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


FACULTY

In addition to the faculty listed here, faculty in other units also participate in IGERT activities. All IGERT activities are open to participation from members of any department.

Participating Faculty in Functional Genomics:

Parker Antin
Professor, Cell Biology and Anatomy

The Antin Lab is concerned with understanding the molecular regulation of early developmental processes in vertebrate embryos. We primarily use the chicken embryo as a model organism, and approach research questions from the dual perspective of how individual molecules function and how their functions can be integrated into regulatory networks. Present projects are focused on mechanisms regulating epithelial-mesenchymal transition (EMT) during gastrulation, endothelial cell development, cardiac myogenesis, and developing genomic and computational tools. We also host the GEISHA high throughput in situ hybridization gene expression project.

Heddwen Brooks
Associate Professor, Physiology

The Brooks Lab has been utilizing microarray technology to study the effects of vasopressin on gene expression in renal medullary cells. Using water restriction (WR) protocols to raise circulating vasopressin, we have identified vasopressin responsive genes in both wild type and AQP1 knockout mice. Due to the lack of a concentrating mechanism in the AQP1 knockout mice osmotically regulated transcripts should not be differentially expressed when vasopressin was increased in these mice. Our aim in applying microarray technology to the KO’s and normal mice was to rapidly identify vasopressin-responsive genes in common between the two physiological models. Our analysis revealed that 25 genes were significantly increased in both studies, i.e. increased in the water restricted wild type mice and increased in water restricted AQP1 KO animals. 15 genes were identified in common as significantly decreased following water restriction. We have focused our studies on two specific pathways that were identified as differentially expressed by in vivo increases in vasopressin: ER stress protein GRP78 and 3beta HSD steroid hormone enzymes.

Carol Dieckmann
Professor, Molecular and Cellular Biology

The Dieckmann Lab is interested in understanding the coordination of organelle/host cell interactions. Two different systems under study are: nuclear control of mitochondrial mRNA expression in yeast mitochondria, and the eyespot assembly in Chlamydomonas.

Mitochondrial tRNA processing is inhibited in yeast strains defective in fatty acid biosynthesis in the organelle. We are trying to understand why gene expression and fatty acid metabolism intersect. Mitochondrial fatty acid synthesis precedes the synthesis of lipoic acid, the swinging arm cofactor of pyruvate dehydrogenase and two other enzyme complexes. We are studying how lipoic acid is synthesized and attached to target proteins in mitochondria, and how this process is controlled.

The eyespot in Chlamydomonas is made up of components in the chloroplast and in the plasma membrane of the cell. We are interested in how the cell controls the assembly of these components into a functional light-sensing structure. Originally isolated as part of a collection of 168 phototaxis-defective mutants, 28 mutants define four genes required for eyespot assembly. eye2 and eye3 mutants are eyeless. min1 mutants have small eyespots and mlt1 mutants have multiple eyespots. We are trying to understand how these mutations affect eyespot assembly and placement relative to the cytoskeleton through a combination of molecular genetics and light, fluorescence and electron microscopy.



Tom Doetschman
Professor, Cell Biology and Anatomy

The functions of the 3 TGF-beta ligands and of FGF2 are being determined using genetically engineered mice. The research has resulted in mouse models for the following human diseases: i) congenital heart defects, ii) cardiac hypertrophy, iii) autoimmune disease and iv) colon cancer. These mouse models are providing a better understanding of the roles that TGF-betas and FGF2s play in the development, prevention and treatment of these diseases.

Bernard Futscher
Professor, Pharmacology and Toxicology

The Futscher lab’s primary research focus is cancer epigenetics. We use comprehensive genomic approaches to investigate the epigenomic dysfunction that drives human cancer. The use of genome-wide approaches guarantees the capture of all of the information regarding epigenetic change in human cancer. From this comprehensive data of the normal and diseased human epigenomes, we employ advanced in silico and molecular biological approaches to generate new knowledge and discover the decisive epigenetic events that drive human carcinogenesis. The long-term objective of these studies is the development of epigenetic markers for toxicant exposure, disease detection and prognostication, and the identification of novel targets for molecularly directed cancer therapy.

David Galbraith
Professor, School of Plant Sciences

The Galbraith laboratory has a long history of development of novel instrumentation, technologies, and methods for analysis of biological systems. Current activities include the development of microarray and NextGeneration sequencing technologies for low-cost, rapid genotyping in combination with expression profiling for the analysis of quantitative trait loci. This technology is been applied for the analysis of agronomic traits such as resistance to disease and abiotic stress. Another project focuses on the use of microarray platforms and high-throughput assays to analyze the effects of small molecule chemical libraries on gene expression.  A final project employs fluorescence-activated cell sorting for the characterization of gene expression within specific cell types. The Galbraith laboratory also designs, produces, and distributes to the research community worldwide DNA microarrays covering a wide number of species.



