|Jody Banks||Plant Molecular and Developmental Biology |
Dr. Jody Banks studies the unique biology of lower vascular plants. Her research focuses on three areas that provide important insights into the evolution of developmental and adaptive traits in plant, especially those that cannot be understood by studying angiosperm model systems. The first research area is sex determination in gametophytes of the fern Ceratopteris richardii. Dr. Banks’ group has identified more than 100 mutants of Ceratopteris that affect the sex of the gametophyte. By comparing the phenotypes of single and different combinations of double or triple mutants, they have ordered these genes into a sex-determining pathway. They are now attempting to clone these genes to understand this pathway at the molecular level. The second research area is on arsenic hyperaccumulation in the fern Pteris vittata. In collaboration with Dr. David Salt’s group at Purdue University, they have characterized two genes likely to be involved in arsenic metabolism in this plant. The third research area deals with the genome sequence of the lycophyte Selaginella moellendorffii and its comparison to other plant genomes. Dr. Banks discovered that this plant has the smallest known plant genome (110Mbp). Because of its phylogenetic position (between bryophyes and ferns) and small genome size, the Joint Genome Institute agreed to shotgun sequence this genome. The whole genome sequence was released by the Joint Genome Institute in December 2007.
|Leonor Boavida||Plant Cell and Developmental Biology|
Dr. Boavida’s lab investigates the cellular and molecular mechanisms that regulate one of the most impressive examples of cell-cell recognition in plant reproduction, the process of fertilization. Fertilization is defined by the fusion of two haploid sex cells or gametes, the sperm and egg which produce a diploid zygote that initiates a very sophisticated developmental program. But this definition does not capture the full scope of cellular events that evolved as a hallmark of flowering plants: the occurrence of two separate gametic fusions (double fertilization). In addition to the sperm-egg cell fusion, a second sperm fuse with a sister female gamete, the central cell to produce the endosperm whose function is to nurture the developing embryo within the seed. This means that flowering plants likely evolved a new signal transduction machinery to ensure a robust recognition between male and female gametes. However, for the majority of these signaling pathways, the function and the interactions of the molecular intermediates remain to be characterized. Our attention is currently focused on the function of Tetraspanins as scaffolding proteins, and other transmembrane partners that have been identified in the surface of plant gametes as potential mediators of gamete interactions. Our goal is to build a comprehensive “fertilization interactome” that will allow us not only to have a better understanding of gamete factors and signaling pathways controlling reproductive success, but also to quiz the network concerning evolutionary aspects of the fertilization process. The lab incorporates unique experimental tools in the research field using genetic, molecular, functional genomics and live cell imaging.
|Nicholas Carpita||Plant Cell Biology |
Dr. Nick Carpita’s research objectives are to characterize the structural and functional architecture of the plant cell wall, to understand the biochemical mechanisms of biosynthesis of its polysaccharides, and to identify the genes that encode the molecular machinery that synthesizes these components. Specific projects include identifying and characterizing cell wall mutants in Arabidopsis and maize by Fourier transform infrared spectra. Potential mutants identified by this novel spectroscopic method are characterized genetically to determine heritability. A systematic protocol was devised to use biochemical, cytological, and spectroscopic methods to characterize the function of cell-wall biogenesis-related genes in Arabidopsis and maize identified through the mutant screen. Dr. Carpita’s group is classifying mutants by artificial neural networks as a database to classify genes of unknown function. They also develop methods to investigate the biosynthesis and topology of cellulose and the mixed-linkage (1→3),(1→4)-β-D-glucan in maize. They use proteomic and immunological approaches to identify the catalytic machinery and its associated polypeptides. We have also begun a program to characterize the regulation by microRNAs and naturally occurring small interfering RNAs of cellulose synthases and suites of similarly regulated genes in networks that form primary and secondary walls. Finally, we desire to apply our knowledge of cell wall biology to solve practical problems in agriculture. Understanding wall composition and architecture and the regulation of the synthesis of its components is an essential tool in enhancing biomass quality and quantity for biofuel production.
