Jaisri Lingappa's Lab

Former PhD Students

Jonathan C. Reed

Jonathan C. Reed

Jon received his BS from Oregon State University (OSU), where he majored in Life Sciences/Botany and studied suppressors of RNA silencing encoded by plant viruses, in the laboratory of Dr. Valerian Dolja.  At OSU, Jon received numerous awards, including two HHMI summer undergraduate research fellowships and the Outstanding Senior Award at Oregon State University.  In 2004, he entered the University of Washington (UW) Molecular and Cellular Biology PhD program, and in 2006, he received an NSF Graduate Research Fellowship to pursue his PhD studies on capsid assembly in the Lingappa lab.   In 2011, he obtained his PhD in Molecular and Cellular Biology and his MS in Epidemiology through a joint UW PhD/MS program.  Jon stayed on in the Lingappa lab as a postdoctoral fellow until 2013, when he joined Prosetta Biosciences and established the Prosetta satellite lab in Seattle.  While at Prosetta, Jon served as Biology Lead and directed two different groups – one screening for anti-viral compounds that act on the subcellular ribonucleoprotein assembly machines that Jon studied while he was in the Lingappa lab, and one screening for anti-parasitic compounds that act on similar ribonucleoprotein complexes in Plasmodium.  In 2017, Jon returned to Jaisri Lingappa’s lab at UW as a Senior Research Scientist to continue his studies of antiretroviral compounds in collaboration with Prosetta and to study the basic science of retroviral assembly.

Research:

As a PhD student in the Lingappa lab, Jon made a fundamental discovery that reshaped our understanding of HIV-1 virus assembly.  He demonstrated that the intermediates (aka assembly machines) that are formed during assembly of the HIV-1 immature capsid are composed of cellular proteins found in RNA granules.  RNA granules are important subcellular host ribonucleoprotein complexes involved in all aspects of RNA metabolism except translation, but had not been implicated previously in HIV-1 assembly.  Jon also used siRNA knockdown approaches in HIV-1 expressing cells to show that DDX6, one of the host RNA granule proteins in the HIV-1 assembly intermediates, facilitates HIV-1 capsid assembly.  In additional experiments, he showed that WT DDX6 rescued the knockdown phenotype, while an enzymatically inactive DDX6 mutant did not.  He also confirmed the importance of DDX6 for facilitating assembly of infectious using siRNA knockdowns of primary blood mononuclear cells (PBMC).  Jon’s seminal PhD studies in support of a model in which HIV-1 Gag co-opts host RNA granules to form assembly machines were published in the Journal of Cell Biology in 2012, adding to growing evidence that HIV-1 capsid assembly in infected cells is host-catalyzed.

As a postdoctoral fellow, Jon developed RT-qPCR techniques for studying how the “assembly machines” facilitate packaging of the HIV-1 genome into newly assembled capsids.  These advances later led to a paper, published in PLOS Pathogens in 2018, showing that the RNA-granule-derived HIV-1 assembly intermediates also contain much of the genomic RNA found in the cytoplasm of HIV-expressing cells.  Thus, by trafficking to these RNA granules, assembling HIV-1 Gag is able to access host facilitators of assembly (e.g. DDX6 and the host enzyme ABCE1) as well as the HIV-1 genomic RNA that it needs to encapsidate in order to produce virus that is infectious.

As a Senior Research Scientist in the Lingappa Lab, Jon demonstrated that the Gag protein of feline immunodeficiency virus (FIV), a non-primate lentivirus, forms RNA-granule-derived assembly intermediates containing ABCE1 and DDX6, as is the case for HIV-1.  This study, published in the Journal of Virology in 2018, also demonstrated that the RNA-granule-derived FIV assembly intermediates contain additional RNA granule proteins, such as DCP-2 (as Jon showed the proximity ligation assay (PLA)), but do not contain the abundant ribosomal protein S6.  Thus, these complexes resemble RNA granules but do not resemble ribosomes.  Jon’s most recent project describes a novel small molecule (PAV117), discovered in collaboration with Prosetta Biosciences, that inhibits replication of HIV-1 in T cell lines and primary T cells with nanomolar potency, most likely acting on HIV-1 assembly intermediates (manuscript in preparation).

Jon’s contributions to the Lingappa Lab are myriad, and include writing manuscripts, editing grants, supervising junior employees, and developing new methods.  He has piloted, optimized, and established a vast number of techniques in the Lingappa lab, including highly sensitive coimmunoprecipitation approaches, quantitative immunogold electron microscopic double labeling, quantitative proximity ligation assay approaches for studying subcellular localization of small molecules, siRNA knockdown and rescue, codon optimization, reverse transcription with quantitative PCR, northern blotting, infectivity assays and other assays for studying efficacy of antiviral small molecules including in primary cells.