Walter Klimecki
Assistant Professor, Pharmacology and Toxicology

The Klimecki laboratory is focused on the factors that determine individual variability in response to environmental toxicants. Human populations that experience a relatively uniform exposure to environmental toxicants frequently demonstrate substantial variability in their response to the toxicant, with a subset of the population relatively sensitive to the effects of the exposure and another segment of the population relatively resistant. We study the toxicity of arsenic, a metalloid to which we are all exposed at some level on a daily basis. In particular regions of the world daily arsenic exposure, frequently through contaminated drinking water, is the cause of substantial morbidity and mortality. Among its many systemic targets in humans is the immune system. Both epidemiological and experimental laboratory studies have established that arsenic damages the immune system. We are particularly interested in immune system damage because of the central role of immune surveillance and response in the gamut of disease that has been associated with arsenic exposure, including cancers (skin, bladder, lung, liver) degenerative diseases, and metabolic/inflammatory diseases (diabetes, atherosclerosis). The laboratory is using lymphoblastoid cell lines (LCL), immortalized cell lines derived from the circulating white blood cells of healthy human donors as a model of the mechanism by which arsenic can damage the immune response. These cell lines offer two distinct benefits, the ability to model normal immune processes such as proliferation and antigen presentation, as well as the ability to study inter-individual variation in these processes by virtue of the commercial availability of thousands of LCL derived from different donors. Our long term goal is to first understand key mechanisms of arsenic-induced disruption of immune function, so that we can learn how those processes vary at the population level. Ultimately this could allow us to predict particularly arsenic-sensitive individuals in an exposed population.



Fernando Martinez
Regents' Professor and Swift-McNear Professor, Pediatrics

Research in the Martinez lab centers on genotyping candidate genes for asthma and chronic obstructive lung disease in humans (Eder 2005; Graves et al. 2005; LeVan et al. 2006). Phylogenetic shadowing is used to identify functionally important regulatory regions. Polymorphisms in such regions are genotyped in affected individuals and their functional consequences are studied in collaboration with Vercelli and Klimecki.

Lisa Nagy
Professor, Molecular and Cellular Biology

The Nagy Lab is interested in exploring the genetic basis of morphological diversity. To do this, we ask how developmental regulatory networks known to pattern a particular aspect of morphology in one organism are modified in other related organisms. At the moment, the focus is on the evolution of arthropod body plans and appendages and axial patterning in molluscs and other lophotrochozoan phyla. Arthropods show a large degree of variation in segmental and limb patterning. Segments, or groups of segments, have repeatedly become specialized for feeding, walking or swimming. Many of the key genes and genetic pathways that regulate segmentation and limb formation have been worked out through molecular genetic analyses in Drosophila or other model organisms. We ask what role developmental regulatory genes play in the evolution of morphological diversity and whether there are properties of developmental systems that constrain or promote phylogenetic change. Other areas of interest include the molecular evolution of the HOX clusters, modeling developmental pathways, the developmental mechanisms underlying phenotypic plasticity and the evolution of life history strategies.



Roy Parker
Regents' Professor, Molecular and Cellular Biology

The Parker laboratory uses three broad approaches to studies the control of mRNA function in eukaryotic cells at posttranscriptional steps. The first employs molecular, biochemical and cell biological methods to identify control steps in the function of eukaryotic mRNAs (Coller & Parker 2005). The second uses functional genomics to identify proteins that govern the life of eukaryotic mRNAs. The third employs microarray technology to examine mRNAs controlled by distinct regulatory nodes. This information is integrated into mathematical models that characterize aspects of mRNA metabolism (Cao & Parker 2003).



Linda Restifo
Professor, Neuroscience

The Restifo Lab’s goal is to understand the genetic bases of normal brain development, and the alterations of brain development that cause neurocognitive disorders such as mental retardation and autism. Our mission is to make developmental brain disorders treatable with safe and effective drug therapies. Our methodological approaches combine the power of a premiere genetic model organism with that of primary neuron culture.

Karen Schumaker
Professor, School of Plant Sciences

Research interests in the Schumaker laboratory focus on understanding the endogenous programs that control plant growth and development and how these programs are altered to enable the plant to adapt to growth in non-optimal conditions. Specifically, our research activities are focused in the following areas.

