Projects
Projects
There are eight participating laboratories each with several projects available for undergraduate research.
Dhingra Laboratory - Genomics/Bioinformatics/Biotechnology
Project available for undergraduate reasearch
Characterization of plastid developmental transitions in fruit: The project focuses on characterization of developmental transitions in the plastids of perennial fruit epidermis such as apple, pear, cherry and grape. Most important metabolic pathways relevant to post-harvest quality involve the plastidial compartment. We are integrating microscopic, bioinformatics and transcriptomics approaches to study this aspect of fruit development. Undergraduate students Emily Rose Rodgers, Michaela Quickstad, Brittany Urso and Jennifer Hartwig have contributed to several aspects of this project and presented their research as poster presentations. The lab is leading the genome sequencing of double haploid apple, pear and cherry and this information will further benefit this project. Some of the interesting genes found in apple are being tested functionally via plastid and nuclear transformation. Kiara Little, a visiting undergraduate student from Fort Valley State University performed chloroplast transformation experiments in summer 2011 to enable functional characterization of some of the genes.
Photosynthesis engineering to enhance plant-based food and fuel production: Plants use C3, C4 or CAM metabolic pathways to increase the efficiency of carbon capture. In collaboration with Gerald Edwards, we are characterizing a novel single cell C3/C4 plant species. Also, we are working on engineering bicarbonate transporters in tobacco using chloroplast transformation. This is an ideal project for an undergraduate student to be involved in to address some of the relevant issues of our times.
Fruit biotechnology: There are several ongoing project related to fruit biotechnology. One of the major ones is using tissue culture methods to rapidly micropropagate recalcitrant perennial cultivars of apples, pears and grapes. Over the years, 12 undergraduate students, Cory Druffel, Christina Duncan, Nohely Valesquez, Danielle Druffel, Justine Poff to name a few, have taken part in protocol development and actual production of tissue culture plants. This continues to be an active area where we have developed novel, environmentally friendly bioreactors with the help of two engineering undergraduate students Payden Waldo and Amanda Porter. This is one project where undergraduate students continue to be trained in. We are also developing early flowering transgenic material in apple using some MADS box genes. This project is conducted by my post-doc Dr. Derick Jiwan and several undergraduate students – Thomas Contreras, Christopher Vincent, Florita Garcia have been involved.
Chloroplast genomics: In 2005, I developed a rapid method to determine chloroplast genome sequence using a simple PCR based approach called ASAP (Dhingra and Folta, 2005). The lab has worked with several other labs in enabling such methodology that usually involves undergraduate or high school students.
As is evident most projects in the lab are a great avenue for undergraduate research training. The students will be offered a choice to participate in any of the projects based on their interest or the PI will engage them in any one of the above mentioned projects.
Schroeder Laboratory - Plant Pathology/Genomics
Project available for undergraduate reasearch
Ecology of Infected Onion Bulbs: One of the first things we did was to start isolating bacteria from infected and symptomatic onion bulbs. Initially, we did not expect E. cloacae to be a big player. What we discovered is that when we isolate from onion bulbs, 50% of the time we do not identify a bacterium that fits into the previously known pathogen groups for onions. For the other 50% of the time, we identify a large % of E. cloacae (~50%) and E. cloacae with the other pathogens. We think there could be some interesting pathogen-pathogen interactions that occur in onion bulbs. We have developed a hybridization probe and PCR primers for definitive identification of E. cloacae to complete this analysis.
Impact of curing temperature and duration on disease progress of bacterial diseases in storage: We have completed two years of data studying the impact of curing temperature and duration on the disease progression of E. cloacae in onion bulbs. We have expanded these studies to include Burkholderia cepacia and Burkholderia gladioli pv. allicola and Pantoea ananatis, P. agglomerans and P. allii. These data were published in Plant Disease. Numerous undergraduates support a postdoc and a graduate student in the completion of this project.
Molecular characterization of E. cloacae: Genetic Diversity: E. cloacae is ubiquitous in nature and is an opportunistic pathogen of humans. We are in the process of completing a multilocus phylogeny demonstrated that strains of E. cloacae obtained from onion bulbs occupy a well-supported clade distinct from isolates of medical origin. An undergraduate research associate, Juan Peña an undergraduate student is completing this work.
Biofilm Formation and Colonization of Onion: The ability to form biofilms can be critical to a bacteria‟s ability to colonize plant tissue. We have generated a mini-Tn5 library of E. cloacae. In addition, a biofilm assay was developed and ~50 congo red mutants were screened for their ability to form biofilms. In conjunction with an undergraduate research associate, Nathan Peterson, it was determined that E. cloacae can move through onion leaf tissue at a rate of approx. 2 cm per week. We would like to complete colonization studies on onion bulb tissue and excised and intact onion leaf tissue. We would like to get an undergraduate involved in this project to complete these experiments.