Publications:

  1. Michon, M, Müller-Schiffmann, A, Lingappa, AF, Yu, SF, Du, L, Deiter, F, Broce, S, Mallesh, S, Crabtree, J, Lingappa, UF, Macieik, A, Müller, L, Ostermann, PN, Andrée, M, Adams, O, Schaal, H, Hogan, RJ, Tripp, RA, Appaiah, U, Anand, SK, Campi, TW, Ford, MJ, Reed, JC, Lin, J, Akintunde, O, Copeland, K, Nichols, C, Petrouski, E, Moreira, AR, Jiang, IT, DeYarman, N, Brown, I, Lau, S, Segal, I, Goldsmith, D, Hong, S, Asundi, V, Briggs, EM, Phyo, NS, Froehlich, M, Onisko, B, Matlack, K, Dey, D, Lingappa, JR, Prasad, DM, Kitaygorodskyy, A, Solas, D, Boushey, H, Greenland, J, Pillai, S, Lo, MK, Montgomery, JM, Spiropoulou, CF, Korth, C, Selvarajah, S, Paulvannan, K, Lingappa, VR. A pan-respiratory antiviral chemotype targeting a transient host multi-protein complex. Open Biol. 2024;14 (6):230363. doi: 10.1098/rsob.230363. PubMed PMID:38889796 .
  2. Michon, M, Müller-Schiffmann, A, Lingappa, AF, Yu, SF, Du, L, Deiter, F, Broce, S, Mallesh, S, Crabtree, J, Lingappa, UF, Macieik, A, Müller, L, Ostermann, PN, Andrée, M, Adams, O, Schaal, H, Hogan, RJ, Tripp, RA, Appaiah, U, Anand, SK, Campi, TW, Ford, MJ, Reed, JC, Lin, J, Akintunde, O, Copeland, K, Nichols, C, Petrouski, E, Moreira, AR, Jiang, IT, DeYarman, N, Brown, I, Lau, S, Segal, I, Goldsmith, D, Hong, S, Asundi, V, Briggs, EM, Phyo, NS, Froehlich, M, Onisko, B, Matlack, K, Dey, D, Lingappa, JR, Prasad, MD, Kitaygorodskyy, A, Solas, D, Boushey, H, Greenland, J, Pillai, S, Lo, MK, Montgomery, JM, Spiropoulou, CF, Korth, C, Selvarajah, S, Paulvannan, K, Lingappa, VR. A Pan-Respiratory Antiviral Chemotype Targeting a Host Multi-Protein Complex. bioRxiv. 2023; :. doi: 10.1101/2021.01.17.426875. PubMed PMID:34931190 PubMed Central PMC8687465.
  3. Lingappa, JR, Lingappa, VR, Reed, JC. Addressing Antiretroviral Drug Resistance with Host-Targeting Drugs-First Steps towards Developing a Host-Targeting HIV-1 Assembly Inhibitor. Viruses. 2021;13 (3):. doi: 10.3390/v13030451. PubMed PMID:33802145 PubMed Central PMC8001593.
  4. Reed, JC, Solas, D, Kitaygorodskyy, A, Freeman, B, Ressler, DTB, Phuong, DJ, Swain, JV, Matlack, K, Hurt, CR, Lingappa, VR, Lingappa, JR. Identification of an Antiretroviral Small Molecule That Appears To Be a Host-Targeting Inhibitor of HIV-1 Assembly. J Virol. 2021;95 (3):. doi: 10.1128/JVI.00883-20. PubMed PMID:33148797 PubMed Central PMC7925099.
  5. Barajas, BC, Tanaka, M, Robinson, BA, Phuong, DJ, Chutiraka, K, Reed, JC, Lingappa, JR. Identifying the assembly intermediate in which Gag first associates with unspliced HIV-1 RNA suggests a novel model for HIV-1 RNA packaging. PLoS Pathog. 2018;14 (4):e1006977. doi: 10.1371/journal.ppat.1006977. PubMed PMID:29664940 PubMed Central PMC5940231.
  6. Reed, JC, Westergreen, N, Barajas, BC, Ressler, DTB, Phuong, DJ, Swain, JV, Lingappa, VR, Lingappa, JR. Formation of RNA Granule-Derived Capsid Assembly Intermediates Appears To Be Conserved between Human Immunodeficiency Virus Type 1 and the Nonprimate Lentivirus Feline Immunodeficiency Virus. J Virol. 2018;92 (9):. doi: 10.1128/JVI.01761-17. PubMed PMID:29467316 PubMed Central PMC5899207.
  7. Tanaka, M, Robinson, BA, Chutiraka, K, Geary, CD, Reed, JC, Lingappa, JR. Mutations of Conserved Residues in the Major Homology Region Arrest Assembling HIV-1 Gag as a Membrane-Targeted Intermediate Containing Genomic RNA and Cellular Proteins. J Virol. 2016;90 (4):1944-63. doi: 10.1128/JVI.02698-15. PubMed PMID:26656702 PubMed Central PMC4734008.
  8. Lingappa, JR, Reed, JC, Tanaka, M, Chutiraka, K, Robinson, BA. How HIV-1 Gag assembles in cells: Putting together pieces of the puzzle. Virus Res. 2014;193 :89-107. doi: 10.1016/j.virusres.2014.07.001. PubMed PMID:25066606 PubMed Central PMC4351045.
  9. Robinson, BA, Reed, JC, Geary, CD, Swain, JV, Lingappa, JR. A temporospatial map that defines specific steps at which critical surfaces in the Gag MA and CA domains act during immature HIV-1 capsid assembly in cells. J Virol. 2014;88 (10):5718-41. doi: 10.1128/JVI.03609-13. PubMed PMID:24623418 PubMed Central PMC4019110.
  10. Reed, JC, Molter, B, Geary, CD, McNevin, J, McElrath, J, Giri, S, Klein, KC, Lingappa, JR. HIV-1 Gag co-opts a cellular complex containing DDX6, a helicase that facilitates capsid assembly. J Cell Biol. 2012;198 (3):439-56. doi: 10.1083/jcb.201111012. PubMed PMID:22851315 PubMed Central PMC3413349.
  11. Klein, KC, Reed, JC, Tanaka, M, Nguyen, VT, Giri, S, Lingappa, JR. HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. J Virol. 2011;85 (14):7419-35. doi: 10.1128/JVI.00288-11. PubMed PMID:21543480 PubMed Central PMC3126549.
  12. Klein, KC, Reed, JC, Lingappa, JR. Intracellular destinies: degradation, targeting, assembly, and endocytosis of HIV Gag. AIDS Rev. 2007;9 (3):150-61. . PubMed PMID:17982940 .
  13. Dooher, JE, Schneider, BL, Reed, JC, Lingappa, JR. Host ABCE1 is at plasma membrane HIV assembly sites and its dissociation from Gag is linked to subsequent events of virus production. Traffic. 2007;8 (3):195-211. doi: 10.1111/j.1600-0854.2006.00524.x. PubMed PMID:17233757 PubMed Central PMC1865004.
  14. Chiba, M, Reed, JC, Prokhnevsky, AI, Chapman, EJ, Mawassi, M, Koonin, EV, Carrington, JC, Dolja, VV. Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon. Virology. 2006;346 (1):7-14. doi: 10.1016/j.virol.2005.09.068. PubMed PMID:16300814 .
  15. Tzanetakis, IE, Reed, J, Martin, RR. Nucleotide sequence, genome organization and phylogenetic analysis of Strawberry pallidosis associated virus, a new member of the genus Crinivirus. Arch Virol. 2005;150 (2):273-86. doi: 10.1007/s00705-004-0410-z. PubMed PMID:15503221 .
  16. Reed, JC, Kasschau, KD, Prokhnevsky, AI, Gopinath, K, Pogue, GP, Carrington, JC, Dolja, VV. Suppressor of RNA silencing encoded by Beet yellows virus. Virology. 2003;306 (2):203-9. doi: 10.1016/s0042-6822(02)00051-x. PubMed PMID:12642093 .

