Dr. Michael Sanderson
Program Director
sanderm@email.arizona.edu

Pennie Liebig
Program Coordinator
genomics@email.arizona.edu

IGERT Program in Genomics
University of Arizona
Biosciences West. 328
1041 E. Lowell Street
Tucson, AZ 85721-0088
Tel: 520-626-0988
Fax: 520-621-9190




IGERT Recruitment Program

IGERT.org


IGERT PROGRAM IN GENOMICS FELLOWS


2009-2010 Cohort

David Andrew
Neuroscience

B.A. Neuroscience and Biology, Oberlin College, 2004

I'm interested in the evolution of nervous systems, in particular how adaptation and environmental forces have shaped neural systems and how nervous systems have contributed to the success of various taxa. I use arthropods as my study system as they provide a wealth of anatomical, behavioral, ecological, and taxonomic diversity unparalleled in the animal kingdom. I approach the topic of neural evolution via two avenues: molecular phylogenetics and comparative morphological studies. It is imperative, when comparing taxa on morphological ground, to have robust phylogenies on which to map anatomical characters. I have therefore built a computational pipeline for phylogenetics that utilizes publicly available expressed sequence tags (ESTs). I compare the results of these extensive analyses to phylogenies derived from neuromorphological data in order to infer principles of nervous system evolution in arthropods.

David graduated in May 2013 and is currently a post-doc at The University of Arizona.



Crystal Brillhart
Microbiology and Pathobiology

B.S. Zoology, Arizona State University, 2001

My research employs a combination of traditional culture techniques as well as genomics-based molecular applications to explore Salmonella infection in oysters and the subsequent risk to consumers of raw oysters. I performed a year-long survey of oysters served on the half-shell in local restaurants, testing the oysters for Salmonella. I serotyped and conducted pulsed-field gel electrophoresis on Salmonella isolates recovered out of the oysters. My study, along with a 2002 survey performed in our laboratory, showed that one particular PFGE pattern of an MDR-AmpC S. Newport predominates in oyster infections. This strain was sequenced using 454 technology and I performed analysis on the sequence including contig assembly and comparison to a reference sequence. To explore its infections in oysters, I created a transposon library in this strain of S. Newport and designed custom microarrays that tiled the entire genome of S. Newport across the microarray. I used the library to conduct Transposon Site Hybridization (TraSH) experiments whereby the microarrays are used in a whole genomics approach to determine which genes are necessary for Salmonella survival in the oyster.

Crystal graduated in May 2011 and is currently a Biological Science Laboratory Technician at the USDA.

Christopher Brownlee
Cell Biology and Anatomy

B.S. General Biology, University of Arizona, 2006

Our lab is using a functional genomics approach in combination with RNAi to silence every Drosophila gene in order to identify genes responsible for the biogenesis of centrosomes; organelles that generate and organize the cell's microtubule cytoskeleton. My project in particular involves characterizing a balance of phosphatase and kinase activities that directly regulates the activity of Polo-like kinase 4 -- a conserved key licensing factor for centrosome assembly. Since cancer cells frequently exhibit centrosome overproduction (or amplification), which in turn promotes chromosomal instability and tumorigenesis, my project will also entail extending our findings to human cancer cells and mining bioinformatic data, such as microarrays and genomes of cancerous cells. Finally, I am currently applying my findings from Drosophila to explain the mechanism by which tumor-causing viruses such as Simian virus 40 promote centrosome amplification.

Patrick Degnan
Ecology and Evolutionary Biology

Postdoctoral Associate, Ecology & Evolutionary Bio., Yale Univ., 2010-Present Ph.D. Ecology & Evolutionary Biology, University of Arizona, 2009
B.S. Biology, Providence College, 2001