|Zhixiang Chen||Molecular Plant-Pathogen Interactions |
Dr. Zhixiang Chen’s research interests are in two related areas of plant defense responses. The first area concerns transcriptional and post-transcriptional regulation of plant-pathogen interactions. A major focus in this area is on a family of plant transcription factors containing the novel WRKY zinc-finger DNA-binding motifs. Genetic and molecular approaches are being utilized to understand the roles, regulation, and action mechanisms of plant WRKY transcription factors in plant disease resistance. Other research in the area is aimed at understanding transcriptional and post-transcriptional regulation of plant-virus interactions. Specific projects include analysis of host transcription factors recruited by plant pararetroviruses for activation of viral transcription and plant RNA-dependent RNA polymerases in plant antiviral defense. The second research area deals with salicylic acid (SA)-mediated plant defense responses. Although the role of SA in plant defense has been extensively studied, SA synthesis and perception by plant cells have not been fully elucidated. In addition, plants differ greatly in both basal SA levels and SA responsiveness, and the underlying molecular basis for the great variation among plant species is unclear. Dr. Chen’s group is investigating several Arabidopsis mutants deficient in pathogen-induced SA accumulation. Some of the mutants may result from mutations of genes encoding enzymes required for SA biosynthesis and are useful to elucidate the SA biosynthetic pathways in plants. They are also studying a SA-binding protein that may play a role in SA signal perception and contribute to the variation of SA responsiveness among plant species. These studies will help understand the fundamental mechanisms of plant disease resistance and provide potential targets for disease control in crop plants.
|Peter Goldsbrough||Plant Molecular Biology |
Dr. Peter Goldsbrough’s research program is focused on two multigene families in Arabidopsis - metallothioneins (MTs) and glutathione S-transferases (GSTs). Metallothioneins are small metal binding proteins encoded by a small gene family. Recent studies with MT-deficient mutants indicates that MTs are involved in the accumulation of copper and zinc in various tissues including roots and shoots, and the redistribution of these metals during senescence and seed development. The primary reaction catalyzed by GSTs is conjugation of glutzthione to a toxic substrate. We have been studying how herbicide safeners induce the expression of GSTs and other components of the xenobiotic detoxification system, and how GSTs can be used to enhance herbicide tolerance in transgenic plants.
Dr. Goldsbrough is currently not accepting graduate students.
|Anjali Iyer-Pascuzzi||Plant Biology|
Dr. Iyer-Pascuzzi’s research investigates the mechanisms that plant roots use to perceive and respond to the environment. There are two primary areas of research in the lab. The first is focused on understanding the molecular basis of plant resistance to bacterial wilt, caused by Ralstonia solanacearum. Ralstonia is a devastating soil-borne pathogen that first infects root systems. Despite the devastation it causes, little is known regarding the networks that underlie resistance or susceptibility, and root responses to R. solanacearum are unclear. Using both tomato and Arabidopsis, we focus on understanding resistance responses at three levels of root development: root cell types, root developmental stages, and root architecture. Current questions include, what are the spatio-temporal dynamics of pathogen invasion in resistant and susceptible genotypes? How are different root cell types and developmental stages affected by bacterial wilt? What are the gene regulatory networks involved in the response to bacterial wilt within each cell type? We use a combination of cell biology, genetics, and genomics approaches to address these questions. The major goal of this research is to identify novel forms of resistance to bacterial wilt. Our second area of research is centered around the role of Nodule Inception-Like Proteins (NLPs) in root development. NLP proteins are a unique family of transcription factors found in a wide diversity of plant species. We are studying the molecular mechanisms through which these proteins mediate root development and stress responses in Arabidopsis.
