School of Plant Sciences

Alexander Bucksch

Associate Professor, Plant Science
Member of the General Faculty
Member of the Graduate Faculty
Primary Department
Department Affiliations
Contact
(520) 621-1977

Work Summary

Alexander Bucksch is an Associate Professor in the School of Plant Sciences at the University of Arizona who develops plant phenotyping methods across all biological and ecological scales with an emphasis on plat roots. As a trained computer scientist, he developed his interest in plant biology & ecology during his undergraduate studies at the Brandenburg Technical University. Since then he developed computational methods to analyze plant morphology in the field as a PhD at the Delft Technical University and as a PostDoc at the Georgia Institute of Technology. Currently, his methods are used by thousands of users within the CyVerse cyberinfrastructure (http://plantit.cyverse.org). During his first faculty appointment at the University of Georgia, he was awarded the NSF CAREER Award, the Fred C. Davison Early Career Award and the Early Career Award of the North American Plant Phenotyping Network for his computational approaches to understand the functions of plant morphologies and their associated formation processes.

Research Interest

An increasing human population faces the growing demand for agricultural products and accurate global climate models that account for individual plant morphologies to sustain human life. Both demands are ultimately rooted in an improved understanding of the mechanistic origins of plant development and their resulting phenotypes. Such understanding requires geometric and topological descriptors to characterize plant phenotypes and to link phenotypes to genotypes. However, the current plant phenotyping framework relies on simple length and diameter measurements, which fail to capture the exquisite architecture of plants. My research aims to set new frontiers in combining plant phenotyping with recent results from shape theory at the interface of geometry and topology. The core technical method I use is to expand and apply the mathematical concept of a “shape descriptor” to the plant sciences. Shape descriptors describe the current state and growth of complex structures, including the rich geometric and topological characteristics of plants. More generally, understanding adaptation of plants to their environments is best observed within imaging data capturing the spatial arrangement of plant organs forming the plant phenotype. Spatial arrangements appear in leafs, branches, roots etc. on all biological and ecological scales. A full understanding the formation of morphological phenotypes requires analysis of the interplay with the underlying formation processes on cellular and genetic scales as well as the interactions on a population and community scale. Applying and extending shape theory for plants is the centerpiece of my current work towards unravelling the formation of plant phenotypes. In doing so, I utilize data collected with self-made imaging instruments from which shapes are extracted to apply shape descriptions.

Betsy Arnold

Professor, Plant Science
Associate Director, Faculty Advancement
Curator, Robert L Gilbertson Mycological Herbarium
Professor, Applied BioSciences - GIDP
Professor, Genetics - GIDP
Professor, BIO5 Institute
Member of the General Faculty
Member of the Graduate Faculty
Primary Department
Department Affiliations
Contact
(520) 396-0854

Work Summary

I am an evolutionary ecologist with expertise in plant microbiomes in both wild and agricultural ecosystems. My group and I use the tools of microbiology, molecular ecology, informatics, systematics, organismal biology, and genomics to study the distributions and impacts of plant-associated microbes worldwide, with study sites that range from the Arctic to tropical rainforests. Our interests in fungal biodiversity, plant-microbe interactions, fungal-bacterial dynamics, and molecular ecology are readily translated to animal systems in diverse settings. We collaborate with agricultural experts in academia and industry, natural products chemists interested in pharmaceutical drug discovery, and academic partners interested in identifying and translating principles of biodiversity research to human endeavors. We are active in outreach, especially with high school researchers, teachers, and classes, and welcome diverse graduate students and undergraduates with an interest in plant microbiology and its applications.

Research Interest

A. Elizabeth (Betsy) Arnold (Ph.D., ecology and evolutionary biology) leads a diverse group of researchers and educators with interests in the ecology, evolution, and potential applications of symbiotic microbes for host health. The special focus of the lab is on the fungal portion of plant microbiomes, with particular interest in foliar endophytic fungi and the soilborne fungi that interact with seeds -- but their interests also include animal-associated fungi, bacterial biodiversity, fungal-bacterial interactions, and the establishment of complex ecological systems in new environments. Their field sites range from the Arctic to tropical rainforests to Biosphere2, and locally, encompass both wild and agricultural systems. Their expertise includes traditional microbiology, phylogenetics, population biology, molecular ecology, genomics, and field biology, as well as fungal identification for stakeholders and medical professionals. Arnold's team collaborates widely on questions related to conservation, agricultural innovation, pharmaceutical drug discovery, and biodiversity discovery in diverse settings worldwide.

Arnold co-directs the National Science Foundation graduate training program in Ecosystem Genomics and is Curator of the Robert L. Gilbertson Mycological Herbarium, the southwest's premier reference collection of fungal biodiversity. She is a Fellow of the Mycological Society of America and the American Association for the Advancement of Science and has published over 140 peer-reviewed publications to date. She has been recognized for her teaching excellence as a Bart Cardon Fellow in the College of Agriculture and Life Sciences (CALS) and by the Mycological Society of America, and for her commitment to diversity by awards from CALS and UArizona. She and her team are active in education and outreach, with strong ties to area high schools as well as a diverse portfolio of undergraduate and graduate teaching and research opportunities.

David A Baltrus

Associate Professor, Plant Sciences
Associate Professor, Animal and Comparative Biomedical Sciences
Associate Professor, BIO5 Institute
Member of the General Faculty
Member of the Graduate Faculty
Primary Department
Department Affiliations
Contact
(520) 626-8215

Work Summary

We are interested in understanding the genetic basis for bacterial interactions with other organisms (be they plants, insects, fungi, other bacteria), and on how evolution shapes these interactions. By better understanding the rules and molecules that structure such relationships, we hope to develop new ways to manipulate these interactions (e.g. through the development of specific antimicrobial compounds) or shape their evolutionary dynamics through time.

