Progress 07/01/09 to 06/30/14
Outputs
Target Audience: Within the University community, the Institute facilitates crosscutting communications among faculty engaged in diverse areas of genomics research. With the sponsorship of retreats and seminar series, MPGI supports the dissemination of scientific knowledge among faculty, students, and staff. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions via its website (www.mpgi.umn.edu) and the seminar series sponsored by the Institute. In addition, a major goal of MPGI is training outstanding students and postdoctoral researchers in this important biological field by providing them with travel awards. These are among the activities designed to bring benefits from genomics to Minnesotans, the nation, and the world. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? MPGI has provided training and professional development for graduate students and postdoctoral researchers by supporting either their attendance at meetings to present research findings, or their travel to other educational institutions for training purposes. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The Microbial and Plant Genomics Institute (MPGI) promotes advances in microbial, plant, and animal genomics, genomics enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multidisciplinary interchange of ideas and applications of cutting edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. The scientific aim of the Institute is to enhance the development of functional and translational genomics concomitantly with the expansion of bioinformatics capabilities and the development of specialized instrumentation. Within the University community, the Institute facilitates interactions among faculty engaged in diverse areas of genomics research by promoting understanding of microbial and plant genomics, and providing access to genomics related technologies. Cooperation among MPGI members helps to assure a strong basis for education in the disciplines of the basic agricultural, environmental, and health sciences. The Institute enhances faculty projects by supporting the educational activities of individual grad students and postdoctoral researchers. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions.
Publications
- Type:
Other
Status:
Other
Year Published:
2014
Citation:
https://www.cbs.umn.edu/sites/all/modules/pubdlcnt/pubdlcnt.php?file=https://www.cbs.umn.edu/sites/default/files/public/downloads/Publications_Jan_June2014.pdf&nid=4272
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Progress 01/01/13 to 09/30/13
Outputs
Target Audience: Within the University community, the Institute facilitates crosscutting communications among faculty engaged in diverse areas of genomics research. With the sponsorship of retreats and seminar series, MPGI supports the dissemination of scientific knowledge among faculty, students, and staff. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions via its website (www.mpgi.umn.edu) and the seminar series sponsored by the Institute. In addition, a major goal of MPGI is training outstanding students and postdoctoral researchers in this important biological field by providing them with travel awards. These are among the activities designed to bring benefits from genomics to Minnesotans, the nation, and the world. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? MPGI has provided training and professional development for 26 graduate students and 19 postdoctoral researchers by supporting either their attendance at meetings to present research findings, or their travel to other educational institutions for training purposes. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The Microbial and Plant Genomics Institute (MPGI) promotes advances in microbial, plant, and animal genomics, genomics enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multidisciplinary interchange of ideas and applications of cutting edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. The scientific aim of the Institute is to enhance the development of functional and translational genomics concomitantly with the expansion of bioinformatics capabilities and the development of specialized instrumentation. Within the University community, the Institute facilitates interactions among faculty engaged in diverse areas of genomics research by promoting understanding of microbial and plant genomics, and providing access to genomics related technologies. Cooperation among MPGI members helps to assure a strong basis for education in the disciplines of the basic agricultural, environmental, and health sciences. The Institute enhances faculty projects by supporting the educational activities of individual grad students and postdoctoral researchers. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
In previous years it was requested that we provide our publications as a .pdf on the MPGI
website as they are quite extensive. Please download .pdf of publications from sidebar at:
https://www.cbs.umn.edu/explore/departments/mpgi/faculty
|
Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: The Microbial and Plant Genomics Institute (MPGI) membership consists of 67 faculty from 4 colleges: The College of Food, Agriculture and Natural Resource Sciences, The College of Biological Sciences, the Academic Health Center and the College of Science and Engineering. MPGI travel awards enabled 32 graduate students and 12 postdoctoral researchers from 26 university-wide labs to attend meetings to present their research and interact with scientists. MPGI coordinated and sponsored a Fall Symposium on the topic of "Systems Biology of Genetic Regulation " hosted by faculty members Chad Myers and Fumiaki Katagiri. The series also served as a one-credit course (PBI05960-002) for 9 students. Each visiting scientist chose a paper for students to read and critique. Students attended the Symposium and a day-long workshop on experimental designs using genomics to study for variation. Science on the Spot is a monthly gathering that has allowed MPGI faculty and members of their lab to present and discuss information on their current research in a social and relaxed environment. These gatherings have expanded opportunities for interdisciplinary connections with other University researchers. PARTICIPANTS: Members of the MPGI are faculty who are interested in the successful development and application of genomics and the resulting societal and environmental impact. The 67 members of MPGI are faculty from departments throughout four colleges at the University of Minnesota: The College of Food, Agricultural, and Natural Resource Sciences (CFANS), the College of Biological Sciences (CBS), the Institute of Technology (IT), and the Academic Health Center (AHC). MPGI directly supports the salary of faculty member M. David Marks, a functional genomics researcher in plant biology, plus support staff member Kit Leffler who is responsible for management and administration of the MPGI seminar series, the MPGI website and other administrative functions. MPGI has provided training and professional development for 32 graduate students and 12 postdoctoral researchers by supporting either their attendance at meetings to present research findings, or their travel to other educational institutions for training purposes. TARGET AUDIENCES: Within the University community, the Institute facilitates crosscutting communications among faculty engaged in diverse areas of genomics research. With the sponsorship of retreats and seminar series, MPGI supports the dissemination of scientific knowledge among faculty, students, and staff. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions via its website (www.mpgi.umn.edu) and the seminar series sponsored by the Institute. In addition, a major goal of MPGI is training outstanding students and postdoctoral researchers in this important biological field by providing them with travel awards. These are among the activities designed to bring benefits from genomics to Minnesotans, the nation, and the world. PROJECT MODIFICATIONS: No significant changes during this reporting period.
Impacts
The Microbial and Plant Genomics Institute (MPGI) promotes advances in microbial and plant genomics, genomics enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multi-disciplinary interchange of ideas and applications of cutting-edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. The scientific aim of the Institute is to enhance the development of functional and translational genomics concomitantly with the expansion of bioinformatics capabilities and the development of specialized instrumentation. Within the University community, the Institute facilitates interactions among faculty engaged in diverse areas of genomics research by promoting understanding of microbial and plant genomics, and providing access to genomics-related technologies. Cooperation among MPGI members helps to assure a strong basis for education in the disciplines of the basic agricultural, environmental, and health sciences. The Institute enhances faculty projects by supporting the educational activities of individual grad students and postdoctoral researchers. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions. In addition, assisting in the training of outstanding students in this important biological field is a major goal.
Publications
- Susana Goncalves; Stephen P. Miller; Maria A. Carrondo; Anthony M. Dean; Pedro M. Matias (Profiled Authors: Antony M Dean; Stephen P Miller). 2012. Induced fit and the catalytic mechanism of isocitrate dehydrogenase. Biochemistry; 51(36):7098 7115.
- Swanson Wagner RA, Briskine R, Schaefer R, Hufford MB, Ross Ibarra J, Myers CL, Tiffin P, Springer NM. 2012. Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci USA, 109(29):11878 11883.
- Tagarelli, A. and George Karypis. 2012. A Segment based Approach to Clustering Multi Topic Documents. Knowledge and Information Systems (in press).
- Takacs, E.M., J. Li, L. Ponnala, D. Janick Buckner, J. Yu, G.J. Muehlbauer, M.C.P. Timmermans, P.S. Schnable, Q. Sun, D. Nettleton and M.J. Scanlon. 2012. Ontogeny of the maize shoot apical meristem. The Plant Cell 24:3219 3234.
- Tegeder M, Ward JM. 2012. Molecular evolution of AAP and LHT amino acid transporters in the plant kingdom. Front. Plant Sci. 3: 00021
- The International Barley Genome Consortium. 2012. A physical, genetical and functional sequence assembly of the barley genome. Nature doi:10.1038/nature11543.
- Tiburcio M, Niang M, Deplaine G, Perrot S, Bischoff E, Ndour PA, Silvestrini F, Khattab A, Milon G, David PH, Hardeman M, Vernick KD, Sauerwein RW, Preiser PR, Mercereau Puijalon O, Buffet P, Alano P, Lavazec C. 2012. A switch in infected erythrocyte deformability at the maturation and blood circulation of Plasmodium falciparum transmission stages. Blood. 119(24):e172 80. PMCID: 3382942.
- Tishchenko, Oksana; Donald G. Truhlar. 2012. Benchmark Ab initio calculations of the barrier height and transition state geometry for hydrogen abstraction from a phenolic antioxidant by a peroxy radical and its use to assess the performance of density functionals. Journal of Physical Chemistry Letters; 3(19):2834 2839.
- Truhlar, Donald G. 2012. Are molecular orbitals delocalized? Journal of Chemical Education; 89(5):573 574.
- Truman, W.M.D. and Glazebrook, J. 2012. Co expression analysis identifies putative targets for CBP60g and SARD1 regulation. BMC Plant Biology, in press.
- Tsuda, K., Qi, Y., Nguyen, L.V., Bethke, G., Tsuda, Y., Glazebrook, J., and Katagiri, F. 2012. An efficient Agrobacterium mediated transient transformation of Arabidopsis. Plant J. 69:713 719. DOI: 10.1111/j.1365 313X.2011.04819.x.
- Unno, Tatsuya & Di, Doris Y W & Jeonghwan, Jang & Suh, Yaeseul & Sadowsky, Michael J & Hur, Hor Gil. 2012. Integrated Online System for a Pyrosequencing Based Microbial Source Tracking Method that Targets Bacteroidetes 16S rDNA. Environ. Sci. Technol. 46:93 987.
- Unrean, Pornkamol; Friedrich Srienc. 2012. Predicting the adaptive evolution of Thermoanaerobacterium saccharolyticum. Journal of Biotechnology; 158(4):259 266.
- Uwe T. Bornscheuer, Gjalt Huisman, Romas J. Kazlauskas, Stefan Lutz, Jeffrey Moore, Karen Robins. 2012. Engineering the third wave of biocatalysis. Nature. 485, 185 194; doi: 10.1038/nature11117.
- Uwe T. Bornscheuer, Romas J. Kazlauskas. 2012, May. Enzymatic catalytic promiscuity and the design of new enzyme catalyzed reactions. Enzyme Catalysis in Organic Synthesis, 3rd edition. K. Drauz, H. Groger, O. pp1695 1733; doi: 10.1002/9783527639861.ch41
- Fang, Gang; Majda Haznadar; Wen Wang; Haoyu Yu; Michael Steinbach; Timothy R. Church; William S. Oetting; Brian van Ness; Vipin Kumar. 2012. High order SNP combinations associated with complex diseases: Efficient discovery, statistical power and functional interactions. PLoS ONE; 7(4):.
- Fengli Fu; Daniel F. Voytas. 2012. Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C2H2 zinc fingers and engineered zinc finger arrays. Nucleic Acids Research; doi: 10.1093/nar/gks1167
- Ferreira, J., Park, Y., Hu, W S., Ko, C.C. 2012. Multipotent progenitor cell aggregates for expansion, osteogenic differentiation and in vivo tracing with AAV vector serotype 6. Gene Therapy, (In press. 2012). doi: 10.1038/gt.2012.16.
- Fink, R.C., E. P. Black, Z. Hou, M. Sugawara, M. J. Sadowsky, and F. Diez Gonzalez. 2012. Transcriptional Responses of Escherichia coli K 12 and O157:H7 Associated with Lettuce Leaves. Appl. Environ. Microbiol. 78:1752 64.
- E. W. Krumholz, H. Yang, P. Weisenhorn, C. S. Henry, I. G. L. Libourel. 2012. Genome wide metabolic network reconstruction of the picoalga Ostreococcus. J. Exp. Bot. 63, 2353.
- Eichten SR, Vaughn MW, Hermanson PJ, Springer NM. 2012. Variation in DNA methylation patterns is more common among maize inbreds than among tissues. The Plant Genome doi: 10.3835/plantgenome2012.06.0009
- Ellis LBM, Wackett LP. 2012. Use of the University of Minnesota Biocatalysis/ Biodegradation Database for Study of Microbial Degradation. Microbial Informatics and Experiment, 2: 1
- Emily Bruns; Martin Carson; Georgiana May (Profiled Author: Georgiana May). 2012. Pathogen and host genotype differently affectpathogen fitness through their effects on differentlife history stages. BMC Evolutionary Biology; ():135 .
- Eom JS, Choi SB, Ward JM, Jeon JS. 2012. The mechanism of phloem loading in rice (Oryza sativa). Mol Cells 33: 431 438
- Epstein, Brendan; Antoine Branca; Joann Mudge; Arvind K. Bharti; Roman Briskine; Andrew D. Farmer; Masayuki Sugawara; Nevin D. Young; Michael J. Sadowsky; Peter Tiffin. 2012. Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae. PLoS Genetics; 8(8):.
- Esther E. McGinnis; Mary H. Meyer; Alan G. Smith. 2012. Analysis of U.S. genetically engineered crop regulation and litigation. Crop Science. 52(3):991 1002.
- Faghmous, James H.; Yashu Chamber; Shyam Boriah; Stefan Liess; Vipin Kumar; Frode Vikebo; Michel Dos Sontos Mesquita. 2012. A novel and scalable spatio temporal technique for ocean eddy monitoring. Proceedings of the National Conference on Artificial Intelligence; 1():281 287.
- Fang Z, Gonzales AM, Durbin ML, Meyer KKT, Miller BH, Volz KM, Clegg MT, Morrell PL. 2012. Tracing the geographic origin of weedy Ipomoea purpurea (common morning glory) in the Southeastern United States. (In Review)
- Fang Z, Eule Nashoba A, Powers C, Kono TY, Morrell PL, Smith KP. 2012. Comparative analysis identifies the contributions of exotic donors to disease resistance in a barley experimental population. (In Review)
- Fisk, S., A. Cuesta Marcos, L. Cistue, J. Russell, K.P Smith, P. Baenziger, Z. Bedo, A. Corey, T. Filichkin, I. Karsai, R. Waugh, P. Hayes. 2012. FR H3: A New QTL to Assist in the Development of Fall Sown Barley with Superior Low Temperature Tolerance. Theor. Appl. Genet. DOI 10.1007/s00122 012 1982 8.
- Flynn, C.M., K.A. Hunt, J.A. Gralnick and F. Srienc. 2012. Construction and elementary model analysis of a metabolic model for Shewanella oneidensis MR 1. Biosystems. 107(2):120 8.
- Frank, K.L., Barnes, A.M.T., Grindle, S.M., Manias, D.A., Schlievert, P.M., and Dunny, G.M. 2012. Use of Recombinase Based In Vivo Expression Technology To Characterize Enterococcus faecalis Gene Expression during Infection Identifies In Vivo Expressed Antisense RNAs and Implicates the Protease Eep in Pathogenesis. Infect. Immun. 80(2):539. DOI: 10.1128/IAI.05964 11.
- Frey, P. A. and Hegeman A. D. 2012. Chemical and Stereochemical Actins of UDP galactose 4 Epimerase, Acc. Chem. Res., in press.
- Gerami Nejad, Forche, A., McClellan, M., and Berman, J. 2012. Analysis of protein function in clinical Candida albicans isolates. Yeast. 29(8):303 309. PMID: 22777821; NIHMSID#390377.
- Giuseppe, A., Sanseverino, W., Rombauts, S., Van der Peer, Y., Bradeen, J., Carputo, D., Frusciante, L., and Ercolano, M.R. 2012. Overview of tomato candidate pathogen recognition genes reveals important Solanum R loci dynamics. New Phytologist.
- Gnanandarajah, J.S., Johnson, T.J., Kim, H.B., Abrahante, J.E., Lulich, J.P., and Murtaugh, M.P. 2012. Comparative fecal microbiota of dogs with and without calcium oxalate stones.
- Goblirsch, B.R., J.A. Frias, L.P. Wackett, and C.M. Wilmot. 2012. Crystal structures of Xanthomonas campestris OleA reveal features that promote head to head condensation of two long chain fatty acids. Biochemistry 51: 4138 4146.
- Gonzales AM, Fang Z, Durbin ML, Meyer KKT, Clegg MT, Morrell PL. 2012. Nucleotide sequence diversity of floral pigment genes in Mexican populations of Ipomoea purpurea (morning glory) accord with a neutral model of evolution. J of Heredity doi:10.1093/jhered/ess059
- Gora PJ, Reinders, A, Ward JM. 2012. A novel fluorescent assay for sucrose transporters. Plant Methods 8: 13
- Grayson T. Wawrzyn; Maureen B. Quin; Swati Choudhary; Fernando Lopez Gallego; Claudia Schmidt Dannert. 2012. Draft genome of omphalotus olearius provides a predictive framework for sesquiterpenoid natural product biosynthesis in basidiomycota. Chemistry and Biology; 19(6):772 783.
- Habibollah, G., C.W. Hiebert, T. Zegeye, S. Liu, M. Dilawari, T. Tsilo, J.A. Anderson, M.N. Rouse, Y. Jin, and T. Fetch. 2012. Inheritance of resistance to Ug99 stem rust in wheat cultivar Norin 40 and genetic mapping of Sr42. Theor. Appl. Genet. 125:817 824.
- Hamilton, M.J., A. R. Weingarden, M. J. Sadowsky, and A. Khoruts. 2012. Standardized Frozen Preparation for Transplantation of Fecal Microbiota for Recurrent Clostridium difficile Infection. Am. J. Gastroenterol. doi: 10.1038/ajg.2011.482. PMID: 22290405
- Valberg S, Sponseller B, Hegeman AD, Earing J, Bender J, Martinson K, Patterson S, and Sweetman L. 2012. Seasonal pasture myopathy/atypical myopathy in North America associated with ingestion of hypoglycin A within seeds of the box elder tree, Equine Vet J, accepted. DOI: 10.1111/j.2042 3306.2012.00684.x
- Wackett, L.P. and L.B.M. Ellis. 2012. MiniReview: Microbial transformation of organic compounds. Micro. Inf. Exp. 2:1 doi:10.1186/2042 5783 2 1
- Wang, Bo; Donald G. Truhlar. 2012. Partial atomic charges and screened charge models of the electrostatic potential. Journal of Chemical Theory and Computation; 8(6):1989 1998.
- Wang, Yingjie; Carlos P. Sosa; Alessandro Cembran; Donald G. Truhlar; Jiali Gao. 2012. Multilevel X Pol: A fragment based method with mixed quantum mechanical representations of different fragments. Journal of Physical Chemistry B; 116(23):6781 6788.
- Wawrzyn, Grayson T.; Sarah E. Bloch; Claudia Schmidt Dannert. 2012. Discovery and characterization of terpenoid biosynthetic pathways of fungi. Methods in Enzymology; 515():83 105.
- Xu, Xuefei; Ewa Papajak; Jingjing Zheng; Donald G. Truhlar. 2012. Multi structural variational transition state theory: Kinetics of the 1,5 hydrogen shift isomerization of the 1 butoxyl radical including all structures and torsional anharmonicity. Physical Chemistry Chemical Physics;14(12):4204 4216.
- Xu, Xuefei; Tao Yu; Ewa Papajak; Donald G. Truhlar. 2012. Multistructural variational transition state theory: Kinetics of the hydrogen abstraction from carbon 2 of 2 methyl 1 propanol by hydroperoxyl radical including all structures and torsional anharmonicity. Journal of Physical Chemistry A; 116(43):10480 10487.
- Yi, T and Morrell, PL. 2012. (in press). Introduction of major exotic economic plants. In: Hong, D and Blackmore, S (eds.). Plants of China.
- Young ND, Bharti AK. 2012. Genome enabled insights into legume biology. Annual Review of Plant Biology 12: 193 201.
- Waybrant B, Pearce TR, Wang P, Sreevatsan S, Kokkoli E. 2012 Sep 12. Development and characterization of an aptamer binding ligand of fractalkine using domain targeted SELEX. Chem Commun (Camb). 48(80):10043 5. PubMed PMID: 22936337.
