12/29/2012

1. Aiken RM, O'Brien DM, Murray L, and Olson BL. 2012. Replacing fallow with continuous cropping reduces crop water productivity of semiarid wheat. Agron. Journal In press.

2. Aiken RM, Klocke NL. 2012. Inferring transpiration control from sap flow heat gauges and the Penman-Monteith equation. Transactions of the ASABE 55: 543-549.

3. Alford S, Rangarajan P, Williams S, and Gillaspy G. 2012. Myo-inositol oxygenase is required for responses to low energy conditions in Arabidopsis thaliana. Frontiers in Plant Physiology 3: 69.

4. Bender RR, Haegele JW, Ruffo M, and Below FE. 2013. Nutrient uptake, partitioning, and remobilization in modern, transgenic insect-protected maize hybrids. Agronomy Journal. 105: 161-170.

5. Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan D, Gurnon J, LadungI I, Lindquist E, Lucas S, Pangilinan J, Proschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Claverie, J, Grigoriev I, Van Etten J, Lomsadze A, and Borodovsky M. 2012. The genome of the polar eukaryotic microalga Coccomyxa subellipsoidae reveals traits of cold adaptation. Genome Biology 13: R39

6. Bogamuwa S, and Jang J-C. 2012. The Arabidopsis Tandem Zinc Finger 4, 5, and 6 are positive regulators of ABA- and negative regulators of GA-mediated control of seed germination. Plant Cell & Environ.(submitted).


7. Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus S, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher S, Johnson S, Benning C, Pellegrini M, Grossman A, and Merchant SS. 2012. Three acyltransferases and a nitrogen responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J. Biol. Chem. 287: 15811-15825.

8. Brueggeman AJ, Gangadharaiah DS, Cserhati MF, Casero D, Weeks DP, Ladunga I. 2012. Activation of the carbon concentrating mechanism by CO2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii. Plant Cell. 24:1860-1875

9. Cannon EKS, Birkett, SM, Braun BL, Kodavali, S, Jennewein DM Yilmaz, A, Antonescu, V, Antonescu, C, Harper LC, Gadiner JM, Schaeffer ML, Campbell, DA, Andorf CM, Andorf D, Lisch D, Koch KE, McCarty DR, Quackenbush J, Grotewold E, Lushbough CM, Sen TZ, and Lawrence,CJ. 2012. POPcorn: an online resource providing access to distributed and diverse maize project data. International Journal of Plant Genomics. Vol. 2011, Article ID 923035, 10 pgs. doi:10.1155/2011/923035.

10. Carmo-Silva AE, Gore MA, Andrade-Sanchez P, French AN, Hunsaker DJ, Salvucci ME. 2012. Decreased CO2 availability and inactivation of Rubisco limit photosynthesis in cotton plants under heat and drought stress in the field. Environ. Exp. Bot. 83: 1-11

11. Carmo-Silva AE, Salvucci ME. 2012. The temperature response of CO2 assimilation, photochemical activities and Rubisco activation in Camelina sativa, a potential bioenergy crop with limited capacity for acclimation to heat stress. Planta 236: 1433-1445

12. Chakraborty M, Kuriata AM, Henderson JN, Salvucci ME, Wachter RM, Levitus M. 2012. Protein oligomerization monitored by fluorescence fluctuation spectroscopy: self-assembly of Rubisco activase. Biophysical Journal 103: 949-958

13. Chan CX, Zauner S, Wheeler GL, Grossman AR, Prochnik S, Blouin N, Zhuang Y, Benning C, Berg GM, Yarish C, Eriksen R, Klein A, Lin S, Levine I, Brawley S, and Bhattacharya D. 2012. Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems. Plant Physiol. 158: 2001-2012.

14. Clouse, SD, Goshe MB, and Huber SC. 2012. Phosphorylation and receptor-like kinase signaling. In: Receptor-Like Kinases in Plants: from signaling to development. B. Kemmerling and F. Tax, Eds., Springer. 313 pp.

15. Donahue J, Ercetin M, and Gillaspy G. 2012. Assaying Inositol and Phosphoinositide Phosphatase Enzymes In Plant Lipid Signaling Protocols (Munnik T. and Heilmann I. Eds) Humana Press (Springer), in press.

16. Fang W, Si Y, Douglass S, Casero D, Merchant SS, Pellegrini M, Ladunga I, Liu P, Spalding MH. 2012. Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell. 24:1876-1893

17. Foudree A, Putarjunan A, Kambakam S, Nolan T, Fussell J, G. Pogorelko and S. Rodermel. 2012. The mechanism of variegation in immutans provides insight into chloroplast biogenesis. (Refereed review) Frontiers in Plant Physiol. (in press).

18. Fu A, Liu H, Yu F, Kambakam S, Luan S, and Rodermel S. 2012. Alternative oxidases (AOX1a and AOX2) can functionally substitute for plastid terminal oxidase in Arabidopsis chloroplasts. Plant Cell 24: 1579-1595.

19. Gentry LF, Ruffo M, and Below FE. 2013. Identifying factors controlling the continuous corn yield penalty. Agron. Journal In press.

20. Gholipoor M, Sinclair TR, Prasad PVV. 2012. Genotypic variation within sorghum for transpiration response to drying soil. Plant Soil 357:35-40.

21. Gillaspy G. 2012. The cellular language of myo-inositol signaling, New Phytol. 192, 823-839.
Torrens-Spence, MP, Gillaspy, G, Zhao, B, Harich, K, White, RH and Li, J. 2012. Biochemical evaluation of a parsley tyrosine decarboxylase results in a novel 4-hydroxyphenylacetaldehyde synthase enzyme, Biochemical and biophysical research communications 418: 211-216.

22. Guan JC, Koch KE, Suzuki M, Wu S, Petruff T, Goulet C, Klee HJ, McCarty DR. 2012. Strigolactone signaling affects branching and ear architecture phenotypes implicated in domestication of maize. Plant Physiol. 160: 1303-1317.

23. Haegele JW and Below FE. 2013. Transgenic corn rootworm protection increases grain yield and nitrogen use of maize. Crop Science. In press.

24. Haegele JW, Cook KA, Nichols DM, and Below FE. 2013. Changes in nitrogen use traits associated with genetic improvement for grain yield of maize hybrids released in different decades. Crop Science. In press.

25. Haider MS, Barnes JD, Cushman JC, 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 stress. J. Exp. Bot. 63: 1985-1996. DOI:10.1093/jxb/err412

26. Henderson JN, Hazra S, Dunkle AM, Salvucci ME, Wachter RM. 2012. Biophysical characterization of higher plant Rubisco activase. Biochimica Biophysica Acta.- Proteins and Proteomics, doi:10.1016/j.bbapap.2012.09.006

27. Huber SC. 2011. Grand challenges in plant physiology: The underpinning of translational research. Front. Plant Physiol. 2: 48. doi: 10.3389/fpls.2011.00048.

28. Hunter CT, Hill Kirienko DH, Sylvester AW, Peter GF, McCarty DR, Koch KE. (2012) Cellulose Synthase-Like D1 is integral to normal cell division, expansion, and leaf development in maize. Plant Physiol. 158: 708-724.

29. Koch KE, Suzuki M, Hunter CT, and McCarty DR. 2011. UniformMu: Release of 8,000 new lines for functional genomics research in maize. MaizeGDB. Website article.
(www.maizegdb.org/documentation/uniformmu/)

30. Kumar S, Sehgal SK, Kumar U, Prasad PVV, Joshi AK, Gill BS. 2012. Genomic characterization of drought tolerant related traits in spring wheat. Euphytica 186: 265-276.

31. Li T, Huang S, Zhao X, Wright DA, Carpenter S, Spalding MH, Weeks DP, Yang B. 2011.
Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res. 39: 6315-6325

32. Li T, Liu B, Spalding MH, Weeks DP, Yang B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature Biotechnology. 30:390-392.

33. Li X, Moellering ER, Liu C, Johnny C, Fedewa M, Sears BB, Kuo M-H, and Benning C. 2012. A galactoglycerolipid lipase is required for triacylglycerol accumulation and survival following nitrogen deprivation in Chlamydomonas reinhardtii. Plant Cell in press.

34. Lin J, Nazarenus TJ, Frey JL, Liang X, Wilson MA, and Stone JM. 2011. A Plant DJ-1 Homolog Is Essential for Arabidopsis thaliana Chloroplast Development. PLoS One 6, e23731.


35. Liu B, and Benning C. 2012. Lipid metabolism in microalgae distinguishes itself. Curr. Opin. Biotechnol., in press.

36. Ma Y, Pollock SV, Xiao Y, Cunnusamy K, Moroney JV. 2011. Identification of a novel gene required for normal pyrenoid formation in Chlamydomonas reinhardtii. Plant Physiol. 156: 884-896.

37. McCarty, DR, Suzuki M, Hunter C, and Koch KE. 2012. Genetic and molecular analysis of UniformMu transposon insertion lines. In Methods in Molecular Biology: Plant Transposable Elements (Thomas Peterson, ed). Springer, New York (in press).

38. McDonald AE, Ivanov AG, Bode R, Maxwell DP, Rodermel SR, Hüner NPA. 2011. Flexibility in photosynthetic electron transport: the physiological role of plastoquinol terminal oxidase (PTOX). (Refereed review) Biochim. Biophys. Acta. 1807: 954-967.

39. McDowell SC, Akmakjian G, Sladek C, Mendoza-Cozatl D, Morrissey JB, Saini N, Mittler R, Baxter I, Salt D, Ward J, Schroeder JI, Guerinot ML, Harper JF. 2012. Elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions. PLoS1. Submitted.

40. McDowell, SC, Poulsen LR, Lòpez-Marquès RL, Palmgren MG,Harper JF. 2012. Loss of the Arabidopsis thaliana P4ATPase ALA3 results in root, shoot, and reproductive phenotypes that are strongly dependent upon growth conditions. PLoS1. Submitted.

41. Meyer MT, Genkov T, Skepper JN, Jouhet J, Mitchell MC, Spreitzer RJ, Griffiths H. 2012. Rubisco small-subunit a-helices control pyrenoid formation in Chlamydomonas. Proc. Natl. Acad. Sci. USA (in press).

42. Moroney JV, Ma Y, Frey WD, Fusilier K, Pham TT, Simms TA, DiMario RJ, Yang J, and Mukherjee B. 2011. The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: expression, intracellular location and physiological roles. Photosyn. Res. 109: 133-149. DOI: 10.1007/s11120-011-9635-3.

43. 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. Bot. J. Linnean Soc.. 168: 117-146. DOI: 10.1111/j.1095-8339.2011.01194.x

44. Ocheltree TW, Nippert JB, Prasad PVV. 2012. Changes in stomatal conductance along grass blades reflect changes in leaf structure. Plant Cell and Environment 35: 1040-1049

45. Oh M-H, Clouse SD, and Huber SC. 2012. Tyrosine phosphorylation of the BRI1 receptor kinase occurs via a posttranslational modification and is activated by the juxtamembrane domain. Front Plant Sci 3: 175. doi: 10.3389/fpls.2012.00175

46. Oh M-H, Kim HS, Wu X, Clouse, SD, Zielinski RE, and Huber SC. 2012. Calcium/calmodulin inhibition of the Arabidopsis BRI1 receptor kinase provides a possible link between calcium- and brassinosteroid-signaling. Biochem. J. 443: 515-523.

47. Oh M-H, Wang X, Clouse SD. and Huber SC. 2012. Deactivation of the Arabidopsis BRI1 receptor kinase by autophosphorylation within the glycine-rich loop involved in ATP binding. Proc. Natl. Acad. Sci. USA, 109: 327-332.

48. Oh M-H, Wu X, Kim HS, Harper JF, Zielinski R, Clouse SD, and Huber SC. 2012. CDPKs are dual-specificity protein kinases and tyrosine autophosphorylation attenuates kinase activity. FEBS Lett. PMID: 23079037

49. Ozdemir, M, Tang C, Ishka MR, Brown E, Groves N, Myers CT, McDowell S, Mittler R, JF Harper 2012. A cyclic nucleotide-gated channel (CNGC16) in pollen is critical for stress tolerance in pollen reproductive development. Plant Physiology. in press.

50. Ozdemir, M, Rato C, Brown E, Rogers S, Goyne A, Frietsch S, Myers CT, Poulsen LR, Malhó R, Harper JF. 2012. Cyclic nucleotide gated channels 7 and 8 are essential for male reproductive fertility. PLoS1. Submitted.

51. Pandurangan S, Pajak A, Molnar SJ, Cober ER, Dhaubhadel S, Hernandez-Sebastia C, Kaiser WM, Nelson, RL, Huber SC, and Marsolais F. 2012. Relationship between asparagine metabolism and protein concentration in soybean seed. J. Exp. Bot. 63: 3173-3184.

52. Parry MAJ, Andralojc PJ, Scales J, Salvucci ME, Carmo-Silva AE, Alonso H, Whitney S. 2012. Rubisco activity and regulation as targets for crop improvement. Journal of Experimental Botany, in press

53. Pedersen CN, Axelsen KB, Harper JF, and Palmgren MG. 2012. Evolution of plant p-type ATPases. Frontiers in Plant Science. 3: 31.

54. Pradhan GP, Prasad PVV, Fritz AK, Kirkham MB, Gill BS. 2012a. High temperature tolerance in Aegilops species and its potential transfer to wheat. Crop Science 52: 292-304

55. Pradhan GP, Prasad PVV, Fritz AK, Kirkham MB, Gill BS. 2012b. Response of Aegilops species to drought stress during reproductive stages of development. Functional Plant Biology 39: 51-59.

56. Pradhan GP, Prasad PVV, Fritz AK, Kirkham MB, Gill BS. 2012c. Effect of drought and high temperature stress on synthetic hexaploid wheat. Functional Plant Biology 39: 190-198

57. Radwan O, Wu, X., Govindarajulu M, Libault M, Neece DJ, Bert,RH, Stacey G, Taylor CG, Huber, SC, and Clough SJ. 2012. A 14-3-3 protein encoded by the SGF14c gene plays a critical role during soybean nodulation. Plant Physiol. in press.

58. Rosso, D, Bode R, Li W, Krol M, Rodermel SR, Maxwell DP, and Hüner NPA. 2012. Redox control of leaf variegation and chloroplast biogenesis in Arabidopsis thaliana. In Photosynthesis: Overviews on Recent Progress and Future Perspectives, ed. S. Itoh, P. Mohanty and K.N. Guruprasad (IK International Publishers, New Delhi), p. 108-119.

59. 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.

60. Scafaro AP, Yamori W, Carmo-Silva AE, Salvucci ME, von Caemmerer S, Atwell BJ. 2012. Rubisco activity is associated with photosynthetic thermo-tolerance in the wild rice Oryza meridionalis. Physiologia Plantarum 146: 99109

61. Spalding E, and JF Harper JF. 2011. The ins and outs of cellular Ca transport. Current Opinion in Plant Biology, 14: 715-720.

62. 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 Biotechnol. J.. 10: 105-124. DOI: 10.1111/j.1467-7652.2011.00648.x

63. Ting L, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B, 2011. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Research 39: 359-372.

64. Ting L, Liu B, Spalding MH, Weeks DP, Yang B. 2012. High Efficiency TALEN-based Gene Editing for Producing Disease Resistance in Crop Plants. Nature Biotechnol. 30: 390-392

65. Vieler A, Brubaker SB, Vick B, and Benning C. 2012. A lipid droplet protein of Nannochloropsis with functions partially analogous to plant oleosins. Plant Physiol. 158: 1562-1569

66. Vieler A, Wu G, Tsai C-H, Bullard B, Cornish AJ, Harvey H, Reca I-B, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Ferguson AA, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston R, Sanjaya, Simpson JP, TerBush A, Warakanont J, Zäuner S, Farre EM, Hegg, EL, Jiang N, Kuo M-H, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu S-H, Benning C. (2012). Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Gen., in press.

67. Wang M, Liu X, Wang R, Li W, Rodermel S, and Yu F. 2012. Overexpression of a putative Arabidopsis BAHD acyltransferase causes dwarfism that can be rescued by brassinosteroid. J. Exp. Bot. (online).

68. Weise SE, Aung K, Jarou ZJ, Hardy AC, Carr DJ, and Sharkey TD. 2012. Engineering starch accumulation by manipulation of phosphate metabolism of starch. Plant Biotechnol. J. 10: 545-554

69. Weise SE, van Wijk KJ, and Sharkey TD. 2011. The role of transitory starch in C3, CAM, and C4 metabolism and opportunities for engineering leaf starch accumulation. . J. Exp. Bot. 62: 3109-3118

70. Weeks DP. 2011. Homologous recombination in Nannochloropsis: A powerful tool in an industrially relevant alga. Proceedings National Academy Sciences 108: 20859-20860.

71. White WG, Vincent ML, Moose SP, and Below FE. 2012. The sugar, biomass and biofuel potential of temperate by tropical maize hybrids. GCB Bioenergy. 4: 496-508. doi: 10.1111/j.1757-1707.2012.01158.x

72. Wu X, Oh, M-H, Kim HS, Schwartz, D, Imai, BS, Yau PM, Clouse SD, and Huber SC. 2013. Transphosphorylation of E. coli proteins during production of recombinant protein kinases provides a robust system to characterize kinase specificity. Frontiers Plant Sci., in revision.

73. Wu X, Vellaichamy, A, Wang D, Zamdborg L, Kelleher NL, Huber SC, and Zhao Y. 2013. Differential lysine acetylation profiles of Erwinia amylovora strains revealed by proteomics. J. Proteome Res., in revision.

74. Yobi A, Wone BWM, Guo L, Alexander DC, Ryals JA, Oliver M, Cushman JC. 2012a. 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.

75. Yobi A, Wone BWM, Guo L, Alexander DC, Ryals JA, Oliver M, Cushman JC. 2012b. Metabolomic profiling in Selaginella lepidophylla reveals adaptations essential for desiccation tolerance. Molec. Plant. DOI: 10.1093/mp/sss155.

76. Yobi A, Schlauch KA, Perryman B, Oliver MJ, Cushman JC. 2012c. 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.

77. Yu F, Park S-S, Liu X, Foudree A, Fu A, Powikrowska M, Khrouchtchova A, Jensen PE, Kriger JN, Gray GR, and Rodermel SR. 2011. SUPPRESSOR OF VARIEGATION4, a new var2 suppressor locus, encodes a pioneer protein that is required for chloroplast biogenesis. Molecular Plant 2: 229-240.

78. Zäuner S, Jochum W, Bigorowski T, and Benning C. 2012. A Cytochrome b5-containing plastid-located fatty acid desaturase from Chlamydomonas reinhardtii. Euk. Cell 11:856-863.

03/01/2014

04/26/2015

02/17/2016

03/02/2017

Publications for all participants are listed along with project summaries in the attached file.