|Gurmukh Johal||Molecular Pathology and Genetics|
Dr. Guri Johal’s interests and expertise are in maize pathology and genetics, and he is involved in three areas of research. The first concerns maize’s interaction with Cochliobolus carbonum, which causes a lethal leaf blight and ear mold disease. A key factor in this pathosystem is HC-toxin, a cyclic tetrapeptide, which is absolutely needed by the pathogen to colonize maize tissues. Exactly how HC-toxin evades maize defenses remains elusive, and unlocking this mystery using a combination of genetic, genomic and molecular approaches constitutes a major thrust of the Johal lab. Efforts include an investigation into the evolutionary origin of the Hm1 disease resistance gene. This gene evolved naturally in maize and it confers complete resistance to C. carbonum by inactivating HC-toxin. An allele of Hm1 confers adult plant resistance, as does the functional allele at the hm2 locus. Why and how these genes behave this way is also pursued. Dr. Johal’s second project concerns a class of mutations that are collectively known as disease lesion mimics (DLMs). These mutants are recognized by their ability to produce symptoms that mimic those that are normally produced during maize’s encounter with various pathogens. The Johal lab has contributed substantially in revealing the biological underpinnings some of these DLMs and is continuing to do so for more and more of these mutants. In addition, DLMs are being used as reporters to uncover natural variation capable of suppressing or enhancing their severity. The cloning and characterization of such natural variants are expected to provide valuable tools and targets for coping with a variety of stresses, both biotic and abiotic. The third project area concerns genes and mechanisms that impact the height and quality of the maize stalk. Again, the approach is to generate and/or identify natural mutants that compromise these stalk traits. The genes underlying these variants are then cloned either by transposon tagging or by map-based cloning approaches. Two recent accomplishments in this area include the cloning of the brittle stalk -2 (bk2) and brachytic-2 (br2) genes. While bk2 encodes a COBRA-like protein required to assemble secondary cell walls, br2 encodes a multidrug resistance protein involved in the polar movement of auxins from the top of the plant to the bottom. An ortholog of the br2 gene was shown to be defective in the sorghum dw3 mutant, which despite its instability has been used extensively in sorghum breeding programs. The molecular mechanism underlying dw3 instability and ways to correct it were also revealed.
|Sharon Kessler||Plant Biology|
The Kessler Lab studies the molecular mechanisms that control pollination and seed yield in flowering plants. Our main focus is cell-to-cell communication between the male and female tissues, specifically how the female cells known as the synergids "talk" to the pollen tube and tell it to burst and release the sperm cells so that double fertilization can occur to produce viable seeds. We are also interested in plant-specific family of seven transmembrane proteins called MLOs which play a role in various signaling processes ranging from pollen tube reception to pathogen infection. Our goal is to assign functions to the 15 members of this large gene family and to understand how their subcellular localization patterns relate to these functions. Based on expression analyses, we suspect that some of the MLO genes play roles in earlier stages of intercellular signaling during reproductive development. We use a combination of genetics, molecular biology, cell biology, and live imaging in the model plant Arabidopsis thaliana to study these important signaling molecules.
|Damon Lisch||Plant Biology|
I am interested in the regulation and evolution of plant transposable elements. Transposable elements, or transposons, are, by far, the most dynamic part of the eukaryotic genome, and the majority, often the vast majority, of plant genomes are composed of these genomic parasites. Although they are an important source of genetic novelty, transposons can also be a significant source of detrimental mutations. Because of this, plants (and indeed all eukaryotes) have evolved a sophisticated “immune system” whose function is to detect and epigenetically silence them. My research centers on determining the means by which transposons are detected and then maintained in a silenced state. To do this, the my lab has focused on MuDR, a transposon in maize that can be reliably and heritably silenced by a naturally occurring derivative of that element. In addition to its role in transposon control, epigenetic silencing is employed by plants and animals for a wide variety of other purposes, and epigenetic silencing pathways in plants are particularly diversified. However, whatever else they do, all of these pathways appear to be involved in transposon silencing as well, making transposons an excellent model for understanding how epigenetic information is encoded and propagated. Finally, transposon mobilization and subsequent silencing can have dramatic effects on the expression of plant genes. Current work in the my lab combines a detailed analysis of MuDR transposon silencing with a global analysis of the effects of transposon silencing on plant gene function and phenotypic variation.
