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John Cushman
Photo of John Cushman

Professor
Biochemistry and Molecular Biology
University of Nevada/Mail Stop 330
1664 North Virginia Street
Reno,  Nevada   89557

 

Office: (775) 784-1918
Lab: 784-6258
Fax: 784-1419
Email: jcushman@unr.edu
Building: Howard Medical Science,  Office 210B

 

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EDUCATION

B.S. 1982 Ursinus College
M.S. 1984 Rutgers University - New Brunswick
Ph.D. 1986 Rutgers University - New Brunswick

 
ACADEMIC & RESEARCH INTEREST
  • Functional Genomics of Crassulacean acid metabolism (CAM): CAM is water-conserving photosynthetic pathway that helps plants survive in seasonally arid climates or those with intermittent water supply (e.g. epiphytic habitats). Our research objectives are to understand how the expression of CAM is controlled by environmental stress (salinity, water deficit) and the circadian clock. Our approach is to conduct integrated transcriptome, proteome, and metabolome analyses using a model facultative CAM species called the common or crystalline ice plant (Mesembryanthemum crystallinum).

 

  • Evolutionary Origins of Crassulacean acid metabolism in Neotropical Orchids: Crassulacean acid metabolism (CAM) has evolved multiple times in 33 families and 328 genera comprising more than 6% of all vascular plant species making it the second most common mode of photosynthesis among vascular plants. Our goal is to understand the molecular mechanisms responsible for the evolution of this important photosynthetic adaptation. Our approach is to survey foliar carbon isotopic composition (delta13C) to map the occurrence of CAM in closely related species within the Oncidiinae, a subtribe within Orchidaceae, and then identify molecular genetic changes specific to plants that exhibit CAM.

 

  • Gene Discovery in Resurrection Species: The long-term goal of this integrated research-education-extension project is to use resurrection plants as models to develop and enhance course offerings in Plant Breeding and Biotechnology and related topics, to develop an integrated research and extension project using Sporobolus as a forage grass, and to gain a basic understanding of the unique gene and gene regulatory networks that are necessary and sufficient for vegetative tissues to withstand dehydration and then rapidly recover upon rehydration that will serve as a case study for advanced teaching modules for crop improvement strategies.

 

  • Improved Abiotic Stress Tolerance in Camelina: The long-term goal of this research program is to improve the drought tolerance and other production traits of Camelina so that is might serve as a biofuel crop within the northern Nevada and the Great Basin. The goals are to test different varieties of Camelina to determine which might be suitable for regional growing conditions, develop improved traits such as heat, drought, and salinity tolerance, herbicide resistance, and shatter resistance of pods, using various genetic approaches, create a transcriptome database for all tissues under abiotic stress conditions, and provide educational outreach to inform stakeholders about the utility of Camelina as a regional biodiesel feedstock.

 

  • Development of Opuntia (Prickly Pear Cactus) as a Low-water-input Oleogenic Biofuel and Biomass Feedstock: The long-term goals of this research program are to enhance existing transcriptome resources for Opuntia ficus-indica, generate oleogenic cactus that accumulates lipids within vegetative and fruit tissues, evaluate such cactus for increased accumulation of lipids and other feedstock characteristics, and provide educational outreach to inform stakeholders using an educatonal display on biofuels production.

 

  • Engineering CAM Photosynthetic Machinery into Bioenergy Crops for Biofuels Production in Marginal Environments: The long-term goal of this research program is to enhance water use efficiency (WUE) and adaptability to hotter/drier climates of C3 species by introducing Crassulacan acid metabolism (CAM) thereby developing new capabilities for biomass production on marginal or abandoned agricultural lands while minimizing water and nitrogen inputs. The specific goals are to define the genetic basis of a set of CAM modules in eudicot and monocot species using network modeling data derived from 'omics data sets, characterize the regulation of carboxylation, decarboxylation, and stomatal control modules using comparative genomic, network/molecular dynamics modeling, and loss-of-function testing, deploy advanced genetic engineering technologies to enable stacking of large numbers of transgenes to improve transgene persistance, and to transfer fully functional CAM modules, and analyze the effects of different CAM modules on stomatal control, CO2 assimilation and transpiration rates, water use efficiency, and biomass yields in Arabidopsis and Poplar.

Our research is funded by the National Science Foundation (NSF), United States Department of Agriculture (NIFA), Department of Energy (DOE), the Nevada Agriculture Foundation (NAF), and the Nevada Agricultural Experiment Station (NAES).

Students and postdoctoral research associates with broad interests in plant molecular genetics and plant biochemistry related to abiotic stress tolerance and bioenergy production systems are welcomed to pursue training opportunities in this laboratory.
 
COURSES & TEACHING RESPONSIBILITIES

 

  • BCH 705 - Molecular Genetics
  • BCH 706 - Functional Genomics
  • BCH 718 - Plant Molecular Biology and Biotechnology
  • BCH794 - Biofuels/biomass Colloquium
  • Biochemistry Graduate Program Director
     
 
AWARDS, HONORS, & PROFESSIONAL RECOGNITION

2011-2013 Foundation Professor

2003 Outstanding CABNR Researcher Award
 
 
COMMUNITY SERVICE

Editor: Progress in Botany; Associate Editor: Plant Cell & Environment

Editorial Board Member: Journal of Experimental Botany, Journal of Plant Physiology
 
REPRESENTATIVE PUBLICATIONS

 

Journals
Yobi A, Schlauch KA, Perryman B, Oliver MJ, Cushman JC. 2013, Biomass production, nutritional, and mineral content of desiccation-sensitive and desiccation-tolerant species of Sporobolus under multiple irrigation regimes., J. Agron. Crop Science. In press.  
Yobi A, Wone BWM, Guo L, Alexander DC, Ryals JA, Oliver M, Cushman JC. 2013, Metabolomic profiling in Selaginella lepidophylla provides new insights in the mechanistic basis of desiccation tolerance., Molec. Plant. In press. DOI: 10.1093/mp/sss155.  
Haider MS, Barnes JD, Cushman JC, and Borland AM 2012, A CAM- and starch-deficient mutant of the facultative CAM species Mesembryanthemum crystallinum reconciles sink demands by repartitioning carbon during acclimation to salinity, Journal of Experimental Botany. 63: 1985-1996.  
Samburova V, Lemos MS, Hiibel SR, Hoekman SK, Cushman JC, Zielinska B. 2012, Analysis of triacylglycerols and free fatty acids in algae using ultra-high-pressure liquid chromatography mass spectrometry., J. Am. Oil Chem. Soc. DOI 10.1007/s11746-012-2138-3.  
Neubig KM, Whitten WM, Williams NH, Blanco MA, Endara L, Burleigh G, Silvera K, Cushman JC, Chase MW 2012, Generic recircumscriptions of Oncidiinae (Orchidaceae: Cymbidieae) based on maximum likelihood analysis of combined DNA datasets., Botanical Journal of the Linnean Society. 168: 117-146.  
Tillett RL, Wheatley MD, Tattersall EAR, Schlauch KA, Cramer, GR, Cushman JC 2012, The Vitis vinifera C-repeat binding protein 4 (VvCBF4) transcriptional factor enhances freezing tolerance in wine grape., Plant Biotechnology Journal. 10:105-124  
Yobi A, Wone BWM, Guo L, Alexander DC, Ryals JA, Oliver M, Cushman JC. 2012, Untargeted global metabolomic profiling reveals novel biochemical differences critical for desiccation tolerance within a sister group comparison of Selaginella species., The Plant J. 72: 983-999.  
Oliver MJ, Guo L, Alexander DC, Ryals JA, Wone BWM, Cushman JC. 2011, A sister group metabolomic contrast using untargeted global metabolomic analysis delineates the biochemical regulation underlying desiccation tolerance in Sporobolus stapfianus., The Plant Cell. 23: 1231-1248.  
Curran A, Chang I-F, Chang C-L, Garg S, Rodriguez Milla M, Barron YD, Li Y, Romanowsky SD, Cushman JC, Gribskov M, Peck SC, Harmon AC, Harper JF. 2011, Calcium-dependent protein kinases from Arabidopsis show substrate specificity differences in an analysis of 102 substrates., Frontiers in Plant Biology. 2: 1-15.  
Tillett RL, Albion RL, Schlauch KA, Cramer GR, and Cushman JC. 2011, mRNA expression profiling of abiotic stress responses in leaf and berry tissue of wine grape (Vitis vinifera) using expressed sequence tags., BMC Plant Biology. 11:86.  
Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S, Kianianmomeni A, Prigge M, Berndt A, Cushman JC, Polle J, Magnuson J, Hegemann P, Deisseroth K. 2011, The microbial opsin family of optogenetic tools., Cell. 147:1446-1457.  
Ramos AA, Polle J, Tran D, Cushman JC, Jin ES, Varela JC. 2011, The unicellular green alga Dunaliella salina Teod. as a model for abiotic stress tolerance: Genetic advances and future prospects., Algae. 26:3-20.  
Deluc LG, Decendit A, Papastomoulis Y, Mérillon J-M, Cushman JC, Cramer GR. 2011, Water deficit increases stilbene metabolism in Cabernet Sauvignon berries., J. Agric. Food Chem. 59: 289-297.  
Sunagawa H, Agarie S, Cushman JC. 2010, Crassulacean acid metabolism alleviates reactive oxygen species in the facultative CAM plant, the common ice plant, Mesembryanthemum crystallinum., Plant Production Science. 13: 256-260.  
Oliver MJ, Cushman JC, Koster KL 2010, Dehydration Tolerance in Plants., Methods in Molecular Biology: Plant Stress Tolerance. 639: 3-24.  
Silvera K, Neubig KM, Whitten WM, Williams NH, Winter K, Cushman JC. 2010, Evolution along the Crassulacan acid metabolism continuum., Functional Plant Biology (Cover article) 37: 995-1010  
Alkayal MF, Albion RL, Tillett RL, Mark S. Lemos, Hernandez-Gomez L, Cushman JC. 2010, Expressed Sequence Tag (EST) profiling in salinity shocked Dunaliella salina reveals high expression of protein synthetic apparatus components., Plant Science. 179:437-449.  
Silvera K, Santiago LS, Cushman JC, Winter K 2010, Incidence of Crassulacean acid metabolism in the Orchidaceae derived from carbon isotope ratios: a checklist of the flora of Panama and Costa Rica., Botanical Journal of the Linnean Society. 163: 194-222.  
Smith DR, Lee RW, Cushman JC, Magnuson JK, Tran D, Polle JEW 2010, The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA., BMC Plant Biology. 10:83.  
Silvera K, Santiago LS, Cushman JC, Winter K. 2009, Crassulacean acid metabolism and epiphytism linked to adaptive radiations in the Orchidaceae., Plant Physiol. 149:1838-1847.  
Uno Y, Rodriguez Milla MA, Maher E, Cushman JC. 2009, Identification of proteins that interact with catalytically active calcium-dependent protein kinases from Arabidopsis., Mol. Gen. Genet. 281:375-390.  
Grimplet J, Ben Jouira H, Wheatley M, Deluc L, Cramer GR, Cushman JC. 2009, Proteomic and selected metabololite analysis of grape berry tissues under well-watered and water-deficit stress conditions., Proteomics. 9:2503-2528.  
Chang IF, Curran A, Woolsey R, Quilici D, Cushman JC, Mittler R, Harmon A, Harper J. 2009, Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana., Proteomics 9:2967-2985.  
Deluc LG, Quilici DR, Decendit A, Grimplet J, Wheatley MD, Schlauch KA, Mérillon J-M, Cushman JC, Cramer GR. 2009, Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay., BMC Genomics. 10:212.  
Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu J-K, Cushman JC, Gollery M, Girke T. 2008, Annotating genes of known and unknown function by large-scale co-expression analysis., Plant Physiol. 147: 41-57.  
Morsy MR, Gouthu S, Orchard S, Thorneycroft D, Harper JF, Mittler R, Cushman JC. 2008, Charting Plant Interactomes: Possibilities and Challenges., Trends in Plant Science. 13: 183-191.  
Song L, Ciftci-Yilmaz S, Harper J, Cushman JC, Mittler R. 2008, Enhanced tolerance to oxidative stress in transgenic Arabidopsis thaliana plants expressing proteins of unknown function., Plant Physiol. 148: 280-292.  
Cushman JC, Agarie S, Albion RL, Elliot SM, Taybi T, Borland AM 2008, Isolation and characterization of mutants of ice plant, Mesembryanthemum crystallinum, deficient in Crassulacean acid metabolism., Plant Physiol. 147: 228-238.  
Cushman JC, Tillett RL, Wood JA, Branco JA, Schlauch KA. 2008, Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)., J. Exp. Botany. 59:1875-1894.  
Book or Chapter(s) in Books
Schlauch KA, Grimplet J, Cushman JC, Cramer GR. 2011, Transcriptomics analysis methods: microarray data processing, analysis and visualization using the Affymetrix GeneChip® Vitis vinifera genome array, Methods and Results in Grapevine Research. Delrot S, Medrano H, Or E, Bavaresco L, Grando S (Eds.). Springer, Chap 22, pp. 317-334.  
Cushman JC, Oliver MJ. 2011, Understanding vegetative desiccation tolerance using integrated functional genomics approaches within a comparative evolutionary framework., Ecological Studies: Desiccation Tolerance in Plants. Eds: Ulrich Luttge, Erwin Beck, and Dorothea Bartels. Springer, Heidelberg. 215: 307-338.  
Tillett RL, Cushman JC 2010, Vitis functional genomics: Open systems for transcriptome analysis., Genetics, Genomics and Breeding of Grapes. Eds: José M. Martinez-Zapater and Anne-Francoise Adam Blondon. Science Publishers, Enfield, New Hampshire. Chapter 10, pp. 235-269.  
Schlauch KA, Grimplet J, Cushman JC, Cramer GR. 2009, Transcriptomics: methods for microarray data analysis and visualization using the Affymetrix GeneChip® Vitis vinifera genome array., In: Methods in Grapevine Research. Eds: Serge Delrot.