PMPB Faculty
| Lorinda K. Anderson |
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Assistant Professor - Department of Biology
Research Web Page Research Interests: We work on the events that occur during the unique first division of meiosis when homologous chromosomes pair, synapse (with the formation of synaptonemal complexes = SCs), and genetically recombine. Using spreads of meiotic chromomosomes and light and electron microscopy (LM and EM), we examine SCs to determine how chromosomes behave during synapsis. Meiotic recombination probably occurs in structures called recombination nodules (RNs) that are associated with SCs during synapsis. RNs are directly visible only by using EM. There are two types of RNs, early RNs (that may be involved in early recombination events and possibly also synapsis) and late RNs (that mark crossover sites). The primary focus of the lab now is in analyzing the role(s) of different recombination-related proteins in the process of synapsis and recombination in tomato using immunofluorescence (LM) as well as immunogold (EM) techniques. We are also examining how the behavior of these proteins is influenced during meiosis in tomato synaptic mutants. We are also examining how chromosomal aberrations (inversion heterozygotes) alter crossover patterns in mice. |
| Patricia A. Bedinger |
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Professor - Department of Biology
Research Web Page Research Interests: The work in my laboratory centers on pollen development and function in higher plants, using Arabidopsis, tomato and maize as model organisms. Our major focus is on the molecular analysis of pollen and pistil proteins that mediate sexual recognition in higher plants via specific protein-protein interactions. |
| Asa Ben-Hur |
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Assistant professor - Department of Computer Science
Research Web Page Research Interests: My research area is computational biology. My recent and ongoing projects focus on prediction of various properties of proteins: their function, interaction partners, and remote homologs. My work involves integrating diverse genomic data including protein sequence, structure, expression, and various annotations using tools of machine learning. |
| Mark A. Brick |
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Professor - Department of Soil and Crop Sciences
Research Web Page Research Interests: I have been involved in teaching, research and outreach at the university level for over 24 years. As the leader of the Colorado State University Dry Bean Breeding Project (DBBP), I am responsible for development of dry edible bean varieties for irrigated and non-irrigated production in Colorado. The DBBP has released 5 varieties in the pinto and black bean market classes since 1995. My research interest are in the area of plant disease resistance and crops for health. I utilize molecular tools to tag diesease resistance genes and better understand the genetic and metabolomic funciton that define the posistve health properities of dry beans in the human diet. I have served as major professor for 25 M.S. and 4 Ph.D. students, authored or co-authored more than 43 refereed publications and over 100 non-refereed bulletins, extension reports and papers. |
| Daniel R. Bush |
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Professor and Chair - Department of Biology
Research Web Page Research Interests: My research focuses on sugar and amino acid allocation from sites of primary assimilation to import-dependent sinks in plants. This is a fundamental process that allows plants to function as multicellular organisms. We use molecular, genetic and biochemical tools to define the mechanisms and regulation of this essential process. |
| Patrick F. Byrne |
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Associate Professor - Department of Soil and Crop Sciences
Research Web Page Research Interests: Our major interest is to apply quantitative and molecular genetics to crop improvement. Emphasis has been on using molecular markers to determine genetic control of abiotic stress tolerance and end-use quality in wheat, and fungal disease resistance in common bean. Recent initiatives have included (1) a public outreach program on methods, benefits, and risks of agricultural biotechnology; (2) studies to estimate the level of pollen-mediated gene flow in maize and wheat under Colorado conditions; and (3) investigation of genetic variation for disease prevention factors in beans and wheat. |
| Stephen Chisholm |
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Assistant Professor - Department of Bioagricultural Sciences and Pest Management
Research Interests: Our laboratory studies interactions between plant pathogens and their hosts. We are particularly interested in bacterial proteins (effectors) delivered to host cells during the infection process. Bacterial pathogens may inject between twenty to thirty unique effectors into host cells during infection. Our current understanding suggests many effector proteins function as enzymes or enzyme inhibitors that interact with host proteins in order to modulate various host cell functions. However, the specific molecular function and host targets of most effectors remain unknown. Currently, we are characterizing the functions of several specific effectors and determining their targets. Furthermore, we are using genomic techniques to identify host variability leading to increased susceptibility and resistance to pathogens. |
| Scott D. Haley |
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Professor - Department of Soil and Crop Sciences