Signal transduction - Mechanisms underlying calcium-mediated development. Plants are continually exposed to endogenous and environmental signals beginning at seed germination through seedling growth and plant maturation to flowering and reproduction. Hormones, light, nutrient availability, gravity, drought, salinity, extremes of temperature, and pest and pathogen interactions are just some of the signals that are perceived and processed by cells in ways that allow the plant to respond and modify growth. A change in cellular calcium has emerged as an essential component of many signaling pathways in plants, underlying growth and development by linking perception of endogenous and environmental cues to cellular responses. A critical unanswered question in plant biology centers on the issue of specificity. How can a simple non-protein messenger be involved in so many signal transduction pathways? Models for specificity suggest it may reside in the temporal, spatial, and kinetic properties of the calcium change and in the array of molecules that sense alterations in cellular calcium levels. Using the model plant Arabidopsis thaliana (Arabidopsis), our research focuses on understanding the role and regulation of the Calcineurin B-like calcium binding proteins in the establishment of developmental specificity. Results from these studies will be critical for designing strategies to modify the responses of plants to endogenous and environmental cues for optimal growth.

Abiotic stress - Mechanisms underlying plant adaptation to salinity. The build-up of salt in agricultural soils is a widespread problem that limits the growth and yield of important crop species nationally and worldwide. While genetic variation for plant growth in salinity (salt tolerance) exists, little is known about the genes and pathways underlying this variation. Molecular genetic studies in Arabidopsis have identified genes contributing to its ability to grow in salinity; these genes are strong candidates for determinants of natural variation in salt tolerance. Understanding the contribution of these genes to this variation in an evolutionary context is one focus of our research. Because salt tolerance is a complex trait that is likely controlled by numerous genes, a second focus of our research is to identify additional genes associated with plant salt tolerance using a two-pronged quantitative trait loci mapping analysis with accessions of Arabidopsis that vary in their response to salt. Understanding the evolutionary forces acting on plant salt tolerance and discovery of genes that underlie natural variation for this trait will be critical for designing strategies to engineer and breed more salt-tolerant crop plants.

S. Patricia Stock
Professor, Entomology and School of Plant Sciences

The Stock Lab is interested is biodiversity of insect-parasitic and pathogenic nematodes and their role in ecosystem function. We actively engaged in biotic survey and inventory projects in different geographic regions of the world, which allow us to make significant contributions toward the discovery of new species, the understanding of the ecology and behavior of insect-parasitic nematodes and their consideration in biological control and integrated pest management programs. Additionally, we are interested in studying the ecology and genetics of nematode populations from agricultural and natural ecosystems, particularly the study of host-parasite relationships and interactions (including plant and insect-parasitic nematodes), such as phoresis, facultative, obligate parasitism, and pathogenesis. A new research area in our program focuses on the study of Steinernema nematodes and their bacterial symbionts (Xenorahbdus spp.) as models for understanding mutualistic interactions between animals and microbes. Current research relates to the study of structural and developmental features of the bacterial receptacle in the nematode hosts to better understand the colonization process. We are also interested in recognizing the chemical signals and physical interactions that occur between the nematode and their symbionts and how these interactions might affect each organism. Furthermore, we also investigate evolutionary histories of both nematode and bacterial symbionts considering a multigene repertoire and study co-evolutionary histories and diversification of these two partners.

Frans Tax with IGERT student Adriana Racolta (R) and collaborator Jia Li (L)
from Lanzhou University in a barley field in Gansu Province, China


Frans Tax
IGERT Steering Committee Member
Associate Professor, Molecular and Cellular Biology

The Tax lab uses receptor kinases as tools to characterize signaling pathways during plant growth and development and in defense responses. Our lab uses reverse genetics to define individual receptor or receptor family functions in the model system of Arabidopsis thaliana. We are also interested in understanding the interrelationship between growth and biotic stresses (in collaboration with the Whiteman lab). Finally, we are exploring whether the functions of receptor kinase families first defined in Arabidopsis are conserved in tomato and barley for crop improvement.

Donata Vercelli
IGERT Steering Committee Member
Professor, Cell Biology and Anatomy

The Vercelli lab, also known as the Functional Genomics Laboratory, seeks to characterize the mechanisms through which natural variation in immune genes contributes to the pathogenesis of complex diseases, particularly respiratory disorders (allergic inflammation, asthma). The lab assesses how genetic variants strongly associated with disease phenotypes affect the function and regulation of the relevant genes (IL13, TLR2 and CD14). The laboratory has tested the impact of coding variants on protein properties and the effect of non-coding variants on transcriptional regulation. A combination of biochemical purification and functional analysis has identified transcription factors that bind differentially to polymorphic alleles. The lab also investigates the epigenetic regulation of gene expression by combining phylogenetic and functional analyses . All of this work relies on extensive resequencing of innate and adaptive immunity genes in reference and population-derived DNA samples of defined disease phenotype. Currently, the lab has moved to in vivo models and is generating BAC transgenic mice that carry alternative haplotypes of the genes of interest to study their expression, epigenetic regulation and phenotypic correlates in a physiologic genomic context. More recently, the lab started conducting genome-wide analyses of DNA methylation and gene expression patterns in relation to specific environmental exposures and genotypes. The ultimate goal of the lab is to establish a new paradigm merging analysis of genetic and environmental determinants of disease, functional studies and patient phenotypes to understand the causes of disease and predict responsiveness to specific treatments.