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Kevin Klein

Kevin Klein

Kevin Klein grew up in Madison, WI and received a BS with Distinction in Biochemistry from the University of Wisconsin. He completed his Ph.D. studies in the Lingappa lab and stayed on as a staff scientist. As a PhD student, Kevin was supported by an ARCS Foundation award and an NIH-funded Virology and Oncology training grant. While in the Lingappa lab, Kevin managed a soccer team called the Dominant Negatives and climbed Mt. Kilimanjaro (19,340′) in Africa, Mt. St. Helens (8,365 feet), Mt. Baker (10,778 feet), and Mt. Rainier (14,411 feet).

In 2010, Kevin, a long-standing brewer, started his own nanobrewery, Northwest Peaks. In 2011, he left the Lingappa Lab to focus full time on his brewery. At Northwest Peaks, Kevin combines his passion for brewing and climbing peaks around Seattle by making new, creative “small batch” beers every month, named after his favorite Pacific Northwest climbs. In 2014, Kevin started The Bergschrund, a great little tap room in Ballard that features Northwest Peaks beers.  You can find the Lingappa lab there having “lab drinks” on a fairly regular basis!

Research:

For his Ph.D. research, Kevin developed a cell-free system for assembling hepatitis C virus (HCV) capsids. At the time, there were no cell culture systems that supported assembly of HCV capsids. Even now, cell culture systems that support assembly of the most common genotypes of HCV are lacking. Kevin utilized this cell-free system to understand mechanisms of capsid formation of HCV and define HCV amino acids required for assembly. The HCV cell-free system established by Kevin is now being used by Prosetta Biosciences to screen for novel inhibitors of HCV assembly that could be used clinically. The success of the HCV cell-free assembly system also led to development of other cell-free assembly systems, including for assembly of alphaviruses.  During his time in the Lingappa lab, Kevin’s technical and conceptual insights contributed to numerous advances in our understanding of HIV-1 assembly and restriction.

