Brief Summary of Minutes of Annual Meeting

Meeting Minutes Outcome of the Business meeting: 1. Jeff Harper and John Cushman (Nevada AES) will host the annual meeting in 2012 in Reno Nevada 2. Marty Spalding and Steve Rodermel (Iowa AES) will organize the annual meeting in 2013 possibly together with Julie Stone (Nebraska AES) in Omaha, NE. 3. The renewal proposal has been completed and will be submitted on time by Christoph Benning on Dec 2011. We expect to hear following the NC AES directors meeting in March or April 2012 4. Christoph Benning will take over from Irwin Goldman as Administrative Advisor and will be supported by MSU AgBioResearch Director Steve Pueppke. 5. It was mentioned by the AA that for the SAES422 Reprort form, funding information is needed. 6. Laura Gentry (Illinois AES), was elected as new member. Agenda of the Meeting: Friday, Nov. 11, 2011 Evening 7:30 Meet in Gatehouse Lobby (Transport by minivan) 8:00 Dinner at Dustys Cellar 10:00 Return to Gatehouse (Transport by minivan) Saturday, Nov. 12, 2011 Morning 7:45 Meet in Gatehouse Lobby (Transport by minivan) 8:00 Breakfast in MSU Biomedical and Physical Science Building (BPS) 8:45 Announcements and introductions, Christoph Benning 9:00 Welcome by MSU AgBioResearch Director Steve Pueppke. 9:15 Christoph Benning, MSU AgBioResearch 9:45 Julie Stone, Nebraska AES 10:15 Gerry Edwards, Washington AES 10:45 Break 11:00 Marty Spalding, Iowa AES 11:30 Don Weeks, Nebraska AES Afternoon 12:00 Lunch and Business Meeting I, 1400 BPS 1:00 Steve Huber, USDA-ARS, Illinois 1:30 JC Jang, Ohio AES 2:00 Glenda Gillaspy, Virginia AES 2:30 Break 2:45 John Cushman, Nevada AES 3:15 Wayne Loescher, MSU AgBioRsearch 3:45 Tom Sharkey, MSU AgBioResearch 4:15 Break 4:30 Laura Gentry, Illinois AES 5:00 Robert Aiken, Kansas AES 5:30 Mike Salvucci, USDA-ARS, Arizona 6:00 Business Meeting II Evening 6:30 Return to Gatehouse (Transport by minivan) 7:30 Meet in Lobby of Gatehouse (Transport by minivan) 8:00 Dinner at Bennings 11:00 Return to Gatehouse (Transport by minivan)

Summary of Accomplishments Presented by Meeting Attendees Objective 1. Plastid Function and Intracellular Communication Christoph Benning (MSU AgBioresearch) presented new findings on chloroplast lipid remodeling and plant stress tolerance related to Objective 1 of the renewal proposal. Lipid composition of cellular membranes is affected by phosphate deprivation leading to the replacement of phospholipids with non-phosphorus glycolipids synthesized at the chloroplast outer envelope membrane. A novel galactolipid remodeling enzyme was described, which is involved in the protection of plants against freezing stress. Activation of this enzyme leads to the formation of oligogalactolipids and triacylglycerols allowing membranes to adjust as the chloroplast shrinks following severe dehydration during freezing and ice formation. Julie Stone (Nebraska AES), a new member, talked about her work with Fumonisin B1 (FB1) a sphingolipid analogue that inhibits ceramide synthases in both plants and animals, and thereby induces programmed cell death. Julie and her coworkers isolated a series of FB1 resistant mutants that she is now studying. One affects a transcription factor causing a change in sphingolipid profiles. Julie also presented her work on Arabidopsis DJ-1 like proteins, which are conserved ubiquitous proteins. A human ortholog is implicated in Parkinsons disease (Park7) and mutations destabilize the dimer. The protein is also overproduced in various tumors. Arabidopsis has three different forms (A, B, and C). AtDJ1C, the current focus of her research, is localized in the plastid. The gene is expressed mostly in young leaves. Homozygous mutants are not viable, but can be rescued with sucrose supplementation and an epitope-tagged version of the wild-type DJ1C protein. DJ1C-interacting partners will be identified using coimmunoprecipitation of DJ1C-containing complexes from chloroplasts isolated from the complemented line. She is proposing to interact with the Benning lab on chloroplast isolation techniques. She will apply omics technologies to characterize these proteins. Two University of Nebraska - Lincoln NSF REU programs were described that contribute to training of undergraduate students involved in her research. Objective 2. Photosynthetic Capture and Photorespiratory Release of CO2 Gerry Edwards presented collaborative work with Asaph Cousins and R. Giuliani (Washington AES) on efforts at overcoming the limitations of C3 photosynthesis, photoinhibition, and sink limitation. The group studies photorespiration in rice and proposes to redesign photosynthesis in this crop. In the long term, it is planned to introduce C4 photosynthetic metabolism into rice. Natural variations in leaf structure and gas exchange in different wild rice species were analyzed and correlated to the diversity in water use and sun versus shade adaptations. One of the wild rice species, Oryzacoarctata, was found to have a cellular arrangement of mesophyll and bundle sheath cells like that