Dissertation Research
The emergence of new genes has been primarily attributed to the re-organization of existing genetic material by processes like gene duplication, horizontal gene transfer, and gene fusion/fission. The possibility of genes arising de novo from previously non-genic regions has been considered extremely unlikely. Despite this notion, genomes of all sequenced organisms contain genes that share no detectable homology to genes in other species. The proto-gene model of de novo gene birth provides one possible mechanism through which these genes might have arisen. This model formalizes an evolutionary continuum from non-genic sequences to proto-genes to genes. It is hypothesized that proto-genes provide the organism with a transient pool of novel sequences to sample from, of which those that lead to an adaptive advantage are retained by natural selection to become de novo genes.
For my dissertation research, I intend to examine the extent and nature of proto-gene adaptiveness systematically. I will: 1) develop a framework that can observe adaptive phenotypes in a high-throughput setup reliably; 2) identify adaptive proto-genes and investigate the source of their phenotypic impact; and 3) examine how adaptive proto-genes associate with the rest of the genome.
Dissertation Mentor
Education & Training
- M.B., B.S.-Smt. NHL Municipal Medical College, Gujarat University, Ahmedabad, Gujarat, India
- M.S.Bioengineering-Swanson School of Engineering, University of Pittsburgh
Research Categories
Representative Publications
Parikh, S.B., Houghton, C., Branden Van Oss, S., Wacholder, A. and Carvunis, A.-R. (2022). Origins, evolution, and physiological implications of de novo genes in yeast. Yeast. https://doi.org/10.1002/yea.3810.
Parikh, S. B.*, Van Oss, S. B.*, Castilho Coelho, N.*, Wacholder, A., Belashov, I., Zdancewicz, S., Michaca, M., Xu, J., Kang, Y. P., Ward, N. P., Yoon, S. J., McCourt, K. M., McKee, J., Ideker, T., VanDemark, A. P., DeNicola, G. M., & Carvunis, A.-R. (2022). On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur thanks to the previously uncharacterized homocysteine synthase Yll058w. The Journal of Biological Chemistry, 298(12), 102697. https://doi.org/10.1016/j.jbc.2022.102697
*these authors contributed equally
Saurin Bipin Parikh, Nelson Castilho Coelho, Anne-Ruxandra Carvunis, LI Detector: A framework for sensitive colony-based screens regardless of the distribution of fitness effects, G3 Genes|Genomes|Genetics, Volume 11, Issue 2, February 2021, jkaa068,
C. Widdowson, J. Ganhotra, M. Faizal, M.Wilko, S. Parikh, Z. Adhami, and M.E. Hernandez. Virtual reality applications in assessing the effect of anxiety on sensorimotor integration in human postural control 2016. 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Orlando, FL. 2016. pp. 33-36. doi: 10.1109/EMBC.2016.7590633
Vakirlis, N., Acar, O., Hsu, B., Castilho Coelho, N., Van Oss, S. B., Wacholder, A., Medetgul-Ernar, K., Bowman, R. W., 2nd, Hines, C. P., Iannotta, J., Parikh, S. B., McLysaght, A., Camacho, C. J., O’Donnell, A. F., Ideker, T., & Carvunis, A. R. (2020). De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nature Communications, 11(1), 781. https://doi.org/10.1038/s41467-020-14500-z