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


2010-2011 Cohort



Alicia Bolt
Pharmacology and Toxicology

B.S. Human Biology, University of Northern Colorado, 2003

I am interested in identifying the Gene by Environment interactions that contribute to individual variation in response to environmental toxicants. I use genomic approaches to identify candidate genes that are involved in sensitivity to arsenic-induced immunotoxicity in an in vitro model of human populations.

Alicia graduated in May 2012 and is currently a post-doc at McGill University.

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.



Daniel DeBlasio
Computer Science

M.S. Computer Science, University of Central Florida, 2009
B.S. Computer Science, University of Central Florida, 2007

My research interests fall into computational approaches to mainly structure based issues. I am interested in modeling biological problems as graphs or trees, then applying computational algorithms to this. I have some background in RNA-Seq assembly and analysis.

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.



Andrew Gloss
Ecology and Evolutionary Biology

B.S. Biology, University of Notre Dame, 2010

I am interested in the evolution of interactions between plants and herbivorous insects, with a focus on how plants perceive attack by insect herbivores, the resulting activation of chemical defense pathways in the plant, and insect strategies of detoxifying and coping with plant defense compounds.  The ongoing development of an herbivorous Drosophilid fly as a genetic model herbivore of the plant model species Arabidopsis thaliana will allow the identification of specific genes vital to these interactions.  I also plan to continue work at the Rocky Mountain Biological Laboratory on a fly species that has specialized on a wild mustard, both of which are closely related to the organisms I'm studying in the lab.  This will allow me to examine the relevance of processes discovered in a controlled lab environment to a variable natural setting in which plants, insects, bacteria, and fungi interact simultaneously.  Ultimately, I hope to provide insight into how species interactions drive local adapation and patterns of genetic variation within and between natural populations.



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.



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.



Zachary Miles
Biochemistry

B.S. in Biochemistry, University of Wisconsin, 2009

I am currently working on the discovery and characterization of enzymes involved in deazapurine biosynthesis. More specifically, I am interested in the biosynthesis of queuosine, a hypermodified nucleoside found in tRNA. Queuosine has been evolutionarily conserved throughout all domains of life, yet its physiological role remains unknown to date. In addition to mechanistic enzymology, our lab uses bioinformatics and whole genome sequencing to identify unknown deazapurine biosynthetic pathways in a wide array of bacterial species. Other members of the Bandarian lab and myself are also interested in prokaryotic RNA modification. In addition to the commonly known RNA nucleosides, (guanosine, cytosine, adenosine, and uracil) there are multiple, lesser abundant modifications, whose structures have still yet to be determined. Currently, we are screening total RNA from a library of E. coli single gene deletion mutants using liquid chromatography and mass spectrometry in an attempt to map the extent of RNA modifications in each mutant strain. By correlating the presence of specific RNA modifications to genes of known function, we hope to identify novel modifications of RNA and their subsequent structures.



Alexander Ochoa
Natural Resources/Wildlife and Fisheries Science

B.S. in Biology, National Autonomous University of Mexico (UNAM), 2008

I'm studying the evolutionary consequences of climate change in the Arizona Sky Islands. This project will focus on the effects of climate change on the genetic diversity and structure of amphibians and reptiles across altitudinal gradients in the Arizona Sky Island System through a classic population genetics approach. Also, this project has the goal of identifying methylation patterns (selective pressures) across genomes in association with different climatic variables.



Marianyoly Ortiz-Ortiz
Soil, Water and Environmental Sciences

B.S. Industrial Microbiology, University Of Puerto Rico, Mayagüez, 2007

My research focus is in the study of the microbial communities in Kartchner Caverns, a carbonate cave near Benson, AZ. Techniques such as pyrosequencing of the 16S rRNA gene and Metagenomics are being used to understand the diversity and variability of the bacterial communities found in the cave.

Marian graduated in December 2012 and is currently a lecturer at the University of Puerto Rico.

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.



Atlantis Russ
Genetics

B.S. Ecology, University of Vermont, 1998
M.S. Conservation Biology, University of Hawaii, 2007

I am interested in the role of microRNAs in establishment and maintenance of cell polarity. We hypothesize that aberrant miRNA expression may contribute to the characteristic deregulation of epithelial cell polarity in breast cancer. My project involves investigations using fly, mouse, and human cell line models to probe for evidence of miRNA misexpression in breast cancer.

Atlantis graduated in May 2013 and is currently in the MD program at The University of Arizona.



Sergei Solonekno
Ecology and Evolutionary Biology

B.S. Cell and Molecular Biology, University of Texas at Austin, 2008

I will be rotating through the laboratories of Dr. Matthew Sullivan, Dr. Noah Whiteman, and Dr. Richard Michod. I spent my last year at UT working in the laboratory of Dr. Mikhail Matz, mostly to study the evolutionary diversity of Cephalopod lens proteins using standard molecular biology techniques. I have also had the opportunity to grow an interest in entomology, marine biology, the evolution of invertebrate ciliation and the study of insect behavior. As part of the IGERT program, I am looking to learn to rigorously apply genomics tools in pursuit of the questions that will drive my PhD dissertation and academic career.

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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