in some Kranz type C4 grasses. In some species the mesophyll cells have lobes in which mitochondria are located in close proximity to the chloroplasts. The group is investigating the significance of these lobes to determine whether they function to facilitate diffusion of atmospheric CO2 to chloroplasts, or to enhance refixation of photorespiredCO2 like C3-C4 intermediates. The CO2 compensation point in plants is a function of Rubisco specificity factor and degree of refixation of photorespiredCO2. In vitro analysis of the specificity factor will be combined with gas exchange to enable modeling of the response of photorespiration to different temperatures. Approaches to measure the CO2 compensation point in vivo and techniques to measure the internal rate of refixation of CO2 using stable isotopes were presented. Marty Spalding, (Iowa AES) presented his newest findings on the carbon concentration mechanism (CCM) in Chlamydomonas. CCM is inducible at low CO2 and there are multiple acclimation states at low and very low CO2 concentrations. Interestingly, one mutant, lcib, does not survive low CO2 concentrations, but is viable under very low CO2 concentrations. His group conducted transcriptomics work using the cia5 mutant and different CO2 concentrations. CIA5(CCM1) is a transcription factor acting as master regulator of CCM. He observed 16 clusters of expressed genes with similar behavior and described examples. For example, cluster 15 contained genes that are induced under low CO2. He also described attempts at ectopic expression of LCIA and LCIB under the control of the Rcbs promoter to increase biomass yields in reactors. Overexpression of both genes caused an increase in final biomass yield. Growth remained the same but the mass of the cells was increased through increase in starch content (60% per DW). The cells showed an increased CO2 assimilation. Crossing the transgenics with the starch deficient mutant sta6 led to increased total fatty acids but decreased biomass yield. Don Weeks (Nebraska AES) also reported on the global transcriptional regulation of CCM by CO2 deprivation, in this case in the wild type. 25% of genes were found to be differentially expressed 4 fold or greater. It was noted that the nature of the CO2 shift is important, e.g., when using a fermenter switching from 4% CO2 to ambient CO2 levels it takes an hour to complete the shift. He also described different clusters of co-regulated genes. For example, photosynthetic genes were strongly reduced under these conditions. It was observed that most genes organized head-to-head (HTH) in the genome are co-regulated by bidirectional promoters. Don provided two examples of HTH gene pairs encoding CCM components that are coordinately expressed at high levels. A search for common TF binding sites identified a CACACA&.motif in up regulated genes, but not in down regulated genes. John Cushman (Nevada AES) described his omics studies on ice plant, in which crassulacean metabolism (CAM) is inducible through salinity or drought stress. CAM plants have about 20% the crop water demand of C3 plants, but can have higher rates of above ground productivity. His lab compared the induced and non-induced states by global transcription profiling. He described an ice plant mutant deficient in CAM that grows more slowly than wild type, lacks nocturnal CO2 uptake and starch. The CAM mutant contains a knockout in the plastidic phosphoglucomutase gene. John described a metabolic profiling study during day-night period following constant conditions of illumination and temperature to evaluate the role of circadian clock regulation of CAM outputs. Rhythmic acid formation following drought stress was observed in the wild type, but not the mutant. Starch was transiently present in wild type, but absent from the mutant. Starch content remained high under continuous conditions. Soluble sugars were found to cycle in the mutant, which was interpreted as a compensatory effect. The metabolite analysis was done commercially (Metabolon). 503 metabolites were identified including 199 known and 304 unnamed compounds. The accumulation of free fatty acids and monoglycerides was observed in the mutant. The mutant showed a lower ABA content and evidence of higher oxidative stress. A reciprocal pattern for reduced and oxidized glutathione was observed over time. Objective 3: Mechanisms Regulating Photosynthate Partitioning Steve Huber (Ilinois ARS) reported on his work on brassinosteroid signaling in particularly the mechanism of deactivation. He focused on the BRI1 receptor kinase, and its auto and transphosphorylation properties. The BRI1 activation loop of the kinase domain becomes phosphorylated during activation. BRI1 is deactivated by dephosphorylation and endocytosis, or phosphorylation of inhibitory sites and calmodulin interaction. He reported on work focusing on the phosphorylation of Ser 891. This phosphorylation occurs in vivo and attenuates brassinosteroid signaling. A phosphomimetic mutant is unresponsive. He reported that transgenic