*Applications will be reviewed on a rolling-basis.
A research opportunity is currently available in the Office of Tissues and Advanced Therapies (OTAT) at the Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA) in Silver Spring, Maryland.
The selected participant will join a research program that examines in silico the adaptation of viruses to hosts and host tissues based on codon usage and tRNA abundance. The codon, codon pair and dinucleotide usage of viral families will be explored in the context of host and tissue tropism, particularly with respect to host and tissue codon usage / tRNA expression. Using data calculated from GTEx RNA-Seq datasets, the participant will generate a database of computationally derived human tissue-specific tRNA abundance. Findings from this investigation will be combined with viral sequence analysis to examine viral fitness and adaptation to human tissues that they infect. Additional data sources will be identified to examine viral codon adaptability in alternate hosts with different tRNA repertoires.
Learning objectives for the participant:
- Possible mechanisms for codon adaptation
- Understanding variability in tRNA availability
- Method development for viral attenuation
The following examples of articles published since 2020 provide examples of the range of work performed in our group; note that a previous ORISE participant is part of several publications:
- Kames J., Holcomb D.D., Alexaki A., Santana-Quintero L., Athey J.C., Hamasaki-Katagiri N., Katneni U., Golikov A., Ibla J.C., Haim B., and Kimchi-Sarfaty C.: TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression. JMB. 2020. https://doi.org/10.1093/oxfordjournals.molbev.a004201
- Kames J., Holcomb D.D., Kimchi O., DiCuccio M., Hamasaki-Katagiri N., Wang T., Komar A.A., Alexaki A., Kimchi-Sarfaty C.: Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design. Scientific Reports. https://doi.org/10.1038/s41598-020-72533-2.
- Katneni U.K., Holcomb, D.D., Hernandez N.E., Hamasaki-Katagiri N., Hunt, R.C., Bar H, Ibla J. and Kimchi-Sarfaty C. 2020. In silico features of ADAMTS13 contributing to plasmatic ADAMTS13 levels in neonates with congenital heart disease. Thrombosis Res. 193:66-76, 2020.
- Katneni K., Alexaki A., Hunt R., Schiller T., DiCuccio M., Buehler P.W., Ibla J.C., and Kimchi-Sarfaty C.: Consumptive Coagulopathy and Thrombosis during Severe COVID-19 Infection: Potential Involvement of VWF/ADAMTS13. https://doi.org/10.1055/s-0040-1715841. Thrombosis and Hemostasis 2020.
- Holcomb D., Alexaki A., Hernandez N., Laurie K., Kames J., Hamasaki-Katagiri N., Komar A.A., DiCuccio M., and Kimchi-Sarfaty C.: Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. PLOS Computational Biology 17(3): e1008805. 2021
- Holcomb D., Hamasaki-Katagiri N., Laurie Kyle, Katneni U., Hernandez N., Kames J., Alexaki A., Bar H. and Kimchi-Sarfaty C.: New approaches to predict the effect of co-occurring variants on protein characteristics. Submitted. 2021
Anticipated Appointment Start Date: September 2021; start date is flexible
This program, administered by ORAU through its contract with the U.S. Department of Energy to manage the Oak Ridge Institute for Science and Education, was established through an interagency agreement between DOE and FDA. The initial appointment is for one year, but may be renewed upon recommendation of FDA contingent on the availability of funds. The participant will receive a monthly stipend commensurate with educational level and experience. Proof of health insurance is required for participation in this program. The appointment is full-time at FDA in the Silver Spring, Maryland, area. Participants do not become employees of FDA, DOE or the program administrator, and there are no employment-related benefits.
If you have questions, send an email to ORISE.FDA.CBER@orau.org. Please include the reference code for this opportunity in your email.