The search for pathogenicity determinants: In an effort to identify genes involved in the production of this necrosis-inducing product and pathogenicity, Dr. Jodi Humann, a postdoctoral research associate and an undergraduate research associate, Austin Bates (now a graduate student in the laboratory) developed an onion slice assay. This assay enabled the high-throughput screening of mini-Tn5 mutants of E. cloacae and the identification of putative pathogenicity-minus mutants. These mutants are currently being characterized. There are numerous opportunities for an undergraduate researcher to mine the genome for genes with potential to contribute to pathogenesis, delete those genes and determine the role in pathogenesis.
Development of a DNA macroarray for the detection of bacterial and fungal storage rot pathogens of onion bulbs: Currently, 11 bacteria, 14 fungi, and 1 yeast are known to cause onion bulb rots in storage, typically without visual symptoms of infection evident in the crop at harvest. This means growers may unknowingly be at risk for substantial losses during storage, after an entire season of expenses. The overall goal of this project is to develop a robust, sensitive, and rapid DNA macroarray to detect and differentiate bulb rot pathogens before bulbs are placed in storage. Numerous undergraduates support a postdoc and a graduate student in the completion of this project.
The diversity of research projects listed above presents numerous opportunities for an undergraduate researcher to complete applied and molecular research in the Schroeder laboratory. Undergraduate researchers would have the opportunity to participate in any of the projects listed above.
Kalyanaraman Laboratory - Computational Biology
Project available for undergraduate reasearch
Design of parallel algorithms for data-intensive applications in computational metagenomics: The aim is to design new parallel algorithms for data-intensive applications in computational biology. More specifically, we are developing graph-theoretic algorithms that can scale to petascale and exascale. These graph kernels have direct applicability to applications stemming from the areas of metagenomics, metaproteomics and phylogenetics. Examples which will be target applications include: i) protein family identification from metagenomic data sets; ii) identification of peptides using tandem mass spectrometry data; and iii) clustering and consolidation of computer-generated phylogenetic trees. Computationally, this involves designing parallel algorithms for large-scale graph construction, implementing graph-theoretic queries and heuristics, clustering of data, sequence matching, string indexing data structures, and database search. Target hardware/architectures include distributed memory machines, and shared memory machines. Parallel paradigms used include MPICH, multi-threading and Map-Reduce. Typical undergraduate research components will include algorithm design and code implementation of research components for deployment on parallel computing platforms including the NSF TeraGrid.
Comparative plant Genomics: This project is in collaboration with the PI (Dhingra). The project aims at developing new computational frameworks for supporting large-scale analysis for genomic sequence data generated from next-generation sequencing platforms. Principal components include i) tree fruit genome/DNA assembly and comparison (e.g., apple, pear, cherry, peach), and ii) implementation of a computational framework to support PCR-enabled targeted resequencing. Algorithmically, the computation involves string matching, building string indexing data structures and pattern matching, and designing combinatorial optimization methods to identify DNA level differentiators across strains. Typical undergraduate research components will include algorithm design, code implementation and webpage creation to support the project‟s software outcomes.
Knowles Laboratory - Plant Physiology/Biochemistry
Research areas in the Knowles laboratory cover – vegetable crop physiology and production with special emphasis on postharvest physiology of potatoes; potato production, variety development, storage, and processing; physiology and biochemistry of seed ageing and factors affecting the productivity of seed potatoes; development of sprout inhibitors; physiology and biochemistry of wound-healing and suberization.
Potatoes are propagated vegetatively from virus-free seed-tubers stored prior to planting. Storage conditions can influence the rate of ageing, which subsequently affects plant growth and crop yield. Using potato as a model, we are investigating metabolic changes associated with loss of vigor and growth potential during ageing. Ongoing studies include a focus on: oxidative processes and associated defense mechanisms in the ageing process; age-induced changes in energy metabolism during sprouting; mechanisms of phospholipid and fatty acid catabolism relative to deterioration in membrane function during ageing; role of NADPH oxidase in the age-induced loss of hypersensitive response and wound-healing ability of tubers; and mechanisms by which proteins become targeted for proteolysis during tuber ageing.
Applied research includes techniques to manipulate apical dominance of seed-tubers to optimize tuber set and size development in relation to market requirements, biochemical/molecular markers of apical dominance and yield potential in seed-tubers, discovery and development of sprout inhibitors, in-season stresses affecting storability and postharvest quality, storage management techniques to preserve processing quality, and potato variety development. My program evaluates the storability, processing quality, and culinary attributes of clones and cultivars in The Pacific Northwest Potato Variety Development Program (WA, ID, OR). We thus have access to potato genotypes with differential susceptibility/resistance to major pathogens, insects, cold/heat tolerance, drought, etc. The germplasm from this program offers a unique opportunity for fundamental research on the metabolic bases of resistance/susceptibility to various biotic and abiotic stresses in potato. This is the project that an undergraduate student will be involved in.
