Recent MPS Graduates

Congrats MPS Grads!
Alexander B. Alleman PhD: Fall 2021 Advisor John Peters Department IBC Current: Post Doctoral researcher in the Marx Laboratory at the University of Idaho Dissertation: Insights into Mechanisms of Redox Homeostasis in Nitrogen-Fixing Azotobacter vinelandii Ph.D. research: Alex attended Western State Colorado University and received a B.A. in Biology and Chemistry. He joined John Peters Lab at Montana State University then followed the lab over to Washington State University in 2017. During his Ph.D. Alex investigated the complexity of nitrogen-fixing bacteria in the soil from ecology to physiology. Publications: Alexander B. Alleman, Florence Mus, John W. Peters. 2021. Low potential electron generating enzymes serve different functions during aerobic nitrogen fixation in Azotobacter vinelandii. bioRxiv. https://doi.org/10.1101/2021.10.06.463449 Alexander B. Alleman, Florence Mus, John W. Peters. 2021. Metabolic Model of the Nitrogen-Fixing Obligate Aerobe Azotobacter vinelandii Predicts Its Adaptation to Oxygen Concentration and Metal Availability. Mbio 12, 6: e02593-21. doi: https://doi.org/10.1128/mBio.02593-21 Alexander B Alleman, Yesuf Assen Mohammed, Kent A McVay, Qasim A Khan, Patrick Carr, John Miller, Zachariah Miller, Jessica Torrion, Peggy Lamb, Florence Mus, Chengci Chen, and John W Peters. 2021. Drivers of Bacterial Community Structure and Co-occurrence in a Northern Great Plains Pulse Crop Rotation System. Applied Soil Ecology. 157, 103737. doi: 10.1016/j.apsoil.2020.103737 Alexander B. Alleman, Gregory A. Prussia, Florence Mus, and John W. Peters. 2019. Acetone Carboxylase. Encyclopedia of Inorganic and Bioinorganic Chemistry. doi: 10.1002/9781119951438.eibc2701
Rachael DeTar PhD: Spring 2021 Advisor: Hans-Henning Kunz / Helmut Kirchhoff Department: SBS / IBC Current: Sloan Lab at Colorado State University Dissertation: The role of KEA1 and KEA2 transporters in plastid ion homeostasis and gene expression PhD research: Rachael graduated with a B.S. in Biology with a botany concentration from Colorado State University in 2014. She has a strong interest in the physiological and biological processes that drive and regulate photosynthesis and nutrient assimilation. Rachael looks forward to continuing her passion for research at WSU. Publications: Loss of salt overly sensitive 1 prevents virescence in chloroplast K+/H+ EFFLUX ANTIPORTER-deficient mutants. DeTar RA, Höhner R, Manavski N, Blackholm M, Meurer J, Kunz HH. Plant Physiol. 2022 Mar 23:kiac142. doi: 10.1093/plphys/kiac142. Online ahead of print. PMID: 35325208 No abstract available. Loss of inner-envelope K+/H+ exchangers impairs plastid rRNA maturation and gene expression. DeTar RA, Barahimipour R, Manavski N, Schwenkert S, Höhner R, Bölter B, Inaba T, Meurer J, Zoschke R, Kunz HH. Plant Cell. 2021 Aug 13;33(7):2479-2505. doi: 10.1093/plcell/koab123. PMID: 34235544 Free PMC article. Comparative analysis of thylakoid protein complexes in state transition mutants nsi and stn7: focus on PSI and LHCII. Koskela MM, Brünje A, Ivanauskaite A, Lopez LS, Schneider D, DeTar RA, Kunz HH, Finkemeier I, Mulo P. Photosynth Res. 2020 Jul;145(1):15-30. doi: 10.1007/s11120-020-00711-4. Epub 2020 Jan 23. PMID: 31975158 Free PMC article. Characterization of filament-forming CTP synthases from Arabidopsis thaliana. Daumann M, Hickl D, Zimmer D, DeTar RA, Kunz HH, Möhlmann T. Plant J. 2018 Oct;96(2):316-328. doi: 10.1111/tpj.14032. Epub 2018 Aug 31. PMID: 30030857
Maiporn Maipoka PhD: Spring 2021 Advisor: Okita Department: IBC Current: Dissertation: The role of the RNA binding protein OsTudor-SN during rice grain development as viewed by transcriptome analysis PhD research: Maiporn obtained a B.S. in Biology from Prince of Songkla University and a M.S. in Botany from Chulalongkorn University, Thailand. She joined MPS program and Professor Thomas Okita’s lab in Fall 2015. She was interested in plant responses to abiotic stress and studied the role of an RNA-binding protein in stress tolerance in rice. Publications:
Raed Al Saharin PhD: Fall 2020 Advisor: Hellmann Department: SBS Current: Dissertation: Characterization and exploring the role of brassica AP2/ERF transcription factors as CUL3-dependent E3 ligase substrates PhD research: Publications:
Hui Min Olivia Oung PhD: Fall 2020 Advisor: Kirchhoff Department: IBC Current: Dissertation: The protection strategies realized in a resurrection plant under drought stress The homoiochlorophyllous resurrection plants adapt unique capabilities against damage caused by reactive oxygen species (ROS) from photosynthesis during desiccation. Under severe drought stress, the plants can maintain most of the photosynthetic apparatus and chlorophylls while minimizing the ROS damage and recover efficiently after re-watering. My research aims to reveal the protection mechanisms under drought stress at different ages of the life cycle in the homoiochlorophyllous resurrection plant Craterostigma pumilum and provides comprehensive information on the regulation of photosynthesis. Publications: Oung HM, Charuvi D, Reich Z, Kirchhoff H. A resurrection plant employs two distinct strategies to protect the photosynthetic machinery against drought. In revision for Plant Physiology. Li M, Mukhopadhyay R, Svoboda V, Oung HM, Mullendore D, Kirchhoff H. (2020) Measuring the dynamic response of the thylakoid architecture in plant leaves by electron microscopy. Plant Direct. 4(11): e00280 Wu TM, Huang JZ, Oung HM, Hsu YT, Tsai YC, Hong CY. (2019) H2O2-based method for rapid detection of transgene-free rice plants from segregating CRISPR/Cas9 genome-edited progenies. Int. J. Mol. Sci. 20: 3885. Pang N., Xie Y, Oung HM, Sonawane BV, Fu X, Kirchhoff H, Cousins AB, Chen S. (2019) Regulation and stimulation of photosynthesis of mixotrophically cultured Haematococcus pluvialis by ribose. Algal Res. 39:101443. Smertenko A., Hewitt SL, Jacques CN, Kacprzyk R, Liu Y, Marcec MJ, Moyo L, Ogden A, Oung HM, Schmidt SA, Serrano-Romero EA. (2018). Phragmoplast microtubule dynamics: a game of zones. J Cell. Sci. 29:131(2). Zia A, Walker BJ, Oung HM, Charuvi D, Jahns P, Cousins AB, Farrant JM, Reich Z, Kirchhoff H. (2016). Protection of the photosynthetic apparatus against dehydration stress in the resurrection plant Craterostigma pumilum. The Plant J. 87, 664–680. Wei FJ, Kuang LY, Oung HM, Cheng SY, Wu HP, Huang LT, Tseng YT, Chiou WY, Hsieh-Feng V, Chung CH, Yu SM, Lee LY, Gelvin SB, Hsing YIC. (2016). Somaclonal variation does not preclude using rice transformants for genetic screening. Plant J. 85(5):648-59. Oung HM, Lin KC, Wu TM, Chandrika NN, Hong CY. (2015). Hygromycin B-induced cell death is partly mediated by reactive oxygen species in rice (Oryza sativa L.). Plant Mol Biol. 89(6):577-88.