Publications:

  1. Reed, JC, Molter, B, Geary, CD, McNevin, J, McElrath, J, Giri, S, Klein, KC, Lingappa, JR. HIV-1 Gag co-opts a cellular complex containing DDX6, a helicase that facilitates capsid assembly. J Cell Biol. 2012;198 (3):439-56. doi: 10.1083/jcb.201111012. PubMed PMID:22851315 PubMed Central PMC3413349.
  2. Klein, KC, Reed, JC, Tanaka, M, Nguyen, VT, Giri, S, Lingappa, JR. HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. J Virol. 2011;85 (14):7419-35. doi: 10.1128/JVI.00288-11. PubMed PMID:21543480 PubMed Central PMC3126549.
  3. Thielen, BK, McNevin, JP, McElrath, MJ, Hunt, BV, Klein, KC, Lingappa, JR. Innate immune signaling induces high levels of TC-specific deaminase activity in primary monocyte-derived cells through expression of APOBEC3A isoforms. J Biol Chem. 2010;285 (36):27753-66. doi: 10.1074/jbc.M110.102822. PubMed PMID:20615867 PubMed Central PMC2934643.
  4. Klein, KC, Reed, JC, Lingappa, JR. Intracellular destinies: degradation, targeting, assembly, and endocytosis of HIV Gag. AIDS Rev. 2007;9 (3):150-61. . PubMed PMID:17982940 .
  5. Thielen, BK, Klein, KC, Walker, LW, Rieck, M, Buckner, JH, Tomblingson, GW, Lingappa, JR. T cells contain an RNase-insensitive inhibitor of APOBEC3G deaminase activity. PLoS Pathog. 2007;3 (9):1320-34. doi: 10.1371/journal.ppat.0030135. PubMed PMID:17892323 PubMed Central PMC1993843.
  6. Lingappa, JR, Dooher, JE, Newman, MA, Kiser, PK, Klein, KC. Basic residues in the nucleocapsid domain of Gag are required for interaction of HIV-1 gag with ABCE1 (HP68), a cellular protein important for HIV-1 capsid assembly. J Biol Chem. 2006;281 (7):3773-84. doi: 10.1074/jbc.M507255200. PubMed PMID:16275648 .
  7. Klein, KC, Dellos, SR, Lingappa, JR. Identification of residues in the hepatitis C virus core protein that are critical for capsid assembly in a cell-free system. J Virol. 2005;79 (11):6814-26. doi: 10.1128/JVI.79.11.6814-6826.2005. PubMed PMID:15890921 PubMed Central PMC1112097.
  8. Lingappa, JR, Newman, MA, Klein, KC, Dooher, JE. Comparing capsid assembly of primate lentiviruses and hepatitis B virus using cell-free systems. Virology. 2005;333 (1):114-23. doi: 10.1016/j.virol.2004.12.024. PubMed PMID:15708597 .
  9. Newman, EN, Holmes, RK, Craig, HM, Klein, KC, Lingappa, JR, Malim, MH, Sheehy, AM. Antiviral function of APOBEC3G can be dissociated from cytidine deaminase activity. Curr Biol. 2005;15 (2):166-70. doi: 10.1016/j.cub.2004.12.068. PubMed PMID:15668174 .
  10. Klein, KC, Polyak, SJ, Lingappa, JR. Unique features of hepatitis C virus capsid formation revealed by de novo cell-free assembly. J Virol. 2004;78 (17):9257-69. doi: 10.1128/JVI.78.17.9257-9269.2004. PubMed PMID:15308720 PubMed Central PMC506955.
  11. Zimmerman, C, Klein, KC, Kiser, PK, Singh, AR, Firestein, BL, Riba, SC, Lingappa, JR. Identification of a host protein essential for assembly of immature HIV-1 capsids. Nature. 2002;415 (6867):88-92. doi: 10.1038/415088a. PubMed PMID:11780123 .
  12. Polyak SJ, Klein KC, Shoji I, Miyamura T, Lingappa JR. Assemble and Interact: Pleiotropic Functions of the HCV Core Protein. In: Tan SL, editor. SourceHepatitis C Viruses: Genomes and Molecular Biology. Norfolk (UK): Horizon Bioscience; 2006. Chapter 3. PubMed PMID:21250388

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Beth Thielen

Beth ThielenBeth Thielen grew up in New Brighton, MN and received her B.S. in Microbiology, summa cum laude, from the University of Minnesota.  While at the University of Minnesota, she also studied health care policy at Denmark’s International Study Program in Copenhagen and worked for 2 years as a certified emergency medical technician (EMT) for the University of Minnesota Emergency Medical Response Team.  Beth joined the Medical Scientist Training Program (MD/PhD program) at the University of Washington (UW) in 2003.  After finishing her first two years of medical school, Beth pursued her Ph.D. studies in the Lingappa lab from 2005 – 2009.  During that time, she received support from the CFAR STD/AIDS training grant, a Poncin scholarship, and an ARCS (Achievement Rewards for College Scientists) award.  She was awarded the Gilbert S. Omenn Award for Academic Excellence at UW in 2008.  She defended her Ph.D. in 2009, obtained her M.D. in 2011, and is currently completing a Medicine Pediatric Residency at the University of Minnesota.  In July 2016, Beth will begin an Infectious Disease Fellowship at the University of Minnesota.