plants with substitutions at Ser 891 have growth phenotypes, such as enhanced growth resulting in increased biomass. He noted that BRI1 binds to immobilized calmodulin (CaM) with its kinase domain. He discovered that CaM affects autophosphorylation of BRI1 and transphosphorylation of E. coli proteins if coproduced in E. coli. In essence, this observation provides the basis for a new assay of BRI1 activity. JC Jang (Ohio, AES) covered work from his lab on sugar signaling. His focus is on sugar responsive Transcription Factors (TFs) such as bZIP1, which is a negative regulator for plant growth in the absence of sugar. He reported on the dimerization of different TFs of the bZIP family. He also reported on TZF1 (Tandem Zinc Finger1). Interestingly, only 10-20% of TZF1-GFP fusion protein was found in nucleus, while most of it was found in punctate patterns in cytosol. These punctate structures were identified as processing (P) bodies and stress granules, which are not the same but have overlapping composition. Both can be induced by stress. The Arabiopsis AtTZF gene family has 11 members. All localize to the nucleus as well as to P-bodies and stress granules as demonstrated by co-localization of GFP fusion proteins and specific marker proteins for P-body and stress granule. He reported that TZF1 is a positive regulator of sugar/ABA signaling and a negative regulator for GA signaling. The expression of the C-terminal fragment of TZF1 causes dominant negative effects and enhances growth, but the plants are sensitive to drought. These findings might provide a strategy to enhance growth of crops such as soybean. Glenda Gillaspy (Virginia AES) reported on the regulation of the energy sensor SnRK1. It is involved in a mechanism that helps plants to respond to low carbon (low energy) conditions. Arabidopsis has three SnRK1 genes. Overexpression leads to gain of function (more biomass) through metabolic reprogramming. On the contrary, RNAi plants were small. Spatial regulation was studied by promoter GUS fusion showing that 1.2 has more restricted expression than 1.1. Her group discovered that the P80 DWD domain protein of previously unknown function interacts directly with SnRK1. Mutants lacking P80 show similar phenotypes to SnRK1 RNAi plants. However, SnRK1.1 overproduction could rescue P80 mutants. The level of SnRK1.1 was found to be low in P80 mutants. SnRK1.1 normally localizes to the cytosol but in the P80 mutant background it was associated with the membrane. Glenda speculated that P80 might form different types of complexes as the expression of 1.2 in the P80 mutant background led to mislocalization. Tom Sharkey (MSU AgBioResearch), a new member, discussed his work defining limitations of photosynthesis with regard to different fates of photosynthate during the day (formation of sucrose) and night (break down of transitory starch formed during the day). He introduced the concept of triosephosphate limitation of photosynthesis. He compared the Arabidopsis tpt mutant, which cannot export carbohydrates during the day, and the starch deficient plastid pgm mutant affected in export of sugars from the plastid during the night. Emphasis was on the role of the proton motive force (PMF). CO2 response curves were determined to be similar at different temperatures. PMF was found to decline at higher CO2 but not at lower temperatures. In the tpt mutant PMF increased with increasing CO2. Tom noted that sucrose and starch syntheses are sensitive to phosphate concentration (inhibitory) and that triosephosphate use (TPU) limitation is balanced by inhibitory effects of Pi and the need for ATP synthesis. Tom pointed out that sucrose production during the day does not need hexokinase while carbohydrate metabolism during the night does. Accordingly, sugar sensing and hexokinase mediated signaling should differ during the night and the day. He reported that down regulation of glucan water dikinase, an enzyme which adds phosphoryl groups to starch and promotes starch break down, increases starch content. Analyzing such a transgenic line, particularly when using inducible promoters, should provide a new approach to study the effect of carbohydrate utilization on photosynthetic capacity in plants. Objective 4: Developmental and Environmental Limitations to Photosynthesis Wayne Loescher (MSU AgBioResearch) showed the results of a large scale global analysis of three transgenic Arabidopsis lines overexpressing three alternative abiotic stress resistance genes: CBF/DREB1 (low temp regulation), M6PR (mannitol synthesis), SOS1 (sodium proton antiporter). These lines were exposed to increasing salt stress. Growth was evaluated and global transcript analyses were conducted. The transgenic lines showed fewer gene expression changes than the wild type - perhaps indicative of salt tolerance. As mannitol serves as a fungal evasion signal, those respective transgenic plants seemed to upregulate biotic stress pathways. In addition, multigenerational studies in the field are under way to test competitiveness