Ted Weinert
Professor, Molecular and Cellular Biology

The Weinert Lab studies regulatory controls called checkpoints that ensure that DNA replication and DNA repair are completed before mitosis. Put simply, normal cells with DNA damage do not replicate their DNA nor do they undergo mitosis. Rather, these damaged cells wait, arresting at checkpoints, until repair is complete, for mitosis with a damaged chromosome is highly deleterious to the cell. We study the genetic and molecular details underlying checkpoint controls in yeast, a typical eukaryotic cell amenable to the extensive genetic analysis required to understand complex biological systems. We have now identified genes and proteins involved in recognizing DNA damage and in subsequent signaling events, and now seek to understand the molecular details of how these regulatory proteins act at the molecular level.

We also investigate the importance of checkpoint controls to the cells genetic integrity by studying the fate of cells that divide with a broken chromosome. Such cells undergo a myriad of chromosomal events, termed genomic instability, the basis for which we are only now beginning to unravel.

Rod Wing
Professor, School of Plant Sciences

The Wing lab is located at the Arizona Genomics Institute (AGI) and has a broad research interest in the area of structural, evolutionary and functional genomics of crop plants. AGI is divided into 5 research/service areas:

1) Evolutionary and functional genomics center (Group Leader: Dr. Rod A. Wing). The primary thrust of the center is the development and interrogation of a within-genus comparative genomic platform, for the genus Oryza, to address fundamental questions in plant evolution, domestication and crop improvement. (see www.ompa.org, and our publication list for more information).

2) BAC library construction center (Group Leader: Dr. Siva S Ammi "Raju" Jetty). The focus of this center is to construct and characterize high-quality, large-insert, deep-coverage bacterial artificial chromosome (BAC) libraries. These libraries serve as entry points into various structural and functional genomics projects within my group and in collaboration with other groups at UA and across the world. Our focus is primarily with agricultural systems but we can make libraries for almost any organism. AGI has produced the majority of BAC libraries used in the plant research field today.

3) BAC/EST resource center (Group Leader: Mr. Dave Kudrna). The focus of this center is to archive and distribute genomic resources at an affordable price to the scientific community. Here, we deposit all BAC libraries that we construct as well as all cDNA libraries that we sequence. We also provide a service to the community by archiving and distributing genomic resources generated by other groups. AGI houses the majority of agriculturally important BAC libraries in the world.

4) DNA sequencing and physical mapping center (Group Leader: Dr. Yeisoo Yu). The center runs a medium throughput DNA sequencing and fingerprinting facility and specializes in genome sequencing, EST sequencing, BAC end sequencing, BAC shotgun sequencing, BAC fingerprinting, and physical mapping. We currently support Roche GSFLX, Illumina GAII, and ABI3730 sequencing platforms.  Over the years AGI has made major contributions to the Arabidopsis, rice, maize, soybean, and Drosophila genome sequencing projects. A major thrust of the center is our participation in the International Oryza Map Alignment Project which aims to generate reference quality genome sequences of all representatives of all 23 speices of Oryza by 2012 (see www.omap.org for more information).

5) Bioinformatics center (Group Leader: Dr. Andrea Zuccolo). The bioinformatics center has two primary functions: a) data analysis; and b) laboratory information management. A major focus is on comparative transposable element annotation and evolutionary analysis across the Oryza phylogeny.

Ramin Yadegari
Associate Professor, School of Plant Sciences

The Yadegari Lab is interested in understanding the regulatory processes that mediate fertilization and the initiation of seed development. The plant life cycle alternates between a diploid sporophyte generation and a haploid gametophyte generation. The angiosperm female gametophyte is critical to the reproductive process. It is the structure within which egg cell production and fertilization take place. Using the model plant Arabidopsis thaliana, we are focusing on two specific processes: (1) development of the female gametophyte and (2) control of seed initiation by gene-regulatory complexes before and after fertilization. For example, we are using a combination of expression-based analyses and genetic resources of Arabidopsis to identify major gene-regulatory networks involved in the differentiation of the female gametophyte cell types. Similarly, using biochemical, molecular and genetic approaches, we are identifying components of the Polycomb-group complexes that mediate epigenetic repression of gene expression before fertilization.


                                                                                                                                                                                       RETURN TO TOP