Poovaiah Laboratory - Plant Physiology/Calcium Signaling
The research in B.W. Poovaiah‟s laboratory is focused on the role of calcium/calmodulin-mediated signaling in plant growth and plant:microbe interactions. By identifying, characterizing and manipulating calcium/calmodulin-binding proteins, Poovaiah‟s laboratory has produced a series of breakthroughs on calcium/calmodulin-mediated regulation of plant growth (Nature 437:741-745, 2005), plant-microbe interactions during bacterial and fungal symbioses (Nature 441:1149-1152, 2006) and plant immune/defense responses (Nature 457:1154-1158, 2009; highlighted in Cell 136:193-195, 2009). Recently, Poovaiah‟s team documented the role of a calcium/calmodulin-regulated receptor-like kinase in cold tolerance in plants (J. Biol. Chem. 285:7119-7126, 2010).
Poovaiah‟s laboratory is actively involved in integrating their findings into the broader educational arena. His laboratory has a long history of active involvement in training undergraduate students in molecular biology/biotechnology and preparing them for careers in science. Prior on-site REU participants have experienced the atmosphere of an active biotechnology research laboratory. Poovaiah‟s laboratory has emphasized minority students and women in their selection process and they have trained numerous undergraduate students. One example is the success of an undergraduate student, Ms. Kayla Simons, who earned a co-authorship in their laboratory‟s most recent publication in Nature (Nature, 2009, 457:1154-1158). WSU has highlighted Kayla‟s success in Poovaiah‟s laboratory in several write-ups emphasizing her undergraduate status and the benefits of the NSF – Research Experience for Undergraduates (REU) program.
Undergraduate students will have the opportunity to carry out research projects in a laboratory setting utilizing standard research laboratory facilities, plant growth rooms and greenhouses. They will be exposed to various cutting-edge techniques used in molecular plant science/biotechnology, physiology, biochemistry and genetics. They will have the unique opportunity to grow and observe various mutant plants that behave differently under varying environmental conditions. In addition, students will be able to get involved in understanding how some of the mutant plants respond to both biotic and abiotic stresses.
Evans Laboratory - Plant Genetics and Breeding
Project available for undergraduate reasearch
Apple breeding program: WSU‟s apple breeding program is based at Washington State University‟s Tree Fruit Research and Extension Center in Wenatchee under the management of the Evans Lab. The breeding program started in 1994 and at any one time has around 15,000 individual fruiting trees of different identities in the ground for assessment. Seedlings derived from controlled REU Site – Plant Genomics and Biotechnology Amit Dhingra crosses (hand-pollinations) are screened for resistance to fireblight (Erwinia amylovora) and mildew (Podosphaera leucotricha) in the greenhouse and field before being budded in the nursery onto a dwarfing precocious rootstock. After planting in the selection orchards, seedlings are assessed for fruit quality both at harvest and after 2 and 4 months in cold-storage. The better individuals are propagated for Phase 2 advanced selection testing at 3 sites in central Washington. After 4 or 5 years in Phase 2 orchards, elite selections are propagated for Phase 3 testing on grower sites. Opportunities are available for undergraduates to learn the different stages of the breeding program and selection techniques as schedules permit through the year. An example of a more specific project could be looking at ways to improve seedling growth in the greenhouse in a new potting system that we recently developed to allow for routine marker-assisted seedling sampling.
DNA screening: In order to improve the efficiency of the breeding program, we have been working in collaborative projects to develop and apply DNA-based markers to the breeding germplasm both to increase the information available when making crossing decisions and to screen and cull seedlings early in the program. Undergraduate students could join the collaborative effort of the Evans and Dhingra Labs to analyze breeding progenies and germplasm collections for variable alleles with a view to develop new DNA-based markers and understand more about the genes and gene products isolated in the Dhingra lab.
Pear rootstock breeding: WSU is initiating a pear rootstock breeding program with the development of a collection of pear germplasm at the university‟s Sunrise orchard. The availability of germplasm together with the new pear genome sequence (Dhingra lab) lends itself to multiple small undergraduate projects looking at the variability of alleles with the different phenotypes available. Very little research, either national or international, is undertaken on pear. The potential for some really useful data from these projects is great.