- Wolf, V.C., A. Gassmann, B.M. Clasen, A.G. Smith, C. Muller. 2012. Genetic and chemical variation of Tanacetum vulgare in plants of native and invasive origin. Biological Control. 61:240 245.
- Wonphatcharachai M, Wang P, Enomoto S, Webby R, Gramer M, Amonsin A, Sreevatsan S. 2012. Neutralizing DNA aptamers against Influenza A H3N2 viruses. J. Clin. Microbiol.
- Xing Liu; Lana Barkawi; Gary Gardner; Jerry D. Cohen. 2012. Transport of indole 3 butyric acid and indole 3 acetic acid in Arabidopsis hypocotyls using stable isotope labeling. Plant Physiology; 158(4):1988 2000.
- Samac, D. A., and Foster Hartnett, D. 2012. Effect of glyphosate application on foliar diseases in glyphosate tolerant alfalfa. Plant Dis. 96:1104 1110.
- Peverati, Roberto; Donald G. Truhlar. 2012. M11 L: A local density functional that provides improved accuracy for electronic structure calculations in chemistry and physics. Journal of Physical Chemistry Letters; 3(1):117 124.
- Peverati, Roberto; Donald G. Truhlar. 2012. Performance of the M11 and M11 L density functionals for calculations of electronic excitation energies by adiabatic time dependent density functional theory. Physical Chemistry Chemical Physics; 14(32):11363 11370.
- Rouse, M.N., I.C. Nava, S. Chao, J.A. Anderson, and Y. Jin. 2012. Identification of markers linked to the race Ug99 effective stem rust resistance gene Sr28 in wheat (Triticum aestivum L.). Theor. Appl. Genet. 125: 877 885.
- Sandford, E.E., Orr, M., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., and Lamont, S. 2012. Strong Concordance Between Transcriptomic Patterns of Spleen and Peripheral Blood Leukocytes in Response to Avian Pathogenic Escherichia coli.
- Sandford, E.E., Orr, M., Shelby, M., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., and Lamont, S.J. 2012. Leukocyte Transcriptome from Chickens Infected with Avian Pathogenic Escherichia coli Identifies Pathways Associated with Resistance. Results In Immunology 2:44 53.
- Shin, S., J.A. Torres Acosta, S.J. Heinen, S. McCormick, M. Lemmens, P.M.K. Paris, F. Berthiller, G. Adam and G.J. Muehlbauer. 2012. Transgenic Arabidopsis thaliana expressing a barley UDP glucosyltransferase exhibit resistance to the mycotoxin deoxynivalenol. J. Exp. Bot. 63:4731 4740.
- Shivaraju, M., Unruh, J., Slaughter, B.D., Mattingly, M., Berman, J. and Gerton J.L. 2012. Cell cycle coupled structural oscillation of centromeric nucleosomes in yeast. Cell. 150(2): 304 316.
- Shu, C. C., Chatterjee, A., Hu, W. S., Ramkrishna, D. 2012. Modeling of Gene Regulatory Processes by Population Mediated Signaling. New Applications of Population Balances. Chem. Eng. Sci., 70, 188 199.
- Seal, Prasenjit; Ewa Papajak; Donald G. Truhlar. 2012. Kinetics of the hydrogen abstraction from carbon 3 of 1 butanol by hydroperoxyl radical: Multi structural variational transition state calculations of a reaction with 262 conformations of the transition state. Journal of Physical Chemistry Letters; 3(2):264 271.
- Seal, Prasenjit; Ewa Papajak; Tao Yu; Donald G. Truhlar. 2012. Statistical thermodynamics of 1 butanol, 2 methyl 1 propanol, and butanal. Journal of Chemical Physics;136(3):.
- Seffernick, J.L., J.S. Erickson, S.M. Cameron, S. Cho, A.G. Dodge, J. Richman, M.J. Sadowsky, and L.P. Wackett. 2012. Defining the cyanuric acid hydrolase (AtzD)/barbiturase protein family. J. Bacteriol. 194:4579 4588.
- Seo. ,J, J.Y. Ryu, J. Han, J. H. Ahn, M. J. Sadowsky, H.G. Hur HG, and Y. Chong. 2012. Amino acid substitutions in naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816 4 result in regio and stereo specific hydroxylation of flavanone and isoflavanone. Appl Microbiol Biotechnol. PMID: 22391970
- Castro Melchor, M., Le, H., and Hu, W S. 2012. Time series microarray data analysis. Adv. Biochem. Eng. Biotechnol., 127, 27 70. (DOI:10.1007/10_2011_116)
- Castell Miller, C. V., and Samac, D. A. 2012. Population genetic structure, gene flow and recombination of Cochliobolus miyabeanus on cultivated wildrice (Zizania palustris). Plant Pathology Doi: 10.1111/j.1365 3059.2011.02581.x
- Cavanagh C, Chao S, Wang S, Huang BE, Stephen S et al. 2012. Genome wide comparative diversity uncovers multiple targets of selection for improvement in a worldwide sample of hexaploid wheat landrace and cultivars. In Review.
- Chander Y, Jindal N, Sreevatsan S, Stallknecht DE, Goyal SM. 2012 Sep 8. Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA. Influenza Other Respi Viruses. doi: 10.1111/irv.12003. [Epub ahead of print] PubMed PMID: 22958470.
- Chandola, Varun; Arindam Banerjee; Vipin Kumar. 2012. Anomaly detection for discrete sequences: A survey. IEEE Transactions on Knowledge and Data Engineering; 24(5):823 839.
- Cui, Y., Lee, M.Y., Huo, N., Bragg, J., Yan, L., Yuan, C., Li, C., Holditch, S.J., Xie, J., Luo, M., Li, D., Yu, J., Martin, J., Schackwitz, W., Gu, Y.Q., Vogel, J.P., Jackson, A.O., Liu, Z., and Garvin, D.F. 2012. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS ONE 7:e38333.
- Curtin SJ, Kantar MB, Yoon HW, Whaley AM, Schlueter JA, Stupar RM. 2012. Co expression of soybean Dicer like genes in response to stress and development. Funct Integr Genomics, In press.
- Curtin SJ, Voytas DF, Stupar RM. 2012. Genome Engineering of Crops with Designer Nucleases. Plant Genome 5: 42 50.
- Dahlem TJ, Hoshijima K, Jurynec MJ, Gunther D, Starker CG, Locke AS, Weis AM, Voytas DF, Grunwald DJ. 2012. Simple methods for generating and detecting locus specific mutations induced with TALENs in the zebrafish genome. PLoS Genet. 8(8):e1002861.
- Da Hye Jung, Kwon Young Choi, Eunok Jung, Wonji Choi, Hyungdon Yun, Romas J. Kazlauskas, Byung Gee Kim. 2012. Bioconversion of p coumaric acid to p hydroxystyrene using phenolic acid decarboxylase from B. amyloliquefaciens in biphasic reaction system. Appl. Environ. Microbiol. 2012, 00, 000 0000; doi: 10.1007/s00253 012 4358 8.
- Dal Bosco C, Dovzhenko A, Liu X, Worner N, Rensch T, Eismann M, Eimer S, Hegermann J, Paponov IA, Ruperti B, Heberle Bors E, Touraev A, Cohen JD, Palme K. 2012. The endoplasmic reticulum localized PIN8 is a pollen specific auxin carrier involved in intracellular auxin homeostasis. Plant Journal 71:860 870.
- Daniel R. Bond; Sarah M. Strycharz Glaven; Leonard M. Tender; Cesar I. Torres (Profiled Author: Daniel R Bond). 2012. On electron transport through geobacter biofilms ChemSusChem;5(6):1099 1105.
- Danzeisen, J.L., Kim, H.B., Isaacson, R.E., Tu, Z.J., and Johnson, T.J. 2011. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment. PLoS ONE 6:e27949.
- Danzeisen, J.L., Wannemuehler, W., Nolan, L.K., and Johnson, T.J. 2012, Sept. Comparison of multilocus sequence analysis and virulence genotyping of Escherichia coli from live birds, retail poultry meat, and human extraintestinal infection. Accepted for publication in Avian Diseases, in press.
- Chen, C., Xiao, Y., Li, X., and Ni, M. 2012. Light regulated stomatal aperture in Arabidopsis. Molecular Plant 5(3): 566 572.
- Choudhary, Swati; Maureen B. Quin; Mark A. Sanders; Ethan T. Johnson; Claudia Schmidt Dannert. 2012. Engineered protein nano compartments for targeted enzyme localization. PLoS ONE; 7(3):.
- Christian ML, Demorest ZL, Starker CG, Osborn MJ, Nyquist MD, Zhang Y, Carlson DF, Bradley P, Bogdanove AJ, Voytas DF. 2012. Targeting G with TAL Effectors: A Comparison of Activities of TALENs Constructed with NN and NK Repeat Variable Di Residues.PLoS One. 7(9):e45383.
- Coursolle, D. and J.A. Gralnick. 2012. Reconstruction of extracellular respiratory pathways for iron(III) reduction in Shewanella oneidensis strain MR 1. Front Microbiol. 3:56.
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- Matthew A. Andersen; Julian M. Alston; Philip G. Pardey. 2012. Erratum: Capital services in U.S. Agriculture: Concepts, comparisons, and the treatment of interest rates: An error and a correction. American Journal of Agricultural Economics; 94(5):1247 1248.
- McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM. 2012. Structural variants in the soybean genome localize to clusters of biotic stress response genes. Plant Physiol 159: 1295 1308.
- Menke, J., Dong, Y., and Kistler, H.C. 2012. Fusarium graminearum Tri12p influences virulence to wheat and trichothecene accumulation. Molecular Plant Microbe Interactions 25:1408 1418.
- Menzel WI, Chen W P, Hegeman AD, and Cohen JD. 2012. Qualitative and Quantitative Screening of Amino Acids in Plant Tissues. High Throughput Phenotyping in Plants: Methods and Protocols, Normanly J. Ed. Methods in Molecular Biology, vol. 918, 165 178.
- Mielke, Steven L.; Donald G. Truhlar. 2012. Accelerating the convergence and reducing the variance of path integral calculations of quantum mechanical free energies by using local reference Potentials. Journal of Chemical Theory and Computation; 8(5):1589 1596.
- Ming Zeng; Ashley T. Haase; Timothy W. Schacker (Profiled Authors: Ashley T Haase; Timothy W Schacker). 2012. Lymphoid tissue structure and HIV 1 infection: Life or death for T cells. Trends in Immunology; 33(6):306 314.
- Ming Zeng; Mirko Paiardini; Jessica C. Engram; Greg J. Beilman; Jeffrey G. Chipman; Timothy W. Schacker; Guido Silvestri; Ashley T. Haase. 2012. Critical role of CD4 T cells in maintaining lymphoid tissue structure for immune cell homeostasis and reconstitution. Blood; 120(9):1856 4867.
- Ming Zeng; Peter J. Southern; Cavan S. Reilly; Greg J. Beilman; Jeffrey G. Chipman; Timothy W. Schacker; Ashley T. Haase. 2012. Lymphoid tissue damage in HIV 1 infection depletes naive T cells and limits T cell reconstitution after antiretroviral therapy. PLoS Pathogens; 8(1):.
- Mitri C, Vernick KD. 2012. Anopheles gambiae pathogen susceptibility: the intersection of genetics, immunity and ecology. Curr Opin Microbiol.
- Morrell PL, Buckler ES, Ross Ibarra J. 2012. Crop genomics: advances and applications. Nat Rev Genet 13: 85 96.
- Mossey, P. and Das, A. 2012. Expression of Agrobacterium tumefaciens octopine Ti plasmid virB8 gene is regulated by translational coupling. Plasmid (in press).
- Mulukutla, B., Crammer, M. and Hu, W. S. 2012. On metabolic shift to lactate consumption in fed batch culture of mammalian cells. Metabol. Eng. 14, 138 49. (PMID:22244936)
- Nachimuthu, Santhanamoorthi; Jiali Gao; Donald G. Truhlar. 2012. A benchmark test suite for proton transfer energies and its use to test electronic structure model chemistries. Chemical Physics; 400():8 12.
- Ning, X, Michael Walters, and George Karypis. 2012. Improved Machine Learning Models for Predicting Selective Compounds. Journal of Chemical Information and Modeling, 52 (1), pp. 38 50.
- Okagaki, R., S. Cho, W.M. Kruger, W.W. Xu, S. Heinen and G.J. Muehlbauer. 2012. The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. Functional & Integrative Genomics DOI 10.1007/s10142 012 0299 7.
- Moeller, D.A., M.A. Geber, V.M. Eckhart, & P. Tiffin. 2012. Reduced pollinator service and elevated pollen limitation at the geographic range limit of an annual plant. Ecology 93:1036 1048.
- Hu, W S. 2012. Cell Culture Bioprocess Engineering. Ebook ( http://www.cellprocessbook.com/ ) and printed book (Amazon).
- Han, Jaebeom; Donald G. Truhlar; Jiali Gao. 2012. Optimization of the explicit polarization (X Pol) potential using a hybrid density functional. Theoretical Chemistry Accounts;131(3):1 15.
- Hansen, Travis; Miki Hondzo; Mara T. Mashek; Douglas G. Mashek; Paul A. Lefebvre. 2012. Algal swimming velocities signal fatty acid accumulation. Biotechnology and Bioengineering.
- Haran KP, Godden S, Boxrud D, Jawahir S, Bender JB, Sreevatsan S. 2012 Mar. Prevalence and Characterization of Staphylococcus aureus, including Methicillin Resistant Staphylococcus aureus from Bulk Tank Milk from Minnesota Dairy Farms. J Clin Microbiol. 50(3):688 95. Epub 2011 Dec 14. PubMed PMID: 22170937; PubMed Central PMCID: PMC3295154.
- Xu, Xuefei; Donald G. Truhlar. 2012. Performance of effective core potentials for density functional calculations on 3d transition metals. Journal of Chemical Theory and Computation; 8(1):80 90.
- Yu, Tao; Jingjing Zheng; Donald G. Truhlar. 2012. Multipath variational transition state theory: Rate constant of the 1,4 hydrogen shift isomerization of the 2 cyclohexylethyl radical. Journal of Physical Chemistry A 2012;116(1):297 308.
- Yu, Tao; Jingjing Zheng; Donald G. Truhlar. 2012. Statistical thermodynamics of the isomerization reaction between n heptane and isoheptane. Physical Chemistry Chemical Physics 2012;14(2):482 494.
- Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF. 2012, Nov 2. TALENs enable efficient plant genome engineering. Plant Physiol.
- Zhang, Peng; Donald G. Truhlar; Jiali Gao. 2012. Fragment based quantum mechanical methods for periodic systems with Ewald summation and mean image charge convention for long range electrostatic interactions. Physical Chemistry Chemical Physics; 14(21):7821 7829.
- Zhang, Peng; Luke Fiedler; Hannah R. Leverentz; Donald G. Truhlar; Jiali Gao. 2012. Erratum: Polarized molecular orbital chemistry. 2. The PMO method (Journal of Chemical Theory and Computation.7 (857 867) DOI:10.1021/ct100638g)) Journal of Chemical Theory and Computation; 8(8):2983 . 09.
- Zhao, Yan; Hou T. Ng; Roberto Peverati; Donald G. Truhlar. 2012. Benchmark database for ylidic bond dissociation energies and its use for assessments of electronic structure methods. Journal of Chemical Theory and Computation; 8(8):2824 2834.
- Zheng, Jingjing; Donald G. Truhlar. 2012. Multi path variational transition state theory for chemical reaction rates of complex polyatomic species: Ethanol + OH reactions. Faraday Discussions; 157():59 88.
- Zheng, Jingjing; Roberta J. Rocha; Marina Pelegrini; Luiz F. A. Ferrao; Edson F. V. Carvalho; Orlando Roberto Neto; Francisco B. C. MacHado; Donald G. Truhlar. 2012.A product branching ratio controlled by vibrational adiabaticity and variational effects: Kinetics of the H + trans N 2H 2 reactions. Journal of Chemical Physics; 136(18):.
- Zheng, Jingjing; Steven L. Mielke; Kenneth L. Clarkson; Donald G. Truhlar. 2012. MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity. Computer Physics Communications; 183(8):1803 1812.
- Zhou, H., G. Muehlbauer and B.J. Steffenson. 2012. Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States. J. Zhejiang Univ. 13:438 451.
- Zhuang, F. George Karypis, Xia Ning, Qing He, and Zhongzhi Shi. 2012. Milti view Learning via Probabilistic Latent Semantic Analysis. Information Sciences, 199, 20 30.
- Abd Allah, A; Wang, P; Richt, J; Sreevatsan. 2012. Y145Stop is sufficient to induce de novo generation of prions. Prion. 6(1):81 8.
- Abrahante, J; Johnson, TJ; Hunter, S; and Maheswaran, S; Haugland, M; Bayles, D; and Briggs, R. 2012. Draft genome sequences of two virulent serotypes of avian Pasteurella multocida. Journal of Bacteriology, October. Andersen, M; Alston, J; Pardey, P. 2012. Capital use intensity and productivity biases. Journal of Productivity Analysis; 37(1):59 71.
- Anderson, JA; Wiersma, JJ; Linkert, GL; Kolmer, JA; Jin, Y; Dill Macky, R; Wiersma, JV; Hareland, GA; and Busch, RH. 2012. Registration of Sabin Wheat. J. Plant Registrations 6:174 179.
- Anderson, JA; Wiersma, JJ; Linkert, GL; Kolmer, JA; Jin, Y; Dill Macky, R; Wiersma, JV; Hareland, GA; and Busch, RH. 2012. Registration of Tom Wheat. J. Plant Registrations 6:180 185.
- Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia J M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross Ibarra J. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics 44(7):808 811.
- George, SJ, Barney, BM, Mitra, D, Igarashi, RY, Guo, Y, Dean, DR, Cramer, SP, Seefeldt, LC. 2012. EXAFS and NRVS Reveal a Conformational Distortion of the FeMo cofactor in the MoFe Nitrogenase Propargyl Alcohol Complex. Journal of Inorganic Biochemistry. 112, pages 85 92.
- Hu, W S., Zeng, A P. 2012. Genomics and Systems Biology of Mammalian Cell Culture. Adv. Biochem. Eng. Biotechnol. Vol. 127. Springer pub.
- Huang, Y., B. Millet, K. Beaubien, S. Dahl, B. Steffenson, K. Smith, G. Muehlbauer. 2012. Haplotype diversity and population structure in cultivated and wild barley evaluated for Fusarium head blight responses. Theor. Appl. Genet. DOI 10.1007/s00122 012 2006 4.
- Hufford, Matthew B.; Xun Xu; Joost Van Heerwaarden; Tanja Pyhajarvi; Jer Ming Chia; Reed A. Cartwright; Robert J. Elshire; Jeffrey C. Glaubitz; Kate E. Guill; Shawn M. Kaeppler; et al. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics; 44(7):808 811.
- Igarashi, D., Tsuda, K., and Katagiri, F. 2012. The Peptide Growth Factor, Phytosulfokine, Attenuates Pattern Triggered Immunity. Plant J. 71, 194 204.
- Jacquemin, Denis; Yan Zhao; Rosendo Valero; Carlo Adamo; Ilaria Ciofini; Donald G. Truhlar. 2012. Verdict: Time dependent density functional theory not guilty of large errors for cyanines. Journal of Chemical Theory and Computation;8(4):1255 1259.
- Johnson, T.J., Bielek, E.M., Fortini, D., Hansen, L.H., Hasman, H., Debroy, C., Nolan, L.K., and Carattoli, A. 2012. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug resistant Enterobacteriaceae. Plasmid 68:43 50.