Research Web Page Research Interests: Dr. Haley serves as project leader of the wheat breeding and genetics program. His research focuses on the genetic improvement of hard red and hard white winter wheat for yield, end-use quality, and biotic and abiotic stresses prevalent in Colorado and the central and southern Great Plains. Current research emphasis in the program includes: Russian wheat aphid resistance, whole-grain near infrared reflectance spectroscopy (NIRs) for wheat quality assessment, molecular marker assisted selection. |
| Ann Hess |
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Assistant Professor - Department of Statistics and Center for Bioinformatics
Research Web Page Research Interests: Microarray Data Analysis and Bioinformatics, Linear and Mixed Models, Experimental Design |
| Hari K. Iyer |
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Professor - Department of Statistics
Research Web Page Research Interests:
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| Paul Kugrens |
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Professor - Department of Biology
Research Web Page Research Interests: Ultrastructural investigations on phytoplankton and heterotrophic flagellates are emphasized in my laboratory. We are studying the phylogeny, systematics and ecology of cryptomonads, an ecologically important group in Colorado, and other related protists, using scanning and transmission electron microscopy. |
| Nora L. Lapitan |
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Professor - Department of Soil and Crop Sciences
Research Web Page Research Interests: I am interested in fundamental understanding of how living organisms function at the level of the gene and genome. I have long been fascinated by the "intelligence" of the DNA - how its structure fits its function, and how the DNA evolves to respond to the needs of the organism. My research projects have focused on investigating genome organization, gene expression and recombination, and identification of genes involved in specific plant phenotypes, with emphasis on converting basic knowledge for practical use in improving plant crops. My current research projects include: 1) the study of molecular and evolutionary mechanisms of interaction between pests and plants; 2) molecular genetic dissection of complex traits in wheat and barley; and 3) use of molecular markers for marker-assisted-selection in breeding. Technologies used in my laboratory include cytogenetic techniques [i.e., microscopy, fluorescence in situ hybridization techniques FISH)], molecular marker technologies, single nucleotide polymorphism analysis, mapping strategies, development of genomics tools such as expressed sequence tags (ESTs) and bacterial artificial chromosome (BAC) libraries, use of bioinformatics tools and software programs, and functional genomics techniques including microarrays. |
| Jan E. Leach |
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Professor - Department of Bioagricultural Sciences and Pest Management
Research Interests: The incorporation of disease resistance genes into plants through breeding practices is the most cost-effective and environmentally sound means to control plant diseases. Although widely practiced, the use of single genes for resistance as a control strategy often fails because plant pathogen populations change so that the resistance genes are no longer effective. The goal of our work is to understand the molecular processes in the interactions between the host and pathogen that ultimately lead to disease resistance or susceptibility to allow for the development of more durable and broad spectrum disease resistance strategies. For these studies, we use a model system that involves interactions between rice (Oryza sativa) and the bacterial blight pathogen Xanthomonas oryzae pv. oryzae or the rice blast pathogen Magnaporthe grisea. One part of our group explores pathogen components that are involved in induction of disease and/or resistance. Another part of the group explores host defense responses, working towards understanding the molecular basis for rice disease resistance governed by multiple genes (quantitative disease resistance) as well as the signal pathways involved in resistance governed by single genes (qualitative disease resistance). |
| John McKay |
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Assistant Professor - Department of Bioagricultural Sciences and Pest Management
Research Web Page Research Interests: I study the evolutionary genomics of local adaptation and range expansion in natural plant populations. Evidence for local adaptation in plants is abundant. What is missing is knowledge of the traits and genes that confer adaptation to specific environments. An understanding of the traits involved in adaptation to particular stresses (e.g. drought) is needed for both applied (crop breeding, conservation, invasive species) and theoretical questions in ecology and evolution. Genomic data are needed to answer whether adaptations are due to: many genetic changes or only a few? New mutations or older alleles that persist at some frequency throughout the species range and history? More generally, understanding the ecological physiology and genomics of adaptation to local environmental stressors is fundamental to our understanding of evolution and biodiversity of both native and invasive species. |
| June I. Medford |
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Associate Professor - Department of Biology
Research Web Page Research Interests: I am interested in how plants grow and develop. Plants, unlike most organisms, develop throughout life meaning that the genes and signals controlling plant development must be continuously operating. Our approach uses molecular and genetic tools with the model plant, Arabidopsis. |