Research:

As a rotation student in the Lingappa lab, Beth established a cell-free system for assembly of Venezuelan equine encephalitis virus (VEEV) capsids. This is the first cell-free system for assembly of an alphavirus capsid.  For her Ph.D. dissertation, Beth studied how the enzymatic activities of the cellular restriction factors APOBEC3G and APOBEC3A are regulated in primary human cells.  APOBEC3 family members, which are cellular proteins that have antiviral activity against HIV-1 and other viruses, are cellular deaminases.  Most studies of APOBEC3 proteins are performed on cells that have been transfected to express APOBEC3 proteins.  In contrast, Beth’s studies focused on the enzymatic activity of APOBEC3 proteins expressed endogenously in primary human cells.  To carry out these studies, she developed a quantitative, FRET-based high-throughput assay for detecting A3G deaminase activity.  Using this assay, she demonstrated that A3G deaminase activity in human T cells is inhibited by an RNase-insensitive inhibitor (PLoS Pathogens 3(9):e135, 2007).  Beth went on to demonstrate that while APOBEC3 deaminase activity remains low in primary human T cells despite treatment with a variety of cytokines, APOBEC3 enzymatic activity in primary human monocytes and macrophages undergoes a dramatic increase upon treatment with interferon alpha or interferon-alpha-inducing TLR ligands  (Journal of Biological Chemistry 285(36): 27753-27766, 2010).  In this paper, Beth used knockdown studies to demonstrate that the increase in deaminase activity in interferon alpha treated primary human monocytes is due entirely to induction of APOBEC3A, another member of the APOBEC3 family.  She also showed that APOBEC3A enzymatic activity in primary human monocytes could be modulated by a variety of other signaling pathways.  In contrast, APOBEC3A enzymatic activity could not be induced by interferon alpha in two different monocytic cell lines.  Thus, in primary human T cells, monocytes, and macrophages, the enzymatic activity of APOBEC3 proteins is under the control of regulatory pathways that are not present in transformed cell lines typically used to study APOBEC3 proteins.

Publications:

  1. Dick, JK, Sangala, JA, Krishna, VD, Khaimraj, A, Hamel, L, Erickson, SM, Hicks, D, Soigner, Y, Covill, LE, Johnson, A, Ehrhardt, MJ, Ernste, K, Brodin, P, Koup, RA, Khaitan, A, Baehr, C, Thielen, BK, Henzler, CM, Skipper, C, Miller, JS, Bryceson, YT, Wu, J, John, CC, Panoskaltsis-Mortari, A, Orioles, A, Steiner, ME, Cheeran, MC, Pravetoni, M, Hart, GT. Antibody-mediated cellular responses are dysregulated in Multisystem Inflammatory Syndrome in Children (MIS-C). bioRxiv. 2024; :. doi: 10.1101/2024.04.16.589585. PubMed PMID:38659969 PubMed Central PMC11042288.
  2. Goren, LR, Lehman, AC, Luquette, M, Howard, C, Thielen, BK. A Lytic Bone Lesion in a 23-month-old Boy from Kenya. Pediatr Rev. 2024;45 (4):225-229. doi: 10.1542/pir.2021-005473. PubMed PMID:38556514 .
  3. Lehman, AC, Goren, LR, Evans, MD, Toles, O, Drozdov, D, Andrews, SL, McAllister, SC, Thielen, BK. Clinical Performance of Plasma Metagenomic Sequencing in Immunocompromised Pediatric Patients. J Pediatric Infect Dis Soc. 2024;13 (5):276-281. doi: 10.1093/jpids/piae024. PubMed PMID:38483068 .
  4. Goren, LR, Adeyi, O, Thielen, BK. Possible Donor-Derived Infection in a Pediatric Liver Transplant Patient With Granulomatous Hepatitis. Cureus. 2023;15 (11):e49136. doi: 10.7759/cureus.49136. PubMed PMID:38130518 PubMed Central PMC10733164.
  5. Thielen, BK, Holzbauer, S, Templen, B, Schafer, IJ, Artus, A, Galloway, R, Ireland, M, Femrite, T, Schleiss, MR. Case Report: Locally Acquired Leptospirosis in a Minnesota Boy and His Dog. Am J Trop Med Hyg. 2024;110 (1):123-126. doi: 10.4269/ajtmh.23-0291. PubMed PMID:37983913 PubMed Central PMC10793009.
  6. Hoover, A, Thielen, BK, Ebens, CL. Fever and neutropenia in pediatric oncology and stem cell transplant patients: an editorial commentary on updated international clinical practice guidelines. Transl Pediatr. 2023;12 (10):1908-1912. doi: 10.21037/tp-23-368. PubMed PMID:37969121 PubMed Central PMC10644023.
  7. Christian, VJ, Sarwar, R, Resch, JC, Lim, S, Somani, A, Larson-Nath, C, McAllister, S, Thielen, BK, Adeyi, O, Chinnakotla, S, Bhatt, H. Use of Cidofovir for Safe Transplantation in a Toddler with Acute Liver Failure and Adenovirus Viremia. Case Rep Transplant. 2022;2022 :9426175. doi: 10.1155/2022/9426175. PubMed PMID:36405892 PubMed Central PMC9668457.
  8. Lofgren, SM, Okafor, EC, Colette, AA, Pastick, KA, Skipper, CP, Pullen, MF, Nicol, MR, Bold, TD, Bangdiwala, AS, Engen, NW, Collins, LB, Williams, DA, Axelrod, ML, Thielen, BK, Hullsiek, KH, Boulware, DR, Rajasingham, R. Feasibility of SARS-CoV-2 Antibody Testing in Remote Outpatient Trials. Open Forum Infect Dis. 2021;8 (11):ofab506. doi: 10.1093/ofid/ofab506. PubMed PMID:35548171 PubMed Central PMC8522439.
  9. Randolph, HE, Fiege, JK, Thielen, BK, Mickelson, CK, Shiratori, M, Barroso-Batista, J, Langlois, RA, Barreiro, LB. Genetic ancestry effects on the response to viral infection are pervasive but cell type specific. Science. 2021;374 (6571):1127-1133. doi: 10.1126/science.abg0928. PubMed PMID:34822289 PubMed Central PMC8957271.
  10. Frosch, AE, Thielen, BK, Alpern, JD, Walz, EJ, Volkman, HR, Smith, M, Wanduragala, D, Holder, W, Boumi, AE, Stauffer, WM. Antimalarial chemoprophylaxis and treatment in the USA: limited access and extreme price variability. J Travel Med. 2022;29 (4):. doi: 10.1093/jtm/taab117. PubMed PMID:34343310 PubMed Central PMC9282095.
  11. Quadri, NS, Thielen, BK, Crichlow, R, Rheault, M, Vraga, EK, Cohen, EL, Erayil, SE, Gulleen, EA, Braman, JP, Krohn, K. 12 Tips for Engaging Medical Students in Health Communications. MedEdPublish (2016). 2021;10 :48. doi: 10.15694/mep.2021.000048.1. PubMed PMID:38486528 PubMed Central PMC10939613.
  12. Fiege, JK, Thiede, JM, Nanda, HA, Matchett, WE, Moore, PJ, Montanari, NR, Thielen, BK, Daniel, J, Stanley, E, Hunter, RC, Menachery, VD, Shen, SS, Bold, TD, Langlois, RA. Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium. PLoS Pathog. 2021;17 (1):e1009292. doi: 10.1371/journal.ppat.1009292. PubMed PMID:33507952 PubMed Central PMC7872261.
  13. Fiege, JK, Thiede, JM, Nanda, H, Matchett, WE, Moore, PJ, Montanari, NR, Thielen, BK, Daniel, J, Stanley, E, Hunter, RC, Menachery, VD, Shen, SS, Bold, TD, Langlois, RA. Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium. bioRxiv. 2020; :. doi: 10.1101/2020.10.19.343954. PubMed PMID:33106802 PubMed Central PMC7587775.
  14. Prince, BT, Thielen, BK, Williams, KW, Kellner, ES, Arnold, DE, Cosme-Blanco, W, Redmond, MT, Hartog, NL, Chong, HJ, Holland, SM. Geographic Variability and Pathogen-Specific Considerations in the Diagnosis and Management of Chronic Granulomatous Disease. Pediatric Health Med Ther. 2020;11 :257-268. doi: 10.2147/PHMT.S254253. PubMed PMID:32801991 PubMed Central PMC7383027.
  15. Quadri, NS, Thielen, BK, Erayil, SE, Gulleen, EA, Krohn, K. Deploying Medical Students to Combat Misinformation During the COVID-19 Pandemic. Acad Pediatr. 2020;20 (6):762-763. doi: 10.1016/j.acap.2020.05.024. PubMed PMID:32502537 PubMed Central PMC7265844.
  16. Ingraham, NE, Lotfi-Emran, S, Thielen, BK, Techar, K, Morris, RS, Holtan, SG, Dudley, RA, Tignanelli, CJ. Immunomodulation in COVID-19. Lancet Respir Med. 2020;8 (6):544-546. doi: 10.1016/S2213-2600(20)30226-5. PubMed PMID:32380023 PubMed Central PMC7198187.
  17. Thielen, BK, Bye, E, Wang, X, Maroushek, S, Friedlander, H, Bistodeau, S, Christensen, J, Reisdorf, E, Shilts, MH, Martin, K, Como-Sabetti, K, Strain, AK, Ferrieri, P, Lynfield, R. Summer Outbreak of Severe RSV-B Disease, Minnesota, 2017 Associated with Emergence of a Genetically Distinct Viral Lineage. J Infect Dis. 2020;222 (2):288-297. doi: 10.1093/infdis/jiaa075. PubMed PMID:32083677 PubMed Central PMC7323494.
  18. Thielen, BK, Barnes, AMT, Sabin, AP, Huebner, B, Nelson, S, Wesenberg, E, Hansen, GT. Widespread Lichtheimia Infection in a Patient with Extensive Burns: Opportunities for Novel Antifungal Agents. Mycopathologia. 2019;184 (1):121-128. doi: 10.1007/s11046-018-0281-6. PubMed PMID:29967971 PubMed Central PMC6445638.
  19. Scott, LA, Dunlop, SJ, Walz, EJ, Wanduragala, DM, Thielen, BK, Smith, ML, Volkman, HR, Walker, PF, Stauffer, WM, Alpern, JD. Prescription drug-dispensing limits in the USA-implications for malaria chemoprophylaxis among VFR travellers. J Travel Med. 2018;25 (1):. doi: 10.1093/jtm/tay039. PubMed PMID:29893891 PubMed Central PMC6676974.
  20. Thielen, BK, Friedlander, H, Bistodeau, S, Shu, B, Lynch, B, Martin, K, Bye, E, Como-Sabetti, K, Boxrud, D, Strain, AK, Chaves, SS, Steffens, A, Fowlkes, AL, Lindstrom, S, Lynfield, R. Detection of Influenza C Viruses Among Outpatients and Patients Hospitalized for Severe Acute Respiratory Infection, Minnesota, 2013-2016. Clin Infect Dis. 2018;66 (7):1092-1098. doi: 10.1093/cid/cix931. PubMed PMID:29069373 PubMed Central PMC5862734.
  21. Iroh Tam, PY, Thielen, BK, Obaro, SK, Brearley, AM, Kaizer, AM, Chu, H, Janoff, EN. Childhood pneumococcal disease in Africa - A systematic review and meta-analysis of incidence, serotype distribution, and antimicrobial susceptibility. Vaccine. 2017;35 (15):1817-1827. doi: 10.1016/j.vaccine.2017.02.045. PubMed PMID:28284682 PubMed Central PMC5404696.
  22. Thielen, BK, McNevin, JP, McElrath, MJ, Hunt, BV, Klein, KC, Lingappa, JR. Innate immune signaling induces high levels of TC-specific deaminase activity in primary monocyte-derived cells through expression of APOBEC3A isoforms. J Biol Chem. 2010;285 (36):27753-66. doi: 10.1074/jbc.M110.102822. PubMed PMID:20615867 PubMed Central PMC2934643.
  23. Lingappa, JR, Thielen, BK. Assembly of immature HIV-1 capsids using a cell-free system. Methods Mol Biol. 2009;485 :185-95. doi: 10.1007/978-1-59745-170-3_13. PubMed PMID:19020826 PubMed Central PMC2678559.
  24. Thielen, BK, Klein, KC, Walker, LW, Rieck, M, Buckner, JH, Tomblingson, GW, Lingappa, JR. T cells contain an RNase-insensitive inhibitor of APOBEC3G deaminase activity. PLoS Pathog. 2007;3 (9):1320-34. doi: 10.1371/journal.ppat.0030135. PubMed PMID:17892323 PubMed Central PMC1993843.
  25. Rheault, MN, Kren, SM, Thielen, BK, Mesa, HA, Crosson, JT, Thomas, W, Sado, Y, Kashtan, CE, Segal, Y. Mouse model of X-linked Alport syndrome. J Am Soc Nephrol. 2004;15 (6):1466-74. doi: 10.1097/01.asn.0000130562.90255.8f. PubMed PMID:15153557 .
  26. Thielen, BK, Barker, DF, Nelson, RD, Zhou, J, Kren, SM, Segal, Y. Deletion mapping in Alport syndrome and Alport syndrome-diffuse leiomyomatosis reveals potential mechanisms of visceral smooth muscle overgrowth. Hum Mutat. 2003;22 (5):419. doi: 10.1002/humu.9191. PubMed PMID:14517961 .