Killinger Laboratory - Food Biotechnology
Project available for undergraduate reasearch
Pre-Harvest Factors Influencing Produce Food Safety: Our laboratory performs observational environmental studies to investigate prevalence of foodborne pathogens (E. coli O157 and Salmonella) and indicator organism levels (total and fecal coliforms as well as generic E. coli) in compost and irrigation water and evaluates the potential transfer to soil and produce in an organic farming system. Components of the compost study were presented as an undergraduate research poster by Loni Watson and Dianne Rider. Pathogen isolates from the organic farming system were the focus of an undergraduate research project and paper by Kelli Wuerth. We are also evaluating irrigation water quality in several regions of Washington to examine the ability of current recommended water quality standards to predict pathogen risk. Components of the irrigation water examination were presented as an undergraduate research poster by Renee Espinosa and Katherine Warren.
Validation of antimicrobial interventions for small-scale and mobile poultry slaughter operations: Our laboratory has performed laboratory and field studies to assess the ability of lactic acid, chlorine and peroxyacetic acid to reduce pathogen and indicator organism levels on poultry carcasses. We have validated a three minute, 2% lactic acid rinse that produced significant reductions in Salmonella and indicator organisms compared to chlorine. Two graduate students have contributed to these projects.
Validation of antimicrobial interventions for apple packing operations: We are conducting laboratory and packing plant studies to validate antimicrobial interventions commonly used in the apple industry, chlorine, chlorine dioxide and peroxyacetic acid. Providing data based on concentrations and application times relevant to the industry is important due to lack of scientific data using industry-relevant parameters. Three concentrations and three to four application times are being examined for each compound. Laboratory examinations involved E. coli O157:H7 and generic E. coli. A literature review and initial studies to develop apple inoculation methods for this project were performed as an undergraduate research project by Elizabeth O’Daffer. Two graduate students and a technician contribute to this project.
Validation of antimicrobial interventions for small-scale, organic leafy greens operations: Our laboratory has performed laboratory and field studies to assess the ability of lactic acid, citric acid and white vinegar to reduce pathogen and indicator organism levels on lettuce. Laboratory studies involve E. coli O157 and field studies utilize indicator organisms. We are working with a producer interested in identifying an organic acid rinse that can be used in small-scale lettuce packing operations. A technician leads project coordination.
Examination of food service rinsing and soaking practices on shredded lettuce contaminated with E. coli O157:H7: The potential for contaminated lettuce to cross-contaminate more lettuce during shredding REU Site – Plant Genomics and Biotechnology Amit Dhingra and soaking of lettuce under typical food service or retail handling practices is being examined in our laboratory. Several combinations of rinsing alone, soaking alone and rinsing both before and after soaking are being examined to explore the potential for wide-spread product contamination with E. coli O157:H7. This project is the focus of Katherine Brann’s undergraduate research project. A technician leads project coordination.
UV-C treatment of pears for microbial reduction and enhancement of fruit quality: This project is a collaborative effort among several laboratories. The effect of UV-C on reduction of generic E. coli and the spoilage mold, Penicillium expansum Link (blue mold) are being examined. Our laboratory contributes microbiological expertise to develop methods and provide laboratory space to conduct studies. A graduate student from another laboratory is performing the laboratory work.
Burke Laboratory - Weed Biology/Biotechnology
The research in I. C. Burke‟s laboratory is focused on herbicide/soil/plant interactions. Recent discoveries include the mechanism of resistance to 2,4-D in prickly lettuce (Weed Technology 2009; Heredity 2011a; J. Ag. Food Chem. 2011b). Burke‟s laboratory has also been studying the behavior of various synthetic growth regulators in selected rangeland weeds and the environment (Pest Manage. Sci. 2011). Each project has involved undergraduate students and exposes them to the interface between applied crop production and the application of analytical chemistry techniques - an interface that is often lacking in more basic research laboratories. The undergraduate student role in Burke‟s laboratory involved completing an analytical analysis using a GC/MS in support of the primary graduate student lead on the project.
Scot Hulbert - Plant Pathology/Biotechnology
Management of diseases and pests through genetics and modifications of cropping systems: The cereal rust diseases are among the most destructive plant pathogens globally and in the Pacific Northwest. We are utilizing the recently derived sequences from several ongoing rust fungus (Puccinia spp.) genome projects to engineer wheat plants that are resistant to these diseases. Rust fungi make haustorial cells that invaginate live plant cells. The haustorial cells draw nutrients from the plant cells and deliver effector proteins into the cells to suppress plant defense responses while the fungi develop. We have found that we can suppress expression of some fungal by expressing interfering RNA (RNAi) constructs within the plant cells. The silencing signals are apparently taken up by the haustorial cells from the plant cells they have colonized. Silencing of certain fungal genes interferes with development of the fungus indicating these genes are essential to the fungus. We are now using these silencing assays to determine which genes are essential for pathogenicity and looking for fungal genes that can be used to engineer resistance to the rust fungi.