- Johnson, T.J., Wannemuehler, Y.W., Kariyawasam, S., Johnson, J.R., Logue, C.M., and Nolan, L.K. 2012. Prevalence of avian pathogenic Escherichia coli strain APEC O1 genomic islands and assessment of its zoonotic potential. Journal of Bacteriology 194:2846 2853.
- Jonkers, W., Dong, Y., Broz, K., and Kistler, H.C. 2012. The Wor1 like protein Fgp1 regulates pathogenicity, toxin synthesis and reproduction in the phytopathogenic fungus Fusarium graminearum. PLoS Pathogens 8(5): e1002724.
- Jonkers, W., Rodriguez Estrada, A.E., Lee, K., Breakspear, A., May, G. and Kistler, H.C. 2012. Metabolome and transcriptome of the interaction between Ustilago maydis and Fusarium verticillioides in vitro. Applied and Environmental Microbiology 78: 3656 3667.
- Jordan, N.R., L. Aldrich Wolfe, S.C. Huerd, D.L. Larson, and G. Muehlbauer. 2012. Soil occupancy effects of invasive and native grassland plant species on composition and diversity of mycorrhizal associations. Invasive Plant Science and Management (In press)
- Joshi D, Harris NB, Waters R, Thacker T, Mathema B, Krieswirth B, Sreevatsan S. 2012 Sep 19. Single nucleotide polymorphisms in Mycobacterium bovis genome resolve phylogenetic relationships. J Clin Microbiol. [Epub ahead of print] PubMed PMID: 22993186.
- Justen VL, Fritz VA, Cohen JD. 2012. Seasonal variation in glucosinolate accumulation in turnips grown under photoselective nettings. Hort Environ Biotechnol 53:108 115.
- Kamber, T., T. Lansdell, C. A. Ishimaru, V. O. Stockwell, T. H. M. Smits, and B. Duffy. 2012. Characterization of the antibacterial peptide herbicolin I biosynthetic operon in Pantoea vagans biocontrol strain C9 1 and incidence in Pantoea species. Appl. Environ. Microbiol. (in press)
- Jareonmit, P., M. Mehta, M. J. Sadowsky, and K. Sajjaphan. 2012. Phylogenetic and phenotypic analyses of arsenic reducing bacteria isolated from an old tin mine area in Thailand. World Journal of Microbiology and Biotechnology. doi:10.1007/s11274 012 1034 1
- Ji Young Ryu, Jiyoung Seo, Joong Hoon Ahn, Michael J. Sadowsky, and Hor Gil Hur. 2012. Transcriptional Control of Isoeugenol Monooxygenase of Pseudomonas nitroreducens Jin1 in E. coli. Biosci. Biotechnol. Biochemi. 76:1891 1896.
- Johnson, T.J. and Lang, K. 2012. IncA/C plasmids: an emerging threat to human and animal health? Mobile Genetic Elements 2:55 58.
- Kane, A.L., D.R. Bond and J.A. Gralnick. 2012. Electrochemical analysis of Shewanella oneidensis engineered to bind gold electrodes. ACS Synth Biol. DOI: 10.1021/sb300042w
- Kantar M, Betts K, Hulke BS, Stupar RM, Wyse D. 2012. Breaking Tuber Dormancy in Helianthus tuberosus L. and Interspecific Hybrids of Helianthus annuus L. x Helianthus tuberosus. Hort Sci 47:1342 1346.
- Katagiri, F. 2012. Toward Predictive Biology in Plant Immunity. Induction of Resistance in Plants by Pathogens, Eds. Rodrigues, F. et al. (Universidade Federal de Vicosa, MG, Brazil), pp. 239 256. ISBN 978 85 8179 025 0.
- Kauffman, C. and George Karypis. 2012. Computational Tools for Protein DNA Interactions. WIREs Data Mining and Knowledge Discovery, 2: 14 28.
- Kauffman, C. Karypis, G. 2012. Coarse and Fine grained Models for Proteins: Evaluation by Decoy Discrimination. Proteins (in press).
- Anderson, MZ; Baller, JA; Dulmage, K; Wigen, L; and Berman, J. 2012. The three clades of the telomere associated 1 TLO gene family of Candida albicans have different splicing, localization and expression features. Eukaryotic Cell, 11(10): 1268 1275.
- Aoki, T; Ward, TJ; Kistler, HC; and ODonnell, K. 2012. Systematics, phylogeny and trichothecene mycotoxin potential of Fusarium head blight pathogens. Mycotoxins 62: 91 102.
- Ashfield, T; Egan, AN; Pfeil, BE; Chen, NWG; Podicheti, R; Ratnaparkhe, MB; Ameline Torregrosa, C; Denny, R; Cannon, S; Doyle, JJ; Geffroy, V; Roe, BA; Saghai Maroof, MA; Young, ND; Innes, RW. 2012. The impact of polyploidy on the evolution of a complex NB LRR resistance gene cluster in soybean. Plant Physiology 159: 344 354.
- Asplen, M; Bruns, E; David, A; Denison, RF; Epstein, B; Kaiser, MC; Kaser, JM; Lacroix, L; Mohl, EK; Quiram, G; et al. 2012. Do trade offs have explanatory power for the evolution of organismal interactions? Evolution; 66(5):1297 1307.
- Bakker, MG; Bradeen, JM; and Kinkel, LL. 2012. Effects of plant host species and plant community richness on streptomycete community structure. FEMS Microbology Ecology.
- Bakker, MG; Tu, ZJ; Bradeen, JM; and Kinkel, LL. 2012. Implications of pyrosequencing error correction for biological data interpretation. PLoS ONE 7(8):e44357.
- Bakule, P; Fleming, DG; Sukhorukov, O; Ishida, K; Pratt, F; Momose, T; Torikai, E; Mielke, SL; Garrett, BC; Peterson, KA; et al. 2012. State selected reaction of muonium with vibrationally excited H 2. Journal of Physical Chemistry Letters; 3(19):2755 2760.
- Baller, JA; Gao, J; Stamenova, R; Curcio, MJ; Voytas, DF. 2012. A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon. Genome Res. 22:704 13.
- Barbieri, M; Marcel, TC; Niks, RE; Francia, E; Pasquariello, M; Mazzamurro, V; Garvin, DF; and Pecchioni, N. 2012. QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L. Genome 55:152 163
- Barnes, AMT; Ballering, KS; Leibman, RS; Wells, CL; Dunny, GM. 2012. Enterococcus faecalis produces abundant extracellular structures containing DNA in the absence of cell lysis during early biofilm formation. MBio 3(4):e00193 12. Doi:101128/mBio00193 12.
- Barney, BM; Mann, RL; Ohlert, JM. 2012. Identification of a Residue Affecting Fatty Alcohol Selectivity in Wax Ester Synthase. Applied and Environmental Microbiology. In Press.
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: The Microbial and Plant Genomics Institute (MPGI) membership consists of 67 faculty from 4 colleges: The College of Food, Agriculture and Natural Resource Sciences, The College of Biological Sciences, the Academic Health Center and the College of Science and Engineering. MPGI travel awards enabled 31 graduate students and 12 postdoctoral researchers from 33 university-wide labs to attend meetings to present their research and interact with scientists.MPGI coordinated and sponsored a Fall Symposium on the topic of "Beyond the Reference: Population Genomics" hosted by faculty members Nathan Springer and Peter Tiffin. The series also served as a one-credit course (PBIO5960-002) for 9 students. Each visiting scientist chose a paper for students to read and critique. Students attended the Symposium and a day-long workshop on experimental designs using genomics to study for variation. The Distinguished Scientist Lectureship Series features research by prominent scientists, particularly in the field of microbial and plant sciences. These lecturers are invited to campus to give seminars, discuss research, and interact with students, faculty, and the public. Science on the Spot is a bi-annual gathering that has allowed MPGI faculty and members of their lab to present and discuss information on their current research in a social and relaxed environment. These gatherings have expanded opportunities for interdisciplinary connections with other University researchers. MPGI has also begun to hold a faculty member lunch every other Wednesday, from Noon to 1 pm at the St. Paul student center. Faculty members are encouraged to bring a lunch and discuss science in an informal setting. PARTICIPANTS: Members of the MPGI are faculty who are interested in the successful development and application of genomics and the resulting societal and environmental impact. The 67 members of MPGI are faculty from departments throughout four colleges at the University of Minnesota: The College of Food, Agricultural, and Natural Resource Sciences (CFANS), the College of Biological Sciences (CBS), the Institute of Technology (IT), and the Academic Health Center (AHC). MPGI directly supports the salary of faculty member M. David Marks, a functional genomics researcher in plant biology, plus support staff member Sandesh Nicol who is responsible for management and administration of the MPGI seminar series, the MPGI website and other administrative functions. MPGI has provided training and professional development for 31 graduate students and 12 postdoctoral researchers by supporting either their attendance at meetings to present research findings, or their travel to other educational institutions for training purposes. TARGET AUDIENCES: Within the University community, the Institute facilitates crosscutting communications among faculty engaged in diverse areas of genomics research. With the sponsorship of retreats and seminar series, MPGI supports the dissemination of scientific knowledge among faculty, students, and staff. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions via its website (www.mpgi.umn.edu) and the seminar series sponsored by the Institute. In addition, a major goal of MPGI is training outstanding students and postdoctoral researchers in this important biological field by providing them with travel awards. These are among the activities designed to bring benefits from genomics to Minnesotans, the nation, and the world. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The Microbial and Plant Genomics Institute (MPGI) promotes advances in microbial and plant genomics, genomics-enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multi-disciplinary interchange of ideas and applications of cutting-edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. The scientific aim of the Institute is to enhance the development of functional and translational genomics concomitantly with the expansion of bioinformatics capabilities and the development of specialized instrumentation. Within the University community, the Institute facilitates interactions among faculty engaged in diverse areas of genomics research by promoting understanding of microbial and plant genomics, and providing access to genomics-related technologies. Cooperation among MPGI members helps to assure a strong basis for education in the disciplines of the basic agricultural, environmental, and health sciences. The Institute enhances faculty projects by supporting the educational activities of individual grad students and postdoctoral researchers. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions. In addition, assisting in the training of outstanding students in this important biological field is a major goal.
Publications
- Ning, Xia and Karypis, George. 2011. In Silico Structure-Activity-Relationship (SAR) Models From Machine Learning: A Review. Drug Development Research, Vol. 72.
- Nirmala J, Drader T, Lawrence PK, Yin C, Hulbert S, Steber CM, Steffenson BJ, Szabo LJ, von Wettstein D, Kleinhofs A. 2011. Concerted action of two avirulent spore effectors activates Reaction to Puccinia graminis 1 (Rpg1)-mediated cereal stem rust resistance. Proc Natl Acad Sci U S A. Aug 30;108(35):14676-81.
- Nonhebel H, Yuan Y, Al-Amier H, Pieck M, Akor E, Ahamed A, Cohen JD, Celenza JL, Normanly J. 2011. Redirection of tryptophan metabolism in tobacco by ectopic expression of an Arabidopsis indolic glucosinolate biosynthetic gene. Phytochemistry 72:37-48.
- Breakspear, A., Pasquali, M., Broz, K., Dong, Y. and Kistler, H.C. 2011. Npc1 is involved in sterol trafficking in the filamentous fungus Fusarium graminearum. Fungal Genetics and Biology. 48: 725-730.
- Brkljacic, J., Grotewold, E., Scholl, R., Mockler, T., Garvin, D.F., Vain, P., Brutnell, T., Sibout, R., Bevan, M., Budak, H., Caicedo, A.L., Gao, C., Gu, Y., Hazen, S.P., Holt, B.F., Hong, S.-Y., Jordan, M., Manzaneda, A.J., Mitchell-Olds, T., Mochida, K., Mur, L.A.J., Park, C.-M., Sedbrook, J., Watt, M., Zheng, S.J., and Vogel, J.P. 2011. Brachypodium as a model for the grasses: Today and the future. Plant Physiology 157:3-13.
- Burkhardt, N.Y., Baldridge, G.D., Williamson, P.C., Billingsley, P.M., Heu, C.C., Felsheim R.F., Kurtti, T.J., Munderloh, U.G. 2011. Development of Shuttle Vectors for Transformation of Diverse Rickettsia Species. PLoS ONE http://dx.plos.org/10.1371/journal.pone.002951
- Burrack, L.S., Applen, S. and J. Berman. 2011. The requirement for the Dam1 complex is dependent upon the number of kinetochore proteins and microtubules. Current Biology, 21:889-896.
- Cameron SM, Durchschein K, Richman JE, Sadowsky MJ, Wackett LP. A New Family of Biuret Hydrolases Involved in S-Triazine Ring Metabolism. 2011. ACS Catal. Aug 1;2011(1):1075-1082.
- Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011. Jul;39(12):e82. Erratum in: Nucleic Acids Res. Sep 1;39(17):7879.
- Qi, Y., Tsuda, K., Nguyen, L.V., Wang, X., Lin, J., Murphy, A.S., Glazebrook, J., Thordal-Christensen, H., and Katagiri, F. 2011. Physical Association of Arabidopsis Hypersensitive Induced Reaction Proteins (HIRs) with the Immune Receptor RPS2. Journal of Biological Chemistry 286: 31297-31307
- Qi, Y., Tsuda, K., Glazebrook, J., and Katagiri, F. 2011. Physical Association of Pattern-Triggered Immunity (PTI) and Effector Triggered Immunity (ETI) Receptors in Arabidopsis. Molecular Plant Pathology. DOI: 10.1111/J.1364-3703.2010.00704.X
- Qian, Y., Paquete C. M., Louro, R. O., Ross, D. E., Labelle, E. V., Bond D. R., and M. Tien. 2011. Mapping the iron binding site(s) on the small tetraheme cytochrome of Shewanella oneidensis MR-1. Biochemistry. Jul 19;50(28):6217-24
- Qu H, Magotti P, Ricklin D, Wu EL, Kourtzelis I, Wu YQ, Kaznessis YN, Lambris JD. 2011. Novel analogues of the therapeutic complement inhibitor compstatin with significantly improved affinity and potency. Mol Immunol . Jan;48(4):481-9.
- Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh C-T, Jia Y, Freeling M, Schnable PS, Springer NM, Vaughn MW. 2011. Heritable epigenetic variation among maize inbreds. PLoS Genetics 7(11), e1002372.
- Dunny GM, Johnson CM. 2011. Regulatory circuits controlling enterococcal conjugation: lessons for functional genomics. Curr Opin Microbiol. 2Apr;14(2):174-80. Review.
- Eberle, C.A., B.M. Clasen, N. O. Anderson and A. G. Smith. 2011. A novel pollen tube growth assay utilizing a transmitting tract-ablated Nicotiana tabacum style. Sexual Plant Reproduction. DOI 10.1007/s00497-011-0177-9.
- Eckhart, V.M., M.A. Geber, W.F. Morris, E.S. Fabio, P. Tiffin, and D.A. Moeller. 2011. The geography of demography: Long-term demographic studies and species distribution models reveal a species border limited by adaptation. American Naturalist 178:S26-S43.
- Eichten SR, Foerster J, de Leon, N, Kai, Y, Yeh C-T, Liu S, Jeddeloh J, Schnable PS, Kaeppleer SM, Springer NM. 2011. B73-Mo17 near isogenic lines (NILs) demonstrate dispersed structural variation in maize. Plant Physiology 156(4): 1679-1690.
- Alston, J.M., M.A. Andersen, J.S. James and P.G. Pardey. 2011. The Economic Returns to U.S. Public Agricultural Research. American Journal of Agricultural Economics 93(5)(2011): 1257-1277.
- Alecu IM, Truhlar DG. 2011. Computational Study of the Reactions of Methanol with the Hydroperoxyl and Methyl Radicals. Part I: Accurate Thermochemistry and Barrier Heights. Journal of Physical Chemistry A 115, 2811-2829.
- Kim HB, Borewicz K, White BA, Singer RS, Sreevatsan S, Tu ZJ, Isaacson RE. 2011. Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs. Vet Microbiol. Nov 21;153(1-2):124-33.
- Kim J, Sadowsky MJ, Hur HG. 2011. Simultaneous synthesis of temperature-tunable peptide and gold nanoparticle hybrid spheres. Biomacromolecules. Jul 11;12(7):2518-23
- King, J.G., Vernick, K.D., and Hillyer, J.F. 2011. Members of the Salivary Gland Surface Protein (SGS) Family Are Major Immunogenic Components of Mosquito Saliva. J Biol Chem 286, 40824-40834
- Kolmer, J, J. Anderson. 2011. First detection in North America of virulence in wheat leaf rust (Puccinia triticina) to seedling plants of wheat with Lr21. Plant Disease 95:1032
- Kolmer, J.A., Garvin, D.F., and Jin, Y. 2011. Expression of a Thatcher wheat adult plant stem rust resistance QTL on chromosome arm 2BL is enhanced by Lr34. Crop Science 51:526-533
- Kulkarni, A. D. and D. G. Truhlar. 2011. Performance of Density Functional Theory and Moller-Plesset Second Order Perturbation Theory for Structural Parameters in Complexes of Ru. Journal of Chemical Theory and Computation 7, 2325-2332
- Lamont EA, He L, Warriner K, Labuza TP, Sreevatsan S. 2011. A single DNA aptamer functions as a biosensor for ricin. Analyst. 2011 Oct 7;136(19):3884-95.
- Lebarbenchon C, Yang M, Keeler SP, Ramakrishnan MA, Brown JD, Stallknecht DE, Sreevatsan S. 2011. Viral replication, persistence in water and genetic characterization of two influenza A viruses isolated from surface lake water. PLoS One. 6(10):e26566.
- Lee JH, Li X, O'Sullivan DJ. 2011. Transcription analysis of a lantibiotic gene cluster from Bifidobacterium longum DJO10A. Appl Environ Microbiol. Sep;77(17):5879-87.
- Leverentz H., J. Gao, and D. G. Truhlar. 2011. Using Multipole Point Charge Distributions to Provide the Electrostatic Potential in the Variational Explicit Polarization (X-Pol) Potential,", Theoretical Chemistry Accounts 129, 3-13
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- Johnson, T.J., Fernandez-Alarcon, C., Bojesen, A.M., Nolan, L.K., Trampel, D.W., and Seemann, T. 2011. Complete genome sequence of Gallibacterium anatis strain UMN179, isolated from a laying hen with peritonitis. J Bacteriol 193:3676-3677.
- Jordan, N., Larson, D., Huerd S. 2011. Evidence of qualitative differences between soil-occupancy effects of invasive versus native grassland plant species. Invasive Plant Science and Management 4:11-21.