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Julia Dooher

Julia Dooher

Julia Dooher grew up in Melrose, MA and received her BS in Biology, Magna cum Laude, from Tufts University. As an undergraduate, she worked in the laboratory of Tom Gilmore at Boston University, and was a recipient of an NSF undergraduate summer research award and Lemelson Fellowship from Hampshire College. As a PhD student in the Lingappa Lab, Julia received an NSF graduate fellowship, an ARCS Foundation award, a UW Magnuson Scholarship, and the 2005 UW Pathobiology Dept. Outstanding Student Award. Julia was awarded her PhD in Pathobiology in December 2005.

After leaving the Lingappa lab, Julia pursued postdoctoral research in Alan Friedman’s lab at Johns Hopkins University (JHU) in Baltimore, MD.  In 2011, she was awarded a Christine Mirzayan Science & Technology Policy Fellowship from the Institute of Medicine at The National Academies.  In 2012, she was awarded an American Association for the Advancement of Science (AAAS) Science & Technology Policy Fellowship in Washington, DC, where she focused on biosecurity.  Julia is currently Senior Professional Staff at the Applied Biological Sciences Group in the Johns Hopkins University Applied Physics Lab.

Research:

While in the Lingappa lab, Julia spearheaded a number of new research directions.  She demonstrated that Gag polypeptides of diverse primate lentiviruses associate with ABCE1 in primate cells, even though these Gag proteins have limited sequence homology. Julia also used apyrase, an enzyme that hydrolyzes ATP, to trap elusive capsid assembly intermediates, allowing such intermediates to be isolated from cells for the first time (Dooher and Lingappa 2004).