Intracellular symbioses between bacteria and insects are numerous, and alter the ecology and evolution of host and symbiont alike. I studied the endosymbiont Hamiltonella defensa, which is not essential for growth or survival of healthy aphids, but protects aphids from attack by parasitoid wasps. During my thesis, I used a variety of sequenced-based techniques to illuminate the population and genome dynamics of H. defensa and to disentangle how these factors contribute to its ability to persist and protect its hosts. In particular, I found that both the presence of a bacteriophage (APSE) and the content of its encoded virulence cassette play crucial roles in modulating the protective phenotype.  I also sequenced the genomes of H. defensa and its sister taxon Regiella insecticola and discovered that they exhibit a streamlined metabolism, but are littered with mobile DNA and putative virulence factors. It was clear that horizontal gene transfer, recombination and rearrangements are common, and phage and plasmids play an important role in resorting genes. Thus, although H. defensa and R. insecticola can protect their hosts from ecological stressors, their facultative lifestyles have resulted in a pattern of genome evolution associated with reproductive parasites rather than long-term mutualists.

Patrick graduated in December 2009 and is currently an Assistant Professor at the University of Illinois.

Robert (Bob) Fitak
Genetics

B.S. Molecular Genetics, Ohio State University, 2006

I am applying genomic tools and next-generation sequencing to the field of conservation genetics. Conservation geneticists can benefit from genomics to better manage the accrued detrimental variation and lost adaptive variation associated with endangered wildlife. I am currently working on two projects. First, in pumas, I am using 454 pyrosequencing of expressed genes to identify SNPs. I will use the SNP genotypes to address several conservation and ecological concerns. Initially, I will use the SNPs to identify suspected adaptive loci associated with their population expansion in North America, then we will identify the origin and migration pattern of puma populations to improve corridor design in the Southwest. Second, I am examining the genetic effects of the Mexican wolf's unique history (extirpated in 1980, reintroduced in 1998) using a 22k SNP chip developed for the domestic dog. I will quantify the ancestry of Mexican wolves from different captive lineages, dogs, and coyotes, in addition to identifying genes fixed by inbreeding which has plagued the population.



Parris Humphrey
Ecology and Evolutionary Biology

B.A. Biology; Science Technology & Society (STS), Bard College, 2006

I study how and to what extent organisms are environmentally specialized, be they parasites to a hosts, bacteria to a carbon source, or plants to a microhabitat. I use a comparative framework to discover lifestyle changes along lineages and investigate the evolutionary genetics and genomic consequences of phenotypic differentiation. At present I can be found studying the evolution of herbivory in a derived Drosophilid fly lineage (Scaptomyza spp.) that has specialized on wild mustard plants (Cardamine spp.). I also examine this interaction against the backdrop of co-occurring antagonists, including pathogenic bacteria that attack the plant and parasitoid wasps that attack the flies. I am also interested in evolutionary patterns of genomic variation across Bacteria and how both neutral and adaptive processes shape gene repertoires within genomes.

Bonnie Hurwitz
Ecology and Evolutionary Biology

B.S. Biochemistry & Molecular Bio., University of California Santa Cruz, 1996

Viruses are ubiquitous in nature and play an integral role in the lifecycle, development and evolution of their diverse hosts. In the ocean, viruses can harm and help their hosts in numerous ways. For example, phage, viruses that infect bacteria, can limit the population size of their hosts and as a result influence carbon and nutrient cycles, or alternatively can transmit genes to the host that confer new function thereby accelerating the host’s evolution and adaptation in a given environment. My interdisciplinary research on ocean viruses incorporates ecology and evolutionary biology, statistics, and bioinformatics to better understand their (i) distribution, diversity and function; (ii) interaction with host species; and (iii) affect on ecosystem function. I am particularly interested in applying large-scale informatics to problems in metagenomics and developing new methodologies to analyze these massive and highly contextualized datasets.

Bonnie graduated in December 2012 and is currently the Program Director of Health Informatics at The University of Arizona.



Jeremy Jonas
Ecology and Evolutionary Biology

B.S. Biology (Pre-Medicine), Edinboro University of Pennsylvania, 2006

My research interests are in evolutionary genetics, particularly in the genetic basis of coat color adaptation and variation in mammals.  Currently, my research involves using a candidate gene approach to investigate the genetic basis of coat color variation among closely related species of mammals.