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: The Microbial and Plant Genomics Institute (MPGI) membership consists of 67 faculty from 4 colleges: CFANS, CBS, IT, and AHC. MPGI funding supports salaries for one Professor and one Administrative Specialist. MPGI travel awards enabled 19 graduate students and 15 postdoctoral researchers from 28 university-wide labs to attend meetings to present their research and interact with scientists. MPGI funded equipment grants for 6 faculty members and shared equipment for the Cargill Building which totaled approximately $400,000. MPGI coordinated and sponsored a Fall Symposium on the topic of "Biological Applications of Next-Generation Sequencing" hosted by faculty members. The series also served as a one-credit course (PBIO5960-002) for 13 students. Each visiting scientist chose a paper for students to read and critique. Students attended the Symposium and a day-long workshop on next-generation sequencing. Other seminars presented by MPGI: The National Academy of Sciences Lectureship Series was changed to the Distinguished Scientists Lectureship Series in 2010. This series features research by prominent scientists, particularly in the field of microbial and plant sciences. These lecturers are invited to campus to give seminars, discuss research, and interact with students, faculty, and the public. Science on the Spot is a new monthly gathering that has allowed MPGI faculty and members of their lab to present and discuss information on their current research in a social and relaxed environment. These gatherings have expanded opportunities for interdisciplinary connections with other University researchers. PARTICIPANTS: Members of the MPGI are faculty who are interested in the successful development and application of genomics and the resulting societal and environmental impact. The 67 members of MPGI are faculty from departments throughout four colleges at the University of Minnesota: The College of Food, Agricultural, and Natural Resource Sciences (CFANS), the College of Biological Sciences (CBS), the Institute of Technology (IT), and the Academic Health Center (AHC). MPGI directly supports the salary of faculty member M. David Marks, a functional genomics researcher in plant biology, plus support staff member Sandesh Nicol who is responsible for management and administration of the MPGI seminar series, the MPGI website and other administrative functions. MPGI has provided training and professional development for 19 graduate students and 15 postdoctoral researchers by supporting either their attendance at meetings to present research findings, or their travel to other educational institutions for training purposes. TARGET AUDIENCES: Within the University community, the Institute facilitates crosscutting communications among faculty engaged in diverse areas of genomics research. With the sponsorship of retreats and seminar series, MPGI supports the dissemination of scientific knowledge among faculty, students, and staff. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions via its website (www.mpgi.umn.edu) and the seminar series sponsored by the Institute. In addition, a major goal of MPGI is training outstanding students and postdoctoral researchers in this important biological field by providing them with travel awards. These are among the activities designed to bring benefits from genomics to Minnesotans, the nation, and the world. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The Microbial and Plant Genomics Institute (MPGI) promotes advances in microbial and plant genomics, genomics-enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multi-disciplinary interchange of ideas and applications of cutting-edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. The scientific aim of the Institute is to enhance the development of functional and translational genomics concomitantly with the expansion of bioinformatics capabilities and the development of specialized instrumentation. Within the University community, the Institute facilitates interactions among faculty engaged in diverse areas of genomics research by promoting understanding of microbial and plant genomics, and providing access to genomics-related technologies. Cooperation among MPGI members helps to assure a strong basis for education in the disciplines of the basic agricultural, environmental, and health sciences. The Institute enhances faculty projects by supporting the educational activities of individual grad students and postdoctoral researchers. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions. In addition, assisting in the training of outstanding students in this important biological field is a major goal.
Publications
- Coursolle, D. and J.A. Gralnick. 2010. Modularity of the Mtr respiratory pathway of Shewanella oneidensis strain MR-1. Mol Microbiol. 77(4):995-1008.
- Dominguez, W., and D. J. OSullivan. 2010. Positive influence of milk on the expression of some stress-induced genes in Bifidobacterium longum. ADSA annual meeting Abstracts Book, Denver, CO.
- Douglas RN, Wiley D, Springer NM, Scanlon MJ (2010) ragged seedling2 encodes an ARGONAUTE7-like protein required for mediolateral expansion, but not dorsiventrality, of maize leaves. Plant Cell 22: 1441-1451.
- Fang G, Kuang R, Pandey G, Steinbach M, Myers CL, Kumar V. 2010. Subspace differential coexpression analysis: problem definition and a general approach. Pac Symp Biocomput:145-156.
- Flynn, J.M., D.E. Ross, K.A. Hunt, D.R. Bond and J.A. Gralnick. 2010. Enabling unbalanced fermentations using engineered electrode-interfaced bacteria. MBio. 1(5):e00190-10.
- Fu Y, Springer NM, Gerhardt D, Ying K, Yeh CT, Wu W, Swanson-Wagner R, DAscenzo M, Millard T, Freeberg L, Ayoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Barbazuk WB, Jeddeloh JA, Schnable PS. 2010. Repeat subtraction-mediated sequence capture from a complex genome. Plant Journal. 62: 898-909.
- Frias, J.A., B.R. Goblirsch, L.P. Wackett, and C.M. Wilmot. (2010). Cloning, purification, and crystallization of the OleC protein from Stenotrophomonas maltophilia involved in head-to-head hydrocarbon biosynthesis. Acta Crystallographica, Section F. 66:1108-1110.
- Gale, C.A., and J. Berman. 2010. Cell Cycle and Growth Control in Candida species. In Candida and candidiasis. Calderone, R. and Clancy, N. Editors. Volume 4. ASM Press. (Solicited review chapter, In press.)
- Gale, L.R., Harrison, S., Ward, T.J., ODonnell, K., Milus, G., Gale, S.W. and Kistler, H.C. (Posted online on 7 Sept 2010). 201x. Nivalenol type populations of Fusarium graminearum and F. asiaticum are prevalent on wheat in southern Louisiana. Phytopathology.
- Gardiner SA, Boddu J, Berthiller F, Hametner C, Stupar RM, Adam G, Muehlbauer GJ. (2010). Transcriptome analysis of the barley-deoxynivalenol interaction: evidence for a role of glutathione in deoxynivalenol detoxification. Mol Plant Microbe Interact. 23: 962 976.
- Katagiri, F. and Tsuda, K. (2010). Understanding the plant immune system. Mol. Plant-Microbe Interact. 23, 1531-1536.
- Katagiri, F. (2010). Systems-wide analysis of the signaling network controlling plant immunity. Genome-Enabled Integration of Research in Plant Pathogen Systems, Eds. Wolpert, T. et al. (APS press, St Paul, MN).
- Keller S. R., M. S. Olson, S. Silim, W. Schroeder, P. Tiffin. 2010. Population structure and migration following rapid range expansion in the balsam poplar, Populus balsamifera. Molecular Ecology 19: 1212-1226
- Keller S. R., Soolanayakanahally R., Guy, R., Silim S., Olson M., and Tiffin P.. 2010. Climate-driven local adaptation in ecophysiology and phenology in balsam poplar, Populus balsamifera (Salicaceae). American Journal of Botany. (In press).
- Kolmer, J.A., J.A. Anderson, and J. Flor. 2010. Chromosome location, linkage with simple sequence repeat markers, and leaf rust resistance conditioned by gene Lr63 in wheat. Crop Sci. 50:2392-2395.
- Koren, A., Tsai, H-J., Tirosh, I., Burrack, L., Barkai, N. and J. Berman. Epigenetic inheritance of centromere location is associated with early DNA replication. 2010. PLoS Genetics, PLoS Genet 6(8): e1001068.
- Kumar, L., Breakspear, A., Kistler, C., Ma, L.-J. and Xie, X. 2010. Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes. BMC Genomics. 11:208.
- Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J. (2010). Genome-wide genetic variation among elite maize inbreds: implications for crop improvement. Nature Genetics. 42(11):1027-1030.
- Lau J., Shaw R.G., Reich P.B., and Tiffin P. 2010 . Species interactions in a changing environment: elevated CO2 alters the ecological and potential evolutionary consequences of competition. Evolutionary Ecology Research 12:435-455.
- Lee, J-H., and D. J. OSullivan. 2010. Genomic insights into bifidobacteria. Microbiol. Mol. Bio. Rev. 74:378-416.
- Lee, J-H., and D. J. OSullivan. 2010. Comparative genomic analysis of eight complete bifidobacteria genomes. 110th ASM annual meeting Abstracts Book, San Diego, CA.
- Nair, S., S.E. Ullrich, T.K. Blake, B. Cooper, C.A. Griffey, P.M. Hayes, D.J. Hole, R.D. Horsley, D.E. Obert, K.P. Smith, G.J. Muehlbauer, and B.-K. Baik. 2010. Variation in kernel hardness and associated traits in U.S. barley breeding lines. Cereal Chem. 87:461-466.
- Olson, MS, A. L. Roberson, N. Takebayashi, S. Silim, W. R. Schroeder, P. Tiffin. 2010. Nucleotide diversity and linkage disequilibirium in Balsam poplar (Populus balsamifera). New Phytologist 186: 526-536.
- Qi, Y., Tsuda, K., Joe, A., Sato, M., Nguyen, L. V., Glazebrook, J., Alfano, J. R., Cohen, J. D., and Katagiri, F. (2010). A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis. Mol. Plant-Microbe Interact. 23, 1573-1583.
- Rep, M. and Kistler H.C. 2010. The genomic organization of plant pathogenicity in Fusarium species. Current Opinion in Plant Biology. 13:420-426.
- Roy, J.K., K.P. Smith, G.J. Muehlbauer, S. Chao, T.J. Close, and B.J. Steffenson. 2010. Association mapping of spot blotch resistance in wild barley. Mol Breeding. 26:243 256.
- Ruzicka, K., L.C. Strader, A. Bailly, H. Yang, J. Blakeslee, L. Langowski, E. Nejedla, H. Fujita, H. Itoh, K. Syono, J. Hejatko, W.M. Gray, E. Martinoia, M. Geisler, B. Bartel, A.S. Murphy, and J. Friml. 2010. Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole-3-butyric acid. Proc. Natl. Acad. Sci. USA. 107:10749-53.
- Springer NM, Jackson SA. (2010) Realizing the potential of genomics for crop improvement. Brief Funct Genomics. 9: 93-94.
- Springer NM, Eichten S, Smith A, Papa CM, Steinway S, Kaeppler SM. 2009. Characterization of a novel maize retrotransposon family SPRITE that shows high levels of variability among maize inbred lines. Maydica. 54: 417-428.
- Sukovich, D.J., J.L Seffernick, J.E. Richman, K.A. Hunt, J.A. Gralnick and L.P. Wackett. 2010. Head-to-head hydrocarbon biosynthetic genes in Shewanella oneidensis strain MR-1. Appl Environ Microbiol. Jun; 76(12):3842-9.
- Sukovich, D.J., J.L. Seffernick, J.E. Richman, J.A. Gralnick and L.P. Wackett. 2010. Widespread head-to-head hydrocarbon biosynthesis in bacteria. Appl Environ Microbiol. Jun; 76(12):3850-62.
- Sukovich, D.J., J.L. Seffernick, J.E. Richman, K.A. Hunt, J.A. Gralnick, and L.P. Wackett (2010) Structure, function and insights into the biosynthesis of a head-to-head hydrocarbon in Shewanella oneidensis strain MR-1. Appl. Environ. Microbiol.76:3842-3849.
- Sukovich, D.J., J.L. Seffernick, J.E. Richman, J.A. Gralnick, and L.P. Wackett. (2010). Widespread head-to-head hydrocarbon biosynthesis in bacteria and role of OleA. Appl. Environ. Microbiol. 76:3850-3862.
- Sun X., and Ni M. (2010). HYPOSENSITIVE TO LIGHT, an alpha/beta fold protein, acts downstream of HY5 to regulate Arabidopsis seedling de-etiolation. Molecular Plant. 10.1093/mp/ssq055.
- Sun X., Shantharaj D., Kang X., and Ni M. (2010). Transcriptional and hormonal signaling control of Arabidopsis seed development. Current Opinion in Plant Biology. 13, 611-620.
- Yu Long-Xi L-X, Liu S., Anderson J.A., Singh R.P., Jin Y., Dubcovsky J., Brown-Guidera G., Bhavani S., Morgounov A., He Z., Huerta-Espino J., Sorrells M.E. 2010. Haplotype diversity of stem rust resistance loci in uncharacterized wheat lines. Mol. Breeding. 26:667 680.
- Yang, S.H., Xu, W., Tesfaye, M., Lamb, J.F., Jung, H.G., VandenBosch, K.A., Vance, C.P., Gronwald, J.W. 2010. Transcript Profiling of Two Alfalfa Genotypes with Contrasting Cell Wall Composition in Stems Using a Cross-Species Platform: Optimizing Analysis by Masking Biased Probes. Biomed Central (BMC) Genomics. 11:323.
- Yang, S.H., Valdes-Lopez, O., Xu, W.W., Bucciarelli, B., Gronwald, J.W., Hernandez, G., Vance, C.P. 2010. Transcript Profiling of Common Bean (Phaseolus vulgaris L.) Using the GeneChip(R) Soybean Genome Array: Optimizing Analysis by Masking Biased Probes. Biomed Central (BMC) Plant Biology. 10:85.
- Yang, X.Y., W.P. Chen, A.K. Rendahl, A.D. Hegeman, W.M. Gray, and J.D. Cohen. 2010. Measuring the turnover rates of Arabidopsis proteins using deuterium oxide: an auxin signaling case study. Plant J. 63:680-695.
- Zacchi, L.M., Selmecki, A.M., Berman,J. and C. A. Davis. 2010. Low dosage of histone H4 leads to growth defects and morphological changes in Candida albicans. PLoS One. 5(5): e10629.
- Zhang, F, Maeder, ML, Unger-Wallace, E, Reyon, D, Hoshaw, JP, Christian, M, Dobbs, D, Peterson, TA, Joung, JK, and Voytas, DF. (2010). High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci USA. 107:12028-12032.
- Akhunov, E.D., Akhunova A.R., Anderson O.D., Anderson J.A., Blake N., Clegg M.T., Coleman-Derr D., Conley E.E., Crossman C.C., Deal K.D., Dubcovsky J., Gill B.S., Gu Y.Q., Hadam J., Heo H., Huo N., Lazo G.R., Luo M.-C., Ma Y.Q., Matthews D.E., McGuire P.E., Morrell P.L., Qualset C.O., Renfro J., Tabanao D., Talbert L.E., Tian C., Toleno D.M., Warburton M.L., You F.M., Zhang W.J., and Dvorak J. (2010). Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics. (In press).
- Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL. (2010). Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods.
- Betancur Lissete, Singh Bir, Rapp Ryan A., Wende Jonathan F., Marks M. David, Roberts Alison W., Haigler Candace H. (2010). Phylogenetically Distinct Cellulose Synthase Genes Support Secondary Wall Thickening in Arabidopsis Shoot Trichomes and Cotton Fiber. J. Integrative Plant Biol. 52: 205-220.
- Berman, J. 2010. News and Views: Evolutionary genomics: When abnormality is beneficial. Nature 468, 183-184.
- Covington, E.D., C.B. Gelbmann, N.J. Kotloski and J.A. Gralnick. 2010. An essential role for UshA in processing of extracellular flavin electron shuttles by Shewanella oneidensis. Mol Microbiol. 78(2):519-32.
- Chen, H., P. L. Morrell, D. M. Toleno, K. E. Lundy, and M. T. Clegg. 2010. Allele-specific PCR can improve the efficiency of experimental resolution of heterozygotes in resequencing studies. Molecular Ecology Resources. 10 (4): 647-658.
- Chen, W.-P., Yang, X.-Y., Hegeman, A. D., Gray, W. M., and Cohen, J. D. (2010). Microscale analysis of amino acids using gas chromatography-mass spectrometry after methyl chloroformate derivatization. J. Chromatogr B 878:2199-2208.
- Christian, M, Cermak, T, Doyle, E, Schmidt, C, Zhang, F, Hummel, A, Bogdanove, A, Voytas, DF. (2010). Targeting DNA double-strand breaks with TAL effector nucleases. Genetics, 186:757-761.
- Dabbert, T., R.J. Okagaki, S. Cho, J. Boddu, and G.J. Muehlbauer. 2010. The genetics of barley low-tillering mutants: low number of tillers-1 (lnt1). Theor. Appl. Genet. 121:705-715.
- Desphande R, Sharma S, Hu WS, Verfaillie CM, Myers CL. 2010. A Scalable Approach for Discovering Conserved Active Subnetworks across Species. PLoS Comput Biol. (In press).
- Dominguez, W., and D. J. OSullivan. 2010. Expression of non-coding RNAs in Bifidobacterium longum during yogurt fermentation. 110th ASM annual meeting Abstracts Book, San Diego, CA.
- Bolon, Y-T., B. Joseph, S.B. Cannon, M.A. Graham, B.W. Diers, A.D. Farmer, G.D. May, G.J. Muehlbauer, J.E. Specht, Z.J. Tu, N. Weeks, W.W. Xu, R.C. Shoemaker, and C.P. Vance. 2010. Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. BMC Plant Biology 10:41.
- Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S,Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pal C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.(2010).The genetic landscape of a cell. Science. 327(5964):425-431.
- Gilding, EK and Marks, MD. (2010). Analysis of purified glabra3‐shapeshifter trichomes reveals a role for NOECK in regulating early trichome morphogenic events. Plant Journal 64:304-317.
- Hamblin, M., T. Close, P. Bhat, S. Chao, K. Abraham, T. Blake, W. Brooks, D. Cooper, C. Griffey, P. Hayes, D. Hole, R. Horsley, D. Obert, K. P. Smith, S. Ullrich, G. Muehlbauer, J-L Jannink. 2010. Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Sci. 50:556-566.
- Hammes UZ, Meier S, Dietrich D, Ward JM, Rentsch D. (2010). Functional properties of the Arabidopsis peptide transporters AtPTR1 and AtPTR5. J. Biol, Chem. (In press).
- Haridas S, Gantt JS. (2010). The mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata. FEMS Microbiol Lett. 308:29-34.
- Haynes K, Wanner L, Thill C, Bradeen JM, Miller J, Novy R, Whitworth J, Corsini D, Vinyard B. (2010). Common scab trials of potato varieties and advanced selections at three U.S. locations. Am J Pot Res. 87:261-276
- Hegeman, A. D. (2010). Plant metabolomics--meeting the analytical challenges of comprehensive metabolite analysis. Brief. Funct. Genomics. 9(2),139-48.
- Heilmann, S. M., Davis, H. T., Jader, L. R., Lefebvre, P. A., Sadowsky, M. F., Schendel, F. J., von Keitz, M. G., and K. J. Valentas. (2010). Hydrothermal carbonization of microalgae. Biomass and Bioenergy. 34: 875-882.
- Hou, Y, Rajagopal, J, Irwin, PA, Voytas, DF. (2010). Retrotransposon vectors for gene delivery in plants. Mobile DNA 1:19.
- Huang Y, Li CY, Pattison DL, Gray W, Park S, Gibson SI. (2010). SUGAR INSENSITIVE3, a RING E3 ligase, is a new player in plant sugar response. Plant Physiol. 152: 1889-1900
- Hunt, K.A., J.M. Flynn, B. Naranjo, I.D. Shikhare and J.A. Gralnick. 2010. Substrate-level phosphorylation is the primary source of energy conservation during anaerobic respiraton of Shewanella oneidensis strain MR-1. J Bacteriol. Jul; 192(13):3345-51.
- Glynn, N. C., Dixon, L. J., Castlebury, L. A., Szabo, L. J., Comstock, J. C. 2010. PCR assays for the sugarcane rust pathogens Puccinia kuehnii and P. melanocephala and detection of a SNP associated with geographical distribution in P. kuehnii. Plant Pathology 59:703-711.
- Hamblin, M.T., T. Close, P. Hayes, S. Chao, G.J. Muehlbauer, J. Abraham, and J-L. Jannink. 2010. Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Sci. 50:556-566.
- Ishimaru, C. A., T. Lansdell, J. Gross, J. Clardy, T. H. Smits, and B. Duffy. 2010. Pantocin A antibiotic produced by Pantoea vagans C9-1: Chemical and genetic characterization. Phytopathology. 100:S54. (Abstract).
- Jia, H., B. Millett, S. Cho, H. Bilgic, K.P. Smith, and G.J. Muehlbauer. 2010. Transcriptome analysis of three barley near-isogenic line pairs carrying contrasting alleles for different Fusarium head blight resistance QTLs. Functional & Integrative Genomics. DOI 10.1007/s10142-010-0192-1.
- Jin, Y., Szabo, L.J., Carson, M. 2010. Century-old mystery of Puccinia striiformis life history solved with the identification of Berberis as an alternate host. Phytopathology 100:432-435.
- Johnson, E.T., D.B. Baron, B. Naranjo, D.R. Bond, C. Schmidt-Dannert and J.A. Gralnick. 2010. Light-driven proton pumping in an engineered bacterium enhances survival and electricity production. Appl Environ Microbiol. Jul; 76(13):4123-9.
- Kamber , T., T. Lansdell, T. H. Smits, V. O. Stockwell, C. Ishimaru, and B. Duffy. 2010. Characterization of the antibacterial peptide herbicolin I biosynthetic operon in the fire blight biocontrol agent Pantoea vagans C9-1. Phytopathology 100:S59 (Abstract).
