Genetics

David A Kudrna

Coordinator, Bac/Est Resource Center
Primary Department
Department Affiliations
Contact
(520) 626-9596

Work Summary

We are a plant genomics lab who specialize in whole genome sequencing and assembly; with analyses of structural variation, gene modeling and transcriptomes. Our work on major projects of rice, corn, barley, etc, allows us to share our technical expertise with other researchers.

Research Interest

We are a plant genomics lab who specialize in whole genome sequencing and assembly; with analyses of structural variation, gene modeling and transcriptomes. Our work on major projects of rice, corn, barley, etc, allows us to share our technical expertise with other researchers. Our research in plant and animal genomes, at the whole genome and transcriptome levels, will impact successful genetic selections toward the goal of feeding the 9 billion people toward the year 2050. Keywords: "Genome Sequencing", "PacBio", "Structural Genomics", "Plant Genetics", "DNA Extraction"

Zhongguo Xiong

Associate Professor, Plant Sciences
Associate Professor, BIO5 Institute
Member of the General Faculty
Member of the Graduate Faculty
Primary Department
Department Affiliations
Contact
(520) 621-9869

Research Interest

Zhongguo Xiong, PhD, is an associate professor in the School of Plant Sciences, College of Agriculture and Life Sciences at the University of Arizona, and a faculty member in the Undergraduate Program of Microbiology. Dr. Xiong is a 2012 winner of the Bill Gates and Melinda Foundation Grand Challenges Explorations in Global Health, and has more than 20 years of research experience on RNA viruses of important crops and native plant species. Dr. Xiong research encompasses a wide range of subjects that include virus diversity, recombination, RNAi suppression, host resistance and resistance-breaking, replication and movement of RNA viruses, and how all these are related to the control and management of viral diseases. He was one of the first researchers to discover ribosomal frameshifting as a gene expression mechanism in plant RNA viruses and to demonstrate recombination between transgene mRNA and genomic RNA of an infecting virus. His recent research on Citrus tristeza virus has revealed its genome stability, unusual for an RNA virus, and the promiscuous recombination between viral strains as the major factor driving Citrus tristeza virus evolution. His recent collaboration with Dr. Martha Hawes has led to the discovery that extracellular DNA, secreted DNases, and proteins are important immunity and pathogenicity factors in the plant-microbe interactions in the rhizosphere. Dr. Xiong has strong ongoing international collaborations on emerging viral diseases of tomato, pepper, papaya, and banana. His recent research interests include genome editing to engineer immunity against viral infection and using the next generation sequencing to explore viral population genomics and genetic diversity and to discover new viruses and novel viral strains.

Rod A Wing

Director, Plant Genomics Institute
Bud Antle Endowed Chair For Excellence, Agriculture-Life Sciences
Professor, Plant Science
Professor, Ecology and Evolutionary Biology
Regents Professor
Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-9595

Work Summary

Harnessing 15MY of natural variation in the genus Oryza (rice) to help solve the 10-billion people question: i.e. how do we feed our world without destroying our world.

Research Interest

Rod Wing, PhD, and his lab, The Arizona Genomics Institute, specialize in building what geneticists call a physical map of a genome- a crucial foundation of any genome sequencing effort. AGI has earned a reputation for providing extremely high-quality maps, as documented in previous sequencing efforts leading to the genome sequences of rice and corn. The genome sequence will allow scientists to locate and identify genes that can improve and strengthen crops and increase yield in order to help solve the Earth’s looming food crisis by creating new strains of the cereal crops that make up 60% of humankind’s diet. Keywords: Genome Biology, Genome Sequencing/Assembly/Annotation, Food Security, Rice

Bruce Walsh

Professor, Ecology and Evolutionary Biology
Professor, Public Health
Professor, Plant Sciences
Adjunct Professor, Animal and Comparative Biomedical Sciences
Adjunct Professor, Molecular and Cellular Biology
Professor, Applied Mathematics - GIDP
Professor, Entomology / Insect Science - GIDP
Professor, Genetics - GIDP
Professor, Statistics-GIDP
Professor, BIO5 Institute
Member of the General Faculty
Member of the Graduate Faculty
Primary Department
Contact
(520) 621-1915