|Dr. Scott McAdam||Plant Evolutionary Physiology|
Evolution of drought tolerance and response in plants, from stomatal behavior to xylem physiology and hormones
|Gordon McNickle||Plant Ecology|
Dr. McNickle's research investigates the strategies used by plants to acquire resources, how interactions among competitors, enemies and mutualistic partners alter these strategies, and how all of these interactions shape species coexistence and community structure - with an emphasis on below ground interactions. Most ecological interactions take on all the essential features of a game, and most work in the lab relies on evolutionary game theory as a central tool to make predications about plant systems. Dr. McNickle relies on a mixture of mathematical modeling to develop explicit hypotheses and field or greenhouse experiments as appropriate to test these hypotheses.
|Tesfaye Mengiste||Molecular Genetics of Plant Immunity to Fungal Pathogens|
Research in the Mengiste lab focuses on molecular mechanisms of plant responses to economically important fungal pathogens which reduce crop productivity worldwide. Critical genetic components of plant resistance are identified through genetic and genomic approaches in the model plant Arabidopsis, and two crop plants tomato and sorghum. By applying genetic, molecular, and biochemical approaches, we seek to determine how these key components regulate plant immune responses required for resistance. Molecular and biochemical mechanisms of tomato resistance are studied with a focus on the role of tomato receptor like kinases, and their substrates to shed light on tomato immune responses to broad host fungal pathogens. In parallel, attempts are made to translate some of the findings into genetic improvement of crops for disease resistance. In sorghum, the natural variation in the germplasm is being explored to identify genes or genomic regions that confer broad-spectrum resistance to anthracnose and grain mold diseases. The overarching goal is to expedite genetic improvement of sorghum to increase productivity in disease prone sorghum producing regions.
Current research areas • Arabidopsis immune response signaling, including the role of receptor kinases, transcription regulators and co-regulators, and chromatin modification in fungal and bacterial resistance.
• Molecular mechanisms of tomato resistance to fungal pathogens, with a focus on role of receptor like kinases, regulators of induced systemic resistance to gray mold disease caused by Botrytis cinerea and early blight caused by Alternaria solani.
• Genetic improvement of sorghum for resistance to fungal pathogens. Mechanisms of sorghum resistance to the parasitic weed Striga hermonthica.
|Christopher Oakley||Ecological and evolutionary genetics of plants|
The Oakley lab is broadly interested in the ecological and evolutionary genetics of plants. One main focus of our research is the genetic basis of local adaptation. Local genotypes are often found to grow, survive, and/or reproduce better than non-local genotypes, suggesting that adaptation to one environment is costly in other environments (fitness tradeoffs across environments). Despite much empirical study, little is known about the mechanisms and genetic basis of local adaptation. Using locally adapted populations of Arabidopsis thaliana from near the northern and southern edge of the native rage, we investigate the genetic basis of local adaptation, adaptive traits (e.g., freezing tolerance), and genetic tradeoffs (fitness tradeoffs attributable to individual loci). We have developed a variety of genetic stocks that we use in field and growth chamber experiments in concert with genetic and genomic approaches.
