User:Elyons
Eric Lyons, Ph.D
Contents
Professionsal Biography
Education:
Undergraduate 1993-1997 UC Berkeley, Molecular and Cell Biology, Immunology:
- Advisers: Loy Volkman, Jan Washburn, and Eric Haas-Stapleton
Three years of research studying host-pathogen relationships between a virus (baculovirus AcMNPV (Autographa californica nucleopolyhedrovirus)) and its lepidopteran (caterpillar) hosts helicoverpa zea (corn earworm), trichoplusia ni (cabbage looper), heliothis virescens (tobacco budworm). AcMNPV is double stranded DNA virus, and as such, has a relatively large genome (133kb) and contains ~150 genes. Its pathogenesis in susceptible hosts is very interesting as it will infect nearly all of the host tissues, convert ~30% of the host's biomass to viral progeny, and cause the host to liquify into a puddle of virus laden goo. Interesting, hosts in late stages of infection will exert a virus controlled climbing behavior, and start climbing up as high as they can before succumbing to the final stage of infection: liquefaction and release of viral progeny. This may serve the virus and help in its dispersion, or it may help other caterpillars by making infected caterpillars more likely to be eaten by larger predators, birds. In either case, this highlights the incredible biological interactions between hosts and pathogens.
My research in the lab focused on a peculiar aspect of baculoviruses. To spread from host to host, the virus has a specific form called occlusion derived virions (ODV) where the virions are packaged in a protective protein complex (occlusions) in order to survive in the environment (which for a virus is a harsh, cold, dry, high UV light exposure world). Some baculoviruses' ODV contain a single copy of their genome, and some contain multiple copies of their genome. This trait is part of the biology of baculoviruses and is what the "M" (multiple) strands for in AcMNPV.
To become infected, a caterpillar eats virus occlusions on the surface of a plant. When the occlusions pass into the gut of the insect, the high pH (caterpillar guts are basic rather than acidic) causes the protective occlusions to break apart and release ODV. These ODV can then infect gut cells and establish a primary site of infection. Next, the virus moves from these infected gut cells into neighboring tracheal cells (insects' respiratory system is different than humans'). Once these cells are infected in a susceptible host, the infection will become systemic and the virus has won.
The question I was after was why would a virus spend the resource to package multiple copies of its genome in a single infectious particle? An infected cell is an infected cell, regardless if 1 or 10 viral genomes were released during the initial phase of infection. It turns out that in order to establish a systemic infection in its host, the virus was under very strong time-sensitive selection to move from its primary cell of infection (gut cells), to a secondary cell of infection (tracheal cells). If it doesn't make it to the secondary cell fast enough, the primary cell would be eliminated by the caterpillar and the infection lost. The gut cells of many caterpillars get sloughed off in a regular fashion when the insect molts, and eliminated out the back end. By packaging multiple copies of its genome in a single virion, and thus infecting a cell with more than one copy of its genome, the virus can bypass the relatively time-consuming step of replicating its genome. Instead, one of the viral genomes can migrate to the nucleus, take over cellular transcription and translation, and immediately make the proteins necessary to package genomes for cell-to-cell movement (known as budded virus). The other genomes can "wait" in the cytoplasm for these proteins to be synthesized, and appropriately assembled or integrated into the cell's plasma membrane. When ready, these genomes can then be used to make budded virus, infect the secondary site of infection, and go systemic.
My first genome biology paper: Washburn, J. O., Lyons, E. H., Haas-Stapleton, E. J., Volkman, L. E. (1999). Multiple Nucleocapsid Packaging of Autographa californica Nucleopolyhedrovirus Accelerates the Onset of Systemic Infection in Trichoplusia ni. J. Virol. 73: 411-416
Masters 1997-1999 UC Berkeley, Microbial Biology:
- Advisers: Norm Pace and Brian Thomas
- Two years of research focusing on two projects:
- Biochemistry of the catalytic RNA subunit of Ribonuclease P (RNase P), the riboprotein responsible for maturing precursor tRNAs by clearving off a 5' leader sequence.
- Characterization of the microbial diversity of cerumen through 16S and 18S ribsomal gene sequences.
Internship 2000-2001 Molcular Sciences Institute, Computational Biology
- Advisors: Drew Endy and Roger Brent
Designed computational systems for systems biology. Main project was the Stochastirator: a program for simulating intracellular biomolecular reaction networks using a stochastic mathematical framework
PhD 2006-2008 UC Berkeley, Plant Biology:
- Adviser: Michael Freeling
Three years of research focusing on:
- Designing and building CoGe: A new kind of comparative genomics platform
- Studying plant genome evolution
Work Experience
2001 Genencore International, Bioinformatics
- Genome assembly and annotation of fungal genomes
- Identification and characterization of metaloproteases from the human genome
2002-2003 Berlex Biosciences, Computational Biologist
- Expression data analysis of human clinical samples, cell culture samples, and animal models for drug target identification
2004 Biotique Systems, Senior Scientific Developer
- Designed system for visualizing pathway and expression data
2005 UC Berkeley, Programmer/Data Analyst III
- Freeling lab. Plant comparative genomics.
Teaching and Educational Outreach
- 1999 Teaching Assistant, UC Berkeley Microbial Biology
- 2002 Mentor for High School Interns, The Molecular Sciences Institute
- 2004-2006 Medical Virology Co-Instructure, UC Berkeley Extension
- 2005-2006 Adviser for Masters Program in Bioinformatics, Amarita Vishwa Vidyapeetham School of Applied Science, Centre For Biotechnology, Kerala India
- 2005-2008 Perl Programming Workshops (8 weeks), UC Berkeley
- Undergraduate Research Advisor UC Berkeley 2005-present
- 2006-present Comparative Genomics Workshops (day long), UC Berkeley
- 2007 Scientific Reviewer High-school Genetics UC Berkeley Lawrence Hall of Science
- 2009 Comparative Genomics Workshop (day long), Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University
- 2010 Comparative Genomics Workshop (day long), Annual meeting for the Socienty of Invertebrate Pathology