Erika Serrano Romero PhD: Fall 2020 Advisor: Cousins Department: SBS Current position: Dissertation: Biochemical and diffusional limitations of C4 photosynthesis PhD research: I am researching Miscanthus Photosynthesis using Gas exchange measurements. In the future I will be working with another C4 biofuels crops such as corn and sugarcane. Publications:
Bruce Williamson Benavides PhD: Fall 2020 Advisor: Dhingra Department: Horticulture Current position: Dissertation: Understanding the molecular basis of Fusarium Solani mediated root rot in Pisum Sativum PhD research: I was born in Costa Rica, where I earned my BS in Biology from the University of Costa Rica. I joined the Molecular Plant Sciences program at WSU in the fall of 2016. I am working in Dr. Amit Dhingra's lab where I study the molecular interaction between peas and root rot disease. My research focuses on the development of molecular markers and new varieties via targeted and non-targeted mutagenesis. I enjoy playing sports, especially soccer and surfing, dancing and listening to ska music, scuba diving and spending time with friends! Publications:
Nathan Grant PhD: Summer 2020 Advisor: Gill Department: CSS Current: Research Molecular Biologist (Research Associate) (USDA-ARS Wheat, Sorghum, and Forage Research Unit, Lincoln, NE) Dissertation: Exploring the natural variation of photosynthesis and abiotic stress in wheat varieties and reduced height mutants PhD research: I received my undergraduate degree in Integrated Plant Sciences: Agricultural Biotechnology from WSU in 2012 where I worked as an undergraduate in Kulvinder Gill's lab mapping reduced height (rht) genes in wheat. As a graduate research assistant, I helped complete the project studying alternative wheat dwarfing genes and characterizing their abiotic resistance from deep planting depths. For our USAID Feed the Future Innovation Lab project, we worked to develop climate resilient wheat, screening over 1200 diverse lines from around the world using various heat trails and afterwards selected a set of complimentary heat tolerant varieties where photosynthetic variation was measured. GO COUGS! Publications: Grant, N., Mohan, A., Schillinger, W.F., & Gill, K.S. (2021) Characterizing reduced height wheat mutants for traits affecting abiotic stress and photosynthesis during seedling growth. Physiologia Plantarum, 172(1), 233-246 doi.org/10.1111/ppl.13321 Erdayani, E., Nagarajan, R., Grant, N.P. & Gill, K.S. (2020). Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat. Scientific Reports, 10, 3948 doi.org/10.1038/s41598-020-60673-4 Bheemanahalli, R., Sunoj, V.S., Saripalli, G., Prasad, P.V., Balyan, H.S., Gupta, P.K., Grant, N., Gill, K.S., & Jagadish, S.V. (2019). Quantifying the Impact of Heat Stress on Pollen Germination, Seed Set, and Grain filling in Spring Wheat. Crop Sciences, 59, 1-13. doi.org/10.2135/cropsci2018.05.0292 Grant, N.P., Mohan, A., Sandhu, D., & Gill, K.S. (2018). Inheritance and Genetic Mapping of the Reduced Height (Rht18) Gene in Wheat. Plants, 7(3), 58-66. doi.org/10.3390/plants7030058 Navarro, C., Yang, Y., Mohan, A., Grant, N., Gill, K.S., & Sandhu, D. (2014). Microsatellites Based Genetic Linkage Map of the Rht3 Locus in Bread Wheat. Molecular Plant Breeding, 5(8), 43-46. doi.org/10.5376/mpb.2014.05.0008
Scott Carle PhD: Spring 2020 Advisor: Garland Campbell Department: CSS Current: Dissertation: Freezing Tolerance and Genetic Marker Maps in Wheat PhD research: Freezing-tolerance is a vital trait for production of wheat in temperate regions. However, cold stress is a difficult trait for breeders to consistently select for. Scott’s research aims to further elucidate the regulation of a major genetic pathway that controls freezing-tolerance in wheat, and also to develop practical markers for the trait to assist wheat breeding programs. Publications:
Yan Liu PhD: Spring 2020 Advisor: Knoblauch Department: SBS Current: Dissertation: Investigation of the Structure and Function of Sieve Element Components PhD research: I researched a kind of phloem protein, forisome, in Dr. Knoblauch's lab. I love to work with green, leafy plants. I also like reading, cooking and hiking in my free time. Publications: Phragmoplast microtubule dynamics - a game of zones, Journal of Cell Science, 2017; Andrei Smertenko, Seanna Hewitt, Caitlin N. Jacques, Rafal Kacprzyk, Yan Liu, Matthew J. Marcec, Lindani Moyo, Aaron Ogdon, Hui Min Oung, Sharol Schmidt and Erika A. Serrano-Romero. Non-Dispersive phloem-protein bodies (NPBs) of Populus trichocarpa consist of a SEOR protein and do not respond to cell wounding and Ca2+, Peer J, 2018; Daniel L. Mullendore, Timothy Ross-Elliott, Yan Liu, Hanjo H. Hellmann, Eric H. Roalson, Winifried S. Peters and Michael Knoblauch.
Seanna Hewitt PhD: Fall 2019 Advisor: Dhingra Department: HORT Current: Dissertation: Transcriptomic characterization of novel fruit ripening pathways PhD research: Food security is a growing issue that necessitates improving the sustainability of agricultural and postharvest systems. The amount of produce that goes to waste, both in the U.S. and throughout the world, is particularly astonishing. My research involves a taking time-course RNAseq and physiology-based approaches to understanding the mechanisms of ripening in non-model systems, primarily pear (Pyrus communis) and other climacteric fruit. The end goal is to uncover ways of reducing waste associated with unpredictable ripening. Interests/Hobbies: When I’m not in the lab, I enjoy running, cycling, hiking, cliff jumping, cooking, traveling, and spending time with friends, family and pets! Publications: Hewitt, S. L., Ghogare, R., Dhingra, A. (2020). Glyoxylic acid overcomes 1-MCP-induced blockage of fruit ripening in Pyrus communis L. var.‘D’Anjou’. Scientific Reports 10(1): 1-14. Hewitt, S. L., Hendrickson, C.A., Dhingra, A. (2020). Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit. Scientific Reports 10(1): 8478. Christian, R.W., Hewitt, S.L., Roalson, E.H. et al. Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. Sci Rep 10, 8281 (2020). https://doi.org/10.1038/s41598-020-64670-5. Sharpe, R., Gustafson, L., Hewitt, S., Kilian, B., Crabb, J., Hendrickson, C., Jiwan, D., Andrews, P., Dhingra, A. (2020) Hendrickson, C Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer. PlosOne. doi:10.1371/journal.pone.0227429. Hendrickson, C., Hewitt, S., Swanson, M., Einhorn, T., Dhingra, A. (2019) Evidence for pre- climacteric activation of AOX transcription during cold-induced conditioning to ripen in European pear (Pyrus communis L.). PlosOne. doi:10.1371/journal.pone.0225886. Bielsa, B., Hewitt, S., Reyes-Chin-Wo, S., Jose Rubio-Cabetas, M., Dhingra, A. (2018) Identification of water use efficiency related genes in ‘Garnem’ almond-peach rootstock using time-course transcriptome analysis. PLoS ONE doi: 10.1371/journal.pone.0205493 Smertenko, A., Hewitt, S. L., Jacques, C. N., Kacprzyk, R., Liu, Y., Marcec, M. J., ... & Serrano-Romero, E. A. (2018). Phragmoplast microtubule dynamics–a game of zones. J Cell Sci, 131(2), jcs203331. Ikiz, D., Gallardo, K., Hewitt, S., Dhingra, A. (2017). Assessing consumer's preferences and willingness to pay for novel sliced packed fresh pears: A latent class approach. Agribusiness: An International Journal. AGR-17-0134.R16. Hewitt S, Kilian B, Hari R, Koepke T, Sharpe R, Dhingra A (2017) Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.). Computational and Structural Biotechnology Journal. doi:http://dx.doi.org/10.1016/j.csbj.2017.03.002 Hewitt, S., Kilian, B., Hari, R., Koepke, T., Sharpe, R., & Dhingra, A. (2017). Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.). Computational and structural biotechnology journal, 15, 290-298 Current Research:
Kaan Koper PhD: Fall 2019 Advisor: Okita Department: IBC Current: Dissertation: The plastidial alpha-glucan phosphorylase has an unexpected role in photosynthesis PhD research: Structure-function relationship of higher plant ADP-glucose pyrophosphorylase (AGPases). This enzyme catalyzes the rate limiting step of starch biosynthesis in plants and certain other mainly photosynthetic organism. In our study, we generated mutant AGPase enzymes with certain amino acid substitutions on known locations. Next we compared the enzyme kinetics, allosterism and assembly profile of the mutant enzyme with that of wild-type enzyme to assess the change in amino acid sequence to function and structure. Publications: Hwang, S.K., Koper, K., Satoh, H., & Okita, T.W. (2016). Rice endosperm starch phosphorylase (Pho1) assembles with disproportinating enzyme (Dpe1) to form a protein complex that enhances synthesis of malto-oligosaccharides. Journal of Biological Chemistry, 291(38), 19994-20007. Seferoglu, A.B., Gul, S., Dikbas, U.M., Koper, K., Baris, Il., Caliskan, M., ...& Kavakli, I. (2016). Glu-370 in the Large Subunit Influences the Substrate Binding, Allosteric, and Heat Stability Properties of Potato ADP-glucose Pyrophosphorylase. bioRxiv, 054106. Cakir, B., Tuncel, A., Green, A.R., Koper, K., Hwang, S.K., Okita, T.W., & Kang, C. (2015). Substrate bining properties of potato tuber ADP-glucose pyrophosphorylase as determined by isothermal titration calorimity. FEBS letters, 589(13), 1444-1449. Seferoglu, A.B., Koper, K., Can, F.B., Cevahir, G., & Kavakli, I.H. (2014). Enhanced heterotetrameric assembly of potato ADP-glucose pyrophosphorylase using reverse genetics. Plant Cell Physiol, 55(8), 1473-1483. doi: 10.1093/pcp/pcu078 Current Research:
Nicholas Mueth PhD: Fall 2019 Advisor: Hulbert Department: Pl Path Current: Instructor, School of Biological Sciences, Washington State University Dissertation: Small RNA_mediated gene regulation on both sides of the wheat stripe rust interaction PhD research: Nicholas "Cole" Mueth is from St. Louis, MO. After three lab rotations during his first year, Cole joined the Hulbert Lab in the Plant Pathology Department. He studied plant-pathogen interactions between wheat and Puccinia, an important group of parasitic rust fungi. By understanding the genetic and biochemical factors that determine pathogen success/failure, Cole hopes to uncover novel plant resistance strategies. He enjoys hiking and biking around the beautiful Northwest landscape. Publications: Ramachandran SR, Mueth NA, Zheng P, & Hulbert SH. 2019. Analysis of miRNAs in two differentially resistant cultivars of wheat during stripe rust infection. Frontiers in Plant Science 10:1574 Yin, C., Schlatter, D., Schroeder, K., Mueth, N.A., Prescott, A., Dhingra, A., Hulbert, S., Paulitz, T.C. Bacterial communities on wheat grown under long-term conventional tillage and no-till in the Pacific Northwest of the US. Phytobiomes 2017, 1:2 Rehder, L.E., Mueth, N.A. Biotechnology and other new production technologies. July 29, 2016. USDA Foreign Agriculture Services. Global Agriculture Information Network Report #GM16011. Rehder, L.E., Mueth, N.A. Food processing ingredients in Germany. September 20, 2016. USDA Foreign Agriculture Services. Global Agriculture Information Network Report #GM16016. Rehder, L.E., Mueth, N.A. German government on potential impacts of T-TIP on agriculture. June 7, 2016. Global Agriculture Information Network Report #GM16007. Rehder, L.E., Mueth, N.A. Parlimentarians discuss future of plant breeding. June 7, 2016. Global Agriculture Information Network Report #GM16008. Mueth, N.A. Biotech in Europe: An insider's view. Cornell Alliance for Science. September 14, 2016. Mueth, N.A., Ramachandran, S.R., Hulbert, S.H. Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici). BMC Genomics 2015, 16:718. Current Research:
Rebecca Weed PhD: Fall 2019 Advisor: Gang Department: IBC Current: Research Assistant, METRIC Core Facility, North Carolina State University Dissertation: Metabolomic changes in grasses due to biotic and abiotic factors PhD research: Rebecca Weed studied under Dr. David Gang in the Institute of Biological Chemistry where she used a metabolomics approach to investigate metabolic changes in two types of grasses: an invasive variety of a marshland grass, Phragmites australis, or Common Reed and wheat. Her research in understanding why P. australis is so invasive helped elucidate when this grass produces allelopathic compounds and potential abiotic factors that trigger the production of those compounds. Her wheat project investigated the impact of Tilletia caries, or Common bunt, infection on wheat. This project led to better understanding of how this fungi can reprogram its host primary and secondary metabolism to its benefit while remaining undetected by the plants immune system. In her free time she enjoyed traveling to different parts of the Northwest to hike, ski, fish, or catch a rock show or hockey game in Spokane. Current Research: Current Research: Rebecca is currently employed at METRIC at NCSU, which is a campus core facility with mass spectrometry, NMR, and x-ray crystallography instrumentation. Her current projects are focused on developing quantitative LC-MS QQQ methods to measure Per- and Polyfluoroalkyl Substances (PFAS), which are by-products from the industrial production of non-stick compounds like Teflon, in order to assist multiple PI's investigations into the impacts and levels of PFAS contamination in North Carolina due to nearby industrial production.
Ryan Christian PhD: Summer 2019 Advisor: Dhingra Department: HORT Current: Technical Director (Genetics/Tissue Culture) Yakima Chief Ranches Dissertation: "Are All Plastids Created Equal? Diversity, Function, and Evolution of Plastid-Targeted Genes and Chloropast Transit Peptides in Plants" Ryan joined the MPS program in the fall of 2013 after graduating from the Honors College at Washington State University with a bachelor’s degree in Agricultural Biotechnology. Ryan's research in Dr. Amit Dhingra’s lab focused on characterizing a set of putative plastid-targeted proteins that are predicted to be involved in energy transduction and nucleic acid binding and are unique to apple (Malus x domestica).
Erika Kruse PhD: Spring 2019 Advisor: Carter Department: CSS Current: Dissertation: Mold & Cold: The Solution is Sweet in Winter Wheat Erika studied crop improvement through breeding. Her project involved understanding resistance to mold and cold in winter wheat. She worked on identifying QTL for snow mold resistance and looking at patterns of sugar accumulation and gene expression as related to resistance to mold and cold. Beyond her studies, Erika loves spending time in the great outdoors; running, hiking, and backpacking. Music is also near and dear to her heart, and she gets her fix not only from listening to music, but through singing and playing guitar. Reading, cooking, zumba, and yoga are a few of her other hobbies. Publications: Kruse, E.B., et al. "Genomic Regions Associated with Tolerance to Freezing Stress and Snow Mold in Winter Wheat." G3 7.3 (2017): 775-780.
April Chen PhD: Fall 2018 Advisor: Gang Department: IBC Current: Dissertation: “(-)-Kolavenyl Diphosphate Synthase and Acetyltransferase Involved in Salvinorin A Biosynthesis Pathway in Salvia Divinorum” April worked on elucidating Salvinorin A biosynthesis pathway in Salvia divinorum. Her research mainly focused on discovering and characterizing enzymes involved in GGPP cyclization and salvinorin compound modifications and in elucidating the means by which such enzymes have evolved in this very unique and interesting plant. Publications: Xiaoyue Chen, Anna Berim, Franck E. Dayan and David R. Gang. 2017. A (-)-kolavenyl diphosphate synthase catalyzes the first step of salvinorin A biosynthesis in Salvia Divinorum. J. Exp. Bot. 68(5):1109-1122. doi: 10.1093/jxb/erw493.
Paul Mihalyov PhD: Fall 2018 Advisor: Pumphrey Department: CSS Current: Co-Founder Dewey Scientific Dissertation: “Reinforcing the Hexaploid Wheat Breeding Pipeline with Genomic Prediction of Quantitative Traits” Paul conducted his research in the Pumphrey lab. His primary focus was wheat breeding for resistance to stem and stripe rusts (Puccinia spp.) which are fungal pathogens with the potential to cause major yield losses for growers. Paul is interested in traditional aspects of plant breeding, but is also researching molecular plant-pathogen interactions in order to improve combat against wheat rusts. Before attending WSU, Paul received his B.S. in Genetics from New Mexico State University. Publications: Mihalyov, P.D., Nicholas, V.A., Bulli, P., Rouse, M.N., and Pumphrey M.O. Multi-locus mixed model analysis of stem rust resistance in winter wheat.(2017) The Plant Genome, 10(2). Gao, Liangliang; Rouse, Matthew N.; Mihalyov, Paul D.; Bulli, Peter; Pumphrey, Michael O.; Anderson, James A. Genetic Characterization of Stem Rust Resistance in a Global Spring Wheat Germplasm Collection. CROP SCIENCE, 57 (5):2575-2589; SEP-OCT 2017
Aaron Ogden PhD: Fall 2018 Advisor: Kahn Department: IBC Current: Dissertation: “Metabolic progression during development of symbiotic nitrogen fixation in the Medicago-Sinorizobium symbiosis and the role of HsIUV and ClpXP protease machinery” Symbiotic nitrogen fixation (SNF) is a critical component of global agriculture, economics, fossil fuel consumption, and nitrogen cycling. The primary location of SNF is within the root nodules formed between members of the bacterial family rhizobiaceae and leguminous plants. To accomplish effective SNF the plant-bacteria pair must coordinate and maintain a drastic metabolic shift from a free-living to a symbiotic state. The progress of this shift can be visualized along the longitudinal axis of indeterminate nodules which at maturity contain metabolically distinct zones. Using both a proteomic and metabolomic approach, my research seeks to evaluate the hypothesis that these zones differentially express particular proteins and metabolites involved in SNF and nodule maturation. Furthermore, bacterial mutant constructs will be generated to explore the role of particular peptides and pathways found unique within each sub-nodule zone. This research will improve our understanding of the metabolism involved in the onset and regulation of SNF engendering its optimization for the more sustainable global agricultural of tomorrow.
