School of Plant Sciences

Ravishankar Palanivelu, PhD, possesses a long-term goal to understand the molecular basis of how cells communicate with each other. His lab employs pollen tube guidance during Arabidopsis thaliana reproduction as a model system to achieve this goal. Currently, the focus remains to understand the molecular mechanisms that underlie pollen tube functions in A. thaliana.A pollen tube's journey to an egg cell within the pistil involves a series of cell-cell interactions such as attraction, repulsion and adhesion (Illustration 1, mov file). While these processes are likely mediated by several guidance signals, only a handful of guidance signals produced by female tissues have been identified. The guidance of pollen tubes into the ovule micropyle is highly reproducible, resembling the polarized migration of axons, yet sharing few genes in common. Dr. Palanivelu’s lab is undertaking a multidisciplinary approach - Genetics, Cell Biology and Biochemistry - to understand the molecular mechanisms that underlie pollen tube functions in A. thaliana. Characterization of pollen tube guidance in A. thaliana holds enormous potential as it focuses on a process that is: 1) very unique to plants, 2) poorly understood at the molecular level, 3) amenable to genetic, cell biological and biochemical techniques, and 4) a rapid way to identify novel plant signals that allow communication between cells possible despite their thick extracellular walls. Additionally, we have recently developed an in vitro pollen tube guidance assay in A. thaliana that monitors both attractive and repulsive interactions between pollen tubes and ovules, processes normally difficult to discern by virtue of them occurring within opaque pistils. These attributes therefore make pollen tube guidance in A. thaliana an ideal model system to study cell-cell interaction in plants.

Marc Orbach, PhD, uses Magnaporthe grisea, the fungal pathogen responsible for the rice blast disease, as a model system to study host-pathogen interactions at the molecular and biochemical level. This pathogen, like many other plant pathogens, interacts with its host in a gene-for-gene manner, where host resistance is induced when the plant contains a resistance gene and the pathogen, a corresponding avirulence gene. The main focus of his research program is to understand what the signals between the pathogen and its host are, that dictate whether the host is able to mount a resistance response. Genetic analysis of M. grisea have identified several avirulence genes that determine what their products are and how these products interact with host plants to induce host defenses. He is also interested in questions of genome stability and the generation of genetic variability in fungi. These questions are of significance in M. grisea because of the apparent ability of this pathogen to rapidly overcome host resistance in the field. Dr. Orbach spends time addressing these questions by studying genome variation in M. grisea at the whole genome level using electrophoretic karyotyping methods. He wishes to specifically analyze the role that a transposable element may play in genome variation and the high rate of mutation observed at some loci.

Rebecca Mosher, PhD, studies how epigenetic information is passed from parent to offspring. Epigenetic information refers to signals laid on top of DNA sequence that affect how and when genes are turned on. Examples of epigenetic signals include chemical modifications of DNA, packaging of DNA around proteins, or the position of DNA in the nucleus. Beginning with Mendel’s observations of pea plants, we have developed a robust understanding of how genetic information in the form of DNA is passed from parent to offspring, but we are only beginning to comprehend how and when epigenetic information is passed from generation to generation. Some epigenetic marks are erased and re-established during reproduction, while others are inherited for many generations. Using plants as models, the Mosher lab studies how tiny RNA molecules place and erase epigenetic marks during reproduction and how the epigenetic marks from the maternal and paternal genomes interact after fertilization.

Research in Dr. McMahon's lab focuses on the analysis of biological diversity, particularly through phylogenetic systematics of plants. Lab-based work includes comparative molecular sequencing, aimed at inferring evolutionary relationships among lineages in the legume family (Fabaceae), and using the resulting phylogenies to infer historical rates and modes of floral morphological evolution. Computational research includes testing data from public molecular sequence databases for the ability to construct large-scale phylogenetic trees for all 1.7 million known species, investigating theoretical limits to phylogenetic inference, and developing software for analyzing the effects of fragmentation in phylogenetic and phylogenomic data sets

