Difference between revisions of "User:Elyons"

From CoGepedia
Jump to: navigation, search
(→‎2010-2011 Senior Scientific Developer, iPlant Collaborative)
 
(16 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
Eric Lyons, Ph.D
 
Eric Lyons, Ph.D
 +
 +
  
 
=Professionsal Biography=
 
=Professionsal Biography=
 
==Education:==
 
==Education:==
−
===Undergraduate:=== 
+
===Undergraduate UC Berkeley, Molecular and Cell Biology, Immunology (1993-1997):=== 
−
1997  UC Berkeley, Molecular and Cell Biology, Immunology
+
*Advisers:  Loy Volkman, Jan Washburn, and Eric Haas-Stapleton
 +
# Characterizing the effects on pathogenicity of multiple genome copies in an insect virus. [[Undergrad Research Summary]]
  
−
Three years of research with Loy Volkman, Jan Washburn, and Eric Haas-Stapleton studying host-pathogen relationships between a virus (baculovirus [http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?oid=27625 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.
+
===Masters UC Berkeley, Microbial Biology (1997-1999):===
−
 
+
*Advisers: Norm Pace and Brian Thomas
−
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.
+
*Two years of research focusing on two projects:
−
 
+
−
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:  [http://jvi.asm.org/cgi/content/full/73/1/411 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:===
+
−
1999 UC Berkeley  Microbial Biology
+
−
 
+
−
Two years of research with Norm Pace and Brian Thomas 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.
 
#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.
 
#Characterization of the microbial diversity of cerumen through 16S and 18S ribsomal gene sequences.
  
−
===PhD:===
+
===Internship  Molcular Sciences Institute, Computational Biology (2000-2001):===
−
2008 UC Berkeley Plant 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
  
−
Three years of research with Michael Freeling focusing on:
+
===PhD  UC Berkeley, Plant Biology (2006-2008):===
 +
*Adviser:  Michael Freeling
 +
Three years of research focusing on:
 
*Designing and building [[CoGe]]:  A new kind of comparative genomics platform
 
*Designing and building [[CoGe]]:  A new kind of comparative genomics platform
 
*Studying plant genome evolution
 
*Studying plant genome evolution
 +
 +
===Postdoc 2009 UC Berkeley, Plant Bioloby:===
 +
*Adviser:  Michael Freeling and Sydney Kustu
 +
*Extending CoGe beyond plant genomes.
 +
*Analyzing the genomes of eight strains of E. coli
 +
 +
  
 
==Work Experience==
 
==Work Experience==
−
===2000-2001 Molcular Sciences Institute, Computational Biology===
+
 
−
#Designed computational systems for systems biology
+
−
##Stochastirator:  program for simulation intracellular biomolecular reaction networks using a stochastic mathematical framework
+
 
===2001  Genencore International, Bioinformatics===
 
===2001  Genencore International, Bioinformatics===
−
#Genome assembly and annotation of fungal genomes
+
# Genome assembly and annotation of fungal genomes
−
#Identification and characterization of metaloproteases from the human genome
+
# 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
+
===2002-2003  Berlex Biosciences, Computational Biologist===
−
===2004 Biotique Systems Senior Scientific Developer===
+
# Expression data analysis of human clinical samples, cell culture samples, and animal models for drug target identification
−
#Designed system for visualizing pathway and expression data
+
 
−
===2005 UC Berkeley Programmer/Data Analyst III===
+
===2004 Biotique Systems, Senior Scientific Developer===
−
#Freeling lab.  Plant comparative genomics.
+
# Designed system for visualizing pathway and expression data
 +
 
 +
===2005 UC Berkeley, Programmer/Data Analyst III===
 +
# Freeling lab.  Plant comparative genomics.
 +
 
 +
===2010-2011 Senior Scientific Developer, iPlant Collaborative, University of Arizona (Tucson)===
 +
# Assisted the Director, Steve Goff, with day to day operations of the project.
 +
# Maintained CoGe on the weekends and evennings
 +
# Leveraged iPlant Cyberinfrastructure to scale CoGe (data storage, computation, user identity management)
 +
 
 +
===2012 Assistant Professor, School of Plant Sciences, University of Arizona (Tuson)===
 +
# Develop and fund a research program studying the structure, dynamics, and evolution of genomes
 +
# Continue to develop CoGe to answer above questions

Latest revision as of 17:18, 13 July 2012

Eric Lyons, Ph.D


Professionsal Biography

Education:

Undergraduate UC Berkeley, Molecular and Cell Biology, Immunology (1993-1997):

  • Advisers: Loy Volkman, Jan Washburn, and Eric Haas-Stapleton
  1. Characterizing the effects on pathogenicity of multiple genome copies in an insect virus. Undergrad Research Summary

Masters UC Berkeley, Microbial Biology (1997-1999):

  • Advisers: Norm Pace and Brian Thomas
  • Two years of research focusing on two projects:
  1. 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.
  2. Characterization of the microbial diversity of cerumen through 16S and 18S ribsomal gene sequences.

Internship Molcular Sciences Institute, Computational Biology (2000-2001):

  • 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 UC Berkeley, Plant Biology (2006-2008):

  • Adviser: Michael Freeling

Three years of research focusing on:

  • Designing and building CoGe: A new kind of comparative genomics platform
  • Studying plant genome evolution

Postdoc 2009 UC Berkeley, Plant Bioloby:

  • Adviser: Michael Freeling and Sydney Kustu
  • Extending CoGe beyond plant genomes.
  • Analyzing the genomes of eight strains of E. coli


Work Experience

2001 Genencore International, Bioinformatics

  1. Genome assembly and annotation of fungal genomes
  2. Identification and characterization of metaloproteases from the human genome

2002-2003 Berlex Biosciences, Computational Biologist

  1. Expression data analysis of human clinical samples, cell culture samples, and animal models for drug target identification

2004 Biotique Systems, Senior Scientific Developer

  1. Designed system for visualizing pathway and expression data

2005 UC Berkeley, Programmer/Data Analyst III

  1. Freeling lab. Plant comparative genomics.

2010-2011 Senior Scientific Developer, iPlant Collaborative, University of Arizona (Tucson)

  1. Assisted the Director, Steve Goff, with day to day operations of the project.
  2. Maintained CoGe on the weekends and evennings
  3. Leveraged iPlant Cyberinfrastructure to scale CoGe (data storage, computation, user identity management)

2012 Assistant Professor, School of Plant Sciences, University of Arizona (Tuson)

  1. Develop and fund a research program studying the structure, dynamics, and evolution of genomes
  2. Continue to develop CoGe to answer above questions
Retrieved from "https://genomevolution.org/wiki/index.php?title=User:Elyons&oldid=5129"