and fitness effects. Laura Gentry (Illinois AES), a new member reported on her work done in collaboration with Fred Below. She conducts field scale research investigating yield penalty of corn during continuous growth and N-fertilization compared to growth under crop rotation conditions. The field trial is currently in its seventh year and the results demonstrated that the yield penalty under continuous conditions increases over the years, but can be compensated by increased N-fertilization. Laura discussed the effects of corn residue and the loss of N into bacterial biomass. She noted that autotoxicity could be involved as corn releases compounds which inhibit its own growth in the next generation. She discussed best practices to achieve agricultural sustainability in view of increasing demands for the production of food and fuels. Rob Aiken (Kansas, AES) presented results of field studies conducted by Vara Prassad on high temperature stress, and the basis of tolerance or susceptibility to drought in soy bean. Pollen viability in response to temperature stress as well as ROS formation and membrane damage were discussed. Rob also described his own field studies on Sorghum under semiarid conditions in Western Kansas. He described methods to determine transpiration and stomatal conductance under field conditions using image analysis. Biomass, and light-use and water-use efficiency were considered. It was concluded that if light use efficiency is increased water-use efficiency increased as well. Mike Salvucci (Arizona-ARS) described his studies on improving RuBisco Activase to achieve higher thermotolerance of photosynthesis. He reported on biochemical approaches to study Rubisco activase structure function relationships. Rubisco activase belongs to the group of AAA+ proteins, which typically remodel other proteins. He reported on the crystallization of the alpha helical domain. This enabled modeling the interaction between RuBisCo activase and RuBisCo and allowed binding competition studies with the alpha helical domain fragment. He is working on the introduction of a heat stable activase into Camelina in a collaborative project with John Cushman. Mike also reported on remote sensor studies of cotton, during which the relationship between heat stress and drought stress is apparent under field conditions. This process is hard to simulate under growth chamber conditions demonstrating the unique value of these field studies. CURRENT FUNDING Steve Rodermel DOE, DE-FG02-10ER20147. The immutans variegation mutant of Arabidopsis. $510,000 (10/01/10-7/31/13). NSF (UCSD PO 10301097-001). Regulation of chloroplast gene expression. $195,000. (07/01/09-06/30/12) UISFL. Global pathways for educating students in biodiversity. $179,000 (10/01/09- 9/30/12) Christoph Benning NSF MCB 0741395. Mechanisms of lipid trafficking between the endoplasmic reticulum and the chloroplast. $546,818 (05/01/08-04/30/11) DOE, DE-FG02-98ER20305. Regulation of Thylakoid Lipid Biosynthesis in Plants. $560,000 (08/01/10-7/31/13 DOE,GLBRC. Multi-investigator project, T. Donahue PI. Funds to CB~$200,000 per year based on annual renewal (09/01/07-08/31/12). Regulation of oil biosynthesis in vegetative tissues and the engineering of biofuel crop plants producing oil in roots and shoot tissues. Aurora Biofuels. Identification of lipid switches in microalgae $250,000 (10/01/2008-09/30/2011). US AFOSR. Regulation of oil biosynthesis in algae. ($561,382 (09/01/11-08/31/14). Cushman, John C. NSF IOS-084373. Regulatory and signaling mechanisms of crassulacean acid metabolism: A photosynthetic adaptation of environmental stress. $988,389 (8/15/09-8/14/12) NSF DBI 0741876. Research Coordination Network (RCN) Program. RCN: An international research and education collaboration for grape functional genomics. $509,420 (9/15/08-9/14/13) Hatch NEV-00372. Improved abiotic stress tolerance of Camelina: A Novel Biofuel Crop for Nevada. $529,900 (7/1/10-6/30/15) DOE, DE-EE0000272. Nevada Renewable Energy Consortium: Municipal Wastewater for Microalgae Biofuel Feedstock Production. $250,000 (10/1/10-9/30/11) DOE, SBIR Phase II DE-SC0001306. High efficiency microalgae biofuel harvest and extraction using ionic liquids. $60,766 (10/1/10-9/30/12) Gerry Edwards IRRI (Bill and Melinda Gates Foundation). Creating the Second Green Revolution by supercharging photosynthesis: C4 Rice (PI, part of a consortium under the leadership of IRRI, The Philippines; co-PI A. Cousins). $334,959 (10/01/08-04/31/12) CRDF. Identifying mechanisms for increasing carbon acquisition and water use efficiency of plants with climate change. (PI, co-PI A Cousins and Russian investigators) $54,886 (9/1/10-9/1/12) USDA. Improving Plant Productivity by Altering Nitrogen Transport Processes. (Co-PI, PI M. Tegeder) $350,000 (12/15/09-12/14/12) USDA. Biosecurity Special Research Grant Aegilops cylindrical. (Co-PI, M. Kahn PI). $28,500 funding available to Edwards (Exp. 7/31/12) Glenda Gillaspy NSF Collaborative Research: Diphospho- and Triphospho-Inositol Phosphates