Research Interest

Bruce Walsh is a Professor of Ecology and Evolutionary Biology at the University of Arizona and also a Professor in the College of Public Health. He is also an Adjunct Professor in the Departments of Animal Sciences, Plant Sciences, and Molecular and Cellular Biology, and the former Chair of two Graduate Interdisciplinary Programs: Genetics and Statistics. Dr. Walsh is internationally known for his work on the genetics of complex traits, and is coauthor of the leading graduate text on Quantitative Genetics. He is a frequently-invited speaker at national and international meetings, being a keynote speaker at the last Two World Congresses in Quantitative Genetics (China and Scotland) as well as at the most recent Gordon Conference in Quantitative Genetics. Dr. Walsh routinely teaches several international graduate/ post-graduate courses each year in areas ranging from animal and plant breeding, to evolutionary genetics, to human applications, and has taught in Australia, Belgium, China, Costa Rica, Denmark, Finland, Holland, Korea, New Zealand, Portugal, Scotland, and Sweden in additional to numerous domestic short courses. Most recently, in conjunction with BIO5, he has started the Tucson Winter Institute in Plant Breeding, whose propose is to train academic and industry plant breeders from around the world in the latest techniques in genomics, statistics, and bioinformatics as they relate to improving plant production. Keywords: "Statistical Genetics" "plant and animal breeding"

Koen Visscher

Associate Professor, Physics
Associate Professor, Molecular and Cellular Biology
Associate Professor, Optical Sciences
Associate Professor, Applied Mathematics - GIDP
Associate Professor, BIO5 Institute
Primary Department
Department Affiliations

Research Interest

Koen Visscher is an Associate Professor in the Department of Physics with an interest in Biological Physics. He holds joint appointments in Molecular and Cellular Biology as well as in the College of Optical Sciences, and is a member of the Applied Mathematics Graduate Interdisciplinary Program. His research focuses on the role of mechanical force in Biology using single-molecule techniques such as optical tweezers. He pioneered the so called molecular force clamp, a feedback controlled optical tweezers that is able to maintain a constant force on a single individual moving motor protein. Recent interests are RNA structure, nucleic acid-protein interactions interactions, and translational recoding via -1 frameshifting.

Carol A Soderlund

Research Associate Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-9600

Research Interest

Carol Soderlund, PhD, is an Associate Research Professor at the BIO5 Institute at the University of Arizona. While working on her PhD in Computer science in 1988, she collaborated with a biologist to develop one of the first gene prediction programs. She received a DOE Human Genome Distinguished Postdoctoral Fellowship hosted by Los Alamos National Laboratory, where she became involved with mapping the human genome. Her work continued at the Sanger Centre in the UK, which was on the forefront of sequencing the human genome. She developed the FPC software, which was used for mapping the human genome, and has since been the primary software package for mapping large genomes.Her primary research objective is to provide environments for biologists to run algorithms (both her own and existing software), with highly interactive graphics for query and display of the data and results. Towards this end, she has published seven software packages for various genomic problems, where the three most important are: (1) The FPC program mentioned above, which is still being used after its initial release 15 years ago and has been extended for next generation sequencing. (2) The SyMAP software for the computation, query and display for synteny for the comparison of plant genomes. (3) The Transcriptome Computational Workbench (TCW) for the analysis of the transcriptome across tissues or conditions, and across the species for finding shared and unique genes.Dr. Soderlund has published over 60 original research papers and 20 book chapters on a range of genomic problems. She has collaborated with a range of scientists on a variety of organisms and genomic problems, where the majority of the collaborations have been on mapping genomes and transcriptome analysis, but she has also been involved in metagenomics, sequencing, and host-pathogen interactions.

Catharine L Smith

Associate Professor, Pharmacology and Toxicology
Associate Professor, Cancer Biology - GIDP
Associate Professor, Genetics - GIDP
Associate Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-8349

Research Interest

Catharine Smith, PhD, focuses on epigenetic mechanisms of gene expression, particularly their regulation through signaling pathways and their modulation by anti-cancer drugs. Epigenetic mechanisms play a very important role in transcriptional regulation of genes but the specifics of these mechanisms require ongoing study. A very exciting new area of research focuses on how these mechanisms are disrupted during tumorigenesis but may also be harnessed to treat cancer. Signaling pathways control the expression of key genes in non-cancerous cells but are often misregulated during the process of oncogenesis. Chromatin proteins and transcription factors that interact with chromatin are often targets of these pathways. Two projects in the lab are directed at the interface of signaling pathways and chromatin. First, Dr. Smith is interested in the mechanism by which the female reproductive steroid, progesterone, regulates target genes in the physiological context of chromatin. Chronic progestin exposure has been linked to increased incidence of breast cancer in post-menopausal women on hormone-replacement therapy. However, the function of the progesterone receptor in mammary tissue and its role in oncogenesis are not well understood. Current studies in this area are directed at the role of chaperone proteins in determining how the progesterone receptor functions at target genes in chromatin and how it is impacted by other signaling pathways.Second, her lab has discovered a novel cAMP signaling pathway that regulates cell cycle progression and are focused on identifying specific components and targets of this pathway.Third, histone deacetylases (HDACs) are key transcriptional regulatory proteins. Inhibitors that target these enzymes have shown great promise as anti-cancer drugs and are currently in clinical trials. However, a lack of knowledge of HDAC biology has made it difficult to predict which tumors will respond to these drugs. HDACs are known to participate in gene repression, but recent work indicates that they are also transcriptional coactivators. Further studies on the mechanism of gene repression through HDAC inhibitors will provide insight into the role of these enzymes as coactivators.