- Kang, H.-G., Oh, C.-S., Sato, M., Katagiri, F., Glazebrook, J., Takahashi, H., Kachroo, P., Martin, G. B., and Klessig, D. F. (2010). Endosome-associated CRT1 functions early in R (resistance) gene-mediated defense signaling. Plant Cell 22, 918-936.
- Liu, J., Allan, D.L., Vance, C.P. 2010. Systemic Signaling and Local Sensing of Phosphate in Common Bean: Cross-Talk Between Photosynthate and MicroRNA399. Molecular Plant. 3(2):428-437.
- Lee, J-H., and D. J. OSullivan. 2010. Secretion of pure tagatose by a lacC mutant of Lactococcus lactis during growth on lactose. 110th ASM annual meeting Abstracts Book, San Diego, CA.
- Lee, J-H., X. Li, and D. J. OSullivan. 2010. Transcriptional analysis of a very broad spectrum lantibiotic produced by Bifidobacterium longum DJO10A. ADSA annual meeting Abstracts Book, Denver, CO.
- Lin JY, Stupar RM, Hans C, Hyten DL, Jackson SA. (2010). Structural and functional divergence of a 1-MMb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris. Plant Cell. 22: 2545-2561.
- Lysoe, E., Pasquali, M., Breakspear, A., and Kistler, H.C. Posted online on 29 Sept 2010. 201x. The transcription factor FgStuAp influences spore development, pathogenicity and secondary metabolism in Fusarium graminearum. Molecular Plant-Microbe Interactions.
- Kim Y.C., Udeshi N.D., Balsbaugh J.L., Shabanowitz J. Hunt D.F., Olszewski N.E. (2010). O-GlcNAcylation of the Plum pox virus capsid protein catalyzed by SECRET AGENT: characterization of O-GlcNAc sites by electron transfer dissociation mass spectrometry. Amino Acids .DOI: 10.1007/s00726-010-0706-0.
- Ma L.-J., van der Does, C., Borkovich, K., Coleman, J., Daboussi, M.-J., Di Pietro, A., Dufresne, M., Freitag, M., Grabherr, M., Henrissat, B., Houterman, P.M., Kang, S., Shim, W.-B., Woloshuk, C., Xie, X., Xu, J.-R., Antoniw, J., Baker, S.E., Bluhm, B.H., Breakspear, A., Brown, D., Butchko, R., Chapman, S., Coulson, R., Coutinho, P.M., Danchin, E., Diener, A., Gale, L.R., Gardiner, D., Goff , S., Hammond-Kosack, K., Hilburn, K., Hua-Van, A., Jonkers, W., Kazan, K., Kodira, C., Koehrsen, M., Kumar, L., Lee, Y.-H., Li, L., Manners, J., Miranda-Saavedra, D., Mukherjee, M., Park, G., Park, J., Park, S.-Y., Proctor, R., Regev, A., Ruiz-Roldan, C., Sain, D., Sakthikumar, S., Sykes, S., Schwartz, D., Turgeon, B.G., Wapinski, I., Yoder, O.., Young, S., Zeng, Q., Zhou, S., Galagan, J., Cuomo, C., Kistler, H.C. and Rep, M. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464: 367-373.
- Malvick D., Syverson R., Mollov D., and Ishimaru C. A. 2010. Goss's bacterial blight and wilt of corn caused by Clavibacter michiganensis subsp. nebraskensis occurs in Minnesota. Plant Disease 94: 1064.
- Massman, J., B. Cooper, R. Horsley, S. Neate, R. Dill-Macky, S. Chao, Y. Dong, P. Schwarz, G.J. Muehlbauer and K.P. Smith. 2010. Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm. Mol. Breeding.
- McGinnis, E. E., M. H. Meyer and A. G. Smith. 2010. Sweet and Sour: A Scientific and Legal Look at Herbicide-Tolerant Sugar Beet. Plant Cell 22: 1653-1657.
- Mergoum, M. K.D. Glover, J.A. Anderson, D. Gigax, J. Berg, P.K. Singh, J.K. Ransom, and P.J. Isakson. 2010. Development and agronomic performance of transgenic roundup ready spring wheat in the North Central Plains of the United States. Agron J. 102:1462-1467.
- Olszewski N.E., West C.M., Sassi S.O., Hartweck L.M. (2010). O-GlcNAc protein modification in plants: Evolution and function. Biochim Biophys Acta 1800: 49-56.
- Pandey G, Zhang B, Chang AN, Myers CL, Zhu J, Kumar V, Schadt EE. 2010. An integrative multi-network and multi-classifier approach to predict genetic interactions. PLoS Comput Biol. 6(9).
- Powers, JS. and P. Tiffin. 2010. Legumes explain more variation in plant traits than leaf habit in 87 Costa Rican tropical dry forest tree species. Functional Ecology. 24: 927-936.
- Pumplin N, Mondo SJ, Topp S, Starker CG, Gantt JS, Harrison MJ. (2010). Medicago truncatula Vapyrin is a novel protein required for arbuscular mycorrhizal symbiosis. Plant J. 61:482-94.
- Sander, JD, Dahlborg, EJ, Goodwin, MJ, Cade, L, Zhang, F, Cifuentes, D, Curtin, SJ, Blackburn, J, Thibodeau-Beganny, S, Qi, Y, Pierick, CJ, Hoffman, E, Maeder, ML, Khayter, C, Reyon, D, Dobbs, D, Langenau, DM, Stupar, RM, Giraldez, AJ, Voytas, DF, Peterson, RT, Yeh, J-RJ, Joung, JK. 2010. Context-dependent assembly (CoDA): efficient selection-free engineering of zinc-finger nucleases. Nature Methods. (In press).
- Sander, JD, Maeder, ML, Reyon, D, Voytas, DF, Joung, JK, Dobbs, D. (2010). ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res., 38:W462-468.
- Sander, JD, Reyon, D, Maeder, ML, Foley, JE, Thibodeau-Beganny, S, Li, X, Regan, MR, Dahlborg, E, Goodwin, MJ, Fu, F, Voytas, DF, Joung, JK, Dobbs, D. (2010). Predicting the success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. BMC Bioinformatics 11:543.
- Sato, M., Tsuda, K., Wang, L., Coller, J., Watanabe, Y., Glazebrook, J., and Katagiri, F. (2010). Network modeling reveals prevalent negative regulatory relationships between signaling sectors in Arabidopsis immune signaling PLoS Pathog. 6(7), e1001011.
- Sbabou, L., Bucciarelli, B., Miller, S.S., Liu, J., Brhada, F., Filali-Maltouf, A., Allan, D., Vance, C.P. 2010. Molecular Analysis of SCARECROW Genes Expressed in White Lupin Cluster Roots. Journal of Experimental Botany. 61(5):1351-1363
- Schlatter, D. C., Samac, D. A., Tesfaye, M., and Kinkel, L. L. 2010. A rapid and specific method for quantifying Streptomyces competitive dynamics in complex soil communities. Appl. Environ. Microbiol. 76:2009-2012.
- Schweiger, W., J. Boddu, S. Shin, B. Poppenberger, F. Berthiller, M. Lemmens, G.J. Muehlbauer, and G. Adam. 2010. Validation of a candidate deoxynivalenol-inactivating UDP-glucosyltransferase from barley by heterologous expression in yeast. Mol. Plant-Microbe Interact. 23:977-986.
- Seffernick, J.L., E. Reynolds, A.A. Federov, E. Federov, S.C. Almo, M.J. Sadowsky, and L.P. Wackett. (2010). X-ray structure and mutational analysis of the atrazine chlorohydrolase TrzN. J. Biol. Chem. 285:30606-30614.
- Seffernick, J.L., A.G. Dodge, M.J. Sadowsky, J.A. Bumpus, and L.P. Wackett. (2010). Bacterial ammeline metabolism by guanine deaminase. J. Bacteriol. 192:1106-1112.
- Selmecki, A.M., Forche, A., and J. Berman. 2010. Genomic Plasticity of the Human Fungal Pathogen Candida albicans. Eukaryotic Cell. 9(7):991-1008.
- Severin, A.J., Peiffer, G., Xu, W.W., Hyten, D.L., Bucciarelli, B., O'Rourke, J.A., Grant, D.M., Farmer, A.D., May, G.D., Vance, C.P., Shoemaker, R.C., Stupar, R.M., Bolon, Y. 2010. An integrative approach to genomic introgression mapping. Plant Physiology.
- Severin AJ, Peiffer G, Xu WW, Hyten DL, Bucciarelli B, O'Rourke JA, Bolon YT, Grant D, Farmer AD, May GD, Vance CP, Shoemaker RC, Stupar RM. (2010). An integrative approach to genomic introgression mapping. Plant Physiol. 154: 3-12.
- Severin, A.J., Woody, J.L., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2010. RNA-Seq Atlas of Glycine max: A Guide to the Soybean Transcriptome. Biomed Central (BMC). Plant Biology. 10:610.
- Severin, A., J.L. Woody, Y-T. Bolon, B. Joseph, B.W. Diers, A.D. Farmer, G.J. Muehlbauer, R. Nelson, D. Grant, J.E. Specht, M.A. Graham, S.B. Cannon, G.D. May, C.P. Vance, and R.C. Shoemaker. 2010. RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. BMC Plant Biology. 10:160.
- Simsek, S., K.L. Whitney, J.-B. Ohm, J. Anderson, and M. Mergoum. 2010. Refrigerated dough quality: effect of environment and genotypes of hard red spring wheat. J Food Sci. Smith, K.P., Rasmusson, D.C. Schiefelbein, E. Wiersma, J.J. Wiersma, J. V. Budde, A.Dill-Macky, R. Steffenson, B. 2010. Registration of Rasmusson Barley 2010. J. Plant Reg. 4:164-167.
- St. Pierre, S., C. Gustus, B.J. Steffenson, R. Dill-Macky , K.P. Smith. 2010. Mapping net form net blotch and septoria speckled leaf blotch resistance loci in barley. Phytopathology. 100:80-84.
- Smits, T. H.M., F. Rezzonico, T. Kamber, A. Goesmann, C. A. Ishimaru, V. O. Stockwell, J. E. Frey, and B. Duffy. 2010. The genome sequence of the biocontrol agent Pantoea vagans strain C9-1. J. Bacteriol.
- Smits, T.H., F. Rezzonico, T. Kamber, C. A. Ishimaru, J. E. Frey, A. Goesmann, V. O. Stockwell, and B. Duffy. 2010. Complete genome sequence of Pantoea vagans biocontrol strain C9-1. Phytopathology. 100:S120. (Abstract).
- Springer NM (2010) Shaping a better rice plant. 42: 475-476.
- Springer NM (2010) Isolation of Plant DNA for PCR and Genotyping Using Organic Extraction and CTAB. Cold Spring Harb Protoc. 2010(11):pdb.prot5515.
- Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM. Published in Advance October 29, 2010. Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor. Genome Research., doi:10.1101/gr.109165.110
- Sun Y, Reinders A, LaFleur KR, Mori T, Ward JM. (2010). Transport activity of rice sucrose transporters OsSUT1 and OsSUT5. Plant Cell Physiol. 51:114-122.
- Swanson-Wagner, R.A., S.R. Eichten, S. Kumari, P. Tiffin, J.C., Stein, D. Ware, and N.M. Springer. 2010. Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor. Genome Research. (In press).
- Stupar RM. (2010). Into the wild: The soybean genome meets its undomesticated relative. Proc Natl Acad Sci USA. (In press).
- Syverson, R. L. and C. A. Ishimaru. 2010. Forward and reverse genetic approaches for functional analyses of Clavibacter michiganensis subsp. Sepedonicus Phytopathology. 100:S124. (Abstract).
- Toyoda, M, K. Jitsumori, B. Mikami, L.P. Wackett, T. Kurihara, and N. Esaki. (2010). Crystallization and preliminary X-ray analysis of L-azetidine-2-carboxylate hydrolase from Pseudomonas sp. strain 2AC. Acta Crystallographica Section F. 66:801-804.
- Tsilo, T.J., J-B. Ohm, G.A. Hareland, and J.A. Anderson. 2010. Association of size-exclusion HPLC of endosperm proteins with dough mixing and breadmaking characteristics in a recombinant inbred population of hard red spring wheat. Cereal Chem. 87:104 111.
- Tsilo, T.J., G.A. Hareland, S. Simsek, S.M. Chao, and J.A. Anderson. 2010. Genome mapping of kernel characteristics in hard red spring wheat breeding lines. Theor. Appl. Genet. 121:717-730.
- Tsilo, T., Y. Jin, and J.A. Anderson. 2010. Identification of flanking markers for the stem rust resistance gene Sr6 in wheat. Crop Sci. 50:1967-1970.
- Tsilo, T., G.A. Hareland, S. Chao, and J.A. Anderson. 2011. Genetic mapping and QTL analysis of flour color and milling yield related traits using recombinant inbred lines in hard red spring wheat. Crop Sci. 51:1-10.
- Tsuda, K. and Katagiri, F. (2010). Comparing signaling mechanisms engaged in pattern-triggered and effector-triggered immunity. Curr. Opin. Plant Biol. 13, 459-465.
- Valdes-Lopez, O., Yang, S.H., Aparicio-Fabre, R., Graham, P.H., Reyes, J., Vance, C.P., Hernandez, G. 2010. MicroRNA Expression Profile in Common Bean (Phaseolus vulgaris) under Nutrient Deficiency Stresses and Manganese Toxicity. New Phytologist. 187(3):805-818.
- Vandersluis B, Bellay J, Musso G, Costanzo M, Papp B, Vizeacoumar FJ, Baryshnikova A, Andrews B, Boone C, Myers CL. Genetic interactions reveal the evolutionary trajectories of duplicate genes. 2010. Mol Syst Biol. 6:429.
- Wackett, L.P. (2010). Engineering microbes to produce biofuels. Curr. Op. Biotech. Nov 9. (Epub ahead of print)
- Wang, B.L., Tang, X.Y., Cheng, L.Y., Zhang, A.Z., Zhang, W.H., Zhang, F.S., Liu, J.Q., Cao, Y., Allan, D.L., Vance, C.P., Shen, J.B. 2010. Nitric Oxide is Involved in Phosphorus Deficiency-Induced Cluster-Root Development and Citrate Exudation in White Lupin. New Phytologist. 187(4):1112-1123.
- Wang, Y., Liu, W., Hou, Z., Wang, C., Zhou, X., Jonkers, W., Ding, S., Kistler, H. C. and Xu, J.-R.. Posted online on 26 Aug 2010. 201x. A novel transcriptional factor important for pathogenesis and ascosporogenesis in Fusarium graminearum. Molecular Plant-Microbe Interactions.
- Waugh, R., D. Marshall, B. Thomas, J. Comadran, J. Russell, T. Close, N. Stein, P. Hayes, G. Muehlbauer, J. Cockram, D. OSullivan, I. Mackay, A. Flavell, AGOUEB, BarleyCAP, and L. Ramsay. 2010. Whole-genome association mapping in elite inbred crop varieties. Genome. 53:967-972.
- Wicker J, Fenner K, Ellis L, Wackett L, Kramer S. (2010). Predicting Biodegradation Products and Pathways: A Hybrid Knowledge-Based and Machine Learning Based Approach Bioinformatics. 2010 Mar 15. 26(6):814-21.
- Wicker, J., K. Fenner, L.B.M. Ellis, L.P. Wackett and S. Kramer. (2010). Predicting biodegradation products and pathways: A hybrid knowledge-based and machine learning based approach. Bioinformatics. 26: 814-821.
- Whitaker VM, Bradeen JM, Debener T, Biber A, Hokanson SC. (2010). Rdr3, a novel locus conferring black spot disease resistance in tetraploid rose: genetic analysis, LRR profiling, and SCAR marker development. Theor Appl Genet . 120:573-585
- Zhou Y., and Ni, M. (2010). SHB1 truncations and mutations alter its association with a signaling protein complex. Plant Cell 22. 703-715.
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: The Microbial and Plant Genomics Institute (MPGI) membership consists of 64 faculty from 4 colleges: CFANS, CBS, IT, and AHC. MPGI funding supports salaries for Professor M. David Marks and Principal Office and Administrative Specialist, Sandesh Nicol. MPGI travel awards enabled 13 graduate students and 6 postdoctoral researchers from 15 university-wide labs to attend meetings to present their research and interact with scientists. MPGI funded three single semester bridging grants for graduate students of MPGI members who demonstrated financial need. The award recipients were: Yiping Qi (Fumi Katagiri, advisor), Xiaodong Sun (Carolyn Silflow, advisor) and Tian Hui (John Ward, advisor). For the 2008-2010 academic years, MPGI awarded two full year Research Assistantships for outstanding 3rd, 4th or 5th year Ph.D. candidates working in microbial or plant genomics. Award recipients were: Katie Ballering (Gary Dunny, advisor) and Yun Zhou (Min Ni, advisor). MPGI coordinated and sponsored a fall seminar series on the topic of "Genomics, Evolution, and Association Mapping" hosted by faculty members Nevin Young, Michael Sadowsky, Peter Tiffin and Ruth Shaw. The series also served as a one-credit course (PBIO5960-001) for several graduate students and Post Docs. Each visiting scientist chose a paper for students to read and critique. After presenting a seminar, the speaker met with students for discussion. Speakers for 2009 included: Sergey Nuzhdin (USC), Ashlee Earl (Broad Institute), Tony Long (UC-Irvine), Ana Caicedo (UMass-Amherst) and Richard Clark (Univ. Utah). Other seminars presented by MPGI: The NAS Lectureship Series features research by National Academy of Sciences members. Prominent scientists, particularly in the field of microbial and plant sciences, are invited to campus to give seminars, discuss research, and interact with students, faculty, and the public. NAS speakers in 2009 were: Jeffrey Palmer (Indiana Univ.-Bloomington) and Jasper Rine (UC-Berkley). The Leading-Edge Technologies Seminars highlight advanced techniques or their applications in the fields of microbial and plant genomics. Researchers who have developed or significantly adapted a technique are invited to give a seminar, meet with faculty, staff, and students, and provide the theoretical principles underlying the technique. Presenters for 2009 were: Richard Martin (AAT Tech), Vinayak Kapatral (IG), William Blank (IG). The Biweekly colloquia series (Spring 2009) has allowed MPGI faculty and members of their lab to present and discuss information on their current research. These seminars have expanded opportunities for interdisciplinary connections with other University researchers. PARTICIPANTS: Members of the MPGI are faculty who are interested in the successful development and application of genomics and the resulting societal and environmental impact. The 64 members of MPGI are faculty from departments throughout four colleges at the University of Minnesota: The College of Food, Agricultural, and Natural Resource Sciences (CFANS), the College of Biological Sciences (CBS), the Institute of Technology (IT), and the Academic Health Center (AHC). MPGI directly supports the salary of faculty member M. David Marks, a functional genomics researcher in plant biology, plus support staff member Sandesh Nicol who is responsible for management and administration of several MPGI seminar series: the National Academy of Sciences Lectureship Seminars, the Leading Edge Technologies Seminars, the Noon time Colloquia, the MPGI Course Seminar series, plus the annual MPGI Retreat. MPGI has provided training and professional development for graduate students and postdoctoral researchers by supporting either their attendance at meetings to present research findings, or their travel to other educational institutions for training purposes. The Microbial and Plant Genomics Institute has provided two full year research assistantships for outstanding graduate students as well as three single semester bridging grants. TARGET AUDIENCES: Within the University community, the Institute facilitates crosscutting communications among faculty engaged in diverse areas of genomics research. With the sponsorship of retreats and seminar series, MPGI supports the dissemination of scientific knowledge among faculty, students, and staff. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions via its website (www.mpgi.umn.edu) and the seminar series sponsored by the Institute. In addition, a major goal of MPGI is training outstanding students and postdoctoral researchers in this important biological field by providing them with fellowships, research assistantships, and travel awards. These are among the activities designed to bring benefits from genomics to Minnesotans, the nation, and the world. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The Microbial and Plant Genomics Institute (MPGI) promotes advances in microbial and plant genomics, genomics-enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multi-disciplinary interchange of ideas and applications of cutting-edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. The scientific aim of the Institute is to enhance the development of functional and translational genomics concomitantly with the expansion of bioinformatics capabilities and the development of specialized instrumentation. Within the University community, the Institute facilitates interactions among faculty engaged in diverse areas of genomics research by promoting understanding of microbial and plant genomics, and providing access to genomics-related technologies. Cooperation among MPGI members helps to assure a strong basis for education in the disciplines of the basic agricultural, environmental, and health sciences. The Institute enhances faculty projects by supporting the educational activities of individual grad students and postdoctoral researchers. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions. In addition, assisting in the training of outstanding students in this important biological field is a major goal.