Julia also used pulse-chase labeling approach to demonstrate that in primate cells HIV-1 Gag enters ABCE1-containing assembly intermediates within minutes after synthesis and exits the assembly pathway just before virus maturation and release begins. Julia’s pulse-chase studies of HIV-1 mutants suggest that when progression of Gag through ABCE1-containing assembly intermediates is slowed, virus release is also delayed; thus, viral-host interactions can affect overall virus production.  Along with Bobbie Schneider at the FHCRC Electron Microscopy lab, Julia piloted immunogold labeling electron microscopy double labeling techniques to demonstrate that ABCE1-containing assembly intermediates can be found at the plasma membrane (Dooher, Schneider, Reed and Lingappa 2007).  Subsequently, the Lingappa lab extended the immunoelectron microscopy techniques Julia initially developed to demonstrate that ABCE1-containing assembly intermediates are also present in the cytoplasm (Klein, Reed et al. 2011) and that assembly intermediates also contain the DEAD-box RNA helicase DDX6 and the Argonaute protein AGO2 (Reed et al. 2012).

At the end of her time in the Lingappa lab, Julia initiated a project in which she used Gag derived from a highly pathogenic HIV-2 isolate to demonstrate that polymorphisms in Gag that arise in vivo can lead to more rapid progression through the assembly pathway.

Publications:

  1. Dooher, JE, Paz-Priel, I, Houng, S, Baldwin, AS Jr, Friedman, AD. C/EBPα, C/EBPα oncoproteins, or C/EBPβ preferentially bind NF-κB p50 compared with p65, focusing therapeutic targeting on the C/EBP:p50 interaction. Mol Cancer Res. 2011;9 (10):1395-405. doi: 10.1158/1541-7786.MCR-11-0072. PubMed PMID:21813505 PubMed Central PMC3196798.
  2. Paz-Priel, I, Houng, S, Dooher, J, Friedman, AD. C/EBPα and C/EBPα oncoproteins regulate nfkb1 and displace histone deacetylases from NF-κB p50 homodimers to induce NF-κB target genes. Blood. 2011;117 (15):4085-94. doi: 10.1182/blood-2010-07-294470. PubMed PMID:21346255 PubMed Central PMC3087533.
  3. Dooher, JE, Schneider, BL, Reed, JC, Lingappa, JR. Host ABCE1 is at plasma membrane HIV assembly sites and its dissociation from Gag is linked to subsequent events of virus production. Traffic. 2007;8 (3):195-211. doi: 10.1111/j.1600-0854.2006.00524.x. PubMed PMID:17233757 PubMed Central PMC1865004.
  4. Lingappa, JR, Dooher, JE, Newman, MA, Kiser, PK, Klein, KC. Basic residues in the nucleocapsid domain of Gag are required for interaction of HIV-1 gag with ABCE1 (HP68), a cellular protein important for HIV-1 capsid assembly. J Biol Chem. 2006;281 (7):3773-84. doi: 10.1074/jbc.M507255200. PubMed PMID:16275648 .
  5. Lingappa, JR, Newman, MA, Klein, KC, Dooher, JE. Comparing capsid assembly of primate lentiviruses and hepatitis B virus using cell-free systems. Virology. 2005;333 (1):114-23. doi: 10.1016/j.virol.2004.12.024. PubMed PMID:15708597 .
  6. Dooher, JE, Lingappa, JR. Cell-free systems for capsid assembly of primate lentiviruses from three different lineages. J Med Primatol. 2004;33 (5-6):272-80. doi: 10.1111/j.1600-0684.2004.00075.x. PubMed PMID:15525328 .
  7. Dooher, JE, Pineda, MJ, Overbaugh, J, Lingappa, JR. Characterization of virus infectivity and cell-free capsid assembly of SIVMneCL8. J Med Primatol. 2004;33 (5-6):262-71. doi: 10.1111/j.1600-0684.2004.00074.x. PubMed PMID:15525327 .
  8. Dooher, JE, Lingappa, JR. Conservation of a stepwise, energy-sensitive pathway involving HP68 for assembly of primate lentivirus capsids in cells. J Virol. 2004;78 (4):1645-56. doi: 10.1128/jvi.78.4.1645-1656.2004. PubMed PMID:14747530 PubMed Central PMC369511.
  9. Barkett, M, Dooher, JE, Lemonnier, L, Simmons, L, Scarpati, JN, Wang, Y, Gilmore, TD. Three mutations in v-Rel render it resistant to cleavage by cell-death protease caspase-3. Biochim Biophys Acta. 2001;1526 (1):25-36. doi: 10.1016/s0304-4165(01)00092-7. PubMed PMID:11287119 .
  10. Wang, Y, Dooher, JE, Koedood Zhao, M, Gilmore, TD. Characterization of mouse Trip6: a putative intracellular signaling protein. Gene. 1999;234 (2):403-9. doi: 10.1016/s0378-1119(99)00168-7. PubMed PMID:10395914 .

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