Analysis of the kinetics and recombinatorial mechanisms of HIV-1 evolution in vivo in humanized mice

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Bradford Berges, MEG 2013 Final Report (submitted Oct 2015)

Evaluation of how well the academic objectives of the proposal were met

Several of my students have moved on to future positions, as follows:
Medical school: Sterling Adams, German Cuadra, Art Lee (still interviewing), and Tyler White (still interviewing)
Graduate school: Steve Hallam

See below in the ‘academic deliverables’ section for further details on presentations, grant funding awarded directly to students, and publications.

Evaluation of the mentoring environment

As in the original proposal, I met with each of my students weekly and we also held weekly group meetings for the entire research lab group. I had the students over to my home for a barbecue and some informal time together. As stated, I always keep my office door open so that students can reach me at any time and they know that they can call/text/email me when I am not on campus.

List of students who participated and what academic deliverables they have produced or it is anticipated they will produce

1. Sterling Adams—

  • ORCA award: Recombination and Evolution of HIV in Vivo
  • Anticipated authorship on a peer-reviewed publication (to be submitted Fall 2015)
  • Conference presentations:
    Bradford K. Berges, Tyler S. Slater, Michael B. Hatch, Sterling G. Adams, Paulo M. Tello, and Christopher P. Koontz. Analysis of human antibody responses to Dengue virus type 2 following experimental infection of humanized Rag2-/-γc-/- mice. American Society for Virology, 2011.

    Tyler Slater, Sterling G. Adams, and Bradford K. Berges. “A Novel ELISA Test to Detect Human Anti-Dengue Antibodies”. American Society of Microbiology Intermountain Branch Meeting, 2011.

2. German Cuadra

  • Published papers:
    1. Tanner, Anne, Hallam, Steven J., Nielsen, Stanton J., Cuadra, German I., and Berges, Bradford K. Development of Human B Cells and Antibodies Following Human Hematopoietic Stem Cell Transplantation to Rag2-/-γc-/- mice. Transpl Immunol 2015, 32:144-150.

    2. Sanchez, F.M., Cuadra, G.I., Nielsen, S.J., Tanner, A., and Berges, B.K. Production and characterization of humanized Rag2-/-γc-/- mice. Methods Mol Biol 2013 1031:19-26.

  • Conference presentations:

    Stanton J. Nielsen, German I. Cuadra, and Bradford K. Berges. “Human B Cell Development and Antibody Responses in Humanized Mice”. Autumn Immunology Conference, 2012.

    German I. Cuadra, Stanton J. Nielsen, and Bradford. K. Berges “Humanized mice as a Model to Study the Development of human B Cells and Antibody Responses”. American Society of Microbiology Intermountain Branch Meeting, 2012.

    Freddy S. Tumbaco, Jamie D. Gardiner, Joel R. Gardner, German R. Cuadra, and Bradford K. Berges. Infection of humanized Rag2-/-γc-/- mice with Kaposi’s Sarcoma-Associated Herpesvirus for studies of AIDS-associated lymphomas. American Society for Virology, 2011.

    German I. Cuadra and Bradford K. Berges. “Humanized Mice as a Model to study Human Gammaherpesvirus Transmission”. American Society of Microbiology Intermountain Branch Meeting, 2011.

3. Art Lee

  • ORCA award: HIV Inhibitors and Their Potential as Anti-HIV Drugs

4. Tyler White

  • ORCA award: Isolation and Characterization of Novel Lytic Phage to Treat MRSA
  • Publication: Jensen, Kyle C., Hair, Bryan B., Wienclaw, Trevor M., Murdock, Mark H., Hatch, Jacob B., Trent, Aaron T., White, Tyler D., Haskell, Kyler J., and Berges, Bradford K. Isolation and Host Range of Bacteriophage with Lytic Activity against Methicillin-Resistant Staphylococcus aureus and Potential use as a Fomite Decontaminant. PLoS ONE 2015, 10(7):e0131714.
  • Conference presentations:
    Jensen, K.C., Wienclaw, T.M., Hatch, J.B., White, T.D., Hair, B.B., Trent, A.T., Haskell, K.J., Berges, B.K. Characterization of Novel Bacteriophage with Lytic Activity Against MRSA and Utility for Decontamination of Fomites Associated with Nosocomial Transmission. American Society for Microbiology, 2015

    White, T.D., Jensen, K.C., Wienclaw, T.M., Hatch, J.B., Hair, B.B, Trent, A.T., and Berges, B.K. Isolation and Characterization of Novel Lytic Phage to Treat Methicillin-Resistant Staphylococcus Aureus. Utah Conference on Undergraduate Research, 2015.

    Trevor M. Wienclaw, Kyle C. Jensen, Jacob B. Hatch, Tyler D. White, Bryan B. Hair, and Bradford K. Berges. Characterization of novel bacteriophage with lytic activity against methicillin-resistant S. aureus. Autumn Immunology Conference, 2014.

    Kyle C. Jensen, Mark H. Murdock, Jacob B. Hatch, Tyler D. White, and Bradford K. Berges. “Isolation and characterization of novel bacteriophage as a control of Methicillin Resistant Staphylococcus Aureus”. American Society of Microbiology Intermountain Branch Meeting, 2014.

5. Steve Hallam

  • ORCA award: Use of humanized mice to study the production of human antibodies
  • Publication: Tanner, Anne, Hallam, Steven J., Nielsen, Stanton J., Cuadra, German I., and Berges, Bradford K. Development of Human B Cells and Antibodies Following Human Hematopoietic Stem Cell Transplantation to Rag2-/-γc-/- mice. Transpl Immunol 2015, 32:144-150.
  • Conference presentations:
    Anne Tanner, Stephanie A. Carlson, Wittnee Decottignies, Steven J. Hallam, Hillary J. Willyerd, Masatoshi Nukui, Eain A. Murphy, and Bradford K. Berges. Human herpesvirus 6A infection of humanized mice and effects on human T cell populations. American Society for Virology, 2014.

    Steven J. Hallam, German I. Cuadra, Stanton J. Nielsen, and Bradford K. Berges. “Immune Development in Humanized Mice as characterized by B cell maturation and antibody production”. American Society of Microbiology Intermountain Branch Meeting, 2014.

6. Taalin Rasmussen

  • Anticipated authorship on a peer-reviewed publication (to be submitted Fall 2015)

Description of the results/findings of the project

Our main roles in this collaborative project are all completed at this point in time, and we are awaiting our collaborators at George Washington University to finish analyzing the HIV genomic sequences and then we can finish writing up the paper and submit it. We produced the humanized mice for this experiment, and also the HIV stocks to be used. We infected the animals, and then we took weekly blood samples for 24 weeks and extracted RNA from them for sequence analysis. We additionally sacrificed mice every 2-3 weeks and dissected out organs and preserved them in RNALater. All of the RNA and organ samples were sent to our collaborators, whose job is to obtain RNA sequences and to analyze them for mutation rates. We anticipate that the paper should be submitted before the end of 2015.

Description of how the budget was spent

The budget was spent in very similar fashion to the original proposal:

3

Tyler White traveled to a meeting to present his results, thus using the travel funds. Most of the rest of the funds were used for supplies, and 2 students were employed (Sterling and German).