Publications
- Katagiri F, Glazebrook J. Overview of mRNA expression profiling using DNA microarrays. Curr Protoc Mol Biol. 2009 Jan;Chapter 22:Unit 22.4.
- Katagiri F, Glazebrook J. Pattern discovery in expression profiling data. Curr Protoc Mol Biol. 2009 Jan;Chapter 22:Unit 22.5.
- Kauffman C, Karypis G. LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction. Bioinformatics. 2009 Dec 1;25(23):3099-107. Epub 2009 Sep 28.
- Kazlauskas R, Lutz S. Engineering enzymes by 'intelligent' design. Curr Opin Chem Biol. 2009 Feb;13(1):1 2. Epub 2009 Mar 9.
- Kazlauskas RJ, Bornscheuer UT. Finding better protein engineering strategies. Nat Chem Biol. 2009 Aug;5(8):526-9.
- Kaznessis YN. Computational methods in synthetic biology. Biotechnol J. 2009 Oct;4(10):1392-405.
- Ketel C, Wang HS, McClellan M, Bouchonville K, Selmecki A, Lahav T, Gerami-Nejad M, Berman J. Neocentromeres form efficiently at multiple possible loci in Candida albicans. PLoS Genet. 2009 Mar;5(3):e1000400. Epub 2009 Mar 6.
- Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, Barbazuk WB, Springer NM, Schnable PS. 2010. High-Throughput Genetic Mapping of Mutants via Quantitative SNP-typing. Genetics.
- Liu S, Yu LX, Singh RP, Jin Y, Sorrells ME, Anderson JA. Diagnostic and co-dominant PCR markers for wheat stem rust resistance genes Sr25 and Sr26. Theor Appl Genet. 2009 Oct 31. [Epub ahead of print]
- Maeder ML, Thibodeau-Beganny S, Sander JD, Voytas DF, Joung JK. Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays. Nat Protoc. 2009;4(10):1471-501. Epub 2009 Sep 17.
- Magotti P, Ricklin D, Qu H, Wu YQ, Kaznessis YN, Lambris JD. Structure-kinetic relationship analysis of the therapeutic complement inhibitor compstatin. J Mol Recognit. 2009 Nov-Dec;22(6):495-505.
- Mantina M, Chamberlin AC, Valero R, Cramer CJ, Truhlar DG. Consistent van der Waals radii for the whole main group. J Phys Chem A. 2009 May 14;113(19):5806-12.
- Mantina M, Valero R, Truhlar DG. Validation study of the ability of density functionals to predict the planar-to-three-dimensional structural transition in anionic gold clusters. J Chem Phys. 2009 Aug 14;131(6):064706.
- Li Q, Skinner PJ, Ha SJ, Duan L, Mattila TL, Hage A, White C, Barber DL, O'Mara L, Southern PJ, Reilly CS, Carlis JV, Miller CJ, Ahmed R, Haase AT. Visualizing antigen-specific and infected cells in situ predicts outcomes in early viral infection. Science. 2009 Mar 27;323(5922):1726-9.
- Li Q, Smith AJ, Schacker TW, Carlis JV, Duan L, Reilly CS, Haase AT. Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection. J Immunol. 2009 Aug 1;183(3):1975-82. Epub 2009 Jul 13.
- Marenich AV, Cramer CJ, Truhlar DG. Performance of SM6, SM8, and SMD on the SAMPL1 test set for the prediction of small-molecule solvation free energies. J Phys Chem B. 2009 Apr 9; 113(14):4538-43.
- Marenich AV, Cramer CJ, Truhlar DG. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B. 2009 May 7; 113(18):6378-96.
- Marks, M.D., Wenger, J.P., Gilding, E., Jilk, R., and Dixon, R.A. (2009). Transcriptome Analysis of Arabidopsis Wild-Type and gl3-sst sim Trichomes Identifies Four Additional Genes Required for Trichome Development. Mol Plant 2, 803-822.
- Marks, M.D., Tian, L., Wenger, J.P., Omburo, S.N., Soto-Fuentes, W., He, J., Gang, D.R., Weiblen, G.D., and Dixon, R.A. (2009). Identification of candidate genes affecting delta(9)-tetrahydrocannabinol biosynthesis in Cannabis sativa. J Exp Bot 60, 3715-3726.
- Maymon I, Greenboim-Wainberg Y, Sagiv S, Kieber JJ, Moshelion M, Olszewski N, Weiss D. Cytosolic activity of SPINDLY implies the existence of a DELLA-independent gibberellin-response pathway. Plant J. 2009 Jun;58(6):979-88. Epub 2009 Feb 18.
- Mazourek M, Cirulli ET, Collier SM, Landry LG, Kang BC, Quirin EA, Bradeen JM, Moffett P, Jahn MM. The fractionated orthology of Bs2 and Rx/Gpa2 supports shared synteny of disease resistance in the Solanaceae. Genetics. 2009 Aug;182(4):1351-64. Epub 2009 May 27.
- Neiman M, Olson MS, Tiffin P. Selective histories of poplar protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates. New Phytol. 2009 Aug;183(3):740-50. Epub 2009 Jun 29.
- Nies-Kraske E, Schacker TW, Condoluci D, Orenstein J, Brenchley J, Fox C, Daucher M, Dewar R, Urban E, Hill B, Guenaga J, Hoover S, Maldarelli F, Hallahan CW, Horn J, Kottilil S, Chun TW, Folino M, Palmer S, Wiegand A, O'Shea MA, Metcalf JA, Douek DC, Coffin J, Haase A, Fauci AS, Dybul M. Evaluation of the pathogenesis of decreasing CD4(+) T cell counts in human immunodeficiency virus type 1-infected patients receiving successfully suppressive antiretroviral therapy. J Infect Dis. 2009 Jun 1;199(11):1648-56.
- Ning X, Rangwala H, Karypis G. Multi-assay-based structure-activity relationship models: improving structure-activity relationship models by incorporating activity information from related targets. J Chem Inf Model. 2009 Nov;49(11):2444-56.
- Moragianni VA, Cohen JD, Smith SE, Schinfeld JS, Somkuti SG, Lee A, Barmat LI. Outcomes of day-1, day 3, and blastocyst cryopreserved embryo transfers. Fertil Steril. 2009 Oct 6. [Epub ahead of print]
- Mulakala C, Kaznessis YN. Path-integral method for predicting relative binding affinities of protein-ligand complexes. J Am Chem Soc. 2009 Apr 1;131(12):4521-8.
- Nissinen R, Xia Y, Mattinen L, Ishimaru CA, Knudson DL, Knudson SE, Metzler M, Pirhonen M. The putative secreted serine protease Chp-7 is required for full virulence and induction of a nonhost hypersensitive response by Clavibacter michiganensis subsp. sepedonicus. Mol Plant Microbe Interact. 2009 Jul;22(7):809-19.
- O'Brian MR, Vance CP, Vandenbosch KA. Legume focus: model species sequenced, mutagenesis approaches extended, and debut of a new model. Plant Physiol. 2009 Nov;151(3):969.
- Oppegard LM, Hamann BL, Streck KR, Ellis KC, Fiedler HP, Khodursky AB, Hiasa H. In vivo and in vitro patterns of the activity of simocyclinone D8, an angucyclinone antibiotic from Streptomyces antibioticus. Antimicrob Agents Chemother. 2009 May;53(5):2110-9. Epub 2009 Mar 9.
- O'Rourke JA, Nelson RT, Grant D, Schmutz J, Grimwood J, Cannon S, Vance CP, Graham MA, Shoemaker RC. Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response. BMC Genomics. 2009 Aug 13; 10:376.
- Pan JJ, May G. Fungal-fungal associations affect the assembly of endophyte communities in maize (Zea mays). Microb Ecol. 2009 Oct;58(3):668-78. Epub 2009 Jun 12.
- Pandey G, Myers CL, Kumar V. Incorporating functional inter-relationships into protein function prediction algorithms. BMC Bioinformatics. 2009 May 12;10:142.
- McNeil, K.J., and A.G. Smith. 2009. A glycine-rich protein that facilitates exine formation during tomato pollen development. Planta, accepted.
- Mielke SL, Truhlar DG. Improved methods for Feynman path integral calculations of vibrational-rotational free energies and application to isotopic fractionation of hydrated chloride ions. J Phys Chem A. 2009 Apr 23; 113(16):4817-27.
- Miller MA, Weibel C, Ferguson D, Landry ML, Kahn JS. WU polyomavirus in patients infected with HIV or hepatitis C virus, Connecticut, USA, 2007. Emerg Infect Dis. 2009 Jul;15(7):1095-7.
- Miller SR, Schultz NE, Truhlar DG, Leopold DG. A study of the ground and excited states of Al3 and Al3(-). II. Computational analysis of the 488 nm anion photoelectron spectrum and a reconsideration of the Al3 bond dissociation energy. J Chem Phys. 2009 Jan 14; 130(2):024304.
- Millett BP, Mollov DS, Iorizzo M, Carputo D, Bradeen JM. Changes in disease resistance phenotypes associated with plant physiological age are not caused by variation in R gene transcript abundance. Mol Plant Microbe Interact. 2009 Mar;22(3):362-8.
- Mitri C, Jacques JC, Thiery I, Riehle MM, Xu J, Bischoff E, Morlais I, Nsango SE, Vernick KD, Bourgouin C. Fine pathogen discrimination within the APL1 gene family protects Anopheles gambiae against human and rodent malaria species. PLoS Pathog. 2009 Sep;5(9):e1000576. Epub 2009 Sep 11.
- Murphy RL, Autran B, Katlama C, Brucker G, Debre P, Calvez V, Clotet B, Clumeck N, Costagliola D, Deeks SG, Dorrell L, Gatell J, Haase A, Klein M, Lazzarin A, McMichael AJ, Papagno L, Schacker TW, Wain Hobson S, Walker BD, Youle M. A step ahead on the HIV collaboratory. Science. 2009 Jun 5;324(5932):1264-5.
- Myers CL, Chiriac C, Troyanskaya OG. Discovering biological networks from diverse functional genomic data. Methods Mol Biol. 2009;563:157-75.
- Negi S, Sukumar P, Liu X, Cohen JD, Muday GK. Genetic dissection of the role of ethylene in regulating auxin-dependent lateral and adventitious root formation in tomato. Plant J. 2009 Sep 29. [Epub ahead of print]
- Piasecki BP, Silflow CD. The UNI1 and UNI2 genes function in the transition of triplet to doublet microtubules between the centriole and cilium in Chlamydomonas. Mol Biol Cell. 2009 Jan;20(1):368-78. Epub 2008 Nov 12.
- Pang, Y.Z., Wenger, J.P., Saathoff, K., Peel, G.J., Wen, J.Q., Huhman, D., Allen, S.N., Tang, Y.H., Cheng, X.F., Tadege, M., et al. (2009). A WD40 Repeat Protein from Medicago truncatula Is Necessary for Tissue-Specific Anthocyanin and Proanthocyanidin Biosynthesis But Not for Trichome Development. Plant Physiol 151, 1114-1129.
- Parekh VV, Lalani S, Kim S, Halder R, Azuma M, Yagita H, Kumar V, Wu L, Kaer LV. PD-1/PD-L blockade prevents anergy induction and enhances the anti-tumor activities of glycolipid-activated invariant NKT cells. J Immunol. 2009 Mar 1;182(5):2816-26.
- Park JH, Ha HJ, Lee WK, Genereux-Vincent T, Kazlauskas RJ. Molecular basis for the stereoselective ammoniolysis of N-alkyl aziridine-2-carboxylates catalyzed by Candida antarctica lipase B. Chembiochem. 2009 Sep 4;10(13):2213-22.
- Piotrowska Z, Vazquez M, Shapiro ED, Weibel C, Ferguson D, Landry ML, Kahn JS. Rhinoviruses are a major cause of wheezing and hospitalization in children less than 2 years of age. Pediatr Infect Dis J. 2009 Jan;28(1):25-9.
- Ramirez NE, Wang P, Lejeune J, Shipitalo MJ, Ward LA, Sreevatsan S, Dick WA. Effect of tillage and rainfall on transport of manure-applied Cryptosporidium parvum oocysts through soil. J Environ Qual. 2009 Oct 29;38(6):2394-401. Print 2009 Nov-Dec.
- Ramakrishnan MA, Tu ZJ, Singh S, Chockalingam AK, Gramer MR, Wang P, Goyal SM, Yang M, Halvorson DA, Sreevatsan S. The feasibility of using high resolution genome sequencing of influenza a viruses to detect mixed infections and quasispecies. PLoS One. 2009 Sep 22;4(9):e7105.
- Sadowsky MJ, Koskinen WC, Bischoff M, Barber BL, Becker JM, Turco RF. Rapid and complete degradation of the herbicide picloram by Lipomyces kononenkoae. J Agric Food Chem. 2009 Jun 10;57(11):4878-82.
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- Janagama HK, Senthilkumar TM, Bannantine JP, Rodriguez GM, Smith I, Paustian ML, McGarvey JA, Sreevatsan S. Identification and functional characterization of the iron-dependent regulator (IdeR) of Mycobacterium avium subsp. paratuberculosis. Microbiology. 2009 Nov;155(Pt 11):3683-90. Epub 2009 Aug 14.
- Jia H, Cho S, Muehlbauer GJ. Transcriptome analysis of a wheat near-isogenic line pair carrying Fusarium head blight-resistant and -susceptible alleles. Mol Plant Microbe Interact. 2009 Nov;22(11):1366-78.
- Jiang S, Lee JH, Kim MG, Myung NV, Fredrickson JK, Sadowsky MJ, Hur HG. Biogenic formation of As-S nanotubes by diverse Shewanella strains. Appl Environ Microbiol. 2009 Nov;75(21):6896-9. Epub 2009 Aug 28.
- Jindal N, Chander Y, de Abin M, Sreevatsan S, Stallknecht D, Halvorson DA, Goyal SM. Amplification of four genes of influenza A viruses using a degenerate primer set in a one step RT-PCR method. J Virol Methods. 2009 Sep;160(1-2):163-6. Epub 2009 May 15.
- Jing Q, Okrasa K, Kazlauskas RJ. Stereoselective hydrogenation of olefins using rhodium-substituted carbonic anhydrase--a new reductase. Chemistry. 2009;15(6):1370-6.
- Jochens H, Stiba K, Savile C, Fujii R, Yu JG, Gerassenkov T, Kazlauskas RJ, Bornscheuer UT. Converting an esterase into an epoxide hydrolase. Angew Chem Int Ed Engl. 2009;48(19):3532-5.
- Johnson ET, Holtzapple E, Schmidt-Dannert C. Combinatorial and evolutionary design of biosynthetic reaction sequences. Adv Enzymol Relat Areas Mol Biol. 2009;76:121-50, 12 p following 150. Review.
- Johnson KJ, Springer NM, Bielinsky AK, Largaespada DA, Ross JA. 2009. Developmental origins of cancer. Cancer Res. 69:6375-6377.
- Johnson, T.J., Logue, C.M., Wannemuehler, Y.M., Kariyawasam, S., Doetkott, C., Debroy, C., White, D.G., and Nolan, L.K. 2009. Examination of the source and extended virulence genotypes of Escherichia coli contaminating retail poultry meat. Foodborne Pathog. Dis. 6:657-667.
- Johnson, T.J., and Nolan, L.K. 2009. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol. Mol. Biol. Rev. 73:750-774. Johnson, T.J. and Nolan, L.K. 2009. Plasmid replicon typing. Methods Mol. Biol. 551:27-35.
- Haun WJ, Danilevskaya O, Meeley RM, Springer NM. 2009. Disruption of Imprinting by Mu Transposon Insertions in the 5' Proximal Regions of the Zea mays Mez1 Locus. Genetics 181:1229-1237.
- Heath KD, Tiffin P. Stabilizing mechanisms in a legume-rhizobium mutualism. Evolution. 2009 Mar;63(3):652-62. Epub 2008 Dec 12.
- Hebert-Magee S, Garvin D, Ahlawat S, Haddad N. Lymphoepithelial cyst of the pancreas with sebaceous differentiation: cytologic diagnosis by fine-needle aspiration. Diagn Cytopathol. 2009 Dec;37(12):937-9.
- Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG. The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics. 2009 Sep 15;25(18):2404-10. Epub 2009 Jun 26.
- Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG. Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data. Methods Mol Biol. 2009;548:273-93.
- Huttlin EL, Chen X, Barrett-Wilt GA, Hegeman AD, Halberg RB, Harms AC, Newton MA, Dove WF, Sussman MR. Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilution. Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17235-40. Epub 2009 Sep 23.
- Henry O, Lopez-Gallego F, Agger SA, Schmidt-Dannert C, Sen S, Shintani D, Cornish K, Distefano MD. A versatile photoactivatable probe designed to label the diphosphate binding site of farnesyl diphosphate utilizing enzymes. Bioorg Med Chem. 2009 Jul 1;17(13):4797-805. Epub 2009 Apr 22.
- Hernandez G, Valdes-Lopez O, Ramirez M, Goffard N, Weiller G, Aparicio-Fabre R, Fuentes SI, Erban A, Kopka J, Udvardi MK, Vance CP. Global changes in the transcript and metabolic profiles during symbiotic nitrogen fixation in phosphorus-stressed common bean plants. Plant Physiol. 2009 Nov; 151(3):1221-38. Epub 2009 Sep 15.
- Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. 2009 Mar;5(3):e1000407. Epub 2009 Mar 20.
- Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG. Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol. 2009 Mar;5(3):e1000322. Epub 2009 Mar 20.
- Ishii S, Sadowsky MJ. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environ Microbiol. 2009 Apr;11(4):733-40. Epub 2009 Feb 19.
- Jacob NM, Kantardjieff A, Yusufi FN, Mulukutla BC, Chuah SH, Yap M, Hu WS. Reaching the depth of the Chinese hamster ovary cell transcriptome. Biotechnol Bioeng. 2009 Oct 30. [Epub ahead of print]
- Jama S, Manivel JC, Abd Alla MD, Stauffer WM. Appendectomy to remember. JTravel Med. 2009 Jul-Aug;16(4):295-6.
- Kilcoyne M, Shah M, Gerlach JQ, Bhavanandan V, Nagaraj V, Smith AD, Fujiyama K, Sommer U, Costello CE, Olszewski N, Joshi L. O-glycosylation of protein subpopulations in alcohol-extracted rice proteins. J Plant Physiol. 2009 Feb 15;166(3):219-32. Epub 2008 Jul 18.
- Kim Y, Cramer CJ, Truhlar DG. Steric effects and solvent effects on SN2 reactions. J Phys Chem A. 2009 Aug 13;113(32):9109-14.
- Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C. DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. 2009 Oct 30. [Epub ahead of print]
- Kuppusamy KT, Ivashuta S, Bucciarelli B, Vance CP, Gantt JS, Vandenbosch KA. Knockdown of CELL DIVISION CYCLE16 reveals an inverse relationship between lateral root and nodule numbers and a link to auxin in Medicago truncatula. Plant Physiol. 2009 Nov;151(3):1155-66. Epub 2009 Sep 29.