Jacob C Schwartz

Associate Research Professor, Pharmacology
Assistant Professor, Chemistry and Biochemistry - Med
Assistant Professor, Chemistry and Biochemistry-Sci
Assistant Professor, Neuroscience - GIDP
Associate Professor, Cancer Biology - GIDP
Associate Professor, Neuroscience - GIDP
Assistant Professor, BIO5 Institute
Primary Department
Contact
(520) 621-0877

Research Interest

Every investigation that they have pursued, even investigating novel disease models, has produced profound discoveries in basic biology and biochemistry. They are currently working in collaborations with labs to exploit three system to explore the basic function of the RNA-binding protein FUS. First, they are collaborating with the lab of Rob Batey (UC Boulder) to investigate the role of RGG-rich domains in mediating RNA recognition. Next they are collaborating with lab of Kate Fitzgerald (U Mass Med) to investigate the role of FUS in transcriptional pause release and initiation as macrophage cells respond to stimulation of Toll-like receptor 4. Lastly, they are collaborating with the lab of Ran Taube (Ben-Gurion U) to investigate the role of FUS as a scaffold protein to promote the formation of the Super Elongation Complex (SEC) both genome-wide and for the Tat gene in HIV. They are also pursuing the role of FUS and noncoding RNAs in DNA damage repair. They believe that the function of FUS in affecting transcription is also crucial to the repair of DNA damage in cells.

Todd A Schlenke

Associate Professor, Entomology
Associate Professor, Entomology / Insect Science - GIDP
Associate Professor, Ecology and Evolutionary Biology
Associate Professor, Molecular and Cellular Biology
Associate Professor, Genetics - GIDP
Associate Professor, Neuroscience - GIDP
Associate Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 621-7167

Research Interest

Dr. Schlenke's research program uses fruit flies in the genus Drosophila to understand the evolutionary genetics of host-parasite interactions. For example, his lab has developed several species of parasitic wasps, which are readily observed infecting Drosophila in nature and can be very specialized to particular host species, as model parasites. These wasps lay single eggs in Drosophila larvae and, once hatched, consume flies from the inside out. Flies mount cellular and behavioral defense responses against wasps, but wasps have adaptations for finding host fly larvae, suppressing host cellular immunity, and manipulating host behavior. The Schlenke lab uses a variety of "omics" tools to understand the molecular genetics of fly cellular immunity and wasp virulence, as well as patterns of host immunity and pathogen virulence coevolution across fly and wasp phylogenies. The Schlenke lab also studies the genetics and neurobiology of behaviors that flies use to avoid being infected by the wasps and to cure themselves once they are infected, including various self-medication behaviors.

Marek Romanowski

Associate Professor, Biomedical Engineering
Associate Professor, Materials Science and Engineering
Associate Professor, Neurosurgery
Member of the Graduate Faculty
Associate Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-1578

Research Interest

Marek Romanowski, PhD, and his work on translating physics into medical products have huge implications for the evolution of personalized medicine. On cue, a tiny pillbox of gold floating in your bloodstream can deliver its medicine exactly to the right cell, one that is sick with cancer, avoiding all of your healthy cells. A gold capsule – about 50 to 200 nanometers in diameter, large enough to do the work of transporting a few molecules of medicine and respond to light signals – is too large to pass out through the kidneys. But on command by an enzyme, it can fall apart into pieces smaller than 10 nanometers, just a few molecules. The new size can easily leave our bodies at no risk. The gold pillbox has many other possible applications. In addition to delivering a drug, it can become a part of a diagnostic test, or deliver genetic material to a cell to permanently modify the cells’ DNA—a key step in gene therapy.