in Plants (PI: Gillaspy) Total Award Amount: $673,426 Total Award Period Covered: 1/1/11- 12/31/14 NSF RET Supplement: Plant Cell Communication and Inositol Trisphosphates Funding Agency: NSF Budget Total: 9,400.00 Start Date: 06/01/2011 End Date: 07/29/2011 Steve Huber United Soybean Board, BBI Oil Project #7222. $40,000 annual (3/1/10-2/29/13) NSF, MCB-1021363. Arabidopsis 2010: Protein interacting networks and site-specific phosphorylation in leucine-rich repeat receptor-like kinase function. Multi-investigator project, S.C. Clouse, PI. Funds to SH lab ~$200,000 per year based on annual renewal (9/1/2010-8/30/2014). NSF, IOS-1022177. Regulation of receptor kinase signaling by tyrosine phosphorylation and calmodulin binding. $499,166 (9/01/2010-8/30/2013). Jeff Harper NSF, MCB-0920624. Calcium Dependent Protein Kinases in Pollen Tube Tip Growth. $390.000 (09/01/09-08/31/12) DOE, DE-FG03-94ER20152. P-type ATPases in Plants  Role of Lipid Flippases in Membrane Biogenesis $390,000 (09/01/09-08/31/12). NIH, 1RO1 GM070813-01. Ca2+-Pumps in Plants: Pollen Growth and Fertilization. $954,000 (04/01/04-08/31/12). JC Jang NSF IOB-053751. The role of AtbZIP1 in sugar regulatory network. $480,000 (02/01/06-01/31/10). OHOA1387. Plant peptide hormone technology in enhancing biomass and fitness to environmental stresses. $50,000 (03/01/2009-04/30/2012). OHOA0794. The novel roles of tandem zinc finger proteins in multi-stress tolerance in plants. $60,000 (07/01/2010-06/30/2012). Karen Koch USDA-NRI- Plant Biochemistry (07-03580). Roles and regulation of sorbitol metabolism in maize. $394,307 (09/01/07  08/31/12). NSF- Plant Genome (08-21952). Functional genomics of transfer cells. Funds to Koch lab ~$150,000 per year (09/09  8/12). BSF- Plant Genome (IOS-1025976). GEPR/LIT Genetic and genomic approaches to understanding long-distance transport and carbon partitioning. Funds to Koch lab ~$140,000 per year (12/10  11/14). BSF- Plant Genome (IOS-1116561). UniformMu: A transposon resource for mutagenesis in maize. Funds to Koch lab ~$200,000 per year based on annual renewal (09/11  08/13). USDA-NIFA (2011-67003-30215). Adapting kernel metabolism to enhance cereal yield under adverse conditions. Funds to Koch lab ~$100,000 per year based on annual renewal (08/11  07/14) David Kraemer NIH, (2 RO1 GM061904) Rieske Headgroup Cytochrome Complexes - Metal Ion Probes Membrane Protein Structure and Function (Co-PI with Dr. Michael Bowman) $2,057,830 (1/1/09-12/31/12) DOE (DE-FG02-04ER15559) The Energy Budget of Steady-State Photosynthesis $540,000 (7/1/08-6/30/12) USDA, Plant Biology (C): Biochemistry (2008-35318-04665) Co-regulation of the light and dark reactions of photosynthesis. $400,000 (1/01/09-12/31/12) DOE (DE-EE0003046) The National Alliance for Advanced Biofuels and Bioproducts an Algal Biofuels Consortium (Lead Consortium Lead: The Donald Danforth Plant Science Center, Executive Director: Jose Olivares, Los Alamos National Lab and Donald Danforth Plant Science Center). $54,000,000 ($660,000 to MSU) (1/01/10-12/31/13) DOE Interdisciplinary Research and Training in the Plant Sciences ($240,000 direct funds) (06/16/2010-08/31/2011) NSF. (RC100150) Plug and Play Photosynthesis for RuBisCO Independent Fuels $3.6M for 7 co-P.I.s, $300,599 to MSU (06/01/2011-05/31/2014) DOE. Center for Advanced Camelina Oil (CECO) 9.3M ($860,000 to MSU, in negotiation), 1/1/12-12/31/15 Jiaxu Li USDA-(NIFA) 2009-04041 Role of histone H3 lysine 36 methylation in regulating developmentally important genes in rice. $134,815 (01/01/10 ? 12/31/11) Wayne Loescher USDA FAS 58-3148-8-159 Enhancing salinity tolerance in canola $60,000 (9/1/09-8/31/12) USDA-CSREES/NIFA 2010-85117-20570 Building Expertise in Plant Breeding that Focuses on Drought Tolerance $500,000 (2/1/10  1/31/14) Mike Salvucci DOE, DE-AI02-97ER20268. Optimizing Rubisco Regulation for Increased Photosynthetic Performance under Climate Change. $381,000 (05/01/2010-04/30/2012). Robert Spreitzer DOE, DE-FG02-00ER15044. Role of the Rubisco Small Subunit. $495,000 (05/01/10-04/30/13). NSF, EPSCoR. Nebraska Center for Algal Biology and Biotechnology. Multi-investigator project. Funds to my lab ~$306,322 (10/01/10-09/30/15). Thomas D. Sharkey NSF, IOS-0950574.Function and regulation of isoprene synthesis in leaves. $590,000 (02/15/11-01/31/14) ZuvaChem Inc. Novel isoprene synthase genes for isoprene production.$300,000. (07/01/11-06/30/14) Julie Stone NSF, DBI-1156692. NSF REU SITE: Training in Redox Biology. PI: Don Becker; co-PI: Julie Stone. $278,500 (4/12-3/15) Univ. Nebraska IANR. Novel Subunits of Serine Palmitoyltransferase, New Players in Sphingolipid Synthesis PI: Ed Cahoon, co-PI: Julie Stone., $60,000 (05/01/2010-04/40/2012) ASPB-SURF. Arabidopsis thaliana Mutants Defective in DJ-1 Homologs. Julie Stone/Amanda Leafgren. $5275 (05/01/2010-04/30/2011) Univ. Nebraska IANR. Plant Stress Biology Initiative Co-PIs: Julie Stone, Gary Brewer, $15,000 (05/2010-04/2012. NSF-DBI-0851747. NSF REU SITE: Training in Redox Biology. PI: Don Becker; co-PI: Julie Stone. $252,250 (4/09-3/12) Don Weeks 2011 NSF, MCB-0952533 Bicarbonate Transport in Chlamydomonas $540,000 (3/15/2010  02/28/2013) NS, EPSCoR-1004094 Building Infrastructure in Nanohybrid Materials and Algal Biology Research $412,000 (10/01/2010  09/30/2015) DOE, DE-EE0001052 Renewable Biofuels from Algae $200,000 (02/01/2010  01/31/2012) DOE  CAB-COMM DE-EE0003373 Consortium for Commercialization of Algae Biofuels and Biotechnology $300,000 (09/01/2010  08/31/2013)