Jordan Zager PhD: Fall 2018 Advisor: Lange Department: IBC Current: Co-Founder Dewey Scientific Dissertation: “Regulation of Terpenoid Biosynthesis in Secretory Cell Types” Research Interest: Glandular trichomes, found on leaf surfaces of many plant species, act as microscopic chemical factories producing a wide range of specialized compounds known as secondary metabolites. Secondary metabolites provide the plant with inborn pest resistance, act to attract pollinators, and have great economic value serving as flavoring agents, fuel derivatives, and medications— both traditional and western. Among the secondary metabolites synthesized in glandular trichomes of cultivated tomato (Solanum lycopersicum) are acyl sugars, flavonoids, mono- and sesquiterpenes. Flavonoids are known to be involved in a myriad of plant processes, including, among others, floral pigmentation, UV screening, polar auxin transport and defense reactions. It was recently demonstrated that the tomato anthocyanin free (af) mutant, which is impaired in the expression of the flavonoid biosynthetic gene chalcone isomerase (CHI), failed to accumulate both flavonoids and terpenoids, and also had a significantly reduced number of glandular trichomes. Using isolated glandular trichomes from cultivated tomato (Solanum lycopersicum) and the af mutant, we have begun to unveil the coordinated mechanisms underlying the biosynthesis of these distinct compound classes. We have characterized flavonoid pathway intermediates accumulating in the af mutant and are now testing if these can regulate terpenoid enzyme activities in plastids. We are also integrating transcriptome, metabolome and enzyme kinetics data in both genome-scale stoichiometric and kinetic based mathematical models to more precisely predict flux distribution among metabolic pathways in glandular trichomes. These computational models will greatly assist in the development of generating novel and precise hypotheses regarding the coordination between secondary metabolism and development of glandular trichomes. These efforts are beginning to shed light into the poorly understood coordination of metabolism in specialized cell types. Hobby: Outdoor enthusiast Publications: Jordan J. Zager, B. Markus Lange. Assessing Flux Distribution Associated with Metabolic Specilization of Glandular Trichomes. Trends in Plant Sciences 2018; 23.7, p 438-647 https://www.sciencedirect.com/science/article/pii/S1360138518300876 Glenn W. Turner, Amber N Parrish, Jordan J Zager, Justin T Fischedick, B Markus Lange. Assessment of flux through oleoresin biosynthesis in epithelial cells of loblolly pine resin ducts. Journal of Experimental Botany, ery338, https://doi.org/10.1093/jxb/ery338
Gracen Smith PhD: Summer 2018 Advisor: Browse Department: IBC Current: We know surprisingly little about what fundamental biological processes are necessary for plant survival in low temperatures. Many studies in the past have used chilling sensitive plants as model organisms. Gracen used a chilling tolerant plant, Arabidopsis thaliana, and screen mutations in the Arabidopsis genome to examine what happen when interruptions are made in genes necessary for normal low temperature growth, and why. Gracen's research project contributed to the discussion about how some plants survive low temperatures, while others exhibit stress responses, and/or die.
Korey Brownstein PhD: Spring 2018 Advisor: Gang Department: IBC Current: Post-Doc The University of Chicago Dissertation: "Using Metabolomics to Investigate Native American Medicinal Plants and Their Uses" Korey received a bachelor’s degree in Interdisciplinary Studies from the University of Missouri. After graduation, he went to the Ha Noi University of Agriculture, Viet Nam (the first American student admitted to this university) on a fellowship to discover new plants and their medicinal uses. In 2012, he was awarded the NSF GRFP to study ethno-phytochemistry. He investigated the uses and chemical composition of Native American and Vietnamese medicinal plants. Publications: Eerkens, J.W., Tushingham, S., Brownstein, K.J., Garibay, R., Perez, K., Murga, E., Kaijankoski, P., Rosenthal, J.S., and Gang, D.R. (2018). Dental calculus as a source of ancient alkaloids: Dection of nicotine by LC-MS in calculus samples from the Americas. Journal of Archaeological Science: Reports, 18, 509-515. Brownstein, K.J., Gargouri, M., Folk, R.W., and Gang, D.R. (2017). Irdoid and phenylethanoid/phenylpropanoid metabolite profiles of Scrophularia and Verbascum species used medicinally in North America. Metabolomics, 13, 133. Brownstein, K.J., Thomas, A.L., Rottinghaus, G.E., Lynch, B.A., Gang, D.R. and Folk, W.R. (2015) Harpagide and related iridoid glycosides in vegetative tissues of cultivated Scrophularia lanceolata and Scrophularia marilandica. Acta Horticulturae, in press. Brownstein, K.J., Knight, M., Ito, Y., Rottinghaus, G.E. and Folk, W.R. (2015) Isolation of the predominant cycloartane glycoside, sutherlandioside B, from Sutherlandia frutescens (L.) R. Br. by spiral countercurrent chromatography. Journal of Liquid Chromatography and Related Technologies, 38, 423-429. Jiang, J., Chuang, D.Y., Zong, Y., Patel, J., Brownstein, K., Lei, W., Lu, C.-H., Simonyi, A., Gu, Z., Cui, J., Rottinghaus, G.E., Fritsche, K.L., Lubahn, D.B., Folk, W.R. and Sun, G.Y. (2014) Sutherlandia frutescens ethanol extracts inhibit oxidative stress and inflammatory responses in neurons and microglial cells. PLOS ONE, 9, e89748. Eerkens, J.W., Tushingham, S., Brownstein, K.J., Garibay, R., Perez, K., Murga, E., Kaijankoski, P., Rosenthal, J.S., and Gang, D.R.
Matthew Garneau PhD: Spring 2018 Advisor: Tegeder Department: SBS Current: Dissertation: "Understanding the physiological role of amino acid transport processes in pea (Pisum sativum L.) metabolism and performance" Matthew was interested in the physiological roles of amino acid transporters during plant reproduction.
Kim Hixson PhD: Spring 2018 Advisor: Lewis Department: IBC Current: PNNL Dissertation: "Network and Multi-omics Analyses of Arabidopsis Arogenate Dehydratase Knock-out and Over-Expression Mutants" Kim studied how changes in arogenate dehydrates composition in plants, affect the downstream or upstream transcript and protein changes in Arabidopsis thaliana. Recent findings have pointed to arogenate dehydratase (ADT) as being the key enzyme or even a key regulation point in the production of phenylalanine (the starting compound in the phenylpropanoid pathway) in plant systems. Controlled carbon flux through the phenylpropanoid pathway someday may be a more environmentally sustainable strategy for producing a myriad of potentially useful chemicals such as high-energy fuels, sunscreens, cosmetics, and plastics. The Lewis group has recently produced several ADT knockout combinations in Arabidopsis that display significant physiological and chemical changes due to changes in ADT composition. To better understand the significant role of these ADTs, Ms. Hixson analyzed the relative transcriptional and proteome changes in chloroplasts and at the whole cell level of leaves, stems, and root tissue at four different times (2, 4, 6, and 8 weeks) during the life of the plant. It is our hope that these data in combination with metabolomic and other chemical composition and physiological data obtained on the same plant tissues will reveal important enzymes that potentially contribute to carbon flux through the phenylpropanoid pathway or upstream and downstream regulatory controls that may be in place that are affected by ADT changes in Arabidopsis.
