a crown domain and a tube-like domain, which embraces a 25-Å-wide channel that could precisely accommodate dsDNA. The constricted channel suggests that gp12 mediates rapid, uni-directional injection of phage DNA into host cells by providing a molecular conduit for DNA translocation. Themore » assembly exhibits a 10-fold symmetry, which may be a common feature among DNA-injection proteins of P22-like phages and may suggest a symmetry mismatch with respect to the 6-fold symmetric phage tail. As a result, the gp12 monomer is highly flexible in solution, supporting a mechanism for translocation of the protein through the conduit of the phage tail toward the host cell envelope, where it assembles into a DNA-injection device.« less

  1. Science Summary

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    conformational changes and auto-proteolysis. Like many human viruses such as HIV and herpes virus, NwV, an insect virus, requires these specific structural changes to become...

  2. Search for: All records | SciTech Connect

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    ... that inhibits the replication of many viruses such as Moloney murine leukemia virus (MLV) and Sindbis virus (SIN) by preventing the accumulation of viral mRNA in the cytoplasm. ...

  3. AFV CoverSheet

    Office of Scientific and Technical Information (OSTI)

    of Latent Genomic Fragments in the Plasma Virus Population Immonen, Taina Tuulia Conway, ... of Latent Genomic Fragments in the Plasma Virus Population Taina T. Immonen 1 *, Jessica ...

  4. Recombination enhances HIV-1 envelope diversity by facilitating...

    Office of Scientific and Technical Information (OSTI)

    plasma virus population Prev Next Title: Recombination enhances HIV-1 envelope diversity by facilitating the survival of latent genomic fragments in the plasma virus ...

  5. Microsoft Word - Ch 1-Ch9-umai-thesis.doc

    Office of Scientific and Technical Information (OSTI)

    ... as the tobacco mosaic virus, collagen, capsid 116, tubulin117, or actin118, 119. ... and dimensionalities were obtained with DNA 180-183, virus 184 and peptides 179. ...

  6. Structure of the cleavage-activated prefusion form of the parainfluenz...

    Office of Scientific and Technical Information (OSTI)

    the parainfluenza virus 5 fusion protein Citation Details In-Document Search Title: Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein ...

  7. Control Center and Data Management Improvements Modernize Bulk...

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    ... Stronger cybersecurity via firewall, anti-virus, and anti-malware protections that ... firewall that includes additional anti-virus and anti-malware protections, more ...

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    nanotemplates of Tobacco mosaic virus using atomic layer deposition, exhibiting ... the patterning and templated synthesis of virus-structured nanomaterials in two- and ...

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    ... NMR study of xenotropic murine leukemia virus-related virus protease in a complex with amprenavir Furukawa, Ayako ; Okamura, Hideyasu ; Morishita, Ryo ; Department of Microbiology, ...

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    ... are host cell targets for the matrix (M) protein of vesicular stomatitis virus (VSV). ... by the vesicular stomatitis virus matrix protein to inhibit host cell nuclear export. ...

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    ... Structure of the Newcastle disease virus hemagglutinin-neuraminidase (HN) ectodomain ... Mutations of the Newcastle disease virus HN stalk region have been shown to affect both F ...

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    ... (2) spinal cord (2) accuracy (1) aids virus (1) animal tissues (1) applied life ... immunodeficiency virus-positive (HIV+) and 3 post-solid organ transplant ID patients. ...

  13. Solid flexible electrochemical supercapacitor using Tobacco mosaic...

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    mosaic virus nanostructures and ALD ruthenium oxide Citation Details In-Document Search Title: Solid flexible electrochemical supercapacitor using Tobacco mosaic virus ...

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    renormalization (3) trajectories (3) aids virus (2) basic biological sciences (2) lattice ... Immunogenic compositions comprising human immunodeficiency virus (HIV) mosaic Nef proteins ...

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    (2) glycoproteins (2) affinity (1) aids virus (1) antibodies (1) antigens (1) ... Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin Receptor Binding ...

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    Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic virus for ... Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic virus for ...

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    ... from the Crimean-Congo Hemorrhagic Fever Virus in Complex with Covalently Bonded ... Crimean-Congo hemorrhagic fever (CCHF) virus is a tick-borne, negative-sense, ...

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    ... and development of computational tools to predict virus-host protein interactions. ... goal 1. We generated and characterized suitable primers for West Nile Virus RNA detection. ...

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    Filter Results Filter by Subject proteins (4) basic biological sciences (3) aids virus (2) ... data, and results from cell-fusion and virus-infectivity assays collectively indicate ...

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    Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands ... Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex Kirchdoerfer, ...

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    ... Anal Carcinoma in Human Immunodeficiency Virus-Positive Patients Receiving Highly Active ... anal carcinoma in human immunodeficiency virus (HIV)-infected patients receiving highly ...

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    ... January 2008 A Novel Approach to Unknown Virus Identification in Clinical Samples. La ... February 2014 A Novel Approach to Unknown Virus Detection in Clinical Samples. La Bauve, ...

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    renormalization (3) trajectories (3) aids virus (2) basic biological sciences (2) lattice ... Full Text Available December 2014 Human immunodeficiency virus type 1 clade M mosaic gag ...

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    ... Filter Results Filter by Subject applied life sciences (9) aids virus (6) glycoproteins ... rearrangements to mediate virus entry into cells and to evade the host immune response. ...

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    ... Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic virus for ... Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic virus for ...

  6. User Facilities: Tools for Seeing Atoms | U.S. DOE Office of...

    Office of Science (SC) Website

    ... Enlarge Photo X-ray diffraction of a single virus particle. Scattering or diffraction ... X-ray diffraction of virus: T. Ekeberg, Uppsala University. Orbitals in metal oxide: ...

  7. Recombination elevates the effective evolutionary rate and facilitates...

    Office of Scientific and Technical Information (OSTI)

    replication competent virus is detected even when other forms may have been transmitted. ... Subject: 59 BASIC BIOLOGICAL SCIENCES HV-1; MTCT; transmittedfounder virus; ...

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    ... of latent genomic fragments in the plasma virus population Immonen, Taina T. ; Conway, ... Virus released from activated latent cells competes against variants that have continually ...

  9. "Title","Creator/Author","Publication Date","OSTI Identifier...

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    ... Virus andor bacteria are pathogens that can be transported by the disclosed method. ... Virus andor bacteria are pathogens that can be transported by the disclosed method. ...

  10. Rational design and adaptive management of combination therapies...

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    therapies for Hepatitis C virus infection Prev Next Title: Rational design and adaptive management of combination therapies for Hepatitis C virus infection Recent ...

  11. Rational Design and Adaptive Management of Combination Therapies...

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    of Combination Therapies for Hepatitis C Virus Infection CrossMark click for updates n ... Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection. ...

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    ... replication competent virus is detected even when other forms may have been transmitted. ... of latent genomic fragments in the plasma virus population Immonen, Taina T. ; Conway, ...

  13. Strategic Priming with Multiple Antigens can Yield Memory Cell...

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    ... Protective vaccines against smallpox (Vaccinia virus) produce T cell populations that are ... CD8+ T cell immunodominance in primary and secondary influenza virus infections. J. Exp. ...

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    of latent genomic fragments in the plasma virus population Immonen, Taina T. ; Conway, ... Virus released from activated latent cells competes against variants that have continually ...

  15. Analysis of the Argonne distance tabletop exercise method.

    SciTech Connect (OSTI)

    Tanzman, E. A.; Nieves, L. A.; Decision and Information Sciences

    2008-02-14

    The purpose of this report is to summarize and evaluate the Argonne Distance Tabletop Exercise (DISTEX) method. DISTEX is intended to facilitate multi-organization, multi-objective tabletop emergency response exercises that permit players to participate from their own facility's incident command center. This report is based on experience during its first use during the FluNami 2007 exercise, which took place from September 19-October 17, 2007. FluNami 2007 exercised the response of local public health officials and hospitals to a hypothetical pandemic flu outbreak. The underlying purpose of the DISTEX method is to make tabletop exercising more effective and more convenient for playing organizations. It combines elements of traditional tabletop exercising, such as scenario discussions and scenario injects, with distance learning technologies. This distance-learning approach also allows playing organizations to include a broader range of staff in the exercise. An average of 81.25 persons participated in each weekly webcast session from all playing organizations combined. The DISTEX method required development of several components. The exercise objectives were based on the U.S. Department of Homeland Security's Target Capabilities List. The ten playing organizations included four public health departments and six hospitals in the Chicago area. An extent-of-play agreement identified the objectives applicable to each organization. A scenario was developed to drive the exercise over its five-week life. Weekly problem-solving task sets were designed to address objectives that could not be addressed fully during webcast sessions, as well as to involve additional playing organization staff. Injects were developed to drive play between webcast sessions, and, in some cases, featured mock media stories based in part on player actions as identified from the problem-solving tasks. The weekly 90-minute webcast sessions were discussions among the playing organizations that were moderated by a highly-qualified public health physician, who reviewed key scenario developments and player actions, as well as solicited input from each playing organization. The exercise control structure included trusted agents who oversaw exercise planning, playing organization points of contact to ensure exercise coordination, and exercise controller/evaluators to initiate and oversee exercise play. A password-protected exercise website was designed for FluNami 2007 to serve as a compartmentalized central information source, and for transmitting exercise documents. During the course of FluNami 2007, feedback on its quality was collected from players and controller/evaluators. Player feedback was requested at the conclusion of each webcast, upon completion of each problem-solving task, and on October 17, 2007, after the final webcast session had ended. The overall average score given to FluNami 2008 by the responding players was 3.9 on a five-point scale. In addition, suggestions for improving the process were provided by Argonne controller/evaluators after the exercise concluded. A series of recommendations was developed based on feedback from the players and controller/evaluators. These included improvements to the exercise scope and objectives, the problem-solving tasks, the scenarios, exercise control, the webcast sessions, the exercise website, and the player feedback process.

  16. Compound-specific effects of diverse neurodevelopmental toxicants on global gene expression in the neural embryonic stem cell test (ESTn)

    SciTech Connect (OSTI)

    Theunissen, P.T.; Robinson, J.F.; Department of Toxicogenomics, Maastricht University, Maastricht; Netherlands Toxicogenomics Centre, Maastricht ; Pennings, J.L.A.; Netherlands Toxicogenomics Centre, Maastricht ; Herwijnen, M.H. van; Kleinjans, J.C.S.; Netherlands Toxicogenomics Centre, Maastricht ; Piersma, A.H.; Netherlands Toxicogenomics Centre, Maastricht; Institute for Risk Assessment Sciences, Faculty of Veterinary Sciences, Utrecht University, Utrecht

    2012-08-01

    Alternative assays for developmental toxicity testing are needed to reduce animal use in regulatory toxicology. The in vitro murine neural embryonic stem cell test (ESTn) was designed as an alternative for neurodevelopmental toxicity testing. The integration of toxicogenomic-based approaches may further increase predictivity as well as provide insight into underlying mechanisms of developmental toxicity. In the present study, we investigated concentration-dependent effects of six mechanistically diverse compounds, acetaldehyde (ACE), carbamazepine (CBZ), flusilazole (FLU), monoethylhexyl phthalate (MEHP), penicillin G (PENG) and phenytoin (PHE), on the transcriptome and neural differentiation in the ESTn. All compounds with the exception of PENG altered ESTn morphology (cytotoxicity and neural differentiation) in a concentration-dependent manner. Compound induced gene expression changes and corresponding enriched gene ontology biological processes (GO–BP) were identified after 24 h exposure at equipotent differentiation-inhibiting concentrations of the compounds. Both compound-specific and common gene expression changes were observed between subsets of tested compounds, in terms of significance, magnitude of regulation and functionality. For example, ACE, CBZ and FLU induced robust changes in number of significantly altered genes (≥ 687 genes) as well as a variety of GO–BP, as compared to MEHP, PHE and PENG (≤ 55 genes with no significant changes in GO–BP observed). Genes associated with developmentally related processes (embryonic morphogenesis, neuron differentiation, and Wnt signaling) showed diverse regulation after exposure to ACE, CBZ and FLU. In addition, gene expression and GO–BP enrichment showed concentration dependence, allowing discrimination of non-toxic versus toxic concentrations on the basis of transcriptomics. This information may be used to define adaptive versus toxic responses at the transcriptome level.

  17. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Battling bird flu by the numbers May 27, 2008 Los Alamos mathematical model gauges epidemic potential of emerging diseases LOS ALAMOS, New Mexico, May 27, 2008-A pair of Los Alamos National Laboratory theorists have developed a mathematical tool that could help health experts and crisis managers determine in real time whether an emerging infectious disease such as avian influenza H5N1 is poised to spread globally. In a paper published recently in the Public Library of Science, researchers Luís

  18. BSM Newsletter February 2016

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    February 2016 At the Bradbury Latest Issue:May 2016 all issues All Issues » submit IN THIS ISSUE What do you think of our new look and feel? A short survey on our new look February most likely month for flu season to peak From our pages Inspecting a microscope A new artifact joins our collection Tobacco and radiation? Our science question of the month Top 10 science stories of the year From our pages Conifer disapperance due to climate change? From our pages EVENTS What's the matter with

  19. May 2016 Events

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    May May 2016 Events Make sure you join us for Pi Day celebration on Monday 3.14 and have some pie! May 14 Sat 11:00 AM From biofuels to predicting the flu Bradbury Science Museum - 1350 Central Ave, Los Alamos, NM 87544, USA Scientist in the Spotlight: A chance to chat with scientists about their work May 19 Thu 5:30 PM Climate change and the Arctic UnQuarked Wine Room - 145 Central Park Square, Los Alamos, New Mexico 87544 USA Join us for convivial discussion on May 19 at 5:30 p.m. at UnQuarked

  20. May Events

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    May May 2016 Events May 2016 event highlights May 9 Mon 8:00 AM Energy Landscapes: From Protein Folding to Molecular Assembly Hilton Santa Fe Historic Plaza - Santa Fe, NM Nanoscale molecular assembly is very common in biology and in nanotechnology. May 14 Sat 11:00 AM From biofuels to predicting the flu Bradbury Science Museum - 1350 Central Ave, Los Alamos, NM 87544, USA Scientist in the Spotlight: A chance to chat with scientists about their work May 16 Mon 8:00 AM Data Science and Optimal

  1. Science on Tap - Forecasting illness

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Science on Tap - Forecasting illness Science on Tap - Forecasting illness WHEN: Mar 17, 2016 5:30 PM - 7:00 PM WHERE: UnQuarked Wine Room 145 Central Park Square, Los Alamos, New Mexico 87544 USA CONTACT: Linda Anderman (505) 665-9196 CATEGORY: Bradbury INTERNAL: Calendar Login Event Description Mark your calendars for this event held every third Thursday from 5:30 to 7 p.m. A short presentation is followed by a lively discussion on a different subject each month. Forecasting the flu (and other

  2. Hybrid fluidized bed combuster

    DOE Patents [OSTI]

    Kantesaria, Prabhudas P. (Windsor, CT); Matthews, Francis T. (Poquonock, CT)

    1982-01-01

    A first atmospheric bubbling fluidized bed furnace is combined with a second turbulent, circulating fluidized bed furnace to produce heat efficiently from crushed solid fuel. The bed of the second furnace receives the smaller sizes of crushed solid fuel, unreacted limestone from the first bed, and elutriated solids extracted from the flu gases of the first bed. The two-stage combustion of crushed solid fuel provides a system with an efficiency greater than available with use of a single furnace of a fluidized bed.

  3. 2011 - 09 | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    9 Sep 2011 Tue, 2011-09-27 15:00 Performance Appraisal Process Begins 9/27/2011 Mon, 2011-09-26 15:00 Occ. Med. Offers Staff Flu Vaccines by Appointment Thu, 2011-09-15 15:00 JLab Adopts Event Policy to Avoid Scheduling Conflicts Tue, 2011-09-13 15:00 CS Parking Lot Closed During Test Lab Exterior Painting Thu, 2011-09-01 15:00 United Way Annual Appeal Underway at JLab Thu, 2011-09-01 15:00 Invitation to Celebrate JLab Founding Director's Contributions

  4. A role for granulocyte-macrophage colony-stimulating factor in the regulation of CD8{sup +} T cell responses to rabies virus

    SciTech Connect (OSTI)

    Wanjalla, Celestine N.; Goldstein, Elizabeth F.; Wirblich, Christoph; Schnell, Matthias J.

    2012-05-10

    Inflammatory cytokines have a significant role in altering the innate and adaptive arms of immune responses. Here, we analyzed the effect of GM-CSF on a RABV-vaccine vector co-expressing HIV-1 Gag. To this end, we immunized mice with RABV expressing HIV-1 Gag and GM-CSF and analyzed the primary and recall CD8{sup +} T cell responses. We observed a statistically significant increase in antigen presenting cells (APCs) in the spleen and draining lymph nodes in response to GM-CSF. Despite the increase in APCs, the primary and memory anti HIV-1 CD8{sup +} T cell response was significantly lower. This was partly likely due to lower levels of proliferation in the spleen. Animals treated with GM-CSF neutralizing antibodies restored the CD8{sup +} T cell response. These data define a role of GM-CSF expression, in the regulation of the CD8{sup +} T cell immune responses against RABV and has implications in the use of GM-CSF as a molecular adjuvant in vaccine development.

  5. Metagenomic analysis of planktonic microbial consortia from a...

    Office of Scientific and Technical Information (OSTI)

    ... % by MG- RAST, 0.1 % by Blast) and virus or plasmid (0.2 % by MG-RAST, 0.07 % by Blast). ... Virus and bacteriophage reads included assignments to Myoviridae, a type of Caudovirus, ...

  6. Domain-level rocking motion within a polymerase that translocates...

    Office of Scientific and Technical Information (OSTI)

    An X-ray crystallographic structure is described for unliganded Vaccinia virus poly(A) ... Vaccinia virus poly(A) polymerase (VP55) is the only known polymerase that can translocate ...

  7. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... The inhibition of PI3K-Akt activation by LY294002 significantly reduced the viral yield, including a reduction in budded viruses and occlusion bodies. The virus production was ...

  8. Microsoft Word - h1n1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The similarity of the Sa antigenic site, in particular, of the 2009 H1N1 virus with the ... viruses in vivo (4), and binds to the Sa antigenic site which is nearly identical in ...

  9. Lessons Learned from Cyber Security Assessments of SCADA and...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... virus scanners or the process of performing a scan may have the effect of a denial of service on most control system networks. Some vendors supply tested virus protection ...

  10. mhtml:file://C:\\Documents and Settings\\kolater\\Local Settings...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... Emails to and from this account may be monitored. Whilst reasonable care has been taken to avoid virus transmission, no responsibility for viruses is taken and it is your ...

  11. EVALUATION REPORT The Department of Energy's Unclassified

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... However, without the latest updates, the systems were at risk of compromise by a virus or ... could result in the distribution of a virus or other malware that could compromise ...

  12. SN-03 Rate Hearing (7i) Files (ratecases/sn03)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    for any problems that may occur. Although these documents have been scanned by BPA anti-virus software, BPA cannot guarantee the files are virus-free. Notes: Some directories may...

  13. Patents -- Ivar Giaever (1976)

    Office of Scientific and Technical Information (OSTI)

    ... used to provide large and widely-distributed surface area for sorting out and separating select viruses, bacteria and other cells from multi-cell, bacteria or virus populations. ...

  14. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... is described for unliganded Vaccinia virus poly(A) polymerase monomer (VP55), showing ... Vaccinia virus poly(A) polymerase (VP55) is the only known polymerase that can translocate ...

  15. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... infection by blocking adsorption of the virus to the cells. * GLTA and GLTB bind to EV71 ... through interacting with the viral particle to block the adsorption of virus to the cells. ...

  16. Biogenic Aerosols Effects on Climate and Clouds Cloud OD Sensor...

    Office of Scientific and Technical Information (OSTI)

    ... Because of our direct connection to the Internet, virus software protection was installed and frequent virus scans were scheduled at night. 4.0 TWST Data Catalog TWST was deployed ...

  17. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... AAnn Arbor660 (AA ca) (H2N2) virus in mice and ferrets to evaluate its use in the event of an H2 influenza pandemic. The AA ca virus was restricted in replication in the ...

  18. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ...erazine-2-carboxamides to the hepatitis C virus polymerase Gentles, Robert G. ; Sheriff, ... These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and ...

  19. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk ... Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of ...

  20. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Structural basis for the antibody neutralization of Herpes simplex virus Lee, Cheng-Chung ... Glycoprotein D (gD) of Herpes simplex virus (HSV) binds to a host cell surface receptor, ...

  1. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Functional analysis of miR-181a and Fas involved in hepatitis B virus-related ... The hepatitis B virus (HBV) is responsible for most of hepatocellular carcinoma (HCC). ...

  2. Structural basis for the antibody neutralization of Herpes simplex...

    Office of Scientific and Technical Information (OSTI)

    of Herpes simplex virus Citation Details In-Document Search Title: Structural basis for the antibody neutralization of Herpes simplex virus The gD-E317-Fab complex ...

  3. Seeing Matter at Atomic and Molecular Scales | U.S. DOE Office...

    Office of Science (SC) Website

    ... Potential Anticancer Agent Using an x-ray beamline, the 3-D structure has been solved for Seneca Valley Virus-001, a virus that attacks certain cancer cells without harming normal ...

  4. Patents -- Ivar Giaever (1976)

    Office of Scientific and Technical Information (OSTI)

    and separating select viruses, bacteria and other cells from multi-cell, bacteria or virus populations. US 3,975,238 METHOD AND APPARATUS FOR DETECTING MOLECULES IN SOLUTIONS --...

  5. Time-Resolved Small-Angle X-ray Scattering Studies Revealed Three Kinetic

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Stages of a T=4 Virus Maturation June 2010 Time-Resolved Small-Angle X-ray Scattering Studies Revealed Three Kinetic Stages of a T=4 Virus Maturation Most eukaryotic viruses, including HIV, influenza and herpes viruses, undergo maturation when transitioning from the noninfectious provirion to the infectious virion. Maturation processes involve reorganization of viral quaternary structure to defend viral gene from the cellular defense mechanism and lead to effective transfection. Nudaurelia

  6. Dr. Andrew Russo

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Disabling a Killer Virus The CAMD Protein Crystallography beamline was used to determine the structure of a protein that the Venezuelan Equine Encephalitis (VEE) virus requires for replication. VEE is a mosquito-borne virus found in Central and South America, and southern Texas. Periodic outbreaks infect tens of thousands of people and kill hundreds of thousands of horses, donkeys and mules. The virus was developed into a biological weapon during the Cold War by both the United States and the

  7. Audit Report: IG-0463 | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    software, including electronic mail, word processing, spreadsheet, database management, application development, statistical analysis, presentation, security and virus protection. ...

  8. Design Construction and Operation of a Supercritical Carbon Dioxide (sCO2) Loop for Investigation of Dry Cooling and Natural Circulation Potential for Use in Advanced Small Modular Reactors Utilizing sCO2 Power Conversion Cycles.

    SciTech Connect (OSTI)

    Middleton, Bobby D.; Rodriguez, Salvador B.; Carlson, Matthew David

    2015-11-01

    This report outlines the work completed for a Laboratory Directed Research and Development project at Sandia National Laboratories from October 2012 through September 2015. An experimental supercritical carbon dioxide (sCO 2 ) loop was designed, built, and o perated. The experimental work demonstrated that sCO 2 can be uti lized as the working fluid in an air - cooled, natural circulation configuration to transfer heat from a source to the ultimate heat sink, which is the surrounding ambient environment in most ca ses. The loop was also operated in an induction - heated, water - cooled configuration that allows for measurements of physical parameters that are difficult to isolate in the air - cooled configuration. Analysis included the development of two computational flu id dynamics models. Future work is anticipated to answer questions that were not covered in this project.

  9. 2012 - 09 | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    9 Sep 2012 Wed, 2012-09-26 15:00 JLab Computing: Microsoft Windows Patch Scheduled for Tonight Wed, 2012-09-26 15:00 Annual United Way Campaign Wed, 2012-09-26 15:00 Machine Shop Work Requests Wed, 2012-09-26 15:00 2012 Vacation Donation Open Enrollment Wed, 2012-09-19 15:00 Don't Use Internet Explorer Unless Necessary: Malware Found Wed, 2012-09-19 15:00 Change in JLab Pay Dates Wed, 2012-09-19 15:00 Performance Appraisal Process Begins 9/25/2012 Wed, 2012-09-12 15:00 Occ. Med. Offers Staff Flu

  10. Forecasting the 2013–2014 influenza season using Wikipedia

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Hickmann, Kyle S.; Fairchild, Geoffrey; Priedhorsky, Reid; Generous, Nicholas; Hyman, James M.; Deshpande, Alina; Del Valle, Sara Y.; Salathé, Marcel

    2015-05-14

    Infectious diseases are one of the leading causes of morbidity and mortality around the world; thus, forecasting their impact is crucial for planning an effective response strategy. According to the Centers for Disease Control and Prevention (CDC), seasonal influenza affects 5% to 20% of the U.S. population and causes major economic impacts resulting from hospitalization and absenteeism. Understanding influenza dynamics and forecasting its impact is fundamental for developing prevention and mitigation strategies. We combine modern data assimilation methods with Wikipedia access logs and CDC influenza-like illness (ILI) reports to create a weekly forecast for seasonal influenza. The methods are appliedmore » to the 2013-2014 influenza season but are sufficiently general to forecast any disease outbreak, given incidence or case count data. We adjust the initialization and parametrization of a disease model and show that this allows us to determine systematic model bias. In addition, we provide a way to determine where the model diverges from observation and evaluate forecast accuracy. Wikipedia article access logs are shown to be highly correlated with historical ILI records and allow for accurate prediction of ILI data several weeks before it becomes available. The results show that prior to the peak of the flu season, our forecasting method produced 50% and 95% credible intervals for the 2013-2014 ILI observations that contained the actual observations for most weeks in the forecast. However, since our model does not account for re-infection or multiple strains of influenza, the tail of the epidemic is not predicted well after the peak of flu season has passed.« less

  11. Forecasting the 2013–2014 influenza season using Wikipedia

    SciTech Connect (OSTI)

    Hickmann, Kyle S.; Fairchild, Geoffrey; Priedhorsky, Reid; Generous, Nicholas; Hyman, James M.; Deshpande, Alina; Del Valle, Sara Y.; Salathé, Marcel

    2015-05-14

    Infectious diseases are one of the leading causes of morbidity and mortality around the world; thus, forecasting their impact is crucial for planning an effective response strategy. According to the Centers for Disease Control and Prevention (CDC), seasonal influenza affects 5% to 20% of the U.S. population and causes major economic impacts resulting from hospitalization and absenteeism. Understanding influenza dynamics and forecasting its impact is fundamental for developing prevention and mitigation strategies. We combine modern data assimilation methods with Wikipedia access logs and CDC influenza-like illness (ILI) reports to create a weekly forecast for seasonal influenza. The methods are applied to the 2013-2014 influenza season but are sufficiently general to forecast any disease outbreak, given incidence or case count data. We adjust the initialization and parametrization of a disease model and show that this allows us to determine systematic model bias. In addition, we provide a way to determine where the model diverges from observation and evaluate forecast accuracy. Wikipedia article access logs are shown to be highly correlated with historical ILI records and allow for accurate prediction of ILI data several weeks before it becomes available. The results show that prior to the peak of the flu season, our forecasting method produced 50% and 95% credible intervals for the 2013-2014 ILI observations that contained the actual observations for most weeks in the forecast. However, since our model does not account for re-infection or multiple strains of influenza, the tail of the epidemic is not predicted well after the peak of flu season has passed.

  12. Activation of the PI3K-Akt pathway by human T cell leukemia virus type 1 (HTLV-1) oncoprotein Tax increases Bcl3 expression, which is associated with enhanced growth of HTLV-1-infected T cells

    SciTech Connect (OSTI)

    Saito, Kousuke; Saito, Mineki; Taniura, Naoko; Okuwa, Takako; Ohara, Yoshiro

    2010-08-01

    Bcl3 is a member of the I{kappa}B family that regulates genes involved in cell proliferation and apoptosis. Recent reports indicated that Bcl3 is overexpressed in HTLV-1-infected T cells via Tax-mediated transactivation, and acts as a negative regulator of viral transcription. However, the role of Bcl3 in cellular signal transduction and the growth of HTLV-1-infected T cells have not been reported. In this study, we showed that the knockdown of Bcl3 by short hairpin RNA inhibited the growth of HTLV-1-infected T cells. Although phosphatidylinositol-3 kinase (PI3K) inhibitor reduced Bcl3 expression, inactivation of glycogen synthase kinase 3 (GSK3), an effector kinase of the PI3K/Akt signaling pathway, restored Bcl3 expression in Tax-negative but not in Tax-positive T cells. Our results indicate that the overexpression of Bcl3 in HTLV-1-infected T cells is regulated not only by transcriptional but also by post-transcriptional mechanisms, and is involved in overgrowth of HTLV-1-infected T cells.

  13. Architecture for removable media USB-ARM

    DOE Patents [OSTI]

    Shue, Craig A.; Lamb, Logan M.; Paul, Nathanael R.

    2015-07-14

    A storage device is coupled to a computing system comprising an operating system and application software. Access to the storage device is blocked by a kernel filter driver, except exclusive access is granted to a first anti-virus engine. The first anti-virus engine is directed to scan the storage device for malicious software and report results. Exclusive access may be granted to one or more other anti-virus engines and they may be directed to scan the storage device and report results. Approval of all or a portion of the information on the storage device is based on the results from the first anti-virus engine and the other anti-virus engines. The storage device is presented to the operating system and access is granted to the approved information. The operating system may be a Microsoft Windows operating system. The kernel filter driver and usage of anti-virus engines may be configurable by a user.

  14. A bio-synthetic interface for discovery of viral entry mechanisms.

    SciTech Connect (OSTI)

    Gutzler, Mike; Maar, Dianna; Negrete, Oscar; Hayden, Carl C.; Sasaki, Darryl Yoshio; Stachowiak, Jeanne C.; Wang, Julia

    2010-09-01

    Understanding and defending against pathogenic viruses is an important public health and biodefense challenge. The focus of our LDRD project has been to uncover the mechanisms enveloped viruses use to identify and invade host cells. We have constructed interfaces between viral particles and synthetic lipid bilayers. This approach provides a minimal setting for investigating the initial events of host-virus interaction - (i) recognition of, and (ii) entry into the host via membrane fusion. This understanding could enable rational design of therapeutics that block viral entry as well as future construction of synthetic, non-proliferating sensors that detect live virus in the environment. We have observed fusion between synthetic lipid vesicles and Vesicular Stomatitis virus particles, and we have observed interactions between Nipah virus-like particles and supported lipid bilayers and giant unilamellar vesicles.

  15. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    deciphers HIV attack plan March 29, 2013 Scientists get inside look at how AIDS virus grooms its assault team LOS ALAMOS, N. M., March 29, 2013-A new study by Los Alamos National Laboratory and University of Pennsylvania scientists defines previously unknown properties of transmitted HIV-1, the virus that causes AIDS. The viruses that successfully pass from a chronically infected person to a new individual are both remarkably resistant to a powerful initial human immune-response mechanism, and

  16. LOS ALAMOS, N.M., Nov. 19, 2013-Researchers at Los Alamos National Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    virus spread and evolution studied through computer modeling November 19, 2013 LOS ALAMOS, N.M., Nov. 19, 2013-Researchers at Los Alamos National Laboratory are investigating the complex relationships between the spread of the HIV virus in a population (epidemiology) and the actual, rapid evolution of the virus (phylogenetics) within each patient's body. "We have developed novel ways of estimating epidemics dynamics such as who infected whom, and the true population incidence of infection

  17. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 Print ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure observations of the adsorption of carbon dioxide

  18. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 ALSNews Vol. 354 Print Tuesday, 24 June 2014 08:51 ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure

  19. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 Print ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure observations of the adsorption of carbon dioxide

  20. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 Print ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure observations of the adsorption of carbon dioxide

  1. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 Print ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure observations of the adsorption of carbon dioxide

  2. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 Print ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure observations of the adsorption of carbon dioxide

  3. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 Print ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure observations of the adsorption of carbon dioxide

  4. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALSNews Vol. 354 Print ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure observations of the adsorption of

  5. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALSNews Vol. 354 Print ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ electronic-structure observations of the adsorption of

  6. ALSNews Vol. 354

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALSNews Vol. 354 ALSNews Vol. 354 Print Tuesday, 24 June 2014 08:51 ALS Capabilities Reveal Multiple Functions of Ebola Virus ebola Researchers at the ALS have demonstrated that a protein of Ebola virus, termedVP40, undergoes dramatic refolding rearrangements to achieve three entirely different structures for three entirely separate functions in the virus life cycle. Read more... Contact: Erica Saphire An Inside Look at a MOF in Action mof Researchers have recorded the first in situ

  7. NNSA Product Aids in Anthrax Clean-up

    National Nuclear Security Administration (NNSA)

    development project funded by NNSA's Chemical and Biological National Security Program. ... was effective against chemical warfare agents, toxins, viruses and anthrax spores. ...

  8. News Item

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mimicking Nature for Homeland Security Biological Nanostructures Facility Director, Ron ... lethal chemical agents or deadly viruses deployed during warfare or a terrorist attack. ...

  9. Modular microfluidic system for biological sample preparation...

    Office of Scientific and Technical Information (OSTI)

    module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter. ...

  10. SEQUEDEX

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases (whether arising from bacteria, parasites, or viruses; characterizing gut, oral and skin microbiomes of humans, livestock, and pets; metagenomics of soils, rivers,...

  11. ALSNews Vol. 338

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    aid in the eventual development of a universal vaccine, protecting against all types of influenza viruses and eliminating the guesswork that limits vaccine effectiveness. Read...

  12. Slide 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    June 15, 2010 2 West Nile Virus - Awareness * Hanford All Employee bulletins * Presidents' Zero Accident Council (PZAC) meeting attendance * AdvanceMed Hanford information links * ...

  13. Nanomaterial Composites for Next Generation Water Filters: Cooperative Research and Development Final Report, CRADA Number CRD-06-197

    SciTech Connect (OSTI)

    Ginley, D.

    2013-04-01

    Under this CRADA, the Parties will produce and test a composite filter element that will remove particles, bacteria and viruses to produce safe drinking water.

  14. Timeline of Events: 2010 | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... of Education, Culture, Sports, Science and Technology. ... learning leadership techniques, and discussing the ... in a process necessary for the virus to infect a host cell. ...

  15. Audit Report: IG-0500 | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    00 Audit Report: IG-0500 April 5, 2001 Virus Protection Strategies and Cyber Security Incident Reporting Information Technology (IT) plays an integral role in the programs and ...

  16. CPL4001840-20151231100208

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    este mensaje, ni se responsabiliza de los posibles perjuicios de cualquier naturaleza derivados de la captura de datos, virus informaticos o manipulaciones efectuadas por terceros....

  17. Science On Tap - Phylogenetics and Epidemics

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and the actual, rapid evolution of the virus (phylogenetics) within each patient's body. "We have developed novel ways of estimating epidemics dynamics such as who infected...

  18. LOS ALAMOS, N.M., Nov. 19, 2013-Researchers at Los Alamos National...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and the actual, rapid evolution of the virus (phylogenetics) within each patient's body. "We have developed novel ways of estimating epidemics dynamics such as who infected...

  19. Discovery and Preclinical Characterization of theCyclopropylindoloben...

    Office of Scientific and Technical Information (OSTI)

    clopropylindolobenzazepine BMS-791325, A Potent Allosteric Inhibitor of the Hepatitis C Virus NS5B Polymerase Citation Details In-Document Search Title: Discovery and Preclinical...

  20. CHEMFINAL1400

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Chemical warfare agents to be detected and identified include nerve and mustard gases; biological agents such as Botulinum toxin, ricin, aflatoxins and an encephalitis virus. The ...

  1. ALSNews Vol. 332

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structured Biomimetic Materials biomemetic materials Researchers have turned a benign virus into an engineering tool for assembling structures that mimic collagen, one of the...

  2. Link Alpha A

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Alvarez Physics Memos AmeriFlux Animal Welfare and Research Committee (AWRC) Anti-virus software Apartment Retrofits for Energy and Indoor Environmental Quality (IEQ)...

  3. STANFORD SYNCHROTRON RADIATION LIGHTSOURCE The Stanford Synchrotron...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    the very nature of bacteria and viruses, exposed how genetic mutations may cause diabetes, and mapped the structures of proteins for use in biology and medicine. Opportunities...

  4. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Filter Results Filter by Subject chem (3) applied life sciences (2) basic biological sciences (2) design (2) glycoproteins (2) affinity (1) aids virus (1) antibodies (1) antigens ...

  5. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... sciences (2) basic biological sciences (2) hydrogen (2) acrolein (1) adducts (1) aids virus (1) animal cells (1) antibodies (1) arginine (1) biological radiation effects (1) ...

  6. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... By separating the diffraction pattern of the virus particles from that of their surroundings, we performed quantitative and high-contrast imaging of a single virion. The structure ...

  7. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... platforms for preclinical and field testing that utilize the assays developed in goal 1. We generated and characterized suitable primers for West Nile Virus RNA detection. ...

  8. Selective deposition of nanostructured ruthenium oxide using...

    Office of Scientific and Technical Information (OSTI)

    Title: Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic virus for micro-supercapacitors in solid Nafion electrolyte Authors: Gnerlich, Markus ; Ben-Yoav, ...

  9. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... (2) quantum mechanics (2) qubits (2) transmission electron microscopy (2) aids virus (1) air pollution control (1) animal cells (1) anisotropy (1) antibodies (1) ...

  10. January 2013 Most Viewed Documents for Biology And Medicine ...

    Office of Scientific and Technical Information (OSTI)

    metropolitana de Sao Paulo, Brasil, utilizando a bromelia Tillandsia usneoides L. como biomonitor Nogueira, Claudio Ailton Development of simulation tools for virus shell assembly. ...

  11. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Structure-Function Analysis of Vaccinia Virus H7 Protein Reveals a Novel Phosphoinositide Binding Fold Essential for Poxvirus Replication Kolli, Swapna ; Meng, Xiangzhi ; Wu, Xiang ...

  12. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Track Viral Evolution - A sensitive technique developed at the Laboratory can identify virus mutations that may jump frommore host to host; and (5) Data for Defense: New ...

  13. Investigation of type-I interferon dysregulation by arenaviruses...

    Office of Scientific and Technical Information (OSTI)

    infection assays, molecular virology analysis of Arenavirus nucleoprotein structure-function, and development of computational tools to predict virus-host protein interactions. ...

  14. Ectopic expression of anti-HIV-1 shRNAs protects CD8{sup +} T...

    Office of Scientific and Technical Information (OSTI)

    ... Country of Publication: United States Language: English Subject: 60 APPLIED LIFE SCIENCES; AIDS VIRUS; ANTIGENS; CELL PROLIFERATION; IMMUNOTHERAPY; IN VITRO; IN VIVO; INSPECTION; ...

  15. SC e-journals, Medicine

    Office of Scientific and Technical Information (OSTI)

    ... Trends in Microbiology Veterinary Research Communications Virchows Archiv Virology Virtual Journal of Biomedical Optics Virus Genes X-Ray Spectrometry Zeitschrift fr Kardiologie

  16. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    platforms for preclinical and field testing that utilize the assays developed in goal 1. We generated and characterized suitable primers for West Nile Virus RNA detection. ...

  17. Broad Distribution of Energetically Important Contacts across...

    Office of Scientific and Technical Information (OSTI)

    Language: ENGLISH Subject: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; AFFINITY; AIDS VIRUS; DISTRIBUTION; HYPOTHESIS; PROTEINS Word Cloud More Like This Full Text ...

  18. February | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    ... String searching is at the core of many security and network applications such as search engines, intrusion detection systems, virus scanners and spam filters. PNNL researchers are ...

  19. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Potential strategies to develop such inhibitors are also discussed. less June 2013 Structural and molecular basis for Ebola virus neutralization by protective human antibodies ...

  20. Self-assembled Ni/TiO{sub 2} nanocomposite anodes synthesized...

    Office of Scientific and Technical Information (OSTI)

    Ni(core)TiOsub 2(shell) nanocomposite anodes were fabricated on three-dimensional, self-assembled nanotemplates of Tobacco mosaic virus using atomic layer deposition, exhibiting ...

  1. The FELICIA bulletin board system and the IRBIS anonymous FTP server: Computer security information sources for the DOE community. CIAC-2302

    SciTech Connect (OSTI)

    Orvis, W.J.

    1993-11-03

    The Computer Incident Advisory Capability (CIAC) operates two information servers for the DOE community, FELICIA (formerly FELIX) and IRBIS. FELICIA is a computer Bulletin Board System (BBS) that can be accessed by telephone with a modem. IRBIS is an anonymous ftp server that can be accessed on the Internet. Both of these servers contain all of the publicly available CIAC, CERT, NIST, and DDN bulletins, virus descriptions, the VIRUS-L moderated virus bulletin board, copies of public domain and shareware virus- detection/protection software, and copies of useful public domain and shareware utility programs. This guide describes how to connect these systems and obtain files from them.

  2. EA-1363: Finding of No Significant Impact

    Broader source: Energy.gov [DOE]

    Joint Environmental Assessment 2002-2006 of the California Department Of Food and Agriculture Curly Top Virus Control Program for Bureau Of Land Management and Department Of Energy

  3. Calendar Year 2001 | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of the Purchase of Protective Force Respirators April 5, 2001 Audit Report: IG-0500 Virus Protection Strategies and Cyber Security Incident Reporting April 3, 2001 Special...

  4. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    developed in goal 1. We generated and characterized suitable primers for West Nile Virus RNA detection. Both optical and electrochemical transduction technologies were...

  5. disease outbreak. Brozik, Susan Marie; Manginell, Ronald Paul...

    Office of Scientific and Technical Information (OSTI)

    developed in goal 1. We generated and characterized suitable primers for West Nile Virus RNA detection. Both optical and electrochemical transduction technologies were...

  6. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    assays developed in goal We generated and characterized suitable primers for West Nile Virus RNA detection Both optical and electrochemical transduction technologies were...

  7. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    of Ligands Targeting a Novel Site on the Integrase Enzyme of Human Immunodeficiency Virus;8197;1 Wielens, Jerome ; Headey, Stephen J. ; Deadman, John J. ; Rhodes, David I. ;...

  8. BSL Fact Sheet_r02_12-08-2005_keb.pub

    National Nuclear Security Administration (NNSA)

    virus, severe acute respiratory syndrome (SARS), monkeypox, and annual outbreaks of influenza. To control epidemics and protect the public health, medical researchers must...

  9. Work with Biological Materials

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    cells, viruses), plant or soil samples (USDA quarantines), recombinant DNA, or blood-borne pathogen. Biological Use Authorization The great majority of biological work at...

  10. Closer to HIV vaccine goal with new insight into viral factors

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    donor's predominant virus subpopulation in the genital tract differed from that in the blood. Comparing the HIV sequence population in each newly infected partner with that in the...

  11. HIV evolution in early infection: selection pressures, patterns...

    Office of Scientific and Technical Information (OSTI)

    host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection...

  12. Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Ekeberg, Tomas

    2015-05-26

    This dataset contains the diffraction patterns that were used for the first three-dimensional reconstruction of a virus using FEL data. The sample was the giant mimivirus particle, which is one of the largest known viruses with a diameter of 450 nm. The dataset consists of the 198 diffraction patterns that were used in the analysis.

  13. Anti-influenza M2e antibody

    DOE Patents [OSTI]

    Bradbury, Andrew M.

    2011-12-20

    Humanized recombinant and monoclonal antibodies specific for the ectodomain of the influenza virus M2 ion channel protein are disclosed. The antibodies of the invention have anti-viral activity and may be useful as anti-viral therapeutics and/or prophylactic/vaccine agents for inhibiting influenza virus replication and for treating individuals infected with influenza.

  14. Viral chemotherapy. Volume 2

    SciTech Connect (OSTI)

    Shugar, D.

    1985-01-01

    This book contains seven chapters. Some of the chapter titles are: Molecular aspects of RNA tumor virus-induced carcinogenesis; Trifluorothymidine; Effects of antiviral nucleoside analogs on purine metabolism; Development of drug resistance and dependence in viruses; and Low molecular weight interferon inducers: Structure and biology.

  15. Anti-influenza M2e antibody

    DOE Patents [OSTI]

    Bradbury, Andrew M.

    2013-04-16

    Humanized recombinant and monoclonal antibodies specific for the ectodomain of the influenza virus M2 ion channel protein are disclosed. The antibodies of the invention have anti-viral activity and may be useful as anti-viral therapeutics and/or prophylactic/vaccine agents for inhibiting influenza virus replication and for treating individuals infected with influenza.

  16. Detection of bioagents using a shear horizontal surface acoustic wave biosensor

    DOE Patents [OSTI]

    Larson, Richard S; Hjelle, Brian; Hall, Pam R; Brown, David C; Bisoffi, Marco; Brozik, Susan M; Branch, Darren W; Edwards, Thayne L; Wheeler, David

    2014-04-29

    A biosensor combining the sensitivity of surface acoustic waves (SAW) generated at a frequency of 325 MHz with the specificity provided by antibodies and other ligands for the detection of viral agents. In a preferred embodiment, a lithium tantalate based SAW transducer with silicon dioxide waveguide sensor platform featuring three test and one reference delay lines was used to adsorb antibodies directed against Coxsackie virus B4 or the negative-stranded category A bioagent Sin Nombre virus (SNV). Rapid detection of increasing concentrations of viral particles was linear over a range of order of magnitude for both viruses, and the sensor's selectivity for its target was not compromised by the presence of confounding Herpes Simplex virus type 1 The biosensor was able to delect SNV at doses lower than the load of virus typically found in a human patient suffering from hantavirus cardiopulmonary syndrome (HCPS).

  17. I Am Science - and So Can You!

    SciTech Connect (OSTI)

    DiChristina, Mariette

    2013-05-08

    Science is humanitys best invention for getting at the truth about how things work (a.k.a. basic research) and solving problems (applied). I can even make a claim that most people are interested in science topicsthey just dont think of them as science. Consider how many of todays top headlines have a critical science underpinning: energy supply, social change from digital innovations, efforts to treat cancer and other diseases, emerging infectious agents like bird flu, climate change, and so on. Clearly, a basic understanding about science is more vital than ever. At the same time, we see two trends: the collapse of traditional science journalism jobs as newspapers have cut thousands of positions and a greater access toand a larger readership forscience-related materials than the world has ever known. Put another way, just when the public needs the Fourth Estate most, its instead drowning in a sea of 24/7 misinformation (a.k.a. the Internet). Whats a busy scientist to do to help engage the lay public? Glad you asked.

  18. Economic and policy implications of pandemic influenza.

    SciTech Connect (OSTI)

    Smith, Braeton J.; Starks, Shirley J.; Loose, Verne W.; Brown, Theresa Jean; Warren, Drake E.; Vargas, Vanessa N.

    2010-03-01

    Pandemic influenza has become a serious global health concern; in response, governments around the world have allocated increasing funds to containment of public health threats from this disease. Pandemic influenza is also recognized to have serious economic implications, causing illness and absence that reduces worker productivity and economic output and, through mortality, robs nations of their most valuable assets - human resources. This paper reports two studies that investigate both the short- and long-term economic implications of a pandemic flu outbreak. Policy makers can use the growing number of economic impact estimates to decide how much to spend to combat the pandemic influenza outbreaks. Experts recognize that pandemic influenza has serious global economic implications. The illness causes absenteeism, reduced worker productivity, and therefore reduced economic output. This, combined with the associated mortality rate, robs nations of valuable human resources. Policy makers can use economic impact estimates to decide how much to spend to combat the pandemic influenza outbreaks. In this paper economists examine two studies which investigate both the short- and long-term economic implications of a pandemic influenza outbreak. Resulting policy implications are also discussed. The research uses the Regional Economic Modeling, Inc. (REMI) Policy Insight + Model. This model provides a dynamic, regional, North America Industrial Classification System (NAICS) industry-structured framework for forecasting. It is supported by a population dynamics model that is well-adapted to investigating macro-economic implications of pandemic influenza, including possible demand side effects. The studies reported in this paper exercise all of these capabilities.

  19. Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gardner, Shea N.; Jaing, Crystal J.; Elsheikh, Maher M.; Peña, José; Hysom, David A.; Borucki, Monica K.

    2014-01-01

    Background . Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results . A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus.more » Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions . This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family.« less

  20. Characterization of a novel insect-specific flavivirus from Brazil: Potential for inhibition of infection of arthropod cells with medically important flaviviruses.

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kenney, Joan L.; Solberg, Owen D.; Langevin, Stanley A.; Brault, Aaron C.

    2014-01-12

    In the past decade, there has been an upsurge in the number of newly described insect-specific flaviviruses isolated pan-globally. We recently described the isolation of a novel flavivirus (tentatively designated ‘Nhumirim virus’; NHUV) that represents an example of a unique subset of apparently insect-specific viruses that phylogenetically affiliate with dual-host mosquito-borne flaviviruses despite appearing to be limited to replication in mosquito cells. We characterized the in vitro growth potential and 3' untranslated region (UTR) sequence homology with alternative flaviviruses, and evaluated the virus’s capacity to suppress replication of representative Culex spp.-vectored pathogenic flaviviruses in mosquito cells. Only mosquito cell linesmore » were found to support NHUV replication, further reinforcing the insect-specific phenotype of this virus. Analysis of the sequence and predicted RNA secondary structures of the 3' UTR indicated NHUV to be most similar to viruses within the yellow fever serogroup and Japanese encephalitis serogroup, and viruses in the tick-borne flavivirus clade. NHUV was found to share the fewest conserved sequence elements when compared with traditional insect-specific flaviviruses. This suggests that, despite apparently being insect specific, this virus probably diverged from an ancestral mosquito-borne flavivirus. Co-infection experiments indicated that prior or concurrent infection of mosquito cells with NHUV resulted in a significant reduction in virus production of West Nile virus (WNV), St Louis encephalitis virus (SLEV) and Japanese encephalitis virus. As a result, the inhibitory effect was most effective against WNV and SLEV with over a 106-fold and 104-fold reduction in peak titres, respectively.« less

  1. Apparatus and method for transforming living cells (Patent) ...

    Office of Scientific and Technical Information (OSTI)

    the cell walls or membrane of host cells one at a time so that a particular substance (e.g. a molecular tag, nucleic acid, bacteria, virus etc.) can be introduced into the cell. ...

  2. Investigation of the mode of binding of a novel series ofN-benzyl...

    Office of Scientific and Technical Information (OSTI)

    of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select...

  3. DEFINING THE EFFECTIVENESS OF UV LAMPS

    Office of Scientific and Technical Information (OSTI)

    ... The infected cell may repair the damaged viral DNA for the virus if the infected cell contains the repair enzymes. 3.3.3 Recovery of Damaged Test Organisms The selection of the ...

  4. LA-8318-MS Informal Report I

    Office of Scientific and Technical Information (OSTI)

    ... D. (E-3) 2-75 QUANTITATION OF CELL FUSION BY TWENTY-ONE STRAINS OF NEWCASTLE DISEASE VIRUS USING FLOW MICROFLUOROMETRY. J. GEN. VIROL., V.41. P.27-36. 1978. CRAM, L. SCOTT (H-10) ...

  5. 'Let the phage do the work': Using the phage P22 coat protein structures as a framework to understand its folding and assembly mutants

    SciTech Connect (OSTI)

    Teschke, Carolyn M., E-mail: Teschke@uconn.ed [Departments of Molecular and Cell Biology, and Chemistry, 91 N. Eagleville Rd., U-3125, University of Connecticut, Storrs, CT 06269-3125 (United States); Parent, Kristin N. [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA (United States)

    2010-06-05

    The amino acid sequence of viral capsid proteins contains information about their folding, structure and self-assembly processes. While some viruses assemble from small preformed oligomers of coat proteins, other viruses such as phage P22 and herpesvirus assemble from monomeric proteins (Fuller and King, 1980). The subunit assembly process is strictly controlled through protein:protein interactions such that icosahedral structures are formed with specific symmetries, rather than aberrant structures. dsDNA viruses commonly assemble by first forming a precursor capsid that serves as a DNA packaging machine. DNA packaging is accompanied by a conformational transition of the small precursor procapsid into a larger capsid for isometric viruses. Here we highlight the pseudo-atomic structures of phage P22 coat protein and rationalize several decades of data about P22 coat protein folding, assembly and maturation generated from a combination of genetics and biochemistry.

  6. EWA Summary.xls

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Guidance Software: Behshad Behnam ph: 703-657-7208 behshad.behnam@guidancesoftware.com DOE PM: Robert Ciochon ph: 202-586-2586 Robert.ciochon@hq.doe.gov IntelMcAfee Anti-virus and ...

  7. Notices DEPARTMENT OF ENERGY Quadrennial Energy Review: Notice...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... Provide documents that are not secured, written in English, and are free of any defects or viruses. Documents should not contain special characters or any form of encryption and, ...

  8. JC3 Bulletin Archive | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    A vulnerability was reported in McAfee VirusScan Enterprise. February 27, 2013 V-100: Adobe Flash Player Bugs Let Remote Users Execute Arbitrary Code Several vulnerabilities were...

  9. C:\\Users\\28105\\Documents\\Choi ICF\\ESPA-LPT work\\RFI\\PDF Conversions...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... You may report the matter by contacting us via our UK Contacts Page or our US Contacts Page (accessed by clicking on the appropriate link) Please ensure you have adequate virus ...

  10. Rf2a and rf2b transcription factors

    DOE Patents [OSTI]

    Beachy, Roger N.; Petruccelli, Silvana; Dai, Shunhong

    2007-10-02

    A method of activating the rice tungro bacilliform virus (RTBV) promoter in vivo is disclosed. The RTBV promoter is activated by exposure to at least one protein selected from the group consisting of Rf2a and Rf2b.

  11. Link Alpha M

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    S T U V W Y Z Macintosh User Group (LBNL-MUG) Mail Services (Facilities Dep't.) MalwareVirus Protection and Prevention Mammary: Human Mammary Epithelial Cell (HMEC) Map: Berkeley...

  12. Environment/Health/Safety (EHS)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    has been in the news. Measles is a highly contagious respiratory disease caused by a virus. It spreads through the air through coughing and sneezing. Measles can be spread days...

  13. Validating Computer-Designed Proteins for Vaccines

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Computed As strange as it sounds, most vaccines are composed of actual dead viruses and bacteria. The idea is that presenting a dead form of the pathogen will fake your body into...

  14. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... ; Bevilacqua, Philip C. ; Golden, Barbara L. ; Penn) The hepatitis delta virus (HDV) ribozyme and HDV-like ribozymes are self-cleaving RNAs found throughout all kingdoms of life. ...

  15. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Hyuk-Soo ; Blobel, Gnter ; Ren, Yi mRNA export factor 1 (Rae1) and nucleoporin 98 (Nup98) are host cell targets for the matrix (M) protein of vesicular stomatitis virus (VSV). ...

  16. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Everything3 Electronic Full Text0 Citations3 Multimedia0 Datasets0 Software0 Filter Results Filter by Subject aids virus (1) applied life sciences (1) basic biological sciences (1) ...

  17. Science and Technology Review December 2011 (Technical Report...

    Office of Scientific and Technical Information (OSTI)

    Track Viral Evolution - A sensitive technique developed at the Laboratory can identify virus mutations that may jump from host to host; and (5) Data for Defense: New Software Finds ...

  18. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Release from PD-1 inhibitory signaling revives 'exhausted' virus-specific T cells in chronic viral infections. Here we present the crystal structure of murine PD-1 in complex with ...

  19. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeFYiiX-like family from Bacillus ...

  20. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Everything17 Electronic Full Text0 Citations17 Multimedia0 Datasets0 Software0 Filter Results Filter by Subject proteins (4) basic biological sciences (3) aids virus (2) applied ...

  1. Search for: All records | DOE Patents

    Office of Scientific and Technical Information (OSTI)

    ... the cell walls or membrane of host cells one at a time so that a particular substance (e.g. a molecular tag, nucleic acid, bacteria, virus etc.) can be introduced into the cell. ...

  2. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Everything4 Electronic Full Text0 Citations4 Multimedia0 Datasets0 Software0 Filter Results Filter by Subject aids virus (1) applied life sciences (1) basic biological sciences (1) ...

  3. Snapshots and Scrapbooks | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    X-ray diffraction pattern of a single Mimivirus particle imaged at the LCLS. In this study, the X-ray pulse lasted a millionth of a billionth of a second and heated the virus to ...

  4. Structural Molecular Biology, SSRL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    cellular sacs full of digestive enzymes that break down bacteria, viruses and worn-out cell parts for recycling. When this recycling process goes awry, it can cause rare metabolic...

  5. CoverSheet

    Office of Scientific and Technical Information (OSTI)

    that would be inappropriate and ineffective. For example, it seems likely that anti-virus tools will be a required compo- nent of the cyber health report scorecard for desktop...

  6. Validating Computer-Designed Proteins for Vaccines

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    apply to a variety of other vaccine targets, such as human immunodeficiency virus and influenza. Wanted: Dead or Computed As strange as it sounds, most vaccines are composed of...

  7. Company/Product Description Contract Number Contract Holders

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Lumension: Ben Boykin ph: 703-956-0347 ben.boykin@lumension.com Rob Gettings Robert.Gettings@hq.doe.gov 301-903-0829 McAfee Anti-virus and anti-spyware software (most McAfee ...

  8. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Stopping executions, saving computers with new malware detection tool October 21, 2009 Virus detection takes a smarter turn with information- based approach Los Alamos, New Mexico, October 13, 2009-In the cyber security world, looking for viruses or other malicious files on computers opens the door to potentially releasing the file and contaminating one's system. In classical terms, if you peer into Medusa's eyes, you're turned to stone. Greek hero Perseus turned a mirror on the monster to

  9. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Computer modeling reveals how surprisingly potent hepatitis C drug works February 19, 2013 LOS ALAMOS, N.M., Feb. 19, 2013-A study by researchers from Los Alamos National Laboratory and a multinational team reveals how daclatasvir, a direct-acting antiviral agent in development for the treatment of hepatitis C virus (HCV), targets one of its proteins and causes the fastest viral decline ever seen with anti-HCV drugs - within 12 hours of treatment. Chronic infection with hepatitis C virus affects

  10. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Relationships between HIV spread and evolution examined November 14, 2013 Thomas Leitner of LANL's Theoretical Biology and Biophysics group and collaborators are investigating the development of HIV from the point of contraction onwards. They are examining the relationships between the spread of the virus in a population (epidemiology) and the evolution of the virus (phylogenetics). The genetic evolution of HIV in infected humans means that unique HIV populations are manifest in each infected

  11. Vaccine to control the viral infection of fish

    DOE Patents [OSTI]

    Leong, Jo-Ann C.

    1994-10-11

    Subunit vaccines and their use for immunizing fish against infection by viruses are disclosed. In particular, plasmid pG8 is constructed by joining, with the plasmid pUC8, DNA which encodes the glycoprotein of infectious hematopoietic necrosis virus (IHNV). E. coli cells are transformed by pG8, whereby pure viral antigen is produced to provide a vaccine for the control of IHNV in fish.

  12. Vaccine to Control the Viral Infection of Fish.

    DOE Patents [OSTI]

    Leong, JoAnn Ching

    1994-10-11

    Subunit vaccines and their use for immunizing fish against infection by viruses are disclosed. In particular, plasmid pG8 is constructed by joining, with the plasmid pUC8, DNA which encodes the glycoprotein of infectious hematopoietic necrosis virus (IHNV). E. coli cells are transformed by pG8, whereby pure viral antigen is produced to provide a vaccine for the control of IHNV in fish. 10 figs.

  13. Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic

    Office of Scientific and Technical Information (OSTI)

    virus for micro-supercapacitors in solid Nafion electrolyte (Journal Article) | SciTech Connect Title: Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic virus for micro-supercapacitors in solid Nafion electrolyte Authors: Gnerlich, Markus ; Ben-Yoav, Hadar ; Culver, James ; Ketchum, D ; Ghodssi, Reza Publication Date: 2015-10-01 OSTI Identifier: 1210848 DOE Contract Number: SC0001160 Resource Type: Journal Article Resource Relation: Journal Name: Journal of Power

  14. Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic

    Office of Scientific and Technical Information (OSTI)

    virus for micro-supercapacitors in solid Nafion electrolyte (Journal Article) | SciTech Connect This content will become publicly available on June 5, 2017 Title: Selective deposition of nanostructured ruthenium oxide using Tobacco mosaic virus for micro-supercapacitors in solid Nafion electrolyte Authors: Gnerlich, Markus Search SciTech Connect for author "Gnerlich, Markus" Search SciTech Connect for ORCID "0000000163589906" Search orcid.org for ORCID

  15. Architecture for removable media USB-ARM (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Patent: Architecture for removable media USB-ARM Citation Details In-Document Search Title: Architecture for removable media USB-ARM A storage device is coupled to a computing system comprising an operating system and application software. Access to the storage device is blocked by a kernel filter driver, except exclusive access is granted to a first anti-virus engine. The first anti-virus engine is directed to scan the storage device for malicious software and report results. Exclusive access

  16. Ig-0500.PDF

    Energy Savers [EERE]

    21 AUDIT REPORT VIRUS PROTECTION STRATEGIES AND CYBER SECURITY INCIDENT REPORTING U.S. DEPARTMENT OF ENERGY OFFICE OF INSPECTOR GENERAL OFFICE OF AUDIT SERVICES APRIL 2001 DOE/IG-0500 April 5, 2001 MEMORANDUM FOR THE SECRETARY FROM: Gregory H. Friedman (Signed) Inspector General SUBJECT: INFORMATION: Audit Report on "Virus Protection Strategies and Cyber Security Incident Reporting" BACKGROUND Information Technology (IT) plays an integral role in the programs and operations of the

  17. LOS ALAMOS, New Mexico, OCTOBER 18, 2010-Los Alamos National Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Consortium to design human trials of mosaic HIV vaccine October 18, 2010 LOS ALAMOS, New Mexico, OCTOBER 18, 2010-Los Alamos National Laboratory researcher Bette Korber is part of an international team of investigators working to design and implement the first human trial of a mosaic HIV vaccine candidate. The vaccine represents a novel strategy for fighting the virus that causes AIDS by attempting to address one of the most daunting challenges in HIV vaccine design: the virus's extensive

  18. T-612: False Positive Detection Generic.dx!yxk in DAT 6329

    Broader source: Energy.gov [DOE]

    This issue can affect all McAfee anti-virus products utilizing this DAT, however it will manifest itself only on endpoints such as VirusScan. Spsgui.exe - This file is typically found only on workstations that have the SAP client installed. This file is loaded by the SAP client when it starts up and is used to send and receive faxes inside the SAP application.

  19. GeoSiphon - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    disease outbreak. (Technical Report) | SciTech Connect Genomics-enabled sensor platform for rapid detection of viruses related to disease outbreak. Citation Details In-Document Search Title: Genomics-enabled sensor platform for rapid detection of viruses related to disease outbreak. Bioweapons and emerging infectious diseases pose growing threats to our national security. Both natural disease outbreak and outbreaks due to a bioterrorist attack are a challenge to detect, taking days after the

  20. Construction and biological activities of the first infectious cDNA clones of the genus Foveavirus

    SciTech Connect (OSTI)

    Meng, Baozhong; Venkataraman, Srividhya; Li, Caihong; Wang, Weizhou; Dayan-Glick, Cathy; Mawassi, Munir

    2013-01-20

    Grapevine rupestris stem pitting-associated virus (GRSPaV, genus Foveavirus, family Betaflexiviridae) is one of the most prevalent viruses in grapevines and is associated with three distinct diseases: rupestris stem pitting, vein necrosis and Syrah decline. Little is known about the biology and pathological properties of GRSPaV. In this work, we engineered a full-length infectious cDNA clone for GRSPaV and a GFP-tagged variant, both under the transcriptional control of Cauliflower mosaic virus 35 S promoter. We demonstrated that these cDNA clones were infectious in grapevines and Nicotiana benthamiana through fluorescence microscopy, RT-PCR, Western blotting and immuno electron microscopy. Interestingly, GRSPaV does not cause systemic infection in four of the most commonly used herbaceous plants, even in the presence of the movement proteins of two other viruses which are known to complement numerous movement-defective viruses. These infectious clones are the first of members of Foveavirus which would allow further investigations into mechanisms governing different aspects of replication for GRSPaV and perhaps related viruses.

  1. Low dose rectal inoculation of rhesus macaques by SIV smE660 or SIVmac251 recapitulates

    SciTech Connect (OSTI)

    Hraber, Peter; Giorgi, Elena E; Keele, Brandon; Li, Hui; Learn, Gerald

    2008-01-01

    We recently developed a novel strategy to identify transmitted HIV-1 genomes in acutely infected humans using single-genome amplification and a model of random virus evolution. Here, we used this approach to determine the molecular features of simian immunodeficiency virus (SIV) transmission in 18 experimentally infected Indian rhesus macaques. Animals were inoculated intrarectally (i.r.) or intravenously (i.v.) with stocks of SIVmac251 or SIVsmE660 that exhibited sequence diversity typical of early-chronic HIV-1 infection. 987 full-length SIV env sequences (median of 48 per animal) were determined from plasma virion RNA 1--5 wk after infection. i.r. inoculation was followed by productive infection by one or a few viruses (median 1; range 1--5) that diversified randomly with near starlike phylogeny and a Poisson distribution of mutations. Consensus viral sequences from ramp-up and peak viremia were identical to viruses found in the inocula or differed from them by only one or a few nucleotides, providing direct evidence that early plasma viral sequences coalesce to transmitted/founder viruses. i.v. infection was >2,000-fold more efficient than i.r. infection, and viruses transmitted by either route represented the full genetic spectra of the inocula. These findings identify key similarities in mucosal transmission and early diversification between SIV and HIV-1, and thus validate the SIV-macaque mucosal infection model for HIV-1 vaccine and microbicide research.

  2. Generation and distribution of PAHs in the process of medical waste incineration

    SciTech Connect (OSTI)

    Chen, Ying; Zhao, Rongzhi; Xue, Jun; Li, Jinhui

    2013-05-15

    Highlights: ? PAHs generation and distribution features of medical waste incineration are studied. ? More PAHs were found in fly ash than that in bottom ash. ? The highest proportion of PAHs consisted of the seven most carcinogenic ones. ? Increase of free oxygen molecule and burning temperature promote PAHs degradation. ? There is a moderate positive correlation between total PCDD/Fs and total PAHs. - Abstract: After the deadly earthquake on May 12, 2008 in Wenchuan county of China, several different incineration approaches were used for medical waste disposal. This paper investigates the generation properties of polycyclic aromatic hydrocarbons (PAHs) during the incineration. Samples were collected from the bottom ash in an open burning slash site, surface soil at the open burning site, bottom ash from a simple incinerator, bottom ash generated from the municipal solid waste (MSW) incinerator used for medical waste disposal, and bottom ash and fly ash from an incinerator exclusively used for medical waste. The species of PAHs were analyzed, and the toxicity equivalency quantities (TEQs) of samples calculated. Analysis results indicate that the content of total PAHs in fly ash was 1.8 10{sup 3} times higher than that in bottom ash, and that the strongly carcinogenic PAHs with four or more rings accumulated sensitively in fly ash. The test results of samples gathered from open burning site demonstrate that Acenaphthylene (ACY), Acenaphthene (ACE), Fluorene (FLU), Phenanthrene (PHE), Anthracene (ANT) and other PAHs were inclined to migrate into surrounding environment along air and surface watershed corridors, while 4- to 6-ring PAHs accumulated more likely in soil. Being consistent with other studies, it has also been confirmed that increases in both free oxygen molecules and combustion temperatures could promote the decomposition of polycyclic PAHs. In addition, without the influence of combustion conditions, there is a positive correlation between total PCDD/Fs and total PAHs, although no such relationship has been found for TEQ.

  3. Nowcasting influenza outbreaks using open-source media report.

    SciTech Connect (OSTI)

    Ray, Jaideep; Brownstein, John S.

    2013-02-01

    We construct and verify a statistical method to nowcast influenza activity from a time-series of the frequency of reports concerning influenza related topics. Such reports are published electronically by both public health organizations as well as newspapers/media sources, and thus can be harvested easily via web crawlers. Since media reports are timely, whereas reports from public health organization are delayed by at least two weeks, using timely, open-source data to compensate for the lag in %E2%80%9Cofficial%E2%80%9D reports can be useful. We use morbidity data from networks of sentinel physicians (both the Center of Disease Control's ILINet and France's Sentinelles network) as the gold standard of influenza-like illness (ILI) activity. The time-series of media reports is obtained from HealthMap (http://healthmap.org). We find that the time-series of media reports shows some correlation ( 0.5) with ILI activity; further, this can be leveraged into an autoregressive moving average model with exogenous inputs (ARMAX model) to nowcast ILI activity. We find that the ARMAX models have more predictive skill compared to autoregressive (AR) models fitted to ILI data i.e., it is possible to exploit the information content in the open-source data. We also find that when the open-source data are non-informative, the ARMAX models reproduce the performance of AR models. The statistical models are tested on data from the 2009 swine-flu outbreak as well as the mild 2011-2012 influenza season in the U.S.A.

  4. Use of Cre/loxP recombination to swap cell binding motifs on the adenoviral capsid protein IX

    SciTech Connect (OSTI)

    Poulin, Kathy L.; Tong, Grace; Vorobyova, Olga; Pool, Madeline; Kothary, Rashmi; Parks, Robin J.

    2011-11-25

    We used Cre/loxP recombination to swap targeting ligands present on the adenoviral capsid protein IX (pIX). A loxP-flanked sequence encoding poly-lysine (pK-binds heparan sulfate proteoglycans) was engineered onto the 3'-terminus of pIX, and the resulting fusion protein allowed for routine virus propagation. Growth of this virus on Cre-expressing cells removed the pK coding sequence, generating virus that could only infect through alternative ligands, such as a tyrosine kinase receptor A (TrkA)-binding motif engineered into the capsid fibre protein for enhanced infection of neuronal cells. We used a similar approach to swap the pK motif on pIX for a sequence encoding a single-domain antibody directed towards CD66c for targeted infection of cancer cells; Cre-mediated removal of the pK-coding sequence simultaneously placed the single-domain antibody coding sequence in frame with pIX. Thus, we have developed a simple method to propagate virus lacking native viral tropism but containing cell-specific binding ligands. - Highlights: > We describe a method to grow virus lacking native tropism but containing novel cell-binding ligands. > Cre/loxP recombination was used to modify the adenovirus genome. > A targeting ligand present on capsid protein IX was removed or replaced using recombination. > Cre-loxP was also used to 'swap' the identity of the targeting ligand present on pIX.

  5. Hematology, Parasitology, and Serology of Free-Ranging Coyotes (Canis latrans) from South Carolina.

    SciTech Connect (OSTI)

    Miller, Debra, Lee; Schrecengost, Joshua; Merrill, Anita; Kilgo, John; Ray, H., Scott; Karl V. Miller, Karl, V.; Baldwin, Charles, A.

    2009-07-01

    ABSTRACT: Blood and feces were collected from 34 adult (19 males, 15 females) and seven juvenile (three males, one female, three not reported) free-ranging coyotes (Canis latrans) on the US Department of Energys Savannah River Site (South Carolina, USA). Significant (P,0.05) hematologic differences by sex were noted for red blood cell counts, hemoglobin, and hematocrit. Biochemical differences by sex occurred only for albumen (P,0.05). Twentyone adults were antibody positive for at least one of four viruses: canine adenovirus type 1 (CAV-1; 68%), West Nile virus (WNV; 60%), Eastern equine encephalitis virus (EEEV; 38%), and Canine distemper virus (CDV; 15%). Of the seven Leptospira serovars tested for, seven (25%) of 28 adults were positive for one or more of five serovars: Pomona, Grippotyphosa, Icterohaemorrhagiae, Bratislava, and Autumnalis. Three (43%) of seven juveniles had seropositivity for a virus, one each for CDV, CAV-1, and WNV. No juveniles were seropositive for EEEV or any of the seven Leptospira serovars. Blood smears of 12 adults were positive for Dirofilaria immitis microfilaria, but blood smears from all juveniles were negative. Parvovirus was identified by electron microscopy from the feces of one adult. Ancylostoma spp., Trichuris spp., and Isospora spp. were observed in fecal samples. These data may aid in understanding the role of coyotes in disease ecology.

  6. Quantitative real-time single particle analysis of virions

    SciTech Connect (OSTI)

    Heider, Susanne; Metzner, Christoph

    2014-08-15

    Providing information about single virus particles has for a long time been mainly the domain of electron microscopy. More recently, technologies have been developed—or adapted from other fields, such as nanotechnology—to allow for the real-time quantification of physical virion particles, while supplying additional information such as particle diameter concomitantly. These technologies have progressed to the stage of commercialization increasing the speed of viral titer measurements from hours to minutes, thus providing a significant advantage for many aspects of virology research and biotechnology applications. Additional advantages lie in the broad spectrum of virus species that may be measured and the possibility to determine the ratio of infectious to total particles. A series of disadvantages remain associated with these technologies, such as a low specificity for viral particles. In this review we will discuss these technologies by comparing four systems for real-time single virus particle analysis and quantification. - Highlights: • We introduce four methods for virus particle-based quantification of viruses. • They allow for quantification of a wide range of samples in under an hour time. • The additional measurement of size and zeta potential is possible for some.

  7. Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhu, Xueyong; Viswanathan, Karthik; Raman, Rahul; Yu, Wenli; Sasisekharan, Ram; Wilson, Ian A.

    2015-11-01

    Avian H5N1 influenza viruses continue to spread in wild birds and domestic poultry with sporadic infection in humans. Receptor binding specificity changes are a prerequisite for H5N1 viruses and other zoonotic viruses to be transmitted among humans. Previous reported hemagglutinin (HA) mutants from ferret-transmissible H5N1 viruses of A/Viet Nam/1203/04 and A/Indonesia/5/05 showed slightly increased, but still very weak, binding to human receptors. From mutagenesis and glycan array studies, we previously identified two H5N1 HA mutants that could more effectively switch receptor specificity to human-like α2-6 linked sialosides with avidity comparable to wild-type H5 HA binding to avian-like α2-3 linked sialosides.more »Here, crystal structures of these two H5 HA mutants free and in complex with human and avian glycan receptor analogues reveal the structural basis for their preferential binding to human receptors. These findings suggest continuous surveillance should be maintained to monitor and assess human-to-human transmission potential of H5N1 viruses.« less

  8. Final Technical Report: Viral Infection of Subsurface Microorganisms and Metal/Radionuclide Transport

    SciTech Connect (OSTI)

    Weber, Karrie A.; Bender, Kelly S.; Li, Yusong

    2013-09-28

    Microbially mediated metabolisms have been identified as a significant factor either directly or indirectly impacting the fate and transport of heavy metal/radionuclide contaminants. To date microorganisms have been isolated from contaminated environments. Examination of annotated finished genome sequences of many of these subsurface isolates from DOE sites, revealed evidence of prior viral infection. To date the role that viruses play influencing microbial mortality and the resulting community structure which directly influences biogeochemical cycling in soils and sedimentary environments remains poorly understood. The objective of this exploratory study was to investigate the role of viral infection of subsurface bacteria and the formation of contaminant-bearing viral particles. This objective was approached by examining the following working hypotheses: (i) subsurface microorganisms are susceptible to viral infections by the indigenous subsurface viral community, and (ii) viral surfaces will adsorb heavy metals and radionuclides. Our results have addressed basic research needed to accomplish the BER Long Term Measure to provide sufficient scientific understanding such that DOE sites would be able to incorporate coupled physical, chemical and biological processes into decision making for environmental remediation or natural attenuation and long-term stewardship by establishing viral-microbial relationships on the subsequent fate and transport of heavy metals and radionuclides. Here we demonstrated that viruses play a significant role in microbial mortality and community structure in terrestrial subsurface sedimentary systems. The production of viral-like particles within subsurface sediments in response to biostimulation with dissolved organic carbon and a terminal electron acceptor resulted in the production of viral-like particles. Organic carbon alone did not result in significant viral production and required the addition of a terminal electron acceptor (nitrate), indicating that nutrients are not limiting viral production, but rather substrates that can be converted into energy for host metabolism. Our results also revealed that cell abundance was not correlated to the mineralization of organic carbon, but rather viruses were positively correlated with carbon mineralization. This is a result of viral-mediated cell lysis and demonstrates that viruses are sensitive indicators of microbial activity. Viruses as an indicator of microbial activity was not unique to batch culture studies as results obtained from an in situ field experiment conducted at the DOE Old Rifle Field site. This study revealed that viral abundance increased in response to the injection of oxygenated groundwater and influx of dissolved organic carbon whereas cell abundance changes were minimal. However, the extent to which viral-mediated cell lysis alters organic matter pools subsequently influencing microbial community structure and biogeochemical function remains a critical question in subsurface biogeochemical cycling. The production of significant numbers of viruses in groundwater has implications for nanoparticulate metal as well as carbon transport in groundwater. We have demonstrated that the virus surface is reactive and will adsorb heavy metals. Thus viruses can promote colloidal contaminant mobility. Interestingly, the presence of heavy metals has a positive effect on infectivity of the phage, increasing phage infection which could lead to further production of viruses. Together, the results indicate that the sorption of metals to the surface of viruses could not only contribute to nanoparticulate metal as well as carbon transport but could also enhance infectivity further contributing to cell lysis which could subsequently influence biogeochemical cycling. As more viruses infect host microbial populations the high concentration of metals would enhance infection, resulting in cell lysis, and decreasing the metabolically active host population while yielding greater numbers of viruses capable of transporting contaminats. Additional studie

  9. Evaluation of an Experimental Re-introduction of Sockeye Salmon into Skaha Lake; Year 2 of 3, 2001 Technical Report.

    SciTech Connect (OSTI)

    Fisher, Christopher; Machin, Deanna; Wright, Howie

    2002-04-01

    This report summarizes the findings from YEAR 2 of a three-year disease risk assessment. The Okanagan Nation Fisheries Commission (ONFC) and the Colville Confederated Tribes (CCT) are investigating the risks involved in re-introducing sockeye salmon into Skaha Lake, part of their historical range (Ernst and Vedan 2000). The disease risk assessment compares the disease and infection status of fish above and below McIntyre Dam (the present limit of sockeye migration). The disease agents identified that are of a particular concern are: infectious pancreatic necrosis virus (IPNV), infectious haematopoietic necrosis virus type 2 (IHNV type2), erythrocytic inclusion body syndrome virus (EIBSV), the whirling disease agent (Myxobolus cerebralis), and the ceratomyxosis agent (Ceratomyxa shasta).

  10. Radioimmunoassays of hidden viral antigens

    SciTech Connect (OSTI)

    Neurath, A.R. (Lindsley F. Kimbell Research Inst., New York, NY); Strick, N.; Baker, L.; Krugman, S.

    1982-07-01

    Antigens corresponding to infectious agents may be present in biological specimens only in a cryptic form bound to antibodies and, thus, may elude detection. We describe a solid-phase technique for separation of antigens from antibodies. Immune complexes are precipitated from serum by polyethylene glycol, dissociated with NaSCN, and adsorbed onto nitrocellulose or polystyrene supports. Antigens remain topographically separated from antibodies after removal of NaSCN and can be detected with radiolabeled antibodies. Genomes from viruses immobilized on nitrocellulose can be identified by nucleic acid hybridization. Nanogram quantities of sequestered hepatitis B surface and core antigens and picogram amounts of hepatitis B virus DNA were detected. Antibody-bound adenovirus, herpesvirus, and measles virus antigens were discerned by the procedure.

  11. Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein

    SciTech Connect (OSTI)

    McBride, Corrin E.; Machamer, Carolyn E.

    2010-09-15

    Coronaviruses are enveloped RNA viruses that generally cause mild disease in humans. However, the recently emerged coronavirus that caused severe acute respiratory syndrome (SARS-CoV) is the most pathogenic human coronavirus discovered to date. The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Coronavirus S proteins are palmitoylated, which may affect function. Here, we created a non-palmitoylated SARS-CoV S protein by mutating all nine cytoplasmic cysteine residues. Palmitoylation of SARS-CoV S was required for partitioning into detergent-resistant membranes and for cell-cell fusion. Surprisingly, however, palmitoylation of S was not required for interaction with SARS-CoV M protein. This contrasts with the requirement for palmitoylation of mouse hepatitis virus S protein for interaction with M protein and may point to important differences in assembly and infectivity of these two coronaviruses.

  12. Structure of the uncleaved ectodomain of the paramyxovirus (hPIV3) fusion protein

    SciTech Connect (OSTI)

    Yin, Hsien-Sheng; Paterson, Reay G.; Wen, Xiaolin; Lamb, Robert A.; Jardetzky, Theodore S. (NWU)

    2010-03-08

    Class I viral fusion proteins share common mechanistic and structural features but little sequence similarity. Structural insights into the protein conformational changes associated with membrane fusion are based largely on studies of the influenza virus hemagglutinin in pre- and postfusion conformations. Here, we present the crystal structure of the secreted, uncleaved ectodomain of the paramyxovirus, human parainfluenza virus 3 fusion (F) protein, a member of the class I viral fusion protein group. The secreted human parainfluenza virus 3 F forms a trimer with distinct head, neck, and stalk regions. Unexpectedly, the structure reveals a six-helix bundle associated with the postfusion form of F, suggesting that the anchor-minus ectodomain adopts a conformation largely similar to the postfusion state. The transmembrane anchor domains of F may therefore profoundly influence the folding energetics that establish and maintain a metastable, prefusion state.

  13. Reduced expression of Autographa californica nucleopolyhedrovirus ORF34, an essential gene, enhances heterologous gene expression

    SciTech Connect (OSTI)

    Salem, Tamer Z.; Department of Microbial Molecular Biology, AGERI, Agricultural Research Center, Giza 12619; Division of Biomedical Sciences, Zewail University, Zewail City of Science and Technology, Giza 12588 ; Zhang, Fengrui; Thiem, Suzanne M.

    2013-01-20

    Autographa californica multiple nucleopolyhedrovirus ORF34 is part of a transcriptional unit that includes ORF32, encoding a viral fibroblast growth factor (FGF) and ORF33. We identified ORF34 as a candidate for deletion to improve protein expression in the baculovirus expression system based on enhanced reporter gene expression in an RNAi screen of virus genes. However, ORF34 was shown to be an essential gene. To explore ORF34 function, deletion (KO34) and rescue bacmids were constructed and characterized. Infection did not spread from primary KO34 transfected cells and supernatants from KO34 transfected cells could not infect fresh Sf21 cells whereas the supernatant from the rescue bacmids transfection could recover the infection. In addition, budded viruses were not observed in KO34 transfected cells by electron microscopy, nor were viral proteins detected from the transfection supernatants by western blots. These demonstrate that ORF34 is an essential gene with a possible role in infectious virus production.

  14. The prevalence of the pre-existing hepatitis C viral variants and the evolution of drug resistance in patients treated with the NS3-4a serine protease inhibitor telaprevir

    SciTech Connect (OSTI)

    Rong, Libin; Ribeiro, Ruy M; Perelson, Alan S

    2008-01-01

    Telaprevir (VX-950), a novel hepatitis C virus (HCV) NS3-4A serine protease inhibitor, has demonstrated substantial antiviral activity in patients infected with HCV genotype 1. Some patients experience viral breakthrough, which has been shown to be associated with emergence of telaprevir-resistant HCV variants during treatment. The exact mechanisms underlying the rapid selection of drug resistant viral variants during dosing are not fully understood. In this paper, we develop a two-strain model to study the pre-treatment prevalence of the mutant virus and derive an analytical solution of the mutant frequency after administration of the protease inhibitor. Our analysis suggests that the rapid increase of the mutant frequency during therapy is not due to mutant growth but rather due to the rapid and profound loss of wild-type virus, which uncovers the pre-existing mutant variants. We examine the effects of backward mutation and hepatocyte proliferation on the pre-existence of the mutant virus and the competition between wild-type and drug resistant virus during therapy. We then extend the simple model to a general model with multiple viral strains. Mutations during therapy do not play a significant role in the dynamics of various viral strains, although they are capable of generating low levels of HCV variants that would otherwise be completely suppressed because of fitness disadvantages. Hepatocyte proliferation may not affect the pretreatment frequency of mutant variants, but is able to influence the quasispecies dynamics during therapy. It is the relative fitness of each mutant strain compared with wild-type that determines which strain(s) will dominate the virus population. The study provides a theoretical framework for exploring the prevalence of pre-existing mutant variants and the evolution of drug resistance during treatment with other protease inhibitors or HCV polymerase inhibitors.

  15. Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Thissen, James B.; McLoughlin, Kevin; Gardner, Shea; Gu, Pauline; Mabery, Shalini; Slezak, Tom; Jaing, Crystal

    2014-06-01

    Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA wasmore » able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.« less

  16. Universal Serial Bus Architecture for Removable Media (USB-ARM)

    Energy Science and Technology Software Center (OSTI)

    2011-03-09

    USB-ARM creates operating system drivers which sit between removable media and the user and applications. The drivers isolate the media and submit the contents of the media to a virtual machine containing an entire scanning system. This scanning system may include traditional anti-virus, but also allows more detailed analysis of files, including dynamic run-time analysis, helping to prevent “zero-day” threats not already identified in anti-virus signatures. Once cleared, the media is presented to the operatingmore » system, at which point it becomes available to users and applications.« less

  17. Reversibly immobilized biological materials in monolayer films on electrodes

    DOE Patents [OSTI]

    Weaver, P.F.; Frank, A.J.

    1993-05-04

    Methods and techniques are described for reversibly binding charged biological particles in a fluid medium to an electrode surface. The methods are useful in a variety of applications. The biological materials may include microbes, proteins, and viruses. The electrode surface may consist of reversibly electroactive materials such as polyvinylferrocene, silicon-linked ferrocene or quinone.

  18. Physicochemical stability and inactivation of human and simian rotaviruses

    SciTech Connect (OSTI)

    Meng, Z.D.; Birch, C.; Heath, R.; Gust, I.

    1987-04-01

    The effects of various physical and chemical treatments on the stability of a human serotype 1 rotavirus and simian agent 11 (SA11) were compared by using a fluorescence focus assay. The infectivity of both strains was retained after storage at room temperature for 14 days, 4 degree C for 22 days, and -20 degree C for 32 days; lyophilization; and treatment at pH 3 to 11. Both viruses were inactivated at pH 12, as was the human virus at pH 2, although this pH resulted in only partial inactivation of SA11. The human virus also appeared to be more sensitive than SA11 to the action of ether and chloroform. The infectivity of both viruses was lost after UV irradiation for 15 min and after treatment with 8% formaldehyde for 5 min, 70% (vol/vol) ethanol for 30 min, and 2% lysol, 2% phenol, and 1% H/sub 2/O/sub 2/ for 1 h each.

  19. Sialic acid-dependent cell entry of human enterovirus D68

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Liu, Yue; Sheng, Ju; Baggen, Jim; Meng, Geng; Xiao, Chuan; Thibaut, Hendrik J.; van Kuppeveld, Frank J. M.; Rossmann, Michael G.

    2015-11-13

    Human enterovirus D68 (EV-D68) is a causative agent of childhood respiratory diseases and has now emerged as a global public health threat. Nevertheless, knowledge of the tissue tropism and pathogenesis of EV-D68 has been hindered by a lack of studies on the receptor-mediated EV-D68 entry into host cells. Here we demonstrate that cell surface sialic acid is essential for EV-D68 to bind to and infect susceptible cells. Crystal structures of EV-D68 in complex with sialylated glycan receptor analogues show that they bind into the ‘canyon’ on the virus surface. The sialic acid receptor induces a cascade of conformational changes inmore » the virus to eject a fatty-acid-like molecule that regulates the stability of the virus. Furthermore, virus binding to a sialic acid receptor and to immunoglobulin-like receptors used by most other enteroviruses share a conserved mechanism for priming viral uncoating and facilitating cell entry.« less

  20. Sialic acid-dependent cell entry of human enterovirus D68

    SciTech Connect (OSTI)

    Liu, Yue; Sheng, Ju; Baggen, Jim; Meng, Geng; Xiao, Chuan; Thibaut, Hendrik J.; van Kuppeveld, Frank J. M.; Rossmann, Michael G.

    2015-11-13

    Human enterovirus D68 (EV-D68) is a causative agent of childhood respiratory diseases and has now emerged as a global public health threat. Nevertheless, knowledge of the tissue tropism and pathogenesis of EV-D68 has been hindered by a lack of studies on the receptor-mediated EV-D68 entry into host cells. Here we demonstrate that cell surface sialic acid is essential for EV-D68 to bind to and infect susceptible cells. Crystal structures of EV-D68 in complex with sialylated glycan receptor analogues show that they bind into the ‘canyon’ on the virus surface. The sialic acid receptor induces a cascade of conformational changes in the virus to eject a fatty-acid-like molecule that regulates the stability of the virus. Furthermore, virus binding to a sialic acid receptor and to immunoglobulin-like receptors used by most other enteroviruses share a conserved mechanism for priming viral uncoating and facilitating cell entry.

  1. SLAC Snapshot

    Broader source: Energy.gov [DOE]

    Biologists have long dreamed of making images of viruses, whole microbes and living cells without freezing slicing or otherwise disturbing them -- learn how researchers at SLAC are making that dream a reality with their help of the world's first hard X-ray free-electron laser.

  2. Programmed cell death

    SciTech Connect (OSTI)

    1995-12-31

    The purpose of this conference to provide a multidisciplinary forum for exchange of state-of-the-art information on the role programmed cell death plays in normal development and homeostasis of many organisms. This volume contains abstracts of papers in the following areas: invertebrate development; immunology/neurology; bcl-2 family; biochemistry; programmed cell death in viruses; oncogenesis; vertebrate development; and diseases.

  3. Reversibly immobilized biological materials in monolayer films on electrodes

    DOE Patents [OSTI]

    Weaver, Paul F. (Golden, CO); Frank, Arthur J. (Lakewood, CO)

    1993-01-01

    Methods and techniques are described for reversibly binding charged biological particles in a fluid medium to an electrode surface. The methods are useful in a variety of applications. The biological materials may include microbes, proteins, and viruses. The electrode surface may consist of reversibly electroactive materials such as polyvinylferrocene, silicon-linked ferrocene or quinone.

  4. Appreciating HIV-1 diversity: subtypic differences in ENV

    SciTech Connect (OSTI)

    Gnanakaran, S; Shen, Tongye; Lynch, Rebecca M; Derdeyn, Cynthia A

    2008-01-01

    Human immunodeficiency virus type 1 (HIV-1) group M is responsible for the current AIDS pandemic and exhibits exceedingly high levels of viral genetic diversity around the world, necessitating categorization of viruses into distinct lineages, or subtypes. These subtypes can differ by around 35% in the envelope (Env) glycoproteins of the virus, which are displayed on the surface of the virion and are targets for both neutralizing antibody and cell-mediated immune responses. This diversity reflects the remarkable ability of the virus to adapt to selective pressures, the bulk of which is applied by the host immune response, and represents a serious obstacle for developing an effective vaccine with broad coverage. Thus, it is important to understand the underlying biological consequences of inter-subtype diversity. Recent studies have revealed that the HIV-1 subtypes exhibit phenotypic differences that result from subtle differences in Env structure, particularly within the highly immunogenic V3 domain, which participates directly in viral entry. This review will therefore explore current research that describes subtypic differences in Env at the genetic and phenotypic level, focusing in particular on V3, and highlighting recent discoveries about the unique features of subtype C Env, which is the most prevalent subtype globally.

  5. Airborne spread of foot-and-mouth disease - model intercomparison

    SciTech Connect (OSTI)

    Gloster, J; Jones, A; Redington, A; Burgin, L; Sorensen, J H; Turner, R; Dillon, M; Hullinger, P; Simpson, M; Astrup, P; Garner, G; Stewart, P; D'Amours, R; Sellers, R; Paton, D

    2008-09-04

    Foot-and-mouth disease is a highly infectious vesicular disease of cloven-hoofed animals caused by foot-and-mouth disease virus. It spreads by direct contact between animals, by animal products (milk, meat and semen), by mechanical transfer on people or fomites and by the airborne route - with the relative importance of each mechanism depending on the particular outbreak characteristics. Over the years a number of workers have developed or adapted atmospheric dispersion models to assess the risk of foot-and-mouth disease virus spread through the air. Six of these models were compared at a workshop hosted by the Institute for Animal Health/Met Office during 2008. A number of key issues emerged from the workshop and subsequent modelling work: (1) in general all of the models predicted similar directions for 'at risk' livestock with much of the remaining differences strongly related to differences in the meteorological data used; (2) determination of an accurate sequence of events is highly important, especially if the meteorological conditions vary substantially during the virus emission period; and (3) differences in assumptions made about virus release, environmental fate, and subsequent infection can substantially modify the size and location of the downwind risk area. Close relationships have now been established between participants, which in the event of an outbreak of disease could be readily activated to supply advice or modelling support.

  6. Three-dimensional colorimetric assay assemblies

    DOE Patents [OSTI]

    Charych, Deborah; Reichert, Anke

    2001-01-01

    A direct assay is described using novel three-dimensional polymeric assemblies which change from a blue to red color when exposed to an analyte, in one case a flue virus. The assemblies are typically in the form of liposomes which can be maintained in a suspension, and show great intensity in their color changes. Their method of production is also described.

  7. Forensic Proteomics of Poxvirus Production

    SciTech Connect (OSTI)

    Wunschel, David S.; Tulman, Edan; Engelmann, Heather E.; Clowers, Brian H.; Geary, Steven J.; Robinson, Aaron C.; Liao, Xiaofen

    2013-08-27

    The field of microbial forensics has recently sought to develop methods to discern biological signatures to indicate production methods for biological agents. Viral agents have received less attention to date. Their obligate propagation in living cells makes purification from cellular material a challenge. This leads to potential carryover of protein-rich signature of their production system. Here we have explored a proteomic analysis of Vaccinia virus as a model poxvirus system in which to compare samples of virus propagated in different cell lines and subjected to different purification schemes. The proteomic data sets indicated viral, host cell and culture medium proteins, and several layers of data analysis were applied to build confidence in the peptide identification and capture information on the taxonomic utility of each. The analysis showed clear shifts in protein profiles with virus purification, with successive gradient purification steps showing different levels of viral protein enrichment. Peptides from cellular proteins, including those present in purified virus preparations, provided signatures which enabled discrimination of cell line substrates, including distinguishing between cells derived from different primate species. The ability to discern multiple aspects of viral production demonstrates the potential value of proteomic analysis as tool for microbial forensics.

  8. Superhydrophobic surfaces

    DOE Patents [OSTI]

    Wang, Evelyn N; McCarthy, Matthew; Enright, Ryan; Culver, James N; Gerasopoulos, Konstantinos; Ghodssi, Reza

    2015-03-24

    Surfaces having a hierarchical structure--having features of both microscale and nanoscale dimensions--can exhibit superhydrophobic properties and advantageous condensation and heat transfer properties. The hierarchical surfaces can be fabricated using biological nanostructures, such as viruses as a self-assembled nanoscale template.

  9. QER- Comment of Petr Gladkov

    Broader source: Energy.gov [DOE]

    We decided all questions ENVIRONMENTALLY CLEAN energy the future of humanity official site ET Energy Corp: http://www.etenergycorp.com/ not official site ET Energy Corp. - For more advanced understanding and a deep dive into the essence of the proposed technologies: https://sites.google.com/site/scisyhpphysicspg1/ This email is free from viruses and malware because avast! Antivirus protection is active.

  10. Low dose rectal inoculation of rhesus macaques by SIV SME660 or SIV MAC251 recapitulates human mucosal infection by HIV-1

    SciTech Connect (OSTI)

    Koraber, Bette; Perelson, Alan; Hraber, Peter; Giorgi, E; Bhattacharya, T

    2009-01-01

    Recently, we developed a novel approach to the identification of transmitted or early founder HIV -1 genomes in acutely infected humans based on single genome amplification and sequencing. Here we tested this approach in 18 acutely infected Indian rhesus macaques to determine the molecular features of SIV transmission. Animals were inoculated intrarectally (IR) or intravenously (IV) with stocks of SIVmac251 or SIVsmE660 that exhibited sequence diversity typical of early-chronic HIV -1 infection. 987 full-length SIV env sequences (median of 48 per animal) were determined from plasma virion RNA one to five weeks after infection. IR inoculation was followed by productive infection by one or few viruses (median 1; range 1-5) that diversified randomly with near star-like phylogeny and a Poisson distribution of mutations. Consensus viral sequences from ramp-up and peak viremia were identical to viruses found in the inocula or differed from them by only one or few nuc1eotides, providing direct evidence that early plasma viral sequences coalesce to transmitted/founder virus( es). IV infection was approximately 10,000-fold more efficient than IR infection, and viruses transmitted by either route represented the full genetic spectra of the inocula. These findings identify key similarities in mucosal transmission and early diversification between SIV and HIV -1.

  11. Mathematical Modeling of Hepatitis C Prevalence Reduction with Antiviral Treatment Scale-Up in Persons Who Inject Drugs in Metropolitan Chicago

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Echevarria, Desarae; Gutfraind, Alexander; Boodram, Basmattee; Major, Marian; Del Valle, Sara; Cotler, Scott J.; Dahari, Harel

    2015-08-21

    New direct-acting antivirals (DAAs) provide an opportunity to combat hepatitis C virus (HCV) infection in persons who inject drugs (PWID). Here we use a mathematical model to predict the impact of a DAA-treatment scale-up on HCV prevalence among PWID and the estimated cost in metropolitan Chicago.

  12. Human retroviruses and AIDS 1994

    SciTech Connect (OSTI)

    Myers, G.; Korber, B.; Wain-Hobson, S.; Jeang, Kuan-Teh; Henderson, L.E.; Pavlakis, G.N.

    1995-01-01

    This compendium, including accompanying floppy diskettes, is the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts it comprises: (I) Nucleic Acid Alignments and Sequences; (II) Amino Acid Alignments; (III) Analysis; (IV) Related Sequences; (V) Database communications.

  13. Role of a reducing environment in disassembly of the herpesvirus tegument

    SciTech Connect (OSTI)

    Newcomb, William W.; Jones, Lisa M.; Dee, Alexander; Chaudhry, Farid; Brown, Jay C.

    2012-09-15

    Initiation of infection by herpes family viruses involves a step in which most of the virus tegument becomes detached from the capsid. Detachment takes place in the host cell cytosol near the virus entry site and it is followed by dispersal of tegument proteins and disappearance of the tegument as a distinct entity. Here we describe the results of experiments designed to test the idea that the reducing environment of the cytosol may contribute to tegument detachment and disassembly. Non-ionic detergent was used to remove the membrane of purified herpes simplex virus under control and reducing conditions. The effects on the tegument were then examined by SDS-PAGE and electron microscopy. Protein analysis demonstrated that most major tegument proteins were removed under both oxidizing and reducing conditions except for UL49 which required a reducing environment. It is proposed therefore that the reducing conditions in the cytosol are involved in removal of UL49 protein. Electron microscopic analysis revealed that capsids produced under oxidizing conditions contained a coating of protein that was absent in reduced virions and which correlated uniquely with the presence of UL49. This capsid-associated layer is suggested to be the location of UL49 in the extracted virion.

  14. Science Headlines

    Office of Science (SC) Website

    -0500 12B69234-E106-461C-B008-1A4F342D3F6Dhttp:1.usa.gov20feQ3S A Respiratory Virus Provides Clues to Possible Treatments Purdue University researchers, working at the...

  15. News

    Office of Science (SC) Website

    glaciers. 12B69234-E106-461C-B008-1A4F342D3F6Dhttp:1.usa.gov20feQ3S A Respiratory Virus Provides Clues to Possible Treatments Purdue University researchers, working at the...

  16. Modular microfluidic system for biological sample preparation

    DOE Patents [OSTI]

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  17. Exploring Viral Genomics at Lawrence Livermore National Laboratory

    SciTech Connect (OSTI)

    Kilpatrick, K; Hiddessen, A

    2007-08-22

    This summer I had the privilege of working at Lawrence Livermore National Laboratory under the Nonproliferation, Homeland and International Security Directorate in the Chemical and Biological Countermeasures Division. I worked exclusively on the Viral Identification and Characterization Initiative (VICI) project focusing on the development of multiplexed polymerase chain reaction (PCR) assays. The goal of VICI is to combine several disciplines such as molecular biology, microfluidics, and bioinformatics in order to detect viruses and identify them in order to effectively and quickly counter infectious disease, natural or engineered. The difficulty in such a countermeasure is that little is known about viral diversity due to the ever changing nature of these organisms. In response, VICI is developing a new microfluidic bioanalytical platform to detect known and unknown viruses by analyzing every virus in a sample by isolating them into picoliter sized droplets on a microchip and individually analyzing them. The sample will be injected into a channel of oil to form droplets that will contain viral nucleic acids that will be amplified using PCR. The multiplexed PCR assay will produce a series of amplicons for a particular virus genome that provides an identifying signature. A device will then detect whether or not DNA is present in the droplet and will sort the empty droplets from the rest. From this point, the amplified DNA is released from the droplets and analyzed using capillary gel electrophoresis in order to read out the series of amplicons and thereby determine the identity of each virus. The following figure depicts the microfluidic process. For the abovementioned microfluidic process to work, a method for detecting amplification of target viral nucleic acids that does not interfere with the multiplexed biochemical reaction is required for downstream sorting and analysis. In this report, the successful development of a multiplexed PCR assay using SYBR Green I as a fluorescent dye to detect amplification of viral DNA that can later be integrated into microfluidic PCR system for sorting and analysis is shown.

  18. Sub-micron filter

    DOE Patents [OSTI]

    Tepper, Frederick; Kaledin, Leonid

    2009-10-13

    Aluminum hydroxide fibers approximately 2 nanometers in diameter and with surface areas ranging from 200 to 650 m.sup.2/g have been found to be highly electropositive. When dispersed in water they are able to attach to and retain electronegative particles. When combined into a composite filter with other fibers or particles they can filter bacteria and nano size particulates such as viruses and colloidal particles at high flux through the filter. Such filters can be used for purification and sterilization of water, biological, medical and pharmaceutical fluids, and as a collector/concentrator for detection and assay of microbes and viruses. The alumina fibers are also capable of filtering sub-micron inorganic and metallic particles to produce ultra pure water. The fibers are suitable as a substrate for growth of cells. Macromolecules such as proteins may be separated from each other based on their electronegative charges.

  19. Nanosize electropositive fibrous adsorbent

    DOE Patents [OSTI]

    Tepper, Frederick; Kaledin, Leonid

    2005-01-04

    Aluminum hydroxide fibers approximately 2 nanometers in diameter and with surface areas ranging from 200 to 650 m.sup.2 /g have been fount to be highly electropositive. When dispersed in water they are able to attach to and retain electronegative particles. When combined into a composite filter with other fibers or particles they can filter bacteria and nano size particulates such as viruses and colloidal particles at high flux through the filter. Such filters can be used for purification and sterilization of water, biological, medical and pharmaceutical fluids, and as a collector/concentrator for detection and assay of mirobes and viruses. The alumina fibers are also capable of filtering sub-micron inorganic and metallic particles to produce ultra pure water. The fibers are suitable as a substrate for growth of cells. Macromolicules such as proteins may be separated from each other based on their electronegative charges.

  20. Nucleic acid sequences encoding D1 and D1/D2 domains of human coxsackievirus and adenovirus receptor (CAR)

    DOE Patents [OSTI]

    Freimuth, Paul I.

    2010-04-06

    The invention provides recombinant human CAR (coxsackievirus and adenovirus receptor) polypeptides which bind adenovirus. Specifically, polypeptides corresponding to adenovirus binding domain D1 and the entire extracellular domain of human CAR protein comprising D1 and D2 are provided. In another aspect, the invention provides nucleic acid sequences encoding these domains and expression vectors for producing the domains and bacterial cells containing such vectors. The invention also includes an isolated fusion protein comprised of the D1 polypeptide fused to a polypeptide which facilitates folding of D1 when expressed in bacteria. The functional D1 domain finds application in a therapeutic method for treating a patient infected with a CAR D1-binding virus, and also in a method for identifying an antiviral compound which interferes with viral attachment. The invention also provides a method for specifically targeting a cell for infection by a virus which binds to D1.

  1. Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Burstein, David; Sun, Christine L.; Brown, Christopher T.; Sharon, Itai; Anantharaman, Karthik; Probst, Alexander J.; Thomas, Brian C.; Banfield, Jillian F.

    2016-02-03

    Here, current understanding of microorganism–virus interactions, which shape the evolution and functioning of Earth’s ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. Wemore » correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides.« less

  2. Predicting Individual Affect of Health Interventions to Reduce HPV Prevalence

    SciTech Connect (OSTI)

    Corley, Courtney D.; Mihalcea, Rada; Mikler, Armin R.; Sanfilippo, Antonio P.

    2011-04-01

    Recently, human papilloma virus has been implicated to cause several throat and oral cancers and hpv is established to cause most cervical cancers. A human papilloma virus vaccine has been proven successful to reduce infection incidence in FDA clinical trials and it is currently available in the United States. Current intervention policy targets adolescent females for vaccination; however, the expansion of suggested guidelines may extend to other age groups and males as well. This research takes a first step towards automatically predicting personal beliefs, regarding health intervention, on the spread of disease. Using linguistic or statistical approaches, sentiment analysis determines a texts affective content. Self-reported HPV vaccination beliefs published in web and social media are analyzed for affect polarity and leveraged as knowledge inputs to epidemic models. With this in mind, we have developed a discrete-time model to facilitate predicting impact on the reduction of HPV prevalence due to arbitrary age and gender targeted vaccination schemes.

  3. Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2014

    SciTech Connect (OSTI)

    Voigt, Christopher

    2014-07-01

    SEED2014 focused on advances in the science and technology emerging from the field of synthetic biology. We broadly define this as technologies that accelerate the process of genetic engineering. It highlighted new tool development, as well as the application of these tools to diverse problems in biotechnology, including therapeutics, industrial chemicals and fuels, natural products, and agriculture. Systems spanned from in vitro experiments and viruses, through diverse bacteria, to eukaryotes (yeast, mammalian cells, plants).

  4. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    culturing tool reveals a full genome from single cells March 15, 2013 Gel microdroplet culturing reveals intraspecies genomic diversity within the human microbiome LOS ALAMOS, N. M., March 15, 2013-A new technique for genetic analysis, "gel microdroplets," helps scientists generate complete genomes from a single cell, thus opening the door to understanding the complex interrelationships of bacteria, viruses and eukaryotes that form "microbiome" communities in soil, in humans,

  5. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Software speeds detection of diseases and cancer-treatment targets December 1, 2014 New technology puts bioinformatics within easy reach of health-care professionals, researchers and others LOS ALAMOS, N.M., Dec. 1, 2014-Los Alamos National Laboratory has released an updated version of powerful, award-winning bioinformatics software that is now capable of identifying DNA from viruses and all parts of the Tree of Life-putting diverse problems such as identifying pathogen-caused diseases,

  6. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mysteries of 'molecular machines' revealed December 22, 2014 EMBARGOED for Monday, December 22, 11 a.m. Eastern Time Phenix software uses X-ray diffraction spots to produce 3-D image LOS ALAMOS, N.M., Dec. 22, 2014-Scientists are making it easier for pharmaceutical companies and researchers to see the detailed inner workings of molecular machines. "Inside each cell in our bodies and inside every bacterium and virus are tiny but complex protein molecules that synthesize chemicals, replicate

  7. DOE Science Showcase - Microbes | OSTI, US Dept of Energy, Office of

    Office of Scientific and Technical Information (OSTI)

    Scientific and Technical Information Microbes Cells of the bacteria Shewanella putrefaciens CN32. Courtesy Department of Energy Microbes - bacteria, fungi, protozoa, algae, and viruses are mysterious engines of life. Microbiomes, or microbe communities, account for 60% of living matter and are the most diverse life form on earth yet little has been known about how they function. Recent advances in gene-sequencing technology have expanded our knowledge of microbiomes, and microbiomes research

  8. How Dynein Binds to Microtubules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    How Dynein Binds to Microtubules Print Cytoplasmic dynein is a protein complex responsible for the transport of a large variety of cargoes, from specific RNAs and proteins to whole organelles, in a directional fashion along microtubules that serve as cellular conveyor belts. Consistent with this central role, cytoplasmic dynein is associated with a number of disease-related processes, including the transport of viruses, neurodegeneration, and the mitotic checkpoint malfunctions that lead to

  9. How Dynein Binds to Microtubules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    How Dynein Binds to Microtubules How Dynein Binds to Microtubules Print Wednesday, 29 April 2009 00:00 Cytoplasmic dynein is a protein complex responsible for the transport of a large variety of cargoes, from specific RNAs and proteins to whole organelles, in a directional fashion along microtubules that serve as cellular conveyor belts. Consistent with this central role, cytoplasmic dynein is associated with a number of disease-related processes, including the transport of viruses,

  10. SSRL HEADLINES March 2014

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    8 - March 2014 View the Archives **Note for Outlook users: For easier reading, please click the bar at the top of this message that reads "This message was converted to plain text" and select "Display as HTML."** Science Highlights thumbnail Structural Rearrangement in Ebola Virus Protein VP40 Creates Multiple Functions - Contact: Erica Ollmann Saphire, The Scripps Research Institute Proteins are molecules with a wide range of functions in all living organisms. As potential

  11. SSRL HEADLINES November 2014

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 - November 2014 View the Archives **Note for Outlook users: For easier reading, please click the bar at the top of this message that reads "This message was converted to plain text" and select "Display as HTML."** Science Highlight thumbnail Antibody Recognition of the Influenza Hemagglutinin by Receptor Mimicry - Contacts: Yoshikazu Kurosawa, Fujita Health University and Ian A. Wilson, The Scripps Research Institute Influenza viruses infect millions of people each year,

  12. What's New with Information Systems? | The Ames Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    What's New with Information Systems? Upgrade to Windows 10 Can you? Should you? Whats new? Find out more here. Questions About Email? Make sure messages from a sender are always recieved. Checking Junk Mail in Thunderbird. GnuPG errors causing blank messages? Embedded Macros & Email Embedded macros are user-written programs commonly used in Microsoft Office products like Word and Excel. These can be used maliciously to infect desktops with viruses. Learn more about why they are no longer

  13. labnews04-15-16.qxp_la02_02-20-04

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    up disease-carrying mosquitoes RED MEANS A DISEASE is present to Sandia researchers Cameron Ball and Robert Meagher as they test their QUASR, quenching of unincorporated amplification signal reporters, a technique to detect the presence of malaria and viruses like West Nile. Simple enough for field labs and handheld devices, QUASR's positive signal is 10 times brighter than a negative signal. (Photo by Dino Vournas) M osquitoes are deadly efficient at spreading disease. Despite vaccines and

  14. News Item

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Researchers Take Cues From Nature in Designing a Programmable Nanomaterial for Biosensing Taking inspiration from the human immune system, researchers at the Molecular Foundry have created a new material that can be programmed to identify an endless variety of molecules. The new material resembles tiny sheets of Velcro, each just one-hundred nanometers across. But instead of securing your sneakers, this molecular Velcro mimics the way natural antibodies recognize viruses and toxins, and could

  15. The Energy

    Energy Savers [EERE]

    NATIONAL AND HOMELAND SECURITY Continued next page Network Interconnectivity The business world is online. So are hackers. The dangers and complica- tions of controlling corporate network access and informa- tion flow from unauthorized users has been a consistent problem since the Inter- net's inception. The guiding principal seems to be that if a programmer can build it, a hacker can destroy it. A virtual back and forth battle of patches and worms, upgrades and viruses has evolved. In addition,

  16. 03-08-2010 NNSA-B-10-0097

    National Nuclear Security Administration (NNSA)

    8-2010 NNSA-B-10-0097 Sandia National Laboratories/New Mexico (SNL/NM) proposes to perform neutron reflectivity and fluorescence microscopy studies of the structure and activity of the negative factor (Nef) protein from Human Immunodeficiency Virus (HIV) bound to lipid membranes. Some of the proposed work with the recombinant proteins - the neutron reflection (NR) - would be performed at national neutron-scattering user facilities across the country; initial work would be performed at the

  17. New global HIV vaccine design shows promise in monkeys

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    New global HIV vaccine design shows promise in monkeys New global HIV vaccine design shows promise in monkeys These vaccines are specifically designed to present the most common forms of parts of the virus that can be recognized by the immune system. October 30, 2013 Bette Korber of Los Alamos National Laboratory, who developed a component of a new vaccine against HIV, now being tested in monkeys. Bette Korber of Los Alamos National Laboratory, who developed a component of a new vaccine against

  18. ORISE: Travelers' Health Campaign | How ORISE is Making a Difference

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Travelers' Health Campaign Travelers' Health Campaign takes critical messages worldwide Travelers' Health Campaign poster Click image to enlarge Traveling can be a dangerous transmitter of germs, bacteria and viruses such as H1N1. That makes airports, ship docks, train stations and bus depots among the most important places to spread the word about healthy practices and precautions. The Oak Ridge Institute for Science and Education (ORISE) has played a key role in preparing to get the

  19. Foreign DNA Capture during CRISPR-CAS Adaptive Immunity

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Foreign DNA Capture during CRISPR-CAS Adaptive Immunity Foreign DNA Capture during CRISPR-CAS Adaptive Immunity Print Thursday, 21 January 2016 16:45 While we humans view bacteria as the enemy, bacteria have enemies too, for example, viruses. To protect themselves, bacteria have developed an adaptive-type immune system that revolves around a unit of DNA known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. A CRISPR unit of DNA is made up of

  20. SREL Reprint #3317

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    7 First case of ranavirus and associated morbidity and mortality in an eastern mud turtle Kinosternon subrubrum in South Carolina Megan E. Winzeler, Matthew T. Hamilton, Tracey D. Tuberville, and Stacey L. Lance Savannah River Ecology Lab, University of Georgia, Drawer E, Aiken, SC 29802, USA Abstract: Ranaviruses are double-stranded DNA viruses that infect amphibians, fish, and reptiles, causing global epidemics in some amphibian populations. It is important to identify new species that may be

  1. SSRL Seminar Series

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Hiring Filamentous Bacteriophage for Targeted Cancer Treatment SSRL Seminar Tuesday, August 24, 2010 11:00 - 12:30 SSRL Conference room -137-322 Chuanbin Mao Department of Chemistry & Biochemistry - University of Oklahoma My research group is actively employing viruses, flagella and bacteria to perform varying functions for the development of nanotechnology and nanomedicine. This talk will highlight our recent work in this area and focus on the use of genetically modifiable bacteriophage

  2. Sandia National Laboratories:

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    15, 2016 Articles CRISPR genome-editing technology CRISPR genome-editing technology Sandia's QUASR enables speedy, accurate detection of West Nile and other viruses Lighting up disease-carrying mosquitoes Sandia CRADA boom sets records, forges ties Bumper crop of partnerships Directed-energy tech receives funding to field weapon for the military Two inspirational Sandia women in ceramic and glass engineering HyRAM logo Hydrogen Risk Assessment Models toolkit now available Maxine Norton, left,

  3. High temperature flow-through device for rapid solubilization and analysis

    DOE Patents [OSTI]

    West, Jason A. A.; Hukari, Kyle W.; Patel, Kamlesh D.; Peterson, Kenneth A.; Renzi, Ronald F.

    2013-04-23

    Devices and methods for thermally lysing of biological material, for example vegetative bacterial cells and bacterial spores, are provided. Hot solution methods for solubilizing bacterial spores are described. Systems for direct analysis are disclosed including thermal lysers coupled to sample preparation stations. Integrated systems capable of performing sample lysis, labeling and protein fingerprint analysis of biological material, for example, vegetative bacterial cells, bacterial spores and viruses are provided.

  4. INL Cyber Security Research (2008) | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    INL Cyber Security Research (2008) INL Cyber Security Research (2008) Cybersecurity research at INL will help protect critical infrastructure control system computers against worms and other viruses. PDF icon INL Cyber Security Research (2008) More Documents & Publications Mitigations for Security Vulnerabilities Found in Control System Networks The NIAC Convergence of Physical and Cyber Technbologies and Related Security Management Challenges Working Group Final Report and Recommendations

  5. High temperature flow-through device for rapid solubilization and analysis

    DOE Patents [OSTI]

    West, Jason A. A.; Hukari, Kyle W.; Patel, Kamlesh D.; Peterson, Kenneth A.; Renzi, Ronald F.

    2009-09-22

    Devices and methods for thermally lysing of biological material, for example vegetative bacterial cells and bacterial spores, are provided. Hot solution methods for solubilizing bacterial spores are described. Systems for direct analysis are disclosed including thermal lysers coupled to sample preparation stations. Integrated systems capable of performing sample lysis, labeling and protein fingerprint analysis of biological material, for example, vegetative bacterial cells, bacterial spores and viruses are provided.

  6. Probing Spatial, Electronic Structures with X-ray Scattering, Spectroscopic

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Techniques | Stanford Synchrotron Radiation Lightsource Probing Spatial, Electronic Structures with X-ray Scattering, Spectroscopic Techniques Wednesday, September 5, 2012 - 10:45am SLAC, Bldg. 137, Room 226 Gang Chen Seminar: Structures at atomic scales are traditionally determined through X-ray crystallography that amplifies scattering intensities by introducing spatial periodicity. For amorphous materials and many macromolecules, such as viruses, proteins and biofilms, it is hard to

  7. Research deciphers HIV attack plan

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Research deciphers HIV attack plan Research deciphers HIV attack plan These findings will help inform vaccine design and interpretation of vaccine trials, and provide new insights into the basic biology of viral/host dynamics of infection. March 29, 2013 Bette Korber Bette Korber Contact Nancy Ambrosiano Communications Office (505) 667-0471 Email The viruses that make it through transmission barriers to infect a new person are particularly infectious and resilient," said Los Alamos National

  8. Real Time Diagnostics for Algae-final-sm

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-time Monitoring And Diagnostics Detecting pathogens and predators to quickly recover from pond crashes Algal Pond Crash Detection Sandia National Laboratories is developing a suite of complementary technologies to help the emerging algae industry detect and quickly recover from algal pond crashes, an obstacle to large-scale algae cultivation for biofuels. Because of the way algae is grown and produced in most algal ponds, they are prone to attack by fungi, rotifers, viruses or other

  9. FNAL central email systems

    SciTech Connect (OSTI)

    Schmidt, Jack; Lilianstrom, Al; Pasetes, Ray; Hill, Kevin; /Fermilab

    2004-10-01

    The FNAL Email System is the primary point of entry for email destined for an employee or user at Fermilab. This centrally supported system is designed for reliability and availability. It uses multiple layers of protection to help ensure that: (1) SPAM messages are tagged properly; (2) All mail is inspected for viruses; and (3) Valid mail gets delivered. This system employs numerous redundant subsystems to accomplish these tasks.

  10. New Microbiome Center to combine UChicago, Marine Biological Laboratory and

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Argonne expertise | Argonne National Laboratory Filamentous cyanobacteria from a tidal pond at Little Sippewissett salt marsh, Falmouth, Mass. Microbial communities - bacteria, viruses and fungi - affect every ecosystem on earth, including human bodies, oceans, our homes and the land around us, and are the focus of a new Microbiome Center jointly headed by Argonne, the Marine Biological Laboratory and the University of Chicago. (Image: S. Emil Ruff, Marine Biological Laboratory) Filamentous

  11. Alamos National Laboratory theoretical biologists Bette Korber, Will Fischer, Sydeaka

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    strategy expands immune responses March 3, 2010 Mosaic vaccines show promise in reducing the spread of deadly virus LOS ALAMOS, New Mexico, March 3, 2010-Two teams of researchers-including Los Alamos National Laboratory theoretical biologists Bette Korber, Will Fischer, Sydeaka Watson, and James Szinger-have announced an HIV vaccination strategy that has been shown to expand the breadth and depth of immune responses in rhesus monkeys. Rhesus monkeys provide the best animal model currently

  12. Software speeds detection of diseases and cancer-treatment targets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Software speeds detection of diseases Software speeds detection of diseases and cancer-treatment targets The Lab has released an updated version of software that is now capable of identifying DNA from viruses and all parts of the Tree of Life. December 1, 2014 With Sequedex, a laptop computer can analyze DNA sequences faster than any current DNA sequencer can create them. With Sequedex, a laptop computer can analyze DNA sequences faster than any current DNA sequencer can create them. Contact

  13. Systems Biology in Prokaryote - Eukaryote Symbiosis | Stanford Synchrotron

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Radiation Lightsource Systems Biology in Prokaryote - Eukaryote Symbiosis Monday, June 25, 2012 - 12:00pm SLAC, SSRL Main Conference Room, 137-322 Allen M. Orville, Brookhaven National Laboratory Frontier challenges for macromolecular crystallography (MX) now include determining structures of trapped reactive intermediates, large macromolecules and viruses, membrane proteins, protein-protein complexes, and protein-nucleic acid complexes. Although structure and function are intimately linked,

  14. Consortium to design human trials of mosaic HIV vaccine

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Human trials of mosaic HIV vaccine Consortium to design human trials of mosaic HIV vaccine The vaccine represents a novel strategy for fighting the virus that causes AIDS by attempting to address one of the most daunting challenges in HIV vaccine design. October 18, 2010 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to

  15. Superhydrophobic surfaces (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Patent: Superhydrophobic surfaces Citation Details In-Document Search Title: Superhydrophobic surfaces Surfaces having a hierarchical structure--having features of both microscale and nanoscale dimensions--can exhibit superhydrophobic properties and advantageous condensation and heat transfer properties. The hierarchical surfaces can be fabricated using biological nanostructures, such as viruses as a self-assembled nanoscale template. Authors: Wang, Evelyn N ; McCarthy, Matthew ; Enright, Ryan ;

  16. An Unusual Mechanism for the Antimicrobial Target Flavine-dependant

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Thymidylate Synthase (FTDS) An Unusual Mechanism for the Antimicrobial Target Flavine-dependant Thymidylate Synthase (FTDS) Classical thymidylate synthases, encoded by the thyA and TYMS genes, are present in most eukaryotes, including humans, and are frequently targeted by chemotherapeutic and antibiotic drugs. A recently discovered class of thymidylate synthases, the FDTSs encoded by the thyX gene has been found primarily in prokaryotes and viruses including several pathogens and biological

  17. Transformation of gram positive bacteria by sonoporation

    DOE Patents [OSTI]

    Yang, Yunfeng; Li, Yongchao

    2014-03-11

    The present invention provides a sonoporation-based method that can be universally applied for delivery of compounds into Gram positive bacteria. Gram positive bacteria which can be transformed by sonoporation include, for example, Bacillus, Streptococcus, Acetobacterium, and Clostridium. Compounds which can be delivered into Gram positive bacteria via sonoporation include nucleic acids (DNA or RNA), proteins, lipids, carbohydrates, viruses, small organic and inorganic molecules, and nano-particles.

  18. Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

    SciTech Connect (OSTI)

    Deymier, Martin J.; Claiborne, Daniel T.; Ende, Zachary; Ratner, Hannah K.; Kilembe, William; Hunter, Eric

    2014-11-15

    The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor.

  19. The Crystal Structure of the RNA-Dependent RNA Polymerase from Human Rhinovirus: A Dual Function Target for Common Cold Antiviral Therapy

    SciTech Connect (OSTI)

    Love, Robert A.; Maegley, Karen A.; Yu, Xiu; Ferre, RoseAnn; Lingardo, Laura K.; Diehl, Wade; Parge, Hans E.; Dragovich, Peter S.; Fuhrman, Shella A.

    2010-11-16

    Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common cold. Given the lack of effective treatments for rhinoviral infections, virally encoded proteins have become attractive therapeutic targets. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp) denoted 3D{sup pol}, which is responsible for replicating the viral genome and for synthesizing a protein primer used in the replication. Here the crystal structures for three viral serotypes (1B, 14, and 16) of HRV 3D{sup pol} have been determined. The three structures are very similar to one another, and to the closely related poliovirus (PV) 3D{sup pol} enzyme. Because the reported PV crystal structure shows significant disorder, HRV 3D{sup pol} provides the first complete view of a picornaviral RdRp. The folding topology of HRV 3D{sup pol} also resembles that of RdRps from hepatitis C virus (HCV) and rabbit hemorrhagic disease virus (RHDV) despite very low sequence homology.

  20. Isolation and characterization of a novel arenavirus harbored by Rodents and Shrews in Zhejiang province, China

    SciTech Connect (OSTI)

    Li, Kun; Lin, Xian-Dan; Wang, Wen; Shi, Mang; Guo, Wen-Ping; Zhang, Xiao-He; Xing, Jian-Guang; and others

    2015-02-15

    To determine the biodiversity of arenaviruses in China, we captured and screened rodents and shrews in Wenzhou city, Zhejiang province, a locality where hemorrhagic fever diseases are endemic in humans. Accordingly, arenaviruses were detected in 42 of 351 rodents from eight species, and in 12 of 272 Asian house shrews (Suncus murinus), by RT-PCR targeting the L segment. From these, a single arenavirus was successfully isolated in cell culture. The virion particles exhibited a typical arenavirus morphology under transmission electron microscopy. Comparison of the S and L segment sequences revealed high levels of nucleotide (>32.2% and >39.6%) and amino acid (>28.8% and >43.8%) sequence differences from known arenaviruses, suggesting that it represents a novel arenavirus, which we designated Wenzhou virus (WENV). Phylogenetic analysis revealed that all WENV strains harbored by both rodents and Asian house shrews formed a distinct lineage most closely related to Old World arenaviruses. - Highlights: • A novel arenavirus (Wenzhou virus) was identified in Zhejiang province, China. • The virus is highly circulating in five species of rats and one species of shrews • More efforts are needed to infer whether it is pathogenic to humans or not.