Publications 2010/2011 1. Ananda, N., P. V. Vadlani, and P. V. V. Prasad. 2011. Evaluation of drought and heat stressed grain sorghum (Sorghum bicolor) for ethanol production. Industrial Crops and Products 33:779-782 2. Buescher, E., T. Achberger, I. Amusan, A. Giannini and others. 2010. Natural genetic variation in selected populations of Arabidopsis thaliana is associated with ionomic differences. PLoS One 5:e11081 3. Carmo-Silva, A. E. and M. E. Salvucci. 2011. The activity of Rubisco's molecular chaperone, Rubisco activase, in leaf extracts. Photosynth.Res. 108:143-155 4. Carmo-Silva, A. E., L. Marri, F. Sparla, and M. E. Salvucci. 2011. Isolation and compositional analysis of a CP12-associated complex of calvin cycle enzymes from Nicotiana tabacum. Protein Pept.Lett. 18:618-624 5. Castruita, M., D. Casero, S. J. Karpowicz, J. Kropat and others. 2011. Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell 23:1273-1292 6. Chan, Z., P. J. Bigelow, W. Loescher, and R. Grumet. 2011. Comparison of salt stress resistance genes in transgenic Arabidopsis thaliana indicates that extent of transcriptomic change may not predict secondary phenotypic or fitness effects. Plant Biotechnol.J. 7. Chan, Z., R. Grumet, and W. Loescher. 2011. Global gene expression analysis of transgenic, mannitol-producing, and salt-tolerant Arabidopsis thaliana indicates widespread changes in abiotic and biotic stress-related genes. J.Exp.Bot. 62:4787-4803 8. Cushman, J. C. and M. J. Oliver. 2011. Understanding vegetative desiccation tolerance using integrated functional genomics approaches within a comparative evolutionary framework, p. 307-338. In: U. Luttge, E. Beck, and D. Bartels (eds.), Ecological Studies: Desiccation Tolerance in Plants. Springer, New York, NY. 9. Deluc, L. G., A. Decendit, Y. Papastomoulis, J.-M. Merillon and others. 2011. Water deficit increases stilbene metabolism in Cabernet Sauvignon berries. J.Agric.Food Chem. 59:289-297 10. Dillard, S. R., K. Van, and M. H. Spalding. 2011. Acclimation to low or limiting CO(2) in non-synchronous Chlamydomonas causes a transient synchronization of the cell division cycle. Photosynth.Res 109:161-168 11. Djanaguiraman, M., P. V. V. Prasad, D. L. Boyle, and W. T. Schapaugh. 2011. High-temperature stress and soybean leaves: Leaf anatomy and photosynthesis. Crop Science 51:2125-2131 12. Djanaguiraman, M., P. V. V. Prasad, and K. Al-Khatib. 2011. Ethylene perception inhibitor 1-MCP decreases oxidative damage of leaves through enhanced antioxidant defense mechanisms in soybean plants grown under high temperature stress. Environmental and Experimental Botany 71:215-223 13. Duanmu, D. and M. H. Spalding. 2011. Insertional suppressors of Chlamydomonas reinhardtii that restore growth of air-dier lcib mutants in low CO(2). Photosynth.Res. 109:123-132 14. Edwards, G. E. and E. V. Voznesenskaya. 2011. C(4) photosynthesis: Kranz forms and single-cell C(4) in terrestrial plants, p. 29-61. In: A. S. Raghavendra and R. F. Sage (eds.), C(4) Photosynthesis and Related CO(2) Concentrating Mechanisms Advances in Photosynthesis and Respiration., vol. 32. Springer, Dordrecht. 15. Foudree, A., M. Aluru, and S. Rodermel. 2010. PDS activity acts as a rheostat of retrograde signaling during early chloroplast biogenesis. Plant Signal.Behav. 5:1629-1632 16. Genkov, T., M. Meyer, H. Griffiths, and R. J. Spreitzer. 2010. Functional hybrid rubisco enzymes with plant small subunits and algal large subunits: engineered rbcS cDNA for expression in chlamydomonas. J Biol Chem 285:19833-19841 17. Gibson, K., J. S. Park, Y. Nagai, S. K. Hwang and others. 2011. Exploiting leaf starch synthesis as a transient sink to elevate photosynthesis, plant productivity and yields. Plant Science 181:275-281 18. Gore, M. A., G. Coyle, B. Friebe, T. A. Coffelt and others. 2011. Complex Ploidy Level Variation in Guayule Breeding Programs. Crop Science 51:210-216 19. Goren, S., S. C. Huber, and D. Granot. 2011. Comparison of a novel tomato sucrose synthase, SlSUS4, with previously described SlSUS isoforms reveals distinct sequence features and differential expression patterns in association with stem maturation. Planta 233:1011-1023 20. Gross, J., K. N. Pelletreau, A. Reyes-Prieto, M. E. Rumpho, and D. Bhattacharya. 2011. Secondary and tertiary endosymbiosis: Plastid evolution and loss, plastid protein import, and photosynthesis in the sea slug Elysia chlorotica, In: R. Bock and V. Knoop (eds.), Advances in Photosynthesis and Respiration - Genomics of Chloroplasts and Mitochondria., vol. In press. Springer. 21. Henderson, J. N., A. M. Kuriata, R. Fromme, M. E. Salvucci and others. 2011. Atomic resolution X-ray structure of the substrate recognition domain of higher plant Rubisco activase. J Biol Chem 22. Huber, S. C., W. M. Kaiser, and V. Jain. 2011. Post Translational Regulation of Nitrate Reductase, p. 21-44. In: V. Jain and A. Kumar (eds.), Nitrogen Use Efficiency in Plants. New India Publishing, New Delhi. 23. Kang, S. G., J. Price, P. C. Lin, J. C. Hong and others. 2010. The Arabidopsis bZIP1 transcription factor is involved in sugar signaling, protein networking, and DNA binding. Mol.Plant 3:361-373 24. Kaye, Y., Y. Golani, Y. Singer, Y. Leshem and others. 2011. Inositol polyphosphate 5-phosphatase7 regulates the production of reactive oxygen species and salt tolerance in Arabidopsis. Plant Physiol 157:229-241 25. Koteyeva, N. K., E. V. Voznesenskaya, J. O. Berry, S. D. Chuong and others. 2011. Development of structural and biochemical characteristics of C(4) photosynthesis in two types of Kranz anatomy in genus Suaeda (family Chenopodiaceae). J Exp.Bot. 62:3197-3212 26. Koteyeva, N. K., E. V. Voznesenskaya, E. H. Roalson, and G. E. Edwards. 2011. Diversity in forms of C4 in the genus Cleome (Cleomaceae). Ann.Bot. 107:269-283 27. Li, T., S. Huang, W. Z. Jiang, D. Wright and others. 2011. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Research 39:359-372 28. Li, T., S. Huang, X. F. Zhao, D. A. Wright and others. 2011. Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Research 39:6315-6325 29. Lin, P. C., M. C. Pomeranz, Y. Jikumaru, S. G. Kang and others. 2011. The Arabidopsis tandem zinc finger protein AtTZF1 affects ABA- and GA-mediated growth, stress and gene expression responses. Plant J. 65:253-268 30. Liu, X., F. Yu, and S. Rodermel. 2010. An Arabidopsis pentatricopeptide repeat protein, SUPPRESSOR OF VARIEGATION7, is required for FtsH-mediated chloroplast biogenesis. Plant Physiol 154:1588-1601 31. Liu, X., F. Yu, and S. Rodermel. 2010. Arabidopsis chloroplast FtsH, var2 and suppressors of var2 leaf variegation: a review. J.Integr.Plant Biol. 52:750-761 32. Liu, X., S. R. Rodermel, and F. Yu. 2010. A var2 leaf variegation suppressor locus, SUPPRESSOR OF VARIEGATION3, encodes a putative chloroplast translation elongation factor that is important for chloroplast development in the cold. BMC Plant Biol. 10:287 33. Ma, Y., S. V. Pollock, Y. Xiao, K. Cunnusamy and others. 2011. Identification of a novel gene, CIA6, required for normal pyrenoid formation in Chlamydomonas reinhardtii. Plant Physiol 156:884-896 34. McDonald, A. E., A. G. Ivanov, R. Bode, D. P. Maxwell and others. 2011. Flexibility in photosynthetic electron transport: the physiological role of plastoquinol terminal oxidase (PTOX). Biochim.Biophys.Acta 1807:954-967 35. McMaster, G., D. A. Edmunds, W. W. Wilhelm, D. C. Nielsen and others. 2011. PhenologyMMS: A program to simulate crop phenological responses to water stress. Computers and "Electron Agric 77:118-125 36. Moroney, J. V., Y. Ma, W. D. Frey, K. A. Fusilier and others. 2011. The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles. Photosynth.Res 109:133-149 37. Mutava, R. N., P. V. V. Prasad, M. R. Tuinstra, M. D. Kofoid and others. 2011. Characterization of sorghum genotypes for traits related to drought tolerance. Field Crops Research 123:10-18 38. Offermann, S., T. W. Okita, and G. E. Edwards. 2011. Resolving the compartmentation and function of C4 photosynthesis in the single-cell C4 species Bienertia sinuspersici. Plant Physiol 155:1612-1628 39. Offermann, S., T. W. Okita, and G. E. Edwards. 2011. How do single cell C4 species form dimorphic chloroplasts? Plant Signal Behav. 6:762-765 40. Oh, M. H., X. Wu, S. D. Clouse, and S. C. Huber. 2011. Functional importance of BAK1 tyrosine phosphorylation in vivo. Plant Signal.Behav. 6:400-405 41. Oh, M. H., J. Sun, D. H. Oh, R. E. Zielinski and others. 2011. Enhancing Arabidopsis leaf growth by engineering the BRASSINOSTEROID INSENSITIVE1 receptor kinase. Plant Physiol 157:120-131 42. Oliver, M. J., L. N. Guo, D. C. Alexander, J. A. Ryals and others. 2011. A sister group contrast using untargeted global metabolomic analysis delineates the biochemical regulation underlying desiccation tolerance in Sporobolus stapfianus. Plant Cell 23:1231-1248 43. Overstreet, L. F., G. D. Hoyt, and J. Imbriani. 2010. Comparing nematode and earthworm communities under combinations of conventional and conservation vegetable production practices. Soil & Tillage Research 110:42-50 44. Parry, M. A. J., M. Reynolds, M. E. Salvucci, C. Raines and others. 2011. Raising yield potential of wheat: Increasing photosynthetic capacity and efficiency. J.Exp.Bot. 62:453-467 45. Pelletreau, K. N., D. Bhattacharya, D. C. Price, J. M. Worful and others. 2011. Sea Slug Kleptoplasty and Plastid Maintenance in a Metazoan. Plant Physiology 155:1561-1565 46. Pengelly, J. L., S. Kwasny, S. Bala, J. R. Evans and others. 2011. Functional analysis of corn husk photosynthesis. Plant Physiol 156:503-513 47. Pomeranz, M., P. C. Lin, J. Finer, and J. C. Jang. 2010. AtTZF gene family localizes to cytoplasmic foci. Plant Signal.Behav. 5:190-192 48. Pomeranz, M., J. Finer, and J. C. Jang. 2011. Putative molecular mechanisms underlying tandem CCCH zinc finger protein mediated plant growth, stress, and gene expression responses. Plant Signal.Behav. 6:647-651 49. Pomeranz, M., L. Zhang, J. Finer, and J. C. Jang. 2011. Can AtTZF1 act as a transcriptional activator or repressor in plants? Plant Signal.Behav. 6:719-722 50. Pomeranz, M. C., C. Hah, P. C. Lin, S. G. Kang and others. 2010. The Arabidopsis tandem zinc finger protein AtTZF1 traffics between the nucleus and cytoplasmic foci and binds both DNA and RNA. Plant Physiol 152:151-165 51. Prasad, P. V. V., K. J. Boote, and L. H. Allen. 2011. Longevity and temperature response of pollen as affected by elevated growth temperature and carbon dioxide in peanut and grain sorghum. Environmental and Experimental Botany 70:51-57 52. Prasad, P. V. V., S. R. Pisipati, I. Momcilovic, and Z. Ristic. 2011. Independent and combined effects of high temperature and drought stress during grain filling on plant yield and chloroplast EF-Tu expression in spring wheat. Journal of Agronomy and Crop Science 197:430-441 53. Rajasekaran, S. A., T. P. Huynh, D. G. Wolle, C. E. Espineda and others. 2010. Na,K-ATPase subunits as markers for epithelial-mesenchymal transition in cancer and fibrosis. Mol.Cancer Ther. 9:1515-1524 54. Rosnow, J., S. Offermann, J. Park, T. W. Okita and others. 2011. In vitro cultures and regeneration of Bienertia sinuspersici (Chenopodiaceae) under increasing concentrations of sodium chloride and carbon dioxide. Plant Cell Rep. 30:1541-1553 55. Rumpho, M. E., K. N. Pelletreau, A. Moustafa, and D. Bhattacharya. 2011. The making of a photosynthetic animal. Journal of Experimental Biology 214:303-311 56. Sanjaya, T. P. Durrett, S. E. Weise, and C. Benning. 2011. Increasing the energy density of vegetative tissues by diverting carbon from starch to oil biosynthesis in transgenic Arabidopsis. Plant Biotechnology Journal 9:874-883 57. Schlauch, K. A., J. Grimplet, J. C. Cushman, and G. R. Cramer. 2011. Transcriptomics analysis methods: microarray data processing, analysis and visualization using the Affymetrix GeneChip® Vitis vinifera genome array, p. 317-334. In: S. Delrot, H. Medrano, E. Or, L. Bavaresco, and S. Grando (eds.), Methods and Results in Grape Vine Research. Springer, New York, NY. 58. Sharkey, T. D. and R. Zhang. 2010. High temperature effects on electron and proton circuits of photosynthesis. J.Integr.Plant Biol. 52:712-722 59. Soule, K. M. and M. E. Rumpho. 2011. Light-regulated photosynthetic gene expression and phosphoribulokinase enzyme activity in the heterokont alga Vaucheria litorea and its symbiotic molluscan partner Elysia chlorotica. J Phycol In press: 60. Sun, J., J. Zhang, C. T. Larue, and S. C. Huber. 2011. Decrease in leaf sucrose synthesis leads to increased leaf starch turnover and decreased RuBP regeneration-limited photosynthesis but not Rubisco-limited photosynthesis in Arabidopsis null mutants of SPSA1. Plant Cell Environ 2011/02/12:592-604 61. Tillet, R. L., R. L. Albion, K. A. Schlauch, G. R. Cramer and others. 2011. mRNA expression profiling of abiotic stress responses in leaf and berry tissue of wine grape (Vitis vinifera) using expressed sequence tags. BMC Plant Biol. 11:86 62. Tillet, R. L. and J. C. Cushman. 2011. Vitis functional genomics: Open systems for transcriptome analysis, p. 235-269. In: J. M. Martinez-Zapater and A.-F. A. Blondon (eds.), Encyclopedia of Plant Genomics. Science Publishers, Enfield 63. Wang, D., B. Calla, S. Vimolmangkang, X. Wu and others. 2011. The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli. PLoS One 6:e25293 64. Wang, Y., D. Duanmu, and M. H. Spalding. 2011. Carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii: inorganic carbon transport and CO(2) recapture. Photosynth.Res 109:115-122 65. Weise, S. E., K. J. van Wijk, and T. D. Sharkey. 2011. The role of transitory starch in C(3), CAM, and C(4) metabolism and opportunities for engineering leaf starch accumulation. J.Exp.Bot 62:3109-3118 66. White, W. G., S. P. Moose, C. F. Weil, M. C. McCann, N. C. Carpita, and F. E. Below. 2011. Tropical Maize: Exploiting Maize Genetic Diversity to Develop a Novel Annual Crop for Lignocellulosic Biomass and Sugar Production., p. 167-179. In: M. S. Buckeridge and G. H. Goldman (eds.), Routes to Cellulosic Ethanol, Part 3. Springer, New York, NY. 67. Wu, X., M. H. Oh, E. M. Schwarz, C. T. Larue and others. 2011. Lysine acetylation is a widespread protein modification for diverse proteins in Arabidopsis. Plant Physiol 155:1769-1778 68. Yu, F., S. S. Park, X. Liu, A. Foudree and others. 2011. SUPPRESSOR OF VARIEGATION4, a new var2 suppressor locus, encodes a pioneer protein that is required for chloroplast biogenesis. Mol.Plant 4:229-240 69. Zhang, R., D. M. Kramer, J. A. Cruz, K. R. Struck and others. 2011. The effects of moderately high temperature on zeaxanthin accumulation and decay. Photosynth.Res. 108:171-181