Dr. Jason Dionisio Fernandes

  • Postdoctoral Researcher, Haussler Wet Lab
  • Genomics Institute
  • 831-459-1014 (Lab)
  • Biomed 455
  • CBSE
  • My primary research interests involve exploring the “molecular details” of evolution. Specifically, I am interested in how particular nucleotide and amino acid changes influence complex phenotypic traits that affect organismal fitness. As a graduate student, I examined how overlapped genes - in which genes share share the same DNA yet encode different proteins via the use of alternative reading frames - balance selective forces. This phenomena is especially common in viruses. My work found, that, contrary to expectations, overlapped genes in HIV can “segregate” along the DNA, such that protein functional motifs alternate and do not overlap. This organization minimizes much of the expected evolutionary constraint. Furthermore, I found that the overlap has evolved in such a way that overall viral fitness is increased by overlapping genes as this “segregated” organization prevents unfit combinations of the genes that would be possible if the genes were encoded separately. This work shed light on how viruses evolve and adapt, which is essential knowledge for rational therapeutic design. As a postdoctoral fellow, my research builds on my doctoral experience with viruses and evolution to explore the role of endogenous retroviruses in human-specific evolution. My work suggests a specific molecular mechanism by which viruses which infected our ancestors long ago and became part of the human genome have been repurposed to modulate biological pathways in a primate-specific manner. I am currently investigating a specific instance of this repurposing in the process of cellular reprogramming, and this work has broad implications for human development, evolution, and disease states.
  • B.S. in Chemical Engineering, Columbia University
  • Ph.D. in Pharmaceutical Science and Pharmacogenomics, UCSF

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