Eric Lyons, PhD is an assistant professor at the University of Arizona School of Plant Sciences. Dr. Lyons is internationally known for his work in understanding the evolution, structure, and dynamics of genomes. Core to his research activities is the development of software systems for managing and analyzing genomic data and cyberinfrastructure for the life sciences.Dr. Lyons has published over 30 original research papers and 5 book chapters, many in collaboration with investigators from around the world. He is a frequent presenter at national and international meetings, and has been invited to teach workshops on the analysis of genomic data to plant, vertebrate, invertebrate, microbe, and health researchers.Prior to joining the faculty in the School of Plant Sciences, Dr. Lyons worked with the iPlant Collaborative developing cyberinfrastructure, and managing its scientific activities. In addition, he spent five years working in industry at biotech, pharmaceutical, and software companies. Dr. Lyons’ core software system for managing and analyzing genomic data is called CoGe, and is available for use at http://genomevolution.org

David Galbraith obtained undergraduate and graduate degrees in Biochemistry from the University of Cambridge, and postdoctoral training as a NATO Fellow at Stanford University. His first academic appointment was at the University of Nebraska Lincoln, and he became Professor of Plant Sciences at the University of Arizona in 1989. His research has focused on the development of instrumentation and methods for the analysis of biological cells, organs, and systems. He is internationally recognized as a pioneer in the development and use of flow cytometry and sorting in plants, developing widely-used methods for the analysis of genome size and cell cycle status, and for the production of somatic hybrids. He also was among the first to develop methods for the analysis of gene expression within specific cell types, using markers based on Fluorescent Protein expression for flow sorting these cells, and microarray platforms for analysis of their transcriptional activities and protein complements. Current interests include applications of highly parallel platforms for transcript and protein profiling of minimal sample sizes, and for analysis of genetic and epigenetic mechanisms that regulate gene expression during normal development and in diseased states, specifically pancreatic cancer. He is also funded to study factors involved in the regulation of bud dormancy in Vitis vinifera, and has interests in biodiversity and improvement of third-world agriculture. He has published more than 180 scholarly research articles, holds several patents, was elected a Fellow of the American Association for Advancement of Science in 2002, and serves on the editorial board of Cytometry Part A. He is widely sought as a speaker, having presented over 360 seminars in academic, industrial and conference settings. He was elected Secretary of the International Society for Advancement of Cytometry in 2016. Keywords: Plant and Animal Cellular Engineering; Biological Instrumentation; Flow Cytometry and Sorting

Bentley A. Fane, PhD, is a Professor in the School of Plant Sciences, College of Agriculture and Life Sciences and holds a joint appointment in the Department of Immunobiology, Arizona College of Medicine. Dr. Fane has an international reputation for his research into virus structure, assembly and evolution. His research focuses on the viruses of the Microviridae, of which he is considered one of the leading experts. He has been instrumental in defining the biochemical and structural parameters that allow these viruses to replicate and produce progeny in as little as five minutes. The rapid lifecycle has facilitated in depth studies into how viruses evolved resistance mechanism to anti-viral proteins targeting particle assembly.He has published over 60 original research paper in leading scientific journals, including Nature, Molecular Cell, and Journal of Virology, in which his publications on the evolution of resistance mechanisms and kinetic traps have been selected by the journal editors as articles of “significant interest.” He is a frequent presenter at national and international meetings, and has been invited to State of the Art and plenary talks at give the American Society for Virology. He presently serves on the Editorial Boards of two leading virology journals: Virology and the Journal of Virology. At the University of Arizona, Dr. Fane has been actively involved in promoting undergraduate research has been honored with teaching awards on the department, college, and university levels. Keywords: Virus structure and assembly, Viral DNA translocation, Viral evolution

Judith Brown, PhD, and her research interests include the molecular epidemiology of whitefly-transmitted geminiviruses (Begomoviruses, Family: Geminiviridae), the basis for virus-vector specificity and the transmission pathway, and the biotic and genetic variation between populations of the whitefly vector, B. tabaci, that influence the molecular epidemiology and evolution of begomoviruses. Keywords: Plant viral genomics, emergent virus phylodynamics, functional genomics of insect-pathogen interactions