A second main focus of our research is the consequences of genetic drift for adaptation and population persistence. A number of factors common in natural populations (e.g., a history of population bottlenecks) can increase both the chance loss of beneficial mutations and the chance fixation of deleterious mutations. Heterosis, the increased fitness in crosses between populations relative to fitness within populations, is thought to be due in part to the masking of these fixed deleterious recessive alleles in the heterozygous state. We are investigating the geographic pattern and genetic basis of heterosis in natural populations of A. thaliana to study the balance between selection and genetic drift in nature.
|Robert Pruitt||Plant Molecular Biology|
Dr. Bob Pruitt’s research is presently focused on two areas that use basic science techniques to address applied problems. The first involves studying the nature of bacterial interactions with plants, with a particular focus on human pathogens that contaminate fresh produce. The goals of this research are to understand how pathogenic bacteria are introduced into the plant system and what bacterial, plant and environmental factors allow them to survive and proliferate. Experiments utilize techniques ranging from traditional microbiology and genetics to modern sequencing methods to examine the microbial communities associated with commercial produce. The second area is to try and develop a modern plant molecular genetic/genomic system to apply to the study of weed science. Availability of a genome sequence together with a comprehensive set of molecular markers would greatly simplify the study of the natural and selected variation in weed traits that affect weed life history as well as those that impact agriculture.
|Christopher Staiger||Plant Cell Biology|
The Staiger laboratory investigates the molecular and cellular mechanisms that underpin cytoskeletal dynamics in living plant cells. We pioneered the use of quantitative image analysis, high spatial and temporal resolution fluorescence microscopy, and reverse-genetic approaches to test a model of actin turnover. This research has uncovered an amazingly dynamic behavior of the plant actin cytoskeleton and novel activities associated with several conserved actin-binding proteins.
|Dan Szymanski||Cell Biology|
Dan Szymanski's lab is trying to understand how protein complexes can function across wide spatial scales to control cell, tissue and organ morphogenesis. His research combines forward genetics, biochemistry, and multivariate live cell imaging. Plant systems include Arabidopsis and soybean leaf development and physiology, cotton fiber morphogenesis, and seed development in rice. Recently, in collaboration with labs in biological and mechanical engineering his group is combining experimental and computational biology to discover how plant cells dynamically reorganize the cytoskeleton and the cell wall during cell morphogenesis. Iterative cycles of multivariate live cell imaging, finite element computational modeling is leading to realistic and predictive models of plant cell growth control that are enabling cellular engineering. Another major project in the lab is the development of a proteomics pipeline that can be used to discover and analyze protein complexes in both model and crop species.
|Mary Alice Webb||Plant Cell Biology|
Dr. Mary Alice Webb’s research interests center around accumulation of crystalline calcium oxalate by plants. Her research has focused on understanding how plants synthesize raphides, crystals with a needle-like morphology that deters herbivory. Previous research examined the structure and development of the raphides and the specialized cells that produce them. Dr. Webb developed a method to isolate raphides along with their associated intravacuolar organic matrix from grape leaves, enabling characterization of matrix structure and biochemistry. The goal of these studies has been to identify and define the role of specific matrix components in crystal initiation and growth within plant cells. Recent research has employed proteomics methodology in a broad approach to identify raphide-associated proteins, and key proteins identified via this method have been selected for further study. For example, Dr. Webb’s laboratory has identified and cloned a cDNA for a putative oxalate transporter from grape with substantial homology to the human oxalate transporter Slc26a6. Future studies include examining its localization in relation to raphide development and assaying its ability to transport oxalate. In another project Dr. Webb’s lab has examined calcium oxalate formation in kidney-like organs, Malpighian tubules, in larvae of silkworm (Bombyx mori). Unlike calcium oxalate stones in human kidneys, calcium oxalate crystals in Malpighian tubules of silkworm accumulate throughout the larval stage of the life cycle with no apparent harm to the organism. However, structural and biochemical studies of the tubules and their content have revealed that they share common features with human kidneys, indicating that silkworm larvae could provide a simple model system for examining aspects of kidney stone formation.
|Gyeongmee Yoon||Plant Biology|
Dr. Yoon’s research interest lies in understanding of the molecular mechanisms of the key steps in the phytohormone ethylene biosynthesis and its signaling pathway using the model plant Arabidopsis thaliana. The gaseous hormone ethylene regulates many important plant growth and developmental processes, including seed germination, root hair formation, nodulation, senescence and response to a variety of developmental and environmental stresses. Two main research projects are currently under way in the lab. First is to investigate the molecular mechanism regulating protein turnover in ethylene biosynthesis. Specifically, we are aiming to understand the roles of phosphorylation in protein turnover of the 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), a key enzyme in the ethylene biosynthesis and the Ethylene Overproducer 1 (ETO1)/ETO1-like (EOL) proteins, ubiquitin ligases that target a subset of ACS for degradation. Besides, we are also interested in identification and characterization of novel proteins regulating ethylene biosynthesis to acquire better insight in the molecular aspects of ethylene biosynthesis regulation. Secondly, we are focusing on elucidation of the roles of Constitutive Triple Response 1 (CTR1), a Raf-like protein kinase that acts as a negative regulator, in the ethylene signaling pathway. Ethylene is perceived by a family of ethylene receptors that are derived from two-component histidine kinase, and the receptors are located at the Endoplasmic Reticulum (ER). Recently, we resolved one of the longstanding questions in the ethylene signaling fields how ethylene signals are transduced from the ER to the nucleus to activate ethylene responsive genes in the nucleus. In the absence of ethylene, CTR1 phosphorylates EIN2, a critical positive regulator in the pathway, which blocks an activating proteolytic cleavage. In response to ethylene, the inactive CTR1 fails to phosphorylate EIN2, which is then cleaved by an unidentified protease, releasing the C-terminal domain that then migrates into the nucleus where it activates the transcription factor EIN3, either directly or indirectly, to regulate ethylene-mediated gene expression. Elucidation of the mechanism for regulating EIN2 in the ethylene signaling pathway bridges the gap between the signaling events from the receptor at the ER to the nucleus. However, this also raises a number of intriguing questions and our lab is particularly interested in understanding: 1) how do the ethylene receptors activate CTR1 in the early step of the ethylene signaling pathway?; 2) how does the ethylene response induced by the activation of EIN2 is turned off in the nucleus?; 3) and what are the roles of CTR1 other than phosphorylating EIN2 at the ER. We use the combination of biochemistry, genetics, cell biology and molecular biology approaches to address these questions.
Endomembrane trafficking is essential for plant growth and development and is involved in multiple aspects of plants' interaction with the environment. Dr. Zhang is interested in understanding the mechanisms of macromolecule transport between different organelles and the temporal and spatial regulation of the trafficking process. She is using high-throughput chemical library screening to identify compounds that target specific trafficking process and then use conditional genetic screening to identify novel cellular components that are involved in the same process. It allows her to observe and document direct and instant cellular response upon trafficking machinery interruption by short-term compound treatment combined with live cell imaging. Mutations in genes that are involved in trafficking process may show altered response to compound in compare with the wild-type plants. Due to the conservation of trafficking machinery between different organisms, her research topic provides opportunities in collaboration with plant pathologist in understanding plant-microbe interaction and biomedical researchers in studying human disease control. Dr. Zhang is currently recruiting talented individuals who are interested in plant cell biology, especially in the subject of endomembrane trafficking. Please contact Dr. Zhang at email@example.com
or 765-496-3855 if you would like to know more information about ongoing projects.
|Yun Zhou||Plant Cell and Developmental Biology|
The research of Dr. Zhou's group focuses on understanding the cellular and molecular mechanisms controlling stem-cell identity and function during plant development, combining both experimental and computational approaches (quantitative cell and developmental biology). We are studying transcriptional circuit, stem cell dynamics, cell-cell communication, and shoot growth and development using combined methods, including molecular genetics, cell biology, live imaging, computational quantification and modeling, biochemistry, and functional genomics. We aim to uncover the fundamental principles of plant stem cell behavior, and potentially boost biomass production and grain/fruit yield through optimizing and programming stem cell numbers and activities.