| Lee Panella |
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Research Geneticist - Crops Research Lab
Research Web Page Research Interests: I am interested in using the genetic resources present in the wild relatives of the sugar beet to improve the performance of cultivated hybrids. This includes using molecular tools and traditional techniques to understand the host pathogen interaction between sugar beet and its major pathogens, as well as the genetic diversity in both pathogen and plant populations. We are discovering the basic genetic mechanisms behind important physiological process, ranging from disease resistance to the biennial control of flowering. |
| Marinus Pilon |
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Associate Professor - Department of Biology
Research Web Page Research Interests: Plant mineral nutrition limits photosynthesis and yield but also affects the nutritional value of crops. Photosynthesis requires the acquisition and correct intracellular delivery of metal ion cofactors. What are the mechanisms for the delivery, assembly and regulation of Cu and Fe cofactors in the chloroplast? To address these questions we use a combination of genetics, biochemistry and whole plant physiology to first identify components involved in metal ion delivery and next study their activity and regulation with the aim to understand homeostasis. We work mainly with Arabidopisis but other plants are also studied. |
| Elizabeth A. H. Pilon-Smits |
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Associate Professor - Department of Biology
Research Web Page Research Interests: In the Pilon-Smits lab we study processes by which plants accumulate and detoxify environmental pollutants, from the molecular level to the field. Our approaches include genomics, genetics, biotechnology, biochemistry, whole-plant physiology, and ecological studies. These studies are aimed to gain knowledge about basic biological processes, and to create plants that may be used for environmental cleanup. |
| Rajinder S. Ranu |
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Professor - Department of Bioagricultural Sciences and Pest Management
Research Web Page Research Interests: Research in our laboratory focuses on the mechanisms of translational regulation of gene expression. For this purpose, Figwort Mosaic Virus (FMV) is being used as a model system. FMV circular double stranded genome of about eight kilobases expresses viral gene by an unconventional mechanism in which full-length viral transcript is used to express multiple genes. The underlying mechanism involved in the expression of multiple genes is not well understood. The spacing of start and stop codons and the overlap of start and stop codons that separate each cistron raised the possibility of translational coupling similar to that observed in prokaryotes. In vitro studies performed with the full-length transcript using rabbit reticulocyte lysates to monitor synthesis of viral gene products suggest the involvement of translational coupling in the expression of these genes. These studies have also raise the possibility that mechanism(s) other than ribosome scanning model in the protein chain initiation may account for these results. In addition, the regulation of protein chain initiation by covalent modification of protein factors is under investigation. |
| A.S.N Reddy |
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Professor - Department of Biology
Research Web Page Research Interests: One of the fundamental questions in plant biology is how hormonal and environmental signals regulate cellular processes and various aspects of plant growth and development. We are interested in understanding the mechanisms by which plant cells sense and respond to various signals. Our current research activities are focused on three areas: i) calcium-mediated signal transduction mechanisms with emphasis on calcium sensors and their target proteins, ii) mechanisms that regulate basic and alternative splicing of pre-messenger RNAs, and iii) designing and testing of novel synthetic signal transduction circuits in plants. |
| Mark P. Simmons |
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Assistant Professor - Department of Biology
Research Web Page Research Interests: My research program consists of two interrelated components: phylogeny and taxonomy of the flowering-plant family Celastraceae (the spindle-tree family), and conceptual aspects of molecular phylogenetics (using genomic data to reconstruct evolutionary relationships among species). The Celastraceae are a large family, primarily of lianas, shrubs, and trees with a sub-cosmopolitan distribution. Within the family, the aril has undergone tremendous diversification and ranges in form from a mucilaginous pulp to a broad wing. I am working to assess overall relationships within the family and track the pattern of aril diversification. For my conceptual research, I am working on problems such as: how alignment changes with increasing genetic distance, the trade-offs of using either nucleotide or amino acid characters, the incorporation of duplicate genes into phylogenetic analyses, the measurement of phylogenetic signal, and the use of morphological characters when entire genomes are sequenced. Molecular phylogentics is playing an increasingly central role in biology, from inferring the diversification of multigene families, to tracking invasive species, conservation of protected species, as evidence in criminal investigations, and fighting bioterrorism. |
| Stephen M. Stack |
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Professor - Department of Biology
Research Web Page Research Interests: Our lab works on chromosomes, with two emphases: 1) Genetic recombination. For this, we study the synaptonemal complex (SC), recombination nodules (RNs), and chiasmata in prophase I of meiosis. RNs are located at crossover sites on SCs where chiasmata will form. We analyze crossover interference by determining the distribution of early and late RNs on SCs in normal and structurally rearranged chromosomes. For this we use electron microscopy of chromosomes from a variety of plant species, including the model species tomato and maize. 2) Sequencing the tomato genome as the model species for the important plant family Solanaceae. Our role in this project is to help confine the sequencing effort to euchromatin where most of the genes are located. For this, we use fluorescence in situ hybridization (FISH) to determine the location of 100-200 kb segments of tomato genomic DNA on tomato pachytene chromosomes in which euchromatin and heterochromatin can be distinguished. These DNA segments are inserts in bacterial artificial chromosomes (BACs) that are part of BAC libraries containing most if not all of the tomato genome. Sequencing can proceed from these anchors BACs with assurance that DNA in euchromatin is being sequenced. |
| Cecil Stushnoff |
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Professor - Department of Horticulture and Landscape Architecture
Research Web Page |
| Henry J. Thompson |
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Professor and Director - Cancer Prevention Laboratory, Department of Horticulture and Landscape Architecture
Research Web Page Research Interests: Thompson's current research deals with establishing the role of antioxidant phytochemicals in whole foods and of antioxidant supplements in cancer prevention in both clinical studies and laboratory model systems. He is particularly interested in how antioxidants modulate the oxidation of DNA and lipids in vivo, and whether changes in the oxidation of these macromolecules alters the risk for cancer. He has a long standing interest in the chemoprevention of breast cancer and maintains an active program of clinical and laboratory research that addresses this topic. Thompson's laboratory also is investigating the mechanisms underlying the cancer inhibitory activity of energy restriction and exercise. The focus of these studies is on identifying the cellular processes and molecular machinery by which these interventions regulate tissue size homeostasis and inhibit the carcinogenic process. |
| Jorge M. Vivanco |
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Associate Professor - Department of Horticulture and Landscape Architecture
Research Web Page Research Interests: Our lab studies plant-plant, plant-microbe and multitrophic interactions that occur in the rhizosphere. In the past, we have focused our attention on underground processes initiated by root exudates, and are now expanding this research to study processes initiated by microbes through the secretion of chemicals and emission of volatiles. A significant part of our effort is focused on understanding the molecular basis of root secretion of phytochemicals. |
| Gayle Volk |
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Plant Physiologist - Department of Horticulture and Landscape Architecture
Research Web Page Research Interests: I am one of three scientists within the Plant Germplasm Preservation Research Unit at the NCGRP. Our facility is part of the USDA-ARS National Plant Germplasm System which collects and maintains more than 450,000 plant accessions. The mission of our unit is to develop improved strategies and technologist for preserving plant genetic diversity in ex situ genebanks. Cryopreservation is one method employed for long-term storage of plant genetic resources. My research program focuses on identifying mechanisms that enable propagules to tolerate low temperature and desiccation stresses using biophysical, ultrastructural, molecular, and physiological techniques. We are also examining the metabolic pathways that lead to repair and recovery of cryopreserved germplasm. With a focus on clonal germplasm collections, we are designing collection and preservation strategies that efficiently capture genetic diversity. We have used AFLPs and SSRs to characterize the genetic diversity of collections and develop core collections. |
| Stephen J. Wallner |
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Professor - Department of Horticulture and Landscape Architecture
Research Web Page |
| Christina Walters |
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Plant Physiologist/Res Leader - USDA National Seed Lab
Research Web Page Research Interests: I am interested in processes that occur during late embryogenesis in plants. During the late stages of embryo maturation, seeds of some species acquire extreme tolerance to desiccation stress and then the ability to survive for long periods in the dry state. The ability to survive these extreme stresses is fundamental to our understanding of seed quality in agriculture and has many applications in the food and pharmaceutical world. The gene products that confer tolerance are poorly understood. Candidate gene products include a family of genes producing LEA (late embryogenic abundant) proteins that are highly soluble but have no known catalytic function. Research efforts in my lab focus on the biophysical properties related to protection mechanisms. Research efforts are also directed towards understanding the physiology of seeds native to the US in order to improve their conservation. |
| Sarah Ward |
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Associate Professor - Soil and Crop Sciences
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