Research Interest

David Baltrus (PhD) is broadly interested in understanding how bacterial evolution is shaped by interactions with other organisms. Questions investigated by the Baltrus lab range from asking how evolutionary events such as the transfer of genes between microbes affects the development of antibiotic resistance to testing how microbiomes impact the development and physiology of plants and animals. The lab approaches these questions by using a variety of existing tools, from screening for mutants using "toothpicks and agar plates" to experimental evolution to comparative genomics. However, Dr. Baltrus is also highly interested in developing new tools that enable sequencing and tracking of bacterial populations and communities of interest (like potential pathogens) in real time under natural conditions.

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"

Ramin Yadegari

Professor, Plant Science
Professor, Molecular and Cellular Biology
Professor, Genetics - GIDP
Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 621-1616

Research Interest

Ramin Yadegari, PhD, is interested in understanding the gene-regulatory processes that mediate fertilization and 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, Dr. Yadegari and his lab 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, they use a combination of expression-based analyses and genetic resources of Arabidopsis to identify major gene-regulatory networks involved in differentiation of the female gametophyte cell types. Similarly, using biochemical, molecular and genetic approaches, they identify components of the Polycomb-group complexes that mediate epigenetic repression of gene expression before fertilization.

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

Karen S Schumaker

Professor, Plant Sciences
Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 621-9635

Research Interest

Karen Schumaker, PhD, understands that activities of living organisms require the performance of chemical, mechanical, osmotic or electrical work. The energy required for this work is supplied by metabolism, respiration, photosynthesis and fermentation. Adenosine triphosphate (ATP) has long been recognized as the universal energy currency, with metabolism supporting the synthesis of ATP and the hydrolysis of ATP being used for the subsequent work. However, ATP is not the only energy currency in living organisms. A second and very different energy currency links metabolism to work by a current of ions passing from one side of a membrane to the other. These ion currents play a major role in energy capture and they support a range of physiological processes from the active transport of nutrients to the removal of toxic ions. To more efficiently capture and utilize energy, it will be necessary to uncover mechanisms regulating these ion currents. In a project funded by the Physical Biosciences Program of the Office of Basic Energy Sciences at the Department of Energy, Dr. Schumaker asks how calcium-binding proteins regulate the activity of specific secondary active transporters to control cellular sodium ion homeostasis during plant growth in saline conditions.The build-up of salt in agricultural soils is a widespread problem that limits the growth and yield of important crop species worldwide. While genetic variation for plant growth in salinity (salt tolerance) exists, little is known about the genes and pathways underlying this variation. In a project funded by the Physiological and Structural Systems Cluster in the Division of Integrative Organismal Systems at the National Science Foundation, Dr. Schumaker’s lab analyzes the molecular evolution of the genes and associated networks that control plant adaptation to soil salinity. To do this, they are assessing the evolutionary forces acting on plant salt tolerance and mapping and isolating genes that underlie natural variation for this trait.

Monica Schmidt

Associate Professor, Plant Science
Associate Professor, Applied BioSciences - GIDP
Associate Professor, Genetics - GIDP
Associate Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-1643

Work Summary

My research focus is on functional foods—designing crops to deliver more than mere calories—by both adding nutritional compounds and eliminating anti-nutritional compounds. I work on enhancing seeds of two of the most globally important crops, soybean and corn.

Research Interest

Monica Schmidt is an Associate Professor in the School of Plant Sciences in the College of Agricultural and Life Sciences at the University of Arizona. Dr. Schmidt’s research interests are in both functional foods and functional genomics. Her research aims at applying molecular biology and genetic techniques to help alleviate current major agricultural problems. As soybean is a global commodity, much of her research focuses on soybean seed traits. Current research is investigating cellular mechanisms to strengthen the metabolic engineering efforts to fortify crops with nutraceutical carotenoids. Since soybean oil is a large component of the American diet, Dr. Schmidt is also investigating means to engineer a more healthy oil composition. Other functional food projects aim at the suppression of deleterious compounds in crops, such as toxins produced from contaminating fungus, in maize and peanuts. She uses techniques of plant biotechnology in over a dozen crops to investigate gene function, at a cellular and entire plant level. Dr. Schmidt has worked with both domestic and international collaborators on value-added traits in seeds of legumes for over a decade and is one of the few academic laboratories that can routinely transform soybean. She has been involved with a number of innovations in tissue culture / transformation techniques (for example, maturation media for soybean, novel gene expression cassette system) and her research on seed manipulation has resulted in a start-up company and patents. Keywords: plant biotechnology, functional foods, soybean, maize

Barry M Pryor

Professor, Agricultural-Biosystems Engineering
Professor, Plant Sciences
Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-5312

Research Interest

Barry M. Pryor, PhD, is an Associate Professor of Plant Pathology at the University of Arizona College of Agriculture and Life Sciences in the School of Plant Sciences. Dr. Pryor is internationally renowned for his work studying fungi in the genus Alternaria, and this research includes study in Alternaria ecology, biology, systematics, mycotoxicology, and the role of Alternaria in childhood-onset asthma. Additional research programs include disease management in agricultural and horticultural crops, characterization of fungal communities in native ecosystems, and cultivation of edible mushrooms and their co-utility in landscape and consumer waster recycling.Dr. Pryor has published over 50 original research and review papers, many in collaboration with investigators from around the world. He has served as Senior Editor for Phytopathology and Plant Disease, which are both premier journals for plant pathology research. He is a frequent presenter at national and international meetings, and is an active member in several plant pathology and mycological societies.