Joseph Kunkel
Genetics

B.S.  Biology, University of New Mexico, 2009

To perceive and react to the state of their environment cells use pathways of protein interaction that cooperate to form networks.  These networks are organized into circuits, which respond to and regulate each other. I am interested in understanding the circuitry that allows a cell to refine and integrate signals from multiple networks, and how cellular circuits coordinate and synthesize this information into the changes in transcription that determine the cell’s response.



Vincent Martinson
Insect Science

B.S. Biotechnology: Microbial Systems, Montana State University, 2005

I am interested in bioprospecting, the search for novel genes that have applications in industry, agriculture, or pharmaceuticals. The microbial symbionts of insects are, specifically, where my bioprospecting interests lie. The high diversity and shear number of both insects and microbes in the world leads me to believe there are useful genes to be found. Using modern techniques to search the wide variety of insects for symbionts will unlock a relatively unexplored region of discovery. This area of science is constantly searching for bacteria and other organisms that contain unique genes/genomes. The search for novel organisms widens our view of the biodiversity on earth by expanding the database of genomes, another exciting side of bioprospecting research.|

Vince graduated in May 2012 and is currently a post-doc at Rochester University.

Mary Paniscus
Genetics

B.S. Biochemistry and Biomedical Science, McMaster University, 2005.

I am describing the sexual dynamics of the bacterial genus Neisseria. Collaboration with the Human Microbiome Project provided the So Lab with sequence data on commensal (nonpathogenic) human-associated Neisseria. I performed bioinformatics in the preliminary exploration of this genus. After finding commensals possess the genetic capacity for sexual recombination with each other and their pathogen relatives, Neisseria meningitidis and Neisseria gonorrhoeae, my data mining continues into the exploration of DNA uptake sequences, their patterns of distribution, and what meaning may be found therein.

Adriana Racolta
Molecular and Cellular Biology

M.S. Molecular Biology, California State University, 2005
B.S. Biology, Babes-Bolyai University, Cluj-Napoca, Romania, 1993

My research is focused on aspects of intercellular communication during plant development. I am interested in elucidating the molecular pathways used by two membrane receptor kinases named RPK1 and TOAD2 in signaling the proper plant development during the early stages of embryogenesis in Arabidopsis thaliana. In my work am trying to find potential ligands, substrates and interacting partners of these kinases and also determine their spatial and temporal requirement during various stages of development.



Jana U'Ren
Plant Science

B.A. Biology, University of Missouri Columbia, 2001

Jana is currently a fifth-year Ph.D. student studying with Dr. Betsy Arnold at University of Arizona. Her dissertation research investigates the evolutionary relationships, biodiversity, and metabolic profiles of fungal endophytes, saprotrophic fungi, and endolichenic fungi associated with diverse plant- and lichen hosts. Her studies also examine the scale of fungal biodiversity and the broad geographical patterns of fungal symbioses.

Jana graduated in December 2011 and is currently a post-doc at The University of Arizona.



Joel Wertheim
Ecology and Evolutionary Biology

Postdoctoral Researcher, Viral Evolution Group, UC San Diego, 2009-Present
Ph.D. Ecology & Evolutionary Biology, University of Arizona, 2009
B.A. Biology, Wesleyan University, 2004

My dissertation was entitled "Reconstructing the evolutionary history of RNA viruses using relaxed molecular clocks." My research was primarily concerned with determining the age of RNA viruses (e.g., HIV, simian immunodeficiency virus, Taura syndrome virus) and investigating the properties of the phylogenetic methods used to make these inferences.

Joel graduated in December 2009 and is currently a Research Scientist at the Center for AIDS Research (UCSD).

Jennifer Wisecaver
Ecology and Evolutionary Biology

B.S. Biological Sciences,Humboldt State University, 2007

My research interests are in the areas of plastid evolution and algal genomics.  As part of my dissertation, I am using a comparative phylogenomics approach to quantify the genetic contribution of Plantae to the chromalveolate algae and evaluate different hypotheses regarding secondary plastid evolution in these algae.  I am also evaluating kleptoplastidy (sequestration of temporary plastids stolen from prey) as a model for understanding the early events in plastid acquisition.

Jennifer graduated in December 2012 and is currently a post-doc at Vanderbilt University.




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