Shantel Martinez Email: shantel.a.martinez@gmail.com PhD: Spring 2018 Advisor: Camille M. Steber Department: CSS Current: Post-Doc, Cornell University Dissertation: Genetic and Hormonal Mechanisms Controlling Grain Dormancy and Preharvest Sprouting Tolerance in White Wheat Ph.D. Research: Shantel completed her Ph.D. under Dr. Camille M. Steber and Dr. Kimberly Garland Campbell. One objective of her research was to identify existing preharvest sprouting tolerant genes in Pacific Northwest white wheat through genome-wide association study (GWAS). The next objective was to generate new sources of preharvest tolerance by screening for an ABA hypersensitive mutant, ERA8, and map the gene through bulk-segregant analysis using exome capture in a backcross population. During graduate school, Shantel was heavily involved in the MPS Seminar Committee, MPS GSO, and was the Director of Professional Development for GPSA. Prior to entering graduate school at WSU, she completed her bachelors in Bioengineering while interning in the Steber and Garland Campbell laboratories. Current Research: For Shantel’s post-doctoral project, she continued to work on improving preharvest sprouting tolerance. One objective is to characterize and map a wheat dormancy gene identified on chromosome 2B. The second objective is to identify preharvest sprouting tolerant QTL in Northeast white wheat through GWAS and then create a genomic selection model for preharvest sprouting. Publications: Martinez, S.A., Godoy J., Huang M., Zhang Z., Carter A.H., Garland Campbell, K.A., and Steber, C.M. (2018). Genome-Wide Association Mapping for Tolerance to Preharvest Sprouting and Low Falling Numbers in Wheat. Frontiers in Plant Science. 9, 1-16. Martinez, S.A., Thompson A.L., Wen N., Murphy L., Sanquinet K.A., M., Steber, C.M., and Garland Campbell, K. (2018). Registration of the Louise/Alpowa Wheat Recombinant Inbred Line Mapping Population. Journal of Plant Registrations. Martinez, S.A., Tuttle, K., Takebayashi, Y., Seo, M., Garland Campbell, K., and Steber, C.M. (2016). The Wheat ABA Hypersensitive ERA8 Mutant is Associated with Increased Preharvest Sprouting Tolerance and Altered Hormone Accumulation. Euphytica. 212, 229-245. Tuttle, K.M., Martinez, S.A., Schramm, E.C., Takebayashi, Y., Seo, M., and Steber, C.M. (2015). Grain dormancy loss is associated with changes in ABA and GA sensitivity and hormone accumulation in bread wheat, Triticum aestivum (L.). Seed Science Research 1–15. Martinez, S.A., Schramm, E.C., Harris, T.J., Kidwell, K.K., Garland-Campbell, K., and Steber, C.M. (2014). Registration of Zak Soft White Spring Wheat Germplasm with Enhanced Response to ABA and Increased Seed Dormancy. Journal of Plant Registrations 8, 217-220.
Lindani Moyo PhD: Spring 2018 Advisor: Pappu Department: Pl Path Current: Dissertation: "Tuber Necrosis-causing Viruses of Potato: Genetic Diversity and Host-pathogen Interactions" A Fulbright Scholar from Bulawayo, Zimbabwe, Lindani joined the Molecular Plant Sciences program in fall 2015. He is interested in plant biotechnology and plant-pathogen interactions. His research in Dr. Hanu Pappu’s lab involved developing genomics resources for potato for virus resistance. Lindani holds a Bachelor of Science (Hons) in Applied Biology and Biochemistry and a Master of Science in Applied Microbiology and Biotechnology both from the National University of Science and Technology (NUST) in Bulawayo, Zimbabwe.
Ragupathi Nagarajan PhD: Spring 2018 Advisor: Kulvinder Gill Department: CSS Current: Post-Doc Oklahoma State Dissertation: "Improving Thermal Stability of Wheat Rubisco Activase (TaRCA) via Molecular Characterization and Genetic Modification" Ragupathi's research project was to develop insertional mutagenesis system using active maize transposable elements in wheat. Before joining MPS program, he worked as a Research Associate in a Washington Grain Commission funded project to develop wheat transgenics for functional studies. Besides his research, he enjoyed photography, movies and traveling.
Wade Roberts PhD: Spring 2018 Advisor: Roalson Department: SBS Current: Post-Doc University of Arkansas Dissertation: Evolutionary genomics of flower diversification in the magic flowers (Achimenes, Gesneriaceae)" Achimenes is a small genus native to Mexico and Central America which displays remarkable variation in floral form among closely related species. There appear to be homoplastic derivations of shape, color, and corolla spurs possibly due to pollinator-mediated selection. In order to begin understanding how this variation evolved, I took a comparative approach across multiple species by combining transcriptome sequencing of developing flowers with phylogenetic, molecular genetic, and biochemical tools. Particular interest involves investigating the functional evolution of the enzymes and transcriptional regulators (MYB-bHLH-WD40) of the Anthocyanin Biosynthetic Pathway, which produces red, purple, and blue pigments. Before attending WSU, Wade received a B.S. in Biology and B.A. in Sculpture from Whitworth University. Publications: Roberts, W.R., and Roalson, E.H. 2018, in press. Transcriptomic evidence of gene flow between species of magic flowers (Achimenes, Gesneriaceae). American Journal of Botany. Roberts, W.R. and Roalson, E.H. 2017. Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). BMC Genomics 18:240.
Fainmarinat Inabuy PhD: Fall 2017 Advisor: Lang Department: IBC Current: Dissertation: "Biosynthesis of Plant Specialized Diterpenoids: Leveraging Metabolic and Transcriptomic Profiling for Gene Discovery" Fainmarinat was a Fulbright scholar from Indonesia. She worked in the group of medicinal-plants, in Dr. Mark Lange's lab. Focus of her research is to elucidate the roles of cytochrome p450 proteins in the biosynthesis pathway of Taxol biosynthesis in Taxus plant, through heterologous expression in yeast. Knowing that what we do nowadays, someday, will greatly contribute to the the treatment of cancer, one of the world's most deadly disease.
James Santiago PhD: Fall 2017 Advisor: Tegeder Department: SBS Current: Dissertation: "Investigating the Function of Leaf Amino Acid Transporters In Source and Sink Physiology in Arabidopsis thaliana" James studied amino acid transporter in the model plant Arabidopsis that we think is responsible for loading of amino acids into the source leaf phloem for long distance transport and how mutation of this transporter affect the whole plant metabolism and physiology including but not limited to Nitrogen and Carbon metabolism, sugar transport, and source-sink relations.
Ryan Boyd PhD: Spring 2017 Advisor: Cousins Department: SBS Current: Dissertation: Variation in Photosynthetic Enzyme Kinetics and Carbon Isotope Fractionation Paremeters Ryan studied the differences in Rubisco kinetics between C3 and C4 grasses and how it relates to amino acid residues evolving under positive selection. My other interests include C4 photosynthesis, temperature response of photosynthetic enzymes, and plant response to climate change factors
Hong-Li Chou PhD: Spring 2017 Advisor: Okita Department: IBC Current: Dissertation: The role of multifunctional RNA finding protein OsTudor-SN in rice storage protein mRNAs transport and localization Research Interests: In-situ RNA/protein labeling. Analysis of functional genes involved in RNA movement. The mechanism of RNA binding proteins in RNA sorting.
Ben Kilian PhD: Spring 2017 Advisor: Dhingra Department: HORT Current: Instructor-Liberty University Dissertation: Identifying the Genetic Mechanism of Ethylene-Inducible Fruit Abscission in Sweet Cherry Ben's research was genetic regulation of pedicel fruit abscission in sweet cherry and the potential implications for growers in the Pacific NW.
Aaron Mahoney PhD: Spring 2017 Advisor: Hulbert/Okubara Department: Pl Path Current: Storm Seeds (Plant Breeding) Dissertation: Genetic Characterization and Rhizosphere Microbial Community Analysis Associated with Root Rot Disease of Wheat Aaron's research was to understand the molecular mechanisms for disease resistance in synthetic wheat lines. The focus includes the genetic and protein interactions between wheat and its pathogens. For my master's, He focused on characterizing transcriptional regulation in Arabidopsis for the stomatal gene MUTE.
Gaganjot Sidhu PhD: Spring 2017 Advisor: Gill Department: CSS Current: Post-Doc, CCS, WSU Dissertation: Understanding the role of auxin and its transport in controlling wheat development Polar auxin transport regulates various aspects of plant development such as embryonic development, shoot and root architecture, and tropic responses. Majority of the understanding of these mechanisms comes from studies on dicot model plant species Arabidopsis thaliana. However, clear morphological and developmental differences exist between monocots and dicots. The focus of his research is to study whether auxin transport route and the associated mechanisms are conserved or diversified in monocots with a special emphasis on wheat crop.
