Courses I teach:

SC111 - Foundations of Chemistry I

SC112 - Foundations of Chemistry II

SC335 - Biochemistry I

SC486C - Molecular Virology

SB251 - Fundamentals of Biology I

SC491/495/496 - 1-3 credit Chemistry Research Project

Research Interests

My students and I employ various molecular biology, biochemical, and biophysical methods to understand the biochemistry of retroviruses such as HIV-1 and the human endogenous retrovirus type K (HERV-K).  Retroviruses have an RNA genome which is converted to DNA and subsequently integrated into the genome of the infected cell. Camouflaging as a host gene, the retroviral genome is then replicated by the host cell’s transcriptional machinery. I am particularly interested in understanding how the newly synthesized, unspliced retroviral RNA genome is exported from the nucleus to the cytoplasm. In HIV-1, this step is carried by the Rev protein which specificially binds to the RRE region on the genomic RNA. This step is essential in retroviral replication and, thus, an ideal target for the development of novel therapeutics. 

Human endogenous retroviruses (HERVs) refer to sequences of viral origin that comprise ~8% of our genome. When retroviruses infect germ cells, the integrated viral DNA is passed on in a Mendelian manner; it becomes endogenized. Most of these sequences have accumulated inactivating mutations but some, such as HERV-K, are actively expressed. HERV-K and HIV-1 exhibit some similarities such as the use of homologous protein and RNA pairs (Rev/RRE and Rec/RcRE) to export unspliced genomic RNA. I am interested in characterizing the Rec protein and understanding the biochemistry of the HERV-K Rec/RcRE interactions. 

My Publications

1. O’Carroll IP and Rein A. 2022. Viral nucleic acids. Online Encyclopedia of Cell Biology, 2nd Edition.
2. Mikhalkevich N, O’Carroll IP, Tkavc R, Lund K, Sukumar G; Dalgard CL, Johnson KR, Li W, Wang T, Nath A and Iordanskiy S. 2021. Macrophage response to gamma radiation is mediated via human endogenous retrovirus-K expression. PLOS Pathogens. 17(2):e1009305
3. O’Carroll IP^&, Fan L, Kroupa T, McShane EK*, Theodore C*, Yates EA, Kondrup K*, Ding J, Martin TS*, Rein A, and Wang Y-X. 2020. Structural mimicry drives HIV Rev-mediated HERV-K expression. Journal of Molecular Biology. 432(24):166711.          *Undergraduate student, ^&Corresponding author.
4. O’Carroll IP, Buck M, Durkin P, and W.S. Farrell. 2020. With anchors aweigh, synchronous instruction is preferred by Naval Academy instructors in small undergraduate chemistry courses. Journal of Chemical Education. 97 (9), 2383-2388. 
5. O’Carroll IP, Thappeta Y, Fan L, Valdez-Ramirez E, Smith S*, Wang Y-X, and Rein A. 2017. Contributions of individual domains to function of the HIV-1 Rev response element. Journal of Virology. Vol. 91, Issue 21, e00746-17. This article was one of Editor’s 4 picks. *Undergraduate student
6. O’Carroll IP and Rein A. 2015. Viral nucleic acids. Online Encyclopedia of Cell Biology.
7. Fang X*, Wang J*, O’Carroll IP*, Mitchell M, Zuo X, Wang Y, Yu P, Rausch JW, Dyba MA, Kjems J, Schwieters CD, Seifert S, Winans R, Watts N, Stahl S, Wingfield P, Byrd RA, LeGrice S, Rein A, Wang Y-X. 2013. A unique topological structure of the HIV-1 Rev response element. Cell, 155(3):594-605.   *Equal contribution by author. 
8. O’Carroll IP, Crist RM, Mirro J, Harvin D, Soheilian F, Kamata A, Nagashima K, and Rein A. 2013. Elements in HIV-1 Gag contributing to virus particle assembly. Virus Research. 171:341-345. 
9. O’Carroll IP, Crist RM, Mirro J, Harvin D, Soheilian F, Kamata A, Nagashima K, and Rein A. 2012. Functional Redundancy in HIV-1 Assembly. Journal of Virology. 86(23):12991-6. 
10. O’Carroll IP and Dos Santos PC.   2011. Genomic analysis of nitrogen fixation.  Methods Mol. Biol. 766:49-65. 
11. Setubal JC, dos Santos P, Goldman BS, Ertesvåg H, Espin G, Rubio LM, Valla S, Almeida NF, Balasubramanian D, Cromes L, Curatti L, Du Z, Godsy E, Goodner B, Hellner-Burris K, Hernandez JA, Houmiel K, Imperial J, Kennedy C, Larson TJ, Latreille P, Ligon LS, Lu J, Maerk M, Miller NM, Norton S, O'Carroll IP, Paulsen I, Raulfs EC, Roemer R, Rosser J, Segura D, Slater S, Stricklin SL, Studholme DJ, Sun J, Viana CJ, Wallin E, Wang B, Wheeler C, Zhu H, Dean DR, Dixon R, and Wood D. 2009. Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. J. Bacteriol. 191(14):4534-45. 
12. Raulfs EC*, O’Carroll IP*, Dos Santos PC, Unciuleac M-C, and Dean DR. In vivo iron-sulfur cluster formation. 2008. Natl. Acad. Sci. USA. 105(25):8591-8596.  *Equal contribution by authors. 
13. Bandyopadhyay S, Naik SG, O’Carroll IP, Huynh B-H, Dean DR, Johnson MK, and Dos Santos PC. 2008. A proposed role for the Azotobacter vinelandii NfuA protein as an intermediate iron-sulfur cluster carrier. Biol. Chem. 283(20):14092-14099. 
14. Smith MB, Ruby S, Horouzhenko S, Buckingham B, Richardson J, Puleri I, Potts E, Jorgensen WL, Arnold E, Zhang W, Hughes SH, Michejda CJ, and Smith RH Jr. 2003. HIV-1 reverse transcriptase variants: molecular modeling of Y181C, V106A, L100I, and K103N mutations with non-nucleoside inhibitors using Monte Carlo simulations in combination with a linear response method. Drug Design Discov. 18(4):151-63.