- Lau JA, Tiffin P. Elevated carbon dioxide concentrations indirectly affect plant fitness by altering plant tolerance to herbivory. Oecologia. 2009 Aug;161(2):401-10. Epub 2009 Jun 6.
- Lee K, Pan JJ, May G. Endophytic Fusarium verticillioides reduces disease severity caused by Ustilago maydis on maize. FEMS Microbiol Lett. 2009 Jul 10. [Epub ahead of print]
- Lee PC, Yoon Y, Schmidt-Dannert C. Investigation of cellular targeting of carotenoid pathway enzymes in Pichia pastoris. J Biotechnol. 2009 Mar 25;140(3-4):227-33. Epub 2009 Feb 7.
- Li Q, Estes JD, Schlievert PM, Duan L, Brosnahan AJ, Southern PJ, Reilly CS, Peterson ML, Schultz-Darken N, Brunner KG, Nephew KR, Pambuccian S, Lifson JD, Carlis JV, Haase AT. Glycerol monolaurate prevents mucosal SIV transmission. Nature. 2009 Apr 23;458(7241):1034-8. Epub 2009 Mar 4.
- Li Q, Seffernick JL, Sadowsky MJ, Wackett LP. Thermostable cyanuric acid hydrolase from Moorella thermoacetica ATCC 39073. Appl Environ Microbiol. 2009 Nov;75(22):6986-91. Epub 2009 Sep 18.
- Li Q, Skinner PJ, Duan L, Haase AT. A technique to simultaneously visualize virus-specific CD8+ T cells and virus-infected cells in situ. J Vis Exp. 2009 Aug 13;(30). pii: 1561. doi: 10.3791/1561.
- Joshi R, Janagama H, Dwivedi HP, Senthil Kumar TM, Jaykus LA, Schefers J, Sreevatsan S. Selection, characterization, and application of DNA aptamers for the capture and detection of Salmonella enterica serovars. Mol Cell Probes. 2009 Feb;23(1):20-8. Epub 2008 Nov 18.
- Jung HW, Tschaplinski TJ, Wang L, Glazebrook J, Greenberg JT. Priming in systemic plant immunity. Science. 2009 Apr 3;324(5923):89-91.
- Kang J-H, Shi F, Jones AD, Marks MD, and Howe, GA (2009) Distortion of trichome morphology by the hairless mutation of tomato affects leaf surface chemistry. Journal of Experimental Botany in press.
- Kantardjieff A, Jacob NM, Yee JC, Epstein E, Kok YJ, Philp R, Betenbaugh M, Hu WS. Transcriptome and proteome analysis of Chinese hamster ovary cells under low temperature and butyrate treatment. J Biotechnol. 2009 Sep 19. [Epub ahead of print]
- Kantardjieff A, Nissom PM, Chuah SH, Yusufi F, Jacob NM, Mulukutla BC, Yap M, Hu WS. Developing genomic platforms for Chinese hamster ovary cells. Biotechnol Adv. 2009 Nov-Dec;27(6):1028-35. Epub 2009 May 24.
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: The Microbial and Plant Genomics Institute (MPGI) membership consists of 66 faculty from 4 colleges: CFANS, CBS, IT, and AHC. MPGI funding supports salaries for Professor M. David Marks, Principal Office and Admin. Specialist Sandesh Nicol, and Associate Admin. Suzanne Livingston (retired). MPGI travel awards enabled 13 graduate students and 8 postdoctoral researchers from 18 university-wide labs to attend meetings to present their research and interact with scientists. MPGI awarded three single semester bridging grants for graduate students of MPGI members who demonstrated financial need. The award recipients were: Yiping Qi (Fumi Katagiri, advisor), Xiaodong Sun (Carolyn Silflow, advisor) and Tian Hui (John Ward, advisor). MPGI also awarded two grants for proposals for shared equipment. Award recipients were Dan Voytas and Nathan Springer. For the 2008-2010 academic years, MPGI awarded two full year Research Assistantships for outstanding 3rd, 4th or 5th year Ph.D. candidates working in microbial or plant genomics. Award recipients were: Katie Ballering (Gary Dunny, advisor) and Yun Zhou (Min Ni, advisor). MPGI coordinated and sponsored a spring seminar series on the topic of "The Importance of Fungal Biology/Interactions" hosted by faculty member Georgiana May (Ecology, Evolution and Behavior). The series also served as a one-credit course (PBIO5960-002) for several graduate students. Each scientist chose a paper for students to read and critique. After presenting a seminar, the speaker met with students for discussion. Speakers for 2008 included: Francois Lutzoni (Duke Univ.), Marilyn Roossinck (Noble Foundation), Nancy Keller (U of W-Madison), Leah Cowen (U of Toronto) and Sarah Watkinson (Univ. of Oxford). Other seminars presented by MPGI: The NAS Lectureship Series features research by National Academy of Sciences members. Prominent scientists, particularly in the field of microbial and plant sciences, are invited to campus to give seminars, discuss research, and interact with students, faculty, and the public. NAS speakers in 2008 were: Jeff Bennetzen (U of Georgia), Hugo Dooner (Rutgers Univ.), Richard Dixon (Noble Foundation) and Jim Tumlinson (Penn State Univ.) The Leading-Edge Technologies Seminars highlight advanced techniques or their applications in the fields of microbial and plant genomics. Researchers who have developed or significantly adapted a technique are invited to give a seminar, meet with faculty, staff, and students, and provide the theoretical principles underlying the technique. Presenters for 2008 were: Amber Volk from Beckman Coulter Inc. The Biweekly colloquia series has allowed MPGI faculty and members of their lab to present and discuss information on their current research. These seminars have expanded opportunities for interdisciplinary connections with other University researchers. MPGI sponsored a one day Mini-symposium titled "Plant Metabolism - Good things made in plants." This was part of the outreach component of the NSF Plant Genome Research Projects. Speakers included Rob Last (Michigan State Univ.), David R. Gang (U of Arizona), Lloyd Sumner (Noble Foundation) and Richard Dixon (Noble Foundation). PARTICIPANTS: Members of the MPGI are faculty who are interested in the successful development and application of genomics and the resulting societal and environmental impact. The 66 members of MPGI are faculty from departments throughout four colleges at the University of Minnesota: The College of Food, Agricultural, and Natural Resource Sciences (CFANS), the College of Biological Sciences (CBS), the Institute of Technology (IT), and the Academic Health Center (AHC). MPGI directly supports the salary of faculty member M. David Marks, a functional genomics researcher in plant biology, plus support staff members Suzanne Livingston (now retired) and Sandesh Nicol who are responsible for management and administration of several MPGI seminar series: the National Academy of Sciences Lectureship Seminars, the Leading Edge Technologies Seminars, the Noon time Colloquia, the MPGI Spring Course Seminars series, plus the annual MPGI Retreat. MPGI has provided training and professional development for graduate students and postdoctoral researchers by supporting either their attendance at meetings to present research findings, or their travel to other educational institutions for training purposes. The Microbial and Plant Genomics Institute has provided two full year research assistantships for outstanding graduate students as well as three single semester bridging grants and two grants for equipment. TARGET AUDIENCES: Within the University community, the Institute facilitates crosscutting communications among faculty engaged in diverse areas of genomics research. With the sponsorship of retreats and seminar series, MPGI supports the dissemination of scientific knowledge among faculty, students, and staff. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions via its website (www.mpgi.umn.edu) and the seminar series sponsored by the Institute. In addition, a major goal of MPGI is training outstanding students and postdoctoral researchers in this important biological field by providing them with fellowships, research assistantships, and travel awards. These are among the activities designed to bring benefits from genomics to Minnesotans, the nation, and the world. PROJECT MODIFICATIONS: MPGI has not had any project modifications in 2008.
Impacts
The Microbial and Plant Genomics Institute (MPGI) promotes advances in microbial and plant genomics, genomics-enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multi-disciplinary interchange of ideas and applications of cutting-edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. The scientific aim of the Institute is to enhance the development of functional and translational genomics concomitantly with the expansion of bioinformatics capabilities and the development of specialized instrumentation. Within the University community, the Institute facilitates interactions among faculty engaged in diverse areas of genomics research by promoting understanding of microbial and plant genomics, and providing access to genomics-related technologies. Cooperation among MPGI members helps to assure a strong basis for education in the disciplines of the basic agricultural, environmental, and health sciences. The Institute enhances faculty projects by supporting the educational activities of individual grad students and postdoctoral researchers. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions. In addition, assisting in the training of outstanding students in this important biological field is a major goal.
Publications
- Karp DR, Carlin S, Cook-Deegan R, Ford DE, Geller G, Glass DN, Greely H, Guthridge J, Kahn J, Kaslow R, Kraft C, Macqueen K, Malin B, Scheuerman RH, Sugarman J. Ethical and practical issues associated with aggregating databases. PLoS Med. 2008 Sep 23;5(9):e190.
- Legrand M, Forche A, Selmecki A, Chan C, Kirkpatrick DT, Berman J. Haplotype mapping of a diploid non-meiotic organism using existing and induced aneuploidies. PLoS Genet. 2008 Jan;4(1):e1. Epub 2007 Nov 20.
- Lewis JM, Mackintosh CA, Shin S, Gilding E, Kravchenko S, Baldridge G, Zeyen R, Muehlbauer GJ. Overexpression of the maize Teosinte Branched1 gene in wheat suppresses tiller development. Plant Cell Rep. 2008 Jul;27(7):1217-25. Epub 2008 Apr 5
- Marks MD, Betancur L, Gilding E, Chen F, Bauer S, Wenger JP, Dixon RA, HaiglerCH. A new method for isolating large quantities of Arabidopsis trichomes for transcriptome, cell wall and other types of analyses. Plant J. 2008 Nov;56(3):483-92. Epub 2008 Aug 4.
- Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, Chua G, Toufighi K, Baryshnikova A, Hayles J, Hoe KL, Kim DU, Park HO, Myers CL, Pandey A, Durocher D, Andrews BJ, Boone C. Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16653-8. Epub 2008 Oct 17.
- Forche A, Alby K, Schaefer D, Johnson AD, Berman J, Bennett RJ. The parasexual cycle in Candida albicans provides an alternative pathway to meiosis for the formation of recombinant strains. PLoS Biol. 2008 May 6;6(5):e110.
- Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. A genomewide functional network for the laboratory mouse. PLoS Comput Biol. 2008 Sep 26;4(9):e1000165.
- Harmon, F., T. Imaizumi, and W.M. Gray. 2008. CUL1 regulates TOC1 protein stability in the Arabidopsis circadian clock. Plant J. 55: 568-579.
- Haun WJ, Springer NM. Maternal and paternal alleles exhibit differential histone methylation and acetylation at maize imprinted genes. Plant J. 2008 Sep 5. [Epub ahead of print]
- Jayapal KP, Philp RJ, Kok YJ, Yap MG, Sherman DH, Griffin TJ, Hu WS. Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor. PLoS ONE. 2008 May 7;3(5):e2097.
- Jones KM, Sharopova N, Lohar DP, Zhang JQ, VandenBosch KA, Walker GC. 2008. Differential response of the plant Medicago truncatula to its symbiont Sinorhizobium meliloti or an exopolysaccharide-deficient mutant. Proc Natl Acad Sci U S A. 105(2):704-9.
- Marsili E, Baron DB, Shikhare ID, Coursolle D, Gralnick JA, Bond DR. Shewanella secretes flavins that mediate extracellular electron transfer. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3968-73. Epub 2008 Mar 3.
- Mehra S, Charaniya S, Takano E, Hu WS. A bistable gene switch for antibiotic biosynthesis: the butyrolactone regulon in Streptomyces coelicolor. PLoS ONE. 2008 Jul 16;3(7):e2724.
- Munkacsi AB, Stoxen S, May G. Ustilago maydis populations tracked maize through domestication and cultivation in the Americas. Proc Biol Sci. 2008 May 7;275(1638):1037-46.
- Qi Y, Katagiri F. Purification of low-abundance Arabidopsis plasma-membrane protein complexes and identification of candidate components. Plant J. 2008 Dec 4. [Epub ahead of print]
- Ren D, Liu Y, Yang KY, Han L, Mao G, Glazebrook J, Zhang S. A fungal-responsive MAPK cascade regulates phytoalexin biosynthesis in Arabidopsis. Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5638-43. Epub 2008 Mar 31.
- Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13.
- Riehle MM, Xu J, Lazzaro BP, Rottschaefer SM, Coulibaly B, Sacko M, Niare O, Morlais I, Traore SF, Vernick KD. Anopheles gambiae APL1 is a family of variable LRR proteins required for Rel1-mediated protection from the malaria parasite, Plasmodium berghei. PLoS ONE. 2008;3(11):e3672. Epub 2008 Nov 7.
- Selmecki A, Gerami-Nejad M, Paulson C, Forche A, Berman J. An isochromosome confers drug resistance in vivo by amplification of two genes, ERG11 and TAC1. Mol Microbiol. 2008 May;68(3):624-41. Epub 2008 Mar 20.
- Spartz, A.K. and W.M. Gray. 2008. Plant hormone receptors: new perceptions. Genes Dev. 22:2139-2148.
- Tsuda K, Sato M, Glazebrook J, Cohen JD, Katagiri F. Interplay between MAMP-triggered and SA-mediated defense responses. Plant J. 2008 Mar;53(5):763-75. Epub 2007 Nov 14. Erratum in: Plant J. 2008 Sep;55(6):1061.
- Zhang, W., H. Ito, M. Quint, H. Huang, L.D. Noel, and W.M. Gray. 2008. Genetic Analysis of CAND1-CULl Interactions in Arabidopsis Supports a Role for CAND1-Mediated Cycling of the SCFTIR1 Complex. Proc. Natl. Acad. Sci. USA. 105: 8470-8475.
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: MPGI membership consists of 65 faculty from 4 colleges: CFANS, CBS, IT, and AHC. MPGI funding supports salaries for Plant Biology Prof. M. D. Marks, Prin. Office/Admin. Spec. S. Nicol, and Assoc. Admin. S. Livingston. MPGI travel awards enabled 11 graduate students and 9 postdoctoral researchers, from 18 university-wide labs, to attend meetings to present their research and interact with scientists. With contributions from CFANS and the Graduate School, MPGI funded graduate student fellowships in the spring semester of 2007 for: Anna Selmecki (J. Berman, advisor) and Carrie Eberle (A. Smith & N. Anderson, co-advisors). For the 2007-08 academic year, MPGI awarded two Research Assistantships for outstanding 3rd or 4th year Ph.D. candidates working in microbial or plant genomics. The award recipients were: Brian Piasecki (C. Silflow, advisor), and Edward Gilding (M. D. Marks, advisor). MPGI coordinated and sponsored a spring seminar series and a one-credit course (PBIO5960-001)
on the topic of "Transport Processes in Plants and Microbes" organized by Assoc. Prof. John Ward, Plant Biology, and Asst. Prof. Jeff Gralnick, Biotechnology Institute. Renowned scientists Julian Schroeder, UC-San Diego; Eric Webb, USC; Andreas Weber, Michigan State U; Dianne Newman, California Institute of Technology; Michael Udvardi, Noble Foundation; and Mary Lou Guerinot, Dartmouth College visited campus over a six-week period (3/20-5/1/07) to present research seminars and participate in the course. Each scientist submitted papers for students to read and critique prior to their arrival on campus, and after presenting a seminar, met with the class for further discussion of their research. Other MPGI seminar series: (A) The NAS Lectureship Series features research by National Academy of Sciences members. Prominent scientists, particularly in the field of microbial and/or plant science, are invited to campus to give seminars, discuss research, and interact with students, faculty,
and the public. The National Academy of Sciences members who presented in 2007 were: Prof. Eugene Nester, U of Washington; Prof. Roy Curtiss, III, , Arizona State U; Prof. Michael Thomashow, Mich State U; and, Dr. Roger Beachy, Pres., Donald Danforth Plant Science Center, St. Louis, MO. (B) The Leading-Edge Technologies Seminars highlight advanced techniques or their applications in the fields of microbial and plant genomics. Researchers who have developed or significantly adapted a technique are invited to give a seminar, meet with faculty, staff, and students, and provide the theoretical principles underlying the technique. Presenters in 2007 were: K. Heidrich and D. Dailey from Illumina Biosciences Corp; G. Hunter, LI-COR Biosciences; and Prof. Wolf Frommer, Carnegie Inst., Stanford U. (C) In the fall of 2007, MPGI held a biweekly colloquia series, "Bioenergy and Biofuels" in which faculty presented their current research on the development of alternative energy sources based on
bioenergy. These well-attended seminars have expanded opportunities for interdisciplinary connections among University researchers, and provide a forum for initiating future collaborations in bioenergy and biofuels.
PARTICIPANTS: Members of the Microbial and Plant Genomics Institute are faculty who are interested in the successful development and application of genomics and the resulting societal and environmental impact. The 65 members of MPGI are faculty from departments throughout four colleges at the University of Minnesota: The College of Food, Agricultural, and Natural Resource Sciences (CFANS), the College of Biological Sciences (CBS), the Institute of Technology (IT), and the Academic Health Center (AHC). MPGI directly supports faculty member M. David Marks, functional genomics researcher in plant biology, plus support staff members Suzanne Livingston and Sandesh Nicol who are responsible for management and administration of several MPGI seminar series: the National Academy of Sciences Lectureship Seminars, the Leading Edge Technologies Seminars, the Bioenergy/Biofuels Colloquia, the MPGI Spring Course Seminars series, plus the annual MPGI Retreat. MPGI has provided training and
professional development for graduate students and postdoctoral researchers by supporting either their attendance at meetings to present research findings, or their travel to other educational institutions for training purposes. With the partnership of the University of Minnesota Graduate School and the College of Food, Agricultural, and Natural Resource Sciences, the Microbial and Plant Genomics Institute has provided two fellowships and two research assistantships for outstanding graduate students and postdoctoral researchers.
TARGET AUDIENCES: Within the University community, the Institute facilitates crosscutting communications among faculty engaged in diverse areas of genomics research. With the sponsorship of retreats and seminar series, MPGI supports the dissemination of scientific knowledge among faculty, students, and staff. Building public awareness about genomics and its applications in a social and ethical context is one of MPGI's outreach functions via its website (http://www.mpgi.umn.edu) and the seminar series sponsored by the Institute. In addition, a major goal of MPGI is training outstanding students and postdoctoral researchers in this important biological field by providing them with fellowships, research assistantships, and travel awards. These are among the activities designed to bring benefits from genomics to Minnesotans, the nation, and the world.
PROJECT MODIFICATIONS: MPGI has not had any project modifications in 2007.
Impacts
The Microbial and Plant Genomics Institute (MPGI) promotes advances in microbial and plant genomics, genomics-enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multi-disciplinary interchange of ideas and applications of cutting-edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. The scientific aim of the Institute is to enhance the development of functional and translational genomics concomitantly with the expansion of bioinformatics capabilities and the development of specialized instrumentation. Within the University community, the Institute facilitates interactions among faculty engaged in diverse areas of genomics research by promoting understanding of microbial and plant genomics, and providing access to genomics-related technologies. Cooperation among MPGI
members helps to assure a strong basis for education in the disciplines of the basic agricultural, environmental, and health sciences. The Institute enhances faculty projects by supporting the educational activities of individual graduate students and postdoctoral researchers. MPGI's outreach functions are centered on building public awareness about genomics and its applications in a social and ethical context. In addition, one of the major goals of the Institute is to assist in the training of outstanding students in this important biological field.
Publications
- Zhao, Y. and D.G. Truhlar. 2007. How well can new-generation density functionals describe protonated epoxides where older functionals fail? Journal of Organic Chemistry 72:295-298.
- Zhao, Y. and D.G. Truhlar. 2007. Size-selective supramolecular chemistry in a hydrocarbon nanoring. Journal of the American Chemical Society 129:8440.