Sierra Beecher PhD: Summer 2016 Advisor: Knoblauch Department: SBS Current: Adjunct Faculty, Biological Sciences - Wagner College Dissertation: "Rheology and Conductivity of Phloem" I studied anatomy, physics, and physiology of the phloem in Dr. Michael Knoblauch's lab at WSU using confocal laser scanning microscopy and molecular biology. I previously worked in New York City teaching biology and environmental science at a private university. I am the proud mother of two fantastic teenagers, and enjoy spending time with them in lovely Palouse.
Brenton Poirier PhD: Summer 2016 Advisor: Lange Department: IBC Current: USDA-Wenatchee, plant pathologist/tree fruits Dissertation: "investigating the Biosynthesis, Function, and Physiological Significance of Isoprenoids in Arabidopsis thaliana" Plant-derived sterols (phytosterols) have a significant impact on human nutrition. Sitosterol, stigmasterol, and campesterol comprise a majority of these sterols, and are found as enriched components of vegetable oil. As a result of their structural similarity, they compete with cholesterol in many cellular processes, and there is a large body of evidence indicating that phytosterols have cholesterol-lowering activities in humans. A great deal of research has been done to study the roles of cholesterol within mammalian cells, but research into the endogenous functions of phytosterols is still in its early stages. We are only now beginning to realize the importance of these molecules at both the cellular and organ level. Aside from their role in regulating membrane fluidity, sterols function as precursors for the synthesis of other molecules. Campesterol, for example, is used to produce brassinosteroids, a class of hormones involved in plant growth and development. As a result, proper sterol biosynthesis is important for multiple cellular processes and is not simply limited to maintaining membrane integrity. The enzymes involved in the main biosynthetic pathway have been identified, but the mechanisms behind the regulation and coordination of synthesis remain unclear. My research is targeted towards understanding the regulation of sterol synthesis in Arabidopsis thaliana using a combination of genetic and biochemical approaches.
Tim Ross-Elliott PhD: Summer 2016 Advisor: Knoblauch Department: SBS Current: Advanced Imaging Specialist, MicRoN Imaging Core, Harvard Medical School Previous: Post-Doc, Dr. Alan Jones, UNC-Chapel Hill Dissertation: "Structural and Functional Aspects of Protophloem Sieve Element Unloading in the Root Tips of Arabidopsis thaliana" In grad school I was interested in understanding factors regulating phloem transport, specifically unloading in sink tissues in Arabidopsis. Using a combination of math modeling and electron and non-invasive light microscopy, we discovered, in collaboration with international research groups, a novel type of plasmodesmata connection necessary for convective unloading of phloem solutes and macromolecules in the root tip unloading zone. This published work built upon previous studies, and parallel research projects at the time, in the Knoblauch lab to further our understanding of long distance phloem translocation, commonly accepted as a pressure flow system and originally hypothesized by Ernst Mϋnch nearly a century ago.
Bilal Cakir PhD: Spring 2016 Advisor: Okita Department: IBC Current: Post-Doc, Yale University Med.-Genetics Dissertation: "Elucidating the Rate Limiting Components of Starch Biosynthesis" Bilal's research topic was to elucidate the structure-function relationships of ADP-glucose pyrophosphorylase (AGPase) a key regulatory enzyme of starch biosynthesis and to use this information to manipulate source-sink relationships in plants.
David Favero PhD: Spring 2016 Advisor: Neff Department: CSS Current: Post-Doc at RIKEN Dissertation: "Transcriptional Control of Arabidopsis Development by AHLS" David's work involved investigating the functions of various members of a family of DNA-binding proteins in plants, the AT-Hook motif Nuclear Localized (AHL) family. David was particularly interested in learning how specificity is accomplished among the 29 members of the family, and how differing protein-protein interactions and tissue expression patterns among family members may contribute to specificity. He earned his bachelor of science degree in Soil and Crop Sciences at Colorado State University, where he participated in research focused on mapping disease resistance genes in common bean. During his free time, he enjoyed being actively involved with a campus club known as Discovery, which is designed to meet the social and spiritual needs of international students here at WSU.
Na Sa PhD: Spring 2016 Advisor: Roje Department: IBC Current: Dissertation: “Identification and Characterization of the Missing Phosphatase on the Riboflavin Biosynthesis Pathway in Arabidopsis Thalina” Na Sa received her M.S. degree in China and then joined Dr. Sanja Roje's lab in August 2011. She worked on investigating the key enzymes in riboflavin (Vitamin B2) biosynthesis pathway. The long-term goal of her research was to advance the understanding of riboflavin biosynthesis and provide means for developing crops with improved riboflavin content.
Kim Cotton PhD: Fall 2015 Advisor: Browse Department: IBC Current: Phytelligince, Inc. Dissertation: Analysis of putative phosphatidic acid phosphatases involved in triacylglycerol synthesis in Arabidopsis The triacylglycerol (TAG) synthesis pathway in plants generates storage lipids which can be used in food, fuel, and industrial and commercial substrates. However, the genes encoding several of the enzymatic steps generating TAG in plants have been largely unstudied due to a lack of molecular data on these genes. Specifically, the phosphatidic acid phosphatase (PAP) reaction catalyzes the dephosphorylation of PA to generate DAG, and is essential for generating not only TAG, but phospholipids as well. In her research, Kimberly is working to identify the PAP(s) involved in TAG synthesis. Putative PAPs involved in TAG synthesis have been identified using homology searches to known yeast and human PAP enzymes and bioinformatics tools. Total fatty acid quantification via GC and visual inspection of T-DNA knockout mutants will be used to determine if any of the PAPs identified using bioinformatics and homology have TAG-deficient phenotypes. Finally, putative PAP proteins involved in TAG biosynthesis will be assayed for PAP activity via activity assays and complementation of the Saccharomyces cerevisiae Δdpp1Δlpp1Δpah1 mutant. Identifying and characterizing the PAP(s) involved in TAG synthesis will lead to a more complete understanding of lipid biosynthesis and potential biotechnology applications such as altered lipid production in crop plants.
Amandeep Dhaliwal PhD: Fall 2015 Advisor: Gill Department: CSS Current: Director of Research Operations - GeneShifters Dissertation: "Molecular Characterization of a Wheat Ortholog of ABC1 (TaABCB1) Gene Involved in Dwarfism via Interrupted Auxin Transport" Important plant growth hormone gibberellic acid (GA)-deficient wheat and rice were instrumental in bringing about the Green Revolution. However, growing evidence suggests that GA-deficient plants put a ceiling for yield especially under limited water conditions. In addition to GA dwarfs, agronomically relevant reduction in plant height with no yield penalty can also be achieved by mutating genes involved in the biology of other plant hormones such as auxin and brassinosteroids. Therefore, focus of my research is to identify and characterize an alternate dwarfing gene system for wheat and other grasses.
Keiko Tuttle PhD: Fall 2015 Advisor: Steber Department: CSS Current: Dissertation: GA Signaling genes, Seed Germination, alpha-amylase production in wheat: Targets for Controlling Pre-Harvest Sprouting and Late Maturity alpha-Amylase Induction. Kiko's research focused on exploring GA signaling in wheat in a translational approach from what we know in Arabidopsis. Discovering and characterizing the changes seen with after-ripening of grain and its effects on breaking dormancy in wheat grain. Finally, using these tools to create targets to advance agriculture in the prevention of Pre-Harvest Sprouting and Late Maturity alpha-amylase.
Ramonjot Kaur PhD: Summer 2015 Advisor: Gill Department: CSS Current: Research Associate Dissertation: Understanding and Utilizing Chromosome Pairing Control in Polyploid Wheat Ramanjot received her B.S from Punjab Agricultural University, India and Joined WSU as a graduate student in the year 2009. Her research focused on understanding chromosomal pairing in polyploid plants with emphasis on wheat. A precise understanding of homologous and homoeologous pairing as a basis of meiotic crossing over is of fundamental importance if transfer of genes for plant improvement from closely or distantly related species is to be undertaken. The research will be a step towards answering many questions related to the fundamental processes of recombination.
Sven Nelson PhD: Spring 2015 Advisor: Camille Steber Department: CSS Current: USDA, University of Missouri, Columbia Dissertation: Transcriptomic and hormonal analyses to elucidate the control of Arabidopsis seed dormancy Sven completed his PhD in the lab of Dr. Camille M. Steber where he investigated the role of GA signaling in Arabidopsis seed dormancy. GA (gibberellin) is a phytohormone that functions antagonistically to ABA (abscisic acid) with regards to seed dormancy; whereas ABA is involved in the onset and maintenance of seed dormancy, GA functions to stimulate seed germination. Prior to entering graduate school at WSU he was a research technician in the laboratory of Dr. Stanley Fields who is well known for his development of the yeast 2-hybrid technique for detecting protein-protein interactions. Prior to that he was living in Japan as an English teacher which is also where he met his wife, Shoko. Publications: Ariizumi, T., Hauvermale, A. L., Nelson, S. K., Hanada, A., Yamaguchi, S., and Steber, C. M. (2013). Lifting DELLA repression of Arabidopsis seed germination by nonproteolytic gibberellin signaling. Plant Physiol 162 (4), 2125–2139. Shramm, E.C., Nelson, S.K., Kidwell, K., and Steber, C.M. (2012) Increased ABA sensitivity results in higher seed dormancy in soft white spring wheat cultivar 'Zak'. Theor Appl Genet 126 (3), 791-803. Schramm, E.C., Nelson, S.K., and Steber, C.M. (2012). Wheat ABA-insensitive mutants result in reduced grain dormancy. Euphytica 188: 35-49. Fowler, D.M., Cooper, S.J., Stephany, J.J., Hendon, N., Nelson, S., and Fields, S. (2010). Suppression of statin effectiveness by copper and zinc in yeast and human cells. Mol. BioSyst 7: 533-544. Cooper, S.J., Finney, G.L., Brown, S.L., Nelson, S.K., Hesselberth, J., Maccoss, M., and Fields, S. (2010). High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. Genome Res 20: 1288-1296.
Reuben Tayengwa PhD: Spring 2015 Advisor: Neff Department: CSS Current: Post-Doc, CCS, WSU Dissertation: Molecular Genetic Analysis of Two Plant-Specific Gene Families, SOFL and AHL, in Arabidopsis Thaliana Worked in the Neff lab where the lab identified a family of three plant-specific proteins in Arabidopsis (SOB5, AtSOFL1 and AtSOFL2) which, when over-expressed, increase levels of specific cytokinins. These proteins have no known function. I am currently using a combination of molecular genetics and biochemical tools to investigate the biological function of these three proteins.
Joo Hyun Lee PhD: Fall 2014 Advisor: Hellmann Department: SBS Current: Post-Doc Seoul National University, College of Agriculture and Life Sciences Dissertation: Functional Impacts of Arabidopsis thaliana Math-BTB/POZ Proteins on the ERF/AP2 Transcription Factor Research Interests: Molecular Biology, protein-protein interaction, signal transduction pathway, abiotic stress tolerance
Richard Sharpe Email: rsharpe@wsu.edu PhD: Fall 2014 Advisor: Edwards Department: SBS Current: Post-Doc Horticulture, WSU Dissertation: Gene Expression Profiling in Single Cell C4 and Related Photosynthetic Species in Suaedoidea Rick's interests included gene expression, chloroplasts and photosynthesis. Unraveling the transcriptome differences between a unique single-cell C4 photosynthetic type higher plant Bienertia sinuspersici and its Kranz C4 photosynthetic type relations was his major focus. Publications: Sharpe, RM and Offermann, S. 2013. One decade after the discovery of single-cell C4 species in terrestrial plants - What did we learn about the minimal requirements of C4 photosynthesis? Photosynthesis Research, March 14. DOI: 10.1007/s11120-013-9810-9. Kirchhoff H, Sharpe RM, Herbstoval M, Yardbrough R, Edwards GE. 2012 Differential Mobility of Pigment-Protein Complexes in Granal and Agranal Thylakoid Membranes of C3 and C4 Plants. Plant Physiology. 161, 1, 497-507. DOI: 10.1104/pp.112.207548. Sharpe RM, Mahajan A, Takacs EM, Stern DB, Cahoon AB. 2011. Developmental and cell type characterization of bundle sheath and mesophyll chloroplast transcript abundance in maize. Curr Genet Cahoon AB, Sharpe RM, Thompson EJ, Ward AD, Mysayphonh C, Linn A. (2010) The complete chloroplast genome of tall fescue (Lolium arundinaceum; Poaceae) and comparison of whole plastomes from the family Poaceae. American Journal of Botany 97:49-58. DOI: 10.3732/ajb.0900008. Sharpe RM, Dunn SN, Cahoon AB. 2008 A Plastome Primer Set for Comprehensive Quantitative Real Time RT-PCR Analysis of Zea mays: A Starter Primer Set for Other Poaceae Species. Plant Methods 4:14. DOI: 10.1186/1746-4811-4-14. Cahoon AB, Takacs EM, Sharpe RM, Stern DB. 208. Nuclear, chloroplast, and mitochondrial transcript abundance along a maize leaf development gradient. Plant Mol Biol. 66, 1-2, 33-46 DOI: 10.1007/s11103-007-9250-z. Farone M, Sharpe R. 2007. Smooth and Rough Colony Variants of Shigella sonnei on Congo Red Agar. Journal of Microbiooty & Biology Education. American Society for Microbiology.
Rhoda Araba Tawiah Brew-Appiah Email: brewappr@wsu.edu PhD: Summer 2014 Advisor: Von Wettstein Department: CSS Current: Associate CSS, WSU Dissertation: Epigenetic and Post-transcriptional Elimination of Celiac Causing Wheat Storage Proteins Rhoda earned a BA in Biochemistry/Molecular Biology from Reed College in Portland, Oregon. Then worked for a year as a research assistant at Oregon Health and Sciences University in Portland, Oregon. Her research focus has been on silencing the Celiac-causing epitopes in bread wheat.
Nuan Wen PhD: Summer 2014 Advisor: vonWettstein Department: CSS Current: Associate CSS, WSU Dissertation: Celiac-Safe Wheat, Reaching One Objective by Two Approaches, Gluten Elimination by Random and Site-Directed Mutagenesis, and Detoxification by Ectopic Expression of 'Glutenases' Nuan came from northeast China to work on celiac safe wheat in Dr. Diter von Wettstein's group.
Jeremy Jewell Email: jbjewell@wsu.edu PhD: Spring 2014 Advisor: Browse Department: IBC Current: Post-Doc IBC Dissertation: Jasmonate Metabolism and Signaling in Abiotic Stress and Male Reproductive Development Jeremy received a bachelor's degree in cell biology with a chemistry minor at Montana State University. He discovered that plants are cool and did a master's in plant science (quantitative trait loci mapping of barley quality traits) also at MSU. Jeremy worked with John Browse on jasmonate signaling and metabolism. Publications: Bhosale R*, Jewell JB*, Hollunder J, Koo AJ, Vuylsteke M, Michoel T, Hilson P, Goossens A, Howe GA, Browse J, Maere S. (*contributed equally). Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants. Plant Cell. 2013 Aug;25(8):2865-77. Bates PD, Jewell JB, Browse J. Rapid separation of developing Arabidopsis seeds from siliques for RNA or metabolite analysis. Plant Methods, 2013 Mar 26;9(1):9.
Stefanie Tietz PhD: Spring 2014 Advisor: Kirchhoff Department: IBC Current: Michigan State University - East Lansing Dissertation: Understanding Structural Flexibility of Photosynthetic Membranes Stefanie studied photosynthesis. Worked on understanding the function of a stress induced switch from a random to a highly-ordered semi-crystalline state in photosynthetic membranes. Her hypothesis for the arrangement is that plants developed this strategy to facilitate molecular diffusion processes in crowded photosynthetic membranes.
Diwaker Tripathi Email: diwaker.tripathi@wsu.edu PhD: Spring 2014 Advisor: Pappu Department: Pl Path Current: Post-Doc in Plant Pathology Dissertation: In Vivo Localization and Interaction Studies of Tospovirus (Genus: Tospovirus; family: Bunyaviridae) Diwaker joined the MPS program at WSU in 2010. Diwaker's research focused on understanding the protein interaction patterns among viruses and their response to chemical inducers of plant defense. He used tospoviruses as a model system and BiFC technique to understand the interaction patterns of viral proteins. A long term goal of his research is to develop an efficient molecular strategy for controlling the damages caused by pathogens in the field.
Scott Schaeffer PhD: Fall 2013 Advisor: Dhingra Department: HORT Current: Research associate at Baylor College of Medicine - studying genetic factors involved in plant nutrient bioavailability Dissertation: Genomics and Morpho-Developmental Characterization of Plastids in Rosaceae Scott's research aimed to use genomics approaches to find novel genes encoding plastid targeted proteins in members of the Rosaceae family and link those to potentially new plastid functions. Scott also functionally characterizing two plastid-localized calcium transporters from apple which may be involved in controlling senescence and possibly Bitter pit, a physiological disorder in apple.
Jianfei Zhao PhD: Fall 2013 Advisor: Neff Department: CSS Current: Post-Doc at University of Pennsylvania Dissertation: Functional and Phylogenetic Analysis of the At-Hook Motif Nuclear Localized Gene Family in Land Plants Jianfei's research project was with a family of DNA-binding proteins in Arabidopsis thaliana.
Joseph Lynch PhD: Summer 2013 Advisor: Roje Department: IBC Current: Post-Doc Biochemistry, Purdue University Dissertation: Characterization of Enzymes Involved in Flavin Cofactor Metabolism Joseph's thesis project looks at flavin cofactor metabolism in plants. Through both in vivo and in vitro approaches, he worked identifying the enzymes responsible for synthesis and degradation of FMN and FAD, and determining how they ensure sufficient levels of these critical cofactors throughout the plant cell.
Aytung Tuncel PhD: Summer 2013 Advisor: Okita Department: IBC Current: Postdoctoral Scientist-Metabolic Biology, John Innes Centre Dissertation: Allosteric Regulation of the Rice Endosperm ADP-Glucose Pyrophosporylase Regulation of starch metabolism in developing rice endosperm. Structure-function relationship of starch regulatory enzyme, ADPglucose pyrophosphorylase.
Jared Bell PhD: Spring 2013 Advisor: Burke Department: CSS Current: Dow Agro Sciences Dissertation: Biochemical and Genetic Characterization of Rubber Production in prickly lettuce (Lactuca serriola L.) Jared's main research interest was characterization of rubber biosynthesis in prickly lettuce (Lactuca serriola) a common, troublesome weed found throughout North America. Prickly lettuce produces long chain polyisoprene (rubber) in specialized vascular tissues called laticifers. Jared's research included: 1.characterize variation in rubber content and quality between collected biotypes, 2. identify genes or QTL responsible for rubber production, 3.begin to develop possible germplasm or breeding lines and, 4.analyze the physical properties of prickly lettuce rubber as compared to current natural rubber sources. The long term goal is to test the feasibility of making this common, drought tolerant, disease and herbicide resistant weed an alternative source of natural rubber. He was also fortunate to work in the development and evaluation of a new experimental herbicide being developed by Dupont called Aminocyclopyrachlor. Using radiolabelled herbicide tracers, we have studied the absorption and translocation of various formulations on broadleaf weed species when applied to leaves. Woody tree species have also been studied using both foliar and basal bark applications. The goal is to describe how this herbicide behaves physiologically in different species to determine optimal application rates and methods.
Jacob Blauer PhD: Spring 2013 Advisor: Knowles Department: HORT Current: Research Scientist and breeder - Forage Genetics Dissertation: Factors Affecting Tuber Ascorbate Content, Physiological Age, Tuber Set and Size Distribution in Potato (Solanum tuberosum L.) PhD research: Physiological aging in seed potatoes and Vitamin C regulation in potatoes during development and storage. I am currently employed as the Agronomy Scientist Manager in the R&D sector with J.R. Simplot Co. - Plant Sciences. My responsibilities are generally two-fold: (1) Member of the discovery/leadership team with 5 other scientists to plan, design, and leverage research opportunities to discover new traits and develop biotech potatoes for the fresh and frozen markets. Our traits focus on various sectors of the potato industry and are targeted towards benefits for growers, processors, and consumers alike. These traits include; reduced waste, reduced inputs, disease resistance, improved shelf-life, and improved health benefits. (2) Manage the Whole Plant Team and all research projects in the R&D greenhouses and research fields. This position requires both management of personnel and experimental design/analysis. Additional, it provides significant opportunities to stream-line production and research to leverage more data and product with fewer resources and reduced inputs. While I get the opportunity to work with researchers both nationally and globally from academia and other companies, I also have the opportunity to pursue my own research interests which are generally around: disease resistance, variety development, processing improvements, postharvest attributes, and texture/flavor. Blauer, J.M., L.O. Knowles, G.N.M. Kumar, A. Dhingra, and N.R. Knowles. 2013. Changes in ascorbate and associated gene expression during development and storage of potato tubers (Solanum tuberosum L.). Postharvest Biology and Technology. 78: 76-91. Blauer, J.M., L.O.Knowles, and N.R. Knowles. 2013. Evidence that tuber respiration is the pacemaker of physiological aging in seed potatoes (Solanum tuberosum L.). Journal of Plant Growth Regulation. 32 (4): 708-720. Blauer, J.M., L.O. Knowles, and N.R. Knowles. 2012. Manipulating Stem Number, Tuber Set and Size Distribution in Specialty Potato Cultivars. American Journal of Potato Research. 90 (5): 470-496.
Berkley Walker PhD: Spring 2013 Advisor: Cousins Department: SBS Current: Assistant Professor, Michigan State University Dissertation: Determining the Response of Leaf Photosynthetic Carbon Metabolism and Energy Balance to Changes in Temperature, C02 and Nitrogen Form PhD research: Berkley used biochemical models to unravel the basic physiology of leaf photosynthesis. He focused on photorespiration and the budget of carbon under elevated temperatures. He is moved into addressing the mechanisms the plant uses to match photosynthetic production of energy with demand. Current Research: Crop plants currently use about 2% of the sun's energy to convert CO2 to biomass under ideal conditions. This 2% is only one-third of the theoretical maximum efficiency for photosynthesis. I am working on ways to increase realized photosynthetic conversion efficiency through aggressive re-engineering of core photosynthesis components. I use a model-led approach ranging from the impact of lighter-green leaves to improved schemes for reducing the energy demand pf photorespiration. Publications: Berkley Walker, Deserah D. Strand, David M. Kramer, Asaph B. Cousins. The response of cyclic electron flow around photosystem I to changes in photorespiration and nitrate assimilation. Plant Physiology. (2014) Wei Sun, Nerea Ubierna, Jian-Ying Ma, Berkley Walker, David M. Kramer, Asaph B. Cousins. The coordination of C4 photosynthesis and the CO2 concentrating mechanism in Zea mays and Miscanthus × giganteus in response to transient changes in light quality. Plant Physiology. (2014) Berkley Walker, Lorenzo Ariza, Sarah Kaines, Murray Badger, Asaph Cousins. Comparison of Rubisco in vivo kinetics and mesophyll conductance between Arabidopsis thaliana and Nicotiana tobacum. Plant, Cell & Environment (2013) Berkley Walker, Asaph Cousins. The influence of temperature on measurements of the CO2 compensation point: Differences between the Laisk and O2 exchange methods. Journal of Experimental Botany (2013)
Amber Hauvermale Email: ahauvermale@wsu.edu PhD: Fall 2012 Advisor: Steber Department: CSS Current: Associate in Research, Crop & Soil Sciences, WSU Dissertation: The Role of the Plant GA Normone Receptor GID1 in Controlling Seed Germination in Arabidopsis thaliana GA signaling, and the mechanisms controlling after-ripening in seeds. Amber completed a masters at the University of Colorado at Colorado Springs and the project was to characterize the novel fatty acid synthase involved in fatty acid production in Schizochytrium sp.
Tyson Koepke PhD: Fall 2012 Advisor: Dhingra Department: HORT Current: Director of Operations at Phytelligence, Inc. Dissertation: Linking Genes and Physiology Utilizing Genomics and Transcriptomics Approaches in Sweet Cherry (Prunus Avium) Growing up on his family farm, Tyson was always intrigued about how plants work in ever changing environments on the farm. This primary observation established a strong desire in him to learn how to make crop plants better for increased yields. To pursue this passion, he completed his bachelors degree in Plant Biotechnology from Montana State University. He continued to explore this field through his Ph. D. research with Dr. Amit Dhingra which leverages genomics and transcriptomics approaches to unravel interesting and agronomically important, physiological traits. One such intriguing trait is the impact of a rootstock on scion performance in perennial crops. In sweet cherry, the rootstock is known to control scion yield by up to 10-fold and his dissertation is focused on understanding which genes of the scion, or fruit producing variety, are modulated by the rootstock to control flower number. Tyson also enjoyed the opportunity to help train and mentor many undergraduates in the Dhingra Lab.