J C Cushman

Summary

Affiliation: University of Nevada
Country: USA

Publications

  1. pmc Tissue-specific mRNA expression profiling in grape berry tissues
    Jerome Grimplet
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
    BMC Genomics 8:187. 2007
  2. doi request reprint Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)
    John C Cushman
    Department of Biochemistry, MS200, University of Nevada, Reno, NV 89557 0014, USA
    J Exp Bot 59:1875-94. 2008
  3. pmc Isolation and characterization of mutants of common ice plant deficient in crassulacean acid metabolism
    John C Cushman
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 0200, USA
    Plant Physiol 147:228-38. 2008
  4. ncbi request reprint Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress
    O V Dyachenko
    Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
    Biochemistry (Mosc) 71:461-5. 2006
  5. pmc What makes species unique? The contribution of proteins with obscure features
    Martin Gollery
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
    Genome Biol 7:R57. 2006
  6. pmc The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Canada
    BMC Plant Biol 10:83. 2010
  7. pmc Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development
    Laurent G Deluc
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557 0014, USA
    BMC Genomics 8:429. 2007
  8. pmc Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay
    Laurent G Deluc
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
    BMC Genomics 10:212. 2009
  9. pmc Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets
    Richard L Tillett
    Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557 0330, USA
    BMC Plant Biol 11:86. 2011
  10. ncbi request reprint Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress
    Elizabeth A R Tattersall
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 0014, USA
    Funct Integr Genomics 7:317-33. 2007

Collaborators

  • Laurent G Deluc
  • Ing Feng Chang
  • Jerome Grimplet
  • Christina Walters
  • Ron Mittler
  • Grant R Cramer
  • Tahar Taybi
  • A M Borland
  • Jeffrey Harper
  • Michael R Sussman
  • Jian Kang Zhu
  • Hans J Bohnert
  • Howard Griffiths
  • H G Nimmo
  • Osamu Ueno
  • Douglas R Cook
  • Thomas Girke
  • Antony N Dodd
  • Alberto Iandolino
  • Miguel A Rodriguez Milla
  • Ali Ergul
  • Yuichi Uno
  • O Rahul Patharkar
  • E Wassim Chehab
  • Richard L Tillett
  • Delphine Vincent
  • Elizabeth A R Tattersall
  • Jose L Soulages
  • Martin Gollery
  • Adrian D Hegeman
  • Mary Ann Cushman
  • David Roy Smith
  • Karen A Schlauch
  • Mustafa Morsy
  • Kevin Horan
  • Sakae Agarie
  • Matthew D Wheatley
  • Julia Bailey-Serres
  • Jared Townsend
  • O V Dyachenko
  • Craig Osborne
  • Susanna F Boxall
  • Francisco Goes da Silva
  • Shin Kore-eda
  • Tilahun Abebe
  • Natalia V Ermolova
  • Kangmin Kim
  • Rebecca L Albion
  • Duc Tran
  • Jurgen E W Polle
  • Jon K Magnuson
  • Robert W Lee
  • Eileen Maher
  • Satyanarayana Gouthu
  • David Thorneycroft
  • Sandra Orchard
  • Charles Jang
  • Christian Shelton
  • Rebekah Woolsey
  • Robert R Blank
  • Yumi Shimizu
  • Karen Schlauch
  • Akihiro Nose
  • Haruki Sunagawa
  • Evan Lomen
  • David A Schooley
  • David R Quilici
  • Ayumu Kondo
  • Teruhisa Nakahara
  • Marlene C Bohlman
  • Kathleen Baumann
  • Toshifumi Shimoda
  • Johann Joets
  • T V Shevchuk
  • Alice C Harmon
  • Byung Woo Han
  • Eileen A Maher
  • N S Zakharchenko
  • Ya I Buryanov
  • Estelle M Hrabak
  • Miguel Rodriguez
  • David Quilici
  • Taliah Mittler
  • George N Phillips
  • Fadi Al-Kayal
  • Elif K Kabuloglu
  • Rubi Figueroa
  • Joan Rowe
  • Jonathan M Foster
  • Hyunju Lim

Detail Information

Publications32

  1. pmc Tissue-specific mRNA expression profiling in grape berry tissues
    Jerome Grimplet
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
    BMC Genomics 8:187. 2007
    ..In order to monitor the influence of water-deficit stress on tissue-specific expression patterns, mRNA expression profiles were also compared from mature berries harvested from vines subjected to well-watered or water-deficit conditions...
  2. doi request reprint Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)
    John C Cushman
    Department of Biochemistry, MS200, University of Nevada, Reno, NV 89557 0014, USA
    J Exp Bot 59:1875-94. 2008
    ....
  3. pmc Isolation and characterization of mutants of common ice plant deficient in crassulacean acid metabolism
    John C Cushman
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 0200, USA
    Plant Physiol 147:228-38. 2008
    ..The CAM-deficient mutants described here constitute important models for exploring regulatory features and metabolic consequences of CAM...
  4. ncbi request reprint Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress
    O V Dyachenko
    Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
    Biochemistry (Mosc) 71:461-5. 2006
    ..crystallinum plants on their adaptation to salt stress and switching-over to CAM metabolism...
  5. pmc What makes species unique? The contribution of proteins with obscure features
    Martin Gollery
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
    Genome Biol 7:R57. 2006
    ....
  6. pmc The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Canada
    BMC Plant Biol 10:83. 2010
    ..This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri...
  7. pmc Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development
    Laurent G Deluc
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557 0014, USA
    BMC Genomics 8:429. 2007
    ....
  8. pmc Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay
    Laurent G Deluc
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
    BMC Genomics 10:212. 2009
    ..While some pathways or enzymes affected by water deficit have been identified, little is known about the global effects of water deficit on grape berry metabolism...
  9. pmc Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets
    Richard L Tillett
    Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557 0330, USA
    BMC Plant Biol 11:86. 2011
    ..To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses...
  10. ncbi request reprint Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress
    Elizabeth A R Tattersall
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 0014, USA
    Funct Integr Genomics 7:317-33. 2007
    ..Funct Integr Genomics 7:111-134, 2007), but the reverse was not true, indicating a larger and more complex response in the acclimation process of a gradual long-term stress...
  11. doi request reprint Proteomic and selected metabolite analysis of grape berry tissues under well-watered and water-deficit stress conditions
    Jerome Grimplet
    Department of Biochemistry and Molecular Biology, University of Nevada Reno, Reno, NV 89557 0200, USA
    Proteomics 9:2503-28. 2009
    ..These results provide novel insights into the likely tissue-specific origins and the influence of water-deficit stress on the accumulation of key flavor and aroma compounds in wine...
  12. ncbi request reprint Transcript profiling of salinity stress responses by large-scale expressed sequence tag analysis in Mesembryanthemum crystallinum
    Shin Kore-eda
    Department of Biochemistry, University of Nevada, MS200, Reno, NV 89557 0014, USA
    Gene 341:83-92. 2004
    ..crystallinum demonstrates the great utility of EST analysis in unraveling the complex set of adaptive mechanisms contributing to water use efficiency (CAM) and salinity tolerance...
  13. ncbi request reprint Proteomic analysis reveals differences between Vitis vinifera L. cv. Chardonnay and cv. Cabernet Sauvignon and their responses to water deficit and salinity
    Delphine Vincent
    Department of Biochemistry and Molecular Biology, MS 200, University of Nevada, Reno, NV 89557, USA
    J Exp Bot 58:1873-92. 2007
    ..Many of the proteins up-regulated in Chardonnay were of unclassified or of unknown function, whereas proteins specifically up-regulated in Cabernet Sauvignon were involved in protein metabolism...
  14. ncbi request reprint Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles
    Grant R Cramer
    Department of Biochemistry and Molecular Biology, MS200, University of Nevada, Reno, NV, 89557 0014, USA
    Funct Integr Genomics 7:111-34. 2007
    ..Water-deficit-treated plants appear to have a higher demand than salinized plants to adjust osmotically, detoxify free radicals (reactive oxygen species), and cope with photoinhibition...
  15. ncbi request reprint The Arabidopsis AtDi19 gene family encodes a novel type of Cys2/His2 zinc-finger protein implicated in ABA-independent dehydration, high-salinity stress and light signaling pathways
    Miguel A Rodriguez Milla
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, 89557 0014, USA
    Plant Mol Biol 61:13-30. 2006
    ....
  16. pmc Temperature-induced extended helix/random coil transitions in a group 1 late embryogenesis-abundant protein from soybean
    Jose L Soulages
    Department of Biochemistry and Molecular Biology, 355 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078 0454, USA
    Plant Physiol 128:822-32. 2002
    ..This feature could constitute the basis of a potential role of LEA proteins in preventing freezing, desiccation, or osmotic stress damage...
  17. pmc Conformation of a group 2 late embryogenesis abundant protein from soybean. Evidence of poly (L-proline)-type II structure
    Jose L Soulages
    Department of Biochemistry and Molecular Biology, 355 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078 0454, USA
    Plant Physiol 131:963-75. 2003
    ....
  18. ncbi request reprint Isolation and characterization of a novel v-SNARE family protein that interacts with a calcium-dependent protein kinase from the common ice plant, Mesembryanthemum crystallinum
    E Wassim Chehab
    Department of Biochemistry and Molecular Biology MS200, 311 Fleischmann Agriculture, University of Nevada, Reno, NV 89557 0014, USA
    Planta 225:783-99. 2007
    ....
  19. ncbi request reprint Expression, purification, and initial characterization of a recombinant form of plant PEP-carboxylase kinase from CAM-induced Mesembryanthemum crystallinum with enhanced solubility in Escherichia coli
    Natalia V Ermolova
    Department of Biochemistry, University of Nebraska Lincoln, George W Beadle Center, 68588 0664, Lincoln, NE, USA
    Protein Expr Purif 29:123-31. 2003
    ..However, these antibodies were effective in immunoprecipitating 32P-based PpcK activity from crude, desalted extracts of maize leaves and soybean root-nodules...
  20. doi request reprint Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana
    Ing Feng Chang
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
    Proteomics 9:2967-85. 2009
    ..More than 80% (101) of these putative clients represent previously unidentified 14-3-3 interactors. These results raise the number of putative 14-3-3 clients identified in plants to over 300...
  21. doi request reprint Identification of proteins that interact with catalytically active calcium-dependent protein kinases from Arabidopsis
    Yuichi Uno
    Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 0200, USA
    Mol Genet Genomics 281:375-90. 2009
    ....
  22. doi request reprint Charting plant interactomes: possibilities and challenges
    Mustafa Morsy
    Department of Biochemistry and Molecular Biology, MS200, University of Nevada, Reno, NV 89557, USA
    Trends Plant Sci 13:183-91. 2008
    ..Bioinformatics approaches for curating and assessing the confidence of these datasets through inter-species comparisons will be crucial in achieving a complete understanding of protein interaction networks in plants...
  23. pmc Autophosphorylation and subcellular localization dynamics of a salt- and water deficit-induced calcium-dependent protein kinase from ice plant
    E Wassim Chehab
    Department of Biochemistry MS200, University of Nevada, Reno, Nevada 89557 0014, USA
    Plant Physiol 135:1430-46. 2004
    ....
  24. ncbi request reprint A novel yeast two-hybrid approach to identify CDPK substrates: characterization of the interaction between AtCPK11 and AtDi19, a nuclear zinc finger protein
    Miguel A Rodriguez Milla
    Department of Biochemistry and Molecular Biology, MS 200, University of Nevada, Reno, NV 89557 0014, USA
    FEBS Lett 580:904-11. 2006
    ..Our data suggest that disruption of the autoinhibitor domain leading to the formation of a constitutively active CDPK may stabilize kinase-substrate interactions without affecting specificity...
  25. pmc Conservation and divergence of circadian clock operation in a stress-inducible Crassulacean acid metabolism species reveals clock compensation against stress
    Susanna F Boxall
    Department of Biology, University of York, York YO10 5YW, United Kingdom
    Plant Physiol 137:969-82. 2005
    ..Importantly, the clock in M. crystallinum is very similar to that in Arabidopsis, indicating that such a clock could control CAM without requiring additional components of the central oscillator or a novel CAM oscillator...
  26. pmc Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development
    Francisco Goes da Silva
    Department of Plant Pathology, University of California, Davis, 95616, USA
    Plant Physiol 139:574-97. 2005
    ..Thus, the combined data set reveals the in silico expression patterns for hundreds of genes in V. vinifera, the majority of which have not been previously studied within this species...
  27. pmc Annotating genes of known and unknown function by large-scale coexpression analysis
    Kevin Horan
    Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
    Plant Physiol 147:41-57. 2008
    ..Finally, the public Plant Gene Expression Database (http://bioweb.ucr.edu/PED) was developed as part of this project to provide efficient access and mining tools for the vast gene expression data of this study...
  28. ncbi request reprint Salt tolerance, salt accumulation, and ionic homeostasis in an epidermal bladder-cell-less mutant of the common ice plant Mesembryanthemum crystallinum
    Sakae Agarie
    Faculty of Agriculture, Saga University, Saga, 840 8502, Japan
    J Exp Bot 58:1957-67. 2007
    ..These results clearly show that EBCs contribute to succulence by serving as a water storage reservoir and to salt tolerance by maintaining ion sequestration and homeostasis within photosynthetically active tissues of M. crystallinum...
  29. ncbi request reprint Integrating diel starch metabolism with the circadian and environmental regulation of Crassulacean acid metabolism in Mesembryanthemum crystallinum
    Antony N Dodd
    Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
    Planta 216:789-97. 2003
    ..We conclude that starch turnover regulates and limits carbon flux through the diel CAM cycle...
  30. ncbi request reprint A novel coiled-coil protein co-localizes and interacts with a calcium-dependent protein kinase in the common ice plant during low-humidity stress
    O Rahul Patharkar
    Department of Molecular Biology, Massachusetts General Hospital, Wellman 11, Boston, MA 02114, USA
    Planta 225:57-73. 2006
    ..McCAP1 is homologous to a family of proteins in Arabidopsis with no known function. Computational threading analysis suggests that McCAP1 is likely to be an intermediate filament protein of the cytoskeleton...
  31. pmc Tolerance of mannitol-accumulating transgenic wheat to water stress and salinity
    Tilahun Abebe
    Department of Plant and Soil Sciences, Oklahoma State University, Stillwater 74078, USA
    Plant Physiol 131:1748-55. 2003
    ....
  32. ncbi request reprint A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases
    Adrian D Hegeman
    University of Wisconsin Biotechnology Center, Madison, 53706, USA
    Proteomics 6:3649-64. 2006
    ..Homology models were generated for the protein kinase and calmodulin-like domains, each containing two of the five conserved sites, to allow intelligent speculation regarding subsequent lines of investigation...