- Zheng, J.J., Y. Zhao, and D.G. Truhlar. 2007. Representative benchmark suites for barrier heights of diverse reaction types and assessment of electronic structure methods for thermochemical kinetics. Journal of Chemical Theory and Computation 3:569-582.
- Zheng, J J., Y. Zhao, and D.G. Truhlar. 2007. Thermochemical kinetics of hydrogen-atom transfers between methyl, methane, ethynyl, ethyne, and hydrogen. Journal of Physical Chemistry A 111:4632-4642.
- Zhou, Y., X.D. Sun, and M. Ni. 2007. Timing of photoperiodic flowering: Light perception and circadian clock. J. Integrative Plant Biology 49:28-34.
- Zlesak, D.C., J.M. Bradeen, and N.O. Anderson. 2007. The use of AFLP markers to resolve clonal origin and integrity in rose, hydrangea, and lily. Floriculture and Ornamental Biotechnology 1:51-60.
- Makarevitch, I., R.M. Stupar, A.L. Iniguez, W. J. Haun, W.B. Barbazulk, S.M. Kaeppler, and N.M. Springer. 2007. Natural variation for Alleles under epigenetic control by the maize chromomethylase Zmet2. Genetics 177:749-760.
- Makarova,K., ASlesarev,YWolf, ASorokin, BMirkin, EKoonin, APavlov, NPavlova, VKaramychev, NPolouchine, VShakhova, , IGrigoriev, YLou, DRohksar, SLucas, KHuang, DGoodstein, THawkins, VPlengvidhya, DWelker, JHughes, YGoh, ABenson, KBaldwin, JLee, IDiaz-Muniz, BDosti, VSmeianov, WWechter, RBarabote, GLorca, EAltermann, R.Barrangou, BGanesan, YXie, HRawsthorne, DTamir, CParker, LMcKay , FBreidt, JBroadbent , RHutkins, DOSullivan , JSteele, GUnlu, MSaier, TKlaenhammer, PRichardson, SKozyavkin, BWeimer, and DMills. 2006. Comparative Genomics of the Lactic Acid Bacteria. PNAS103:15611-616.
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- Gralnick, J.A. and D.K. Newman. 2007. Extracellular respiration. Molecular Microbiology 65:1-11.
- Griffin, T.J., G. Seth, H.W. Xie, S. Bandhakavi, and W.S. Hu. 2007. Advancing mammalian cell culture engineering using genome-scale technologies. Trends in Biotechnology 25:401-408.
- Griffin, T.J., H. Xie, S. Bandhakavi, J. Popko, A. Mohan, J.V. Carlis, and L. Higgins. 2007. iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. J Proteome Res 6:4200-4209.
- Gupta, R., T. Garg, G. Pandey, M. Steinbach and V. Kumar. 2007. Comparative Study of Various Genomic Data Sets for Protein Function Prediction and Enhancements Using Association Analysis. Proceedings of the Workshop on Data Mining for Biomedical Informatics, held in conjunction with SIAM International Conference on Data Mining.
- Sanderfoot, A. 2007. Increases in the number of SNARE genes parallels the rise of multicellularity among the green plants. Plant Physiology 144:6-17.
- Gyenis, L., S.J. Yun, K.P. Smith, B.J. Steffenson, E. Bossolini, M.C. Sanguineti, and G.J. Muehlbauer. 2007. Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross. Genome 50:714-723.
- Haase, A. 2007. The role of apoptosis in CD4 T cell depletion and injury to the mucosal lining in the gut. Journal of Medical Primatology 36:290-290.
- Haun, W.J., S. Laoueille-Duprat, M.J. OConnell, C. Spillane, U. Grossniklaus, A.R. Phillips, S.M. Kaeppler, and N.M. Springer. 2007. Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs. Plant Journal 49:325-337.
- Heath, K.D. and P. Tiffin. 2007. Context dependence in the coevolution of plant and rhizobial mutualists. Proceedings of the Royal Society B-Biological Sciences 274:1905-1912.
- Voth, P.D., B.E. Lockhart, and G. May. 2007. Evolutionary history of the Ustilago maydis virus H1 throughout the Americas. Phytopathology 97:S118-S119.
- van het Hoog, M., T.Rast, M.Martchenko, S.Grindle, D.Dignard, H.Hogues, C.Cuomo, M.Berriman, S.Scherer, B.Magee, M.Whiteway, H.Chibana, A.Nantel, and P.Magee. 2007. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biology 8(4):R52.
- van Leeuwen, H., D.Kliebenstein, M.West, K.Kim, R.vanPoecke, F.Katagiri, R.Michelmore, R.Doerge, and D.Clair. 2007. Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid. Plant Cell 19:2099-2110.
- van Poecke, R.M.P., M. Sato, L. Lenarz-Wyatt, S. Weisberg, and F. Katagiri. 2007. Natural variation in RPS2-mediated resistance among Arabidopsis accessions: correlation between gene expression profiles and phenotypic responses. Plant Cell, DOI 10.1105.tpc.107.053827.
- Voth, P.D., M.A. Turner, B.E. Lockhart, and G. May. 2007. Exclusion phenomenon in Ustilago maydis virus H1: Not all that exclusive. Phytopath. 97:S118-S118.
- Wackett, L.P. 2007. Pathways to discovering new microbial metabolism for functional genomics and biotechnology. Advances in Applied Microbiology, pp. 219-232.
- Weinig, C., M.T. Brock, J.A. Dechaine, and S.M. Welch. 2007. Resolving the genetic basis of invasiveness and predicting invasions. Genetica 129:205-216.
- Weinig, C., J.A. Johnston, C.G. Willis, and J.N. Maloof. 2007. Antagonistic multilevel selection on size and architecture in variable density settings. Evolution 61:58-67.
- Whitaker, V.M., K. Zuzek, S.C. Hokanson, and J.M. Bradeen. 2007. Culturing and long-term storage of virulent races of the rose blackspot pathogen, Diplocarpon rosae Wolf. Acta Horticulturae 751:199-205.
- Whitaker, V.M., S.C. Hokanson, and J. Bradeen. 2007. Distribution of rose black spot (Diplocarpon rosae) genetic diversity in eastern north America using amplified fragment length polymorphism and implications for resistance screening. J. Amer. Soc. for Hort. Science 132:534-540.
- Wlaschin, K.F. and W.S. Hu. 2007. A scaffold for the chinese hamster genome. Biotechnology and Bioengineering 98:429-439.
- Wlaschin, K., and W.S. Hu. 2007. Engineering Cell Metabolism for High Density Cell Culture via Manipulation of Sugar Transport. J. Biotechnol., 131,168-176. Wolf, S.M., J.P. Kahn, and T. Working Grp Genetic. 2007. Genetic testing and the future of disability insurance: Ethics, law & policy. Journal of Law Medicine & Ethics 35:6-32.
- Wright, B.D., P.G. Pardey, C. Nottenburg and B. Koo. 2007. Agricultural Innovation: Economic Incentives and Institutions. Chapter in R.E. Evenson and P. Pingali (eds.). Handbook of Agricultural Economics: Volume 3 Amsterdam: Elsevier.
- Xie, Y., W. Pan, K.S. Jeong, and A. Khodursky. 2007. Incorporating prior information via shrinkage: a combined analysis of genome-wide location data and gene expression data. Statistics in Medicine 26:2258-2275.
- Yan, T., M.J. Hamilton, and M.J. Sadowsky. 2007. High throughput and quantitative procedure for determining sources of Escherichia coli in waterways using host-specific DNA marker genes. Appl. Environ. Microbiol. 73:890896.
- Yan, T. and M.J. Sadowsky. 2007. Determining sources of fecal bacteria in waterways. Environmental Monitoring and Assessment 129:97-106.
- Yee, J.C., M. de Leon Gatti, R.J. Philp, M. Yap, and W.S. Hu. 2007.Genomic and proteome exploration of CHO and hybridoma cells under sodium butyrate treatment. Biotechnol. Bioeng. Published Online: Oct 10 2007, DOI: 10.1002/bit.21665.
- Zhao, Y. and D.G. Truhlar. 2007. Attractive noncovalent interactions in the mechanism of Grubbs second-generation Ru catalysts for olefin metathesis. Organic Letters 9:1967-1970.
- Zeng, Z., J.Y. Wang, L.Z. Zhou, and G. Karypis. 2007. Out-of-core coherent closed quasi-clique mining from large dense graph databases. Acm Transactions on Database Systems 32.
- Zhang, Y., Z.H. Li, and D.G. Truhlar. 2007. Computational requirements for simulating the structures and proton activity of silicaceous materials. Journal of Chemical Theory and Computation 3:593-604.
- Zhang, Y., H. Lin, and D.G. Truhlar. 2007. Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined quantum-mechanical and molecular-mechanical calculations. Journal of Chemical Theory and Computation 3:1378-1398.
- Zhao, Y. and D.G. Truhlar. 2007. Density functionals for noncovalent interaction energies of biological importance. Journal of Chemical Theory and Computation 3:289-300.
- Hernandez, G., M. Ramirez, O. Valdes-Lopez, M. Tesfaye, M.A. Graham, T. Czechowski, A. Schlereth, M. Wandrey, A. Erban, F. Cheung, H.C. Wu, M. Lara, C.D. Town, J. Kopka, M.K. Udvardi, and C.P. Vance. 2007. Phosphorus stress in common bean: Root transcript and metabolic responses. Plant Physiology 144:752-767.
- Heyden, A., H. Lin, and D.G. Truhlar. 2007. Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. Journal of Physical Chemistry B 111:2231-2241.
- Hillyer, J.F., C. Barreau, and K D. Vernick. 2007. Efficiency of salivary gland invasion by malaria sporozoltes is controlled by rapid sporozoite destruction in the mosquito haemocoel. International Journal for Parasitology 37:673-681.
- Holtzapple, E. and C. Schmidt-Dannert. 2007. Biosynthesis of isoprenoid wax ester in Marinobacter hydrocarbonoclasticus DSM 8798: Identification and characterization of isoprenoid coenzyme A synthetase and wax ester synthases. J. Bacteriology 189:3804-3812.
- Horevaj, P., E. Milus, L.R. Gale, and C. Kistler. 2007. Resistance in soft red winter wheat lines to deoxynivalenol and nivalenol chemotypes of Fusarium graminearum. Phytopath. 97:S48-S48.
- Hossler, P., B.C. Mulukutla, and W.S. Hu. 2007. Systems analysis of N-Glycan Processing in Mammalian Cells. PlosOne, 2(8) e713.
- Ishii, S., D.L. Hansen, R.E. Hicks, and M.J. Sadowsky. 2007. Beach sand and sediments are temporal sinks and sources of Escherichia coli in Lake Superior. Environmental Science & Technology 41:2203-2209.
- Ishii, S., K.P. Meyer, and M.J. Sadowsky. 2007. Relationship between phylogenetic groups, genotypic clusters, and virulence gene profiles of Escherichia coli strains from diverse human and animal sources. Applied and Environmental Microbiology 73:5703-5710.
- Jaque, P., A.V. Marenich, C.J. Cramer, and D.G. Truhlar. 2007. Computational electrochemistry: The aqueous Ru3+vertical bar Ru2+ reduction potential. Journal of Physical Chemistry C 111:5783-5799.
- Jasper, A.W., N.E. Schultz, and D.G. Truhlar. 2007. Transferability of orthogonal and nonorthogonal tight-binding models for aluminum clusters and nanoparticles. Journal of Chemical Theory and Computation 3:210-218.
- Jayapal, K.P., W. Lian, F. Glod, D.H. Sherman, and W.S. Hu. 2007. Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans. BMC Genomics 8:229doi:10.1186/1471-2164-8-229.
- Jayapal, K. R., K. F. Wlaschin, , M. G. S. Yap, and W. S. Hu. 2007. Recombinant protein therapeutics from CHO cells - 20 years and counting. Chemical Engineering Progress 103:40-47.
- Kahn, J. 2007. Comments on: Applying justice in clinical trials for diverse population. J. Tilburt, et al. Clinical Trials 4:270-270.
- Kahn, J.P. 2007. Baseball, alcohol and public health. American Journal of Bioethics 7:3-3.
- Kahn, J.P. 2007. Beyond Disclosure: The Necessity of Trust in Biomedical Research, Cleveland Clinic Journal of Medicine, 74(Supplement 2):S49-S50.
- Kahn, J.P. 2007. Organs and stem cells: Policy lessons and cautionary tales. Hastings Center Report 37:11-12.
- Kahn, J. 2007. What Vaccination Programs Mean for Research, The American Journal of Bioethics, 7(3):3-4.
- Kahn, J.P. 2007. Why Public Health and Politics Don't Mix, The American Journal of Bioethics, 7(11): 3-4.
- Kahn, J.P. and S.M. Wolf. 2007. Understanding the role of genetics in disability insurance. Journal of Law Medicine & Ethics 35:5-5.
- Katagiri, F. and M. Sato. 2007. Expression profiles as detailed snapshots of biological states. Transgenic Research 16:399-403.
- Kaznessis, Y.N. 2007. Models for synthetic biology. BMC Syst Biol. 1(1):47.
- Kelly, C.P., C.J. Cramer, and D.G. Truhlar. 2007. Single-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide. Journal of Physical Chemistry B 111:408-422.
- Khandelia, H. and Y.N. Kaznessis. 2007. Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: Molecular dynamics simulations. Journal of Physical Chemistry B 111:242-250.
- Khandelia, H. and Y.N. Kaznessis. 2007. Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation. Biochimica Et Biophysica Acta-Biomembranes 1768:509-520.
- Khodursky, A.B. 2007. Evolution, adaptation, and supercoiling. Journal of Bacteriology 189:5789-5791.
- Koo, B., P.G. Pardey, and K. Qian. 2007. Reforming the Agricultural Research and Intellectual Property Rights Systems of China, in A. Gulati and S. Fan (eds.) The Dragon and the Elephant: Agricultural and Rural Reforms in China and India. Baltimore: Johns Hopkins Univ. Press.
- Kostoff, R.N., J.A. delRio, H.D. Cortes, C. Smith, A. Smith, C. Wagner, L. Leydesdorff, G. Karypis, G. Malpohl, and R. Tshiteya. 2007. Clustering methodologies for identifying country core competencies. Journal of Information Science 33:21-40.
- Kristich, C.J., J.R. Chandler, and G.M. Dunny. 2007. Development of a host-genotype-independent counterselectable marker and a high-frequency conjugative delivery system and their use in genetic analysis of Enterococcus faecalis. Plasmid 57:131-144.
- Kristich, C.J., C.L. Wells, and G.M. Dunny. 2007. A eukaryotic-type Ser/Thr kinase in Enterococcus faecalis mediates antimicrobial resistance and intestinal persistence. Proceedings of the National Academy of Sciences of the United States of America 104:3508-3513.
- Ksoll, W.B., S. Ishii S, M.J. Sadowsky, and R.E. Hicks. 2007. Presence and sources of fecal coliform bacteria in epilithic periphyton communities of Lake Superior. Appl. Environ. Microbiol. 73:3771-3778.
- Kuramochi, M. and G. Karypis. 2007. Discovering frequent geometric subgraphs. Information Systems 32:1101-1120.
- Lamb, J.F.S., H.J.G. Jung, C.C. Sheaffer, and D.A. Samac. 2007. Alfalfa leaf protein and stem cell wall polysaccharide yields under hay and biomass management systems. Crop Science 47:1407-1415.
- Langham, A.A. and Y.N. Kaznessis. 2007. Testing of protegrin-like antimicrobial peptides using molecular dynamics simulations. Biophysical Journal:249A-250A.
- Langham, A.A., A.J. Waring, and Y.N. Kaznessis. 2007. Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data. BMC Biochem 8:11.
- Bilgic, H., Cho, S., Garvin, D.F., and Muehlbauer, G.J. 2007. Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines. Genome 50:898-906.
- Boddu, J., S.H. Cho, and G.J. Muehlbauer. 2007. Transcriptome analysis of trichothecene-induced gene expression in barley. Molecular Plant-Microbe Interactions 20:1364-1375.
- Bolintineanu, D.S., A.A. Langham, H.T. Davis, and Y.N. Kaznessis. 2007. Molecular dynamics simulations of three protegrin-type antimicrobial peptides: interplay between charges at the termini, beta-sheet structure and amphiphilic interactions. Molecular Simulation 33:809-819.
- Bradeen, J.M., and P.W. Simon. 2007. Carrot. In: C. Kole (ed.) Genome Mapping and Molecular Breeding in Plants. Berlin: Springer-Verlag. pp. 161-184.
- Brautaset, T., O.M. Jakobsen, K.D. Josefsen, M.C. Flickinger, and T.E. Ellingsen. 2007. Bacillus methanolicus: a candidate for industrial production of amino acids from methanol at 50 degrees C. Applied Microbiology and Biotechnology 74:22-34.
- Brock, M.T., P. Tiffin, and C. Weinig. 2007. Sequence diversity and haplotype associations with phenotypic responses to crowding: GIGANTEA affects fruit set in Arabidopsis thaliana. Molecular Ecology 16:3050-3062.
- Accinelli, C., W.C. Koskinen, J.M. Becker, and M.J. Sadowsky. 2007. Environmental fate of two sulfonamide antimicrobial agents in soil. J. Agric. Food Chemistry 55:2677-2682.
- Alla, M.D.A., G.L. White, T.B. Rogers, M.E. Cary, D.W. Carey, and J.I. Ravdin. 2007. Adherence-inhibitory intestinal immunogylobulin A antibody response in baboons elicited by use of a synthetic intranasal lectin-based amebiasis subunit vaccine. Infection and Immunity 75:3812-3822.
- Alston, J.M. and P.G. Pardey. 2007. Public Funding for Research into Specialty Crops. Department of Applied Economics Staff Paper No. P07-09, St Paul, U. of Minnesota.
- Andersen, M.A., J.M. Alston, and P.G. Pardey. 2007. Capital Use Intensity and Productivity Biases. Department of Applied Economics Staff Paper No. P07-06, St Paul, U. of Minnesota.
- Anderson, J.A. 2007. Marker-assisted selection for Fusarium head blight resistance in wheat. Int J Food Microbiol 119:51-53.
- Anderson, J.A., R.H. Busch, D.V. McVey, J.A. Kolmer, Y. Jin, G.L. Linkert, J.V. Wiersma, R. Dill-Macky, J.J. Wiersma, and G.A. Hareland. 2007. Registration of Ada wheat. Crop Science 47:434-435.
- Atkinson, L.M., C.R. Hollingsworth, J.E. Larsen, D.A. Samac, and C.D. Motteberg. 2007. Aster yellows incidence and distribution within commercial small grains fields in Minnesota. Phytopathology 97:S5-S5.
- Aversano, R., M.R. Ercolano, L. Frusciante, L. Monti, J.M. Bradeen, G. Cristinzio, A. Zoina, N. Greco, S. Vitale, and D. Carputo. 2007. Resistance traits and AFLP characterization of diploid primitive tuber-bearing potatoes. Genetic Resources and Crop Evolution. 54: 1797-1806.
- Byappanahalli, M.N., R.L. Whitman, D.A. Shively, J. Ferguson, S. Ishii, and M.J. Sadowsky. 2007. Population structure of Cladophora-borne Escherichia coli in nearshore water of Lake Michigan. Water Res. 41:3649-3654.
- Carson, T. D., D. B. White, and A. G. Smith. 2007. Distinguishing creeping bluegrass (Poa annua var. reptans) genotypes using inter-simple sequence repeat markers. Hortscience 42:373-377.
- Chandola, V. and V. Kumar. 2007. Summarization - compressing data into an informative representation. Knowledge and Information Systems 12:355-378.
- Chang, Y.L., S. Cho, H.C. Kistler, C.S. Hsieh, and G. J. Muehlbauer. 2007. Bacterial artificial chromosome-based physical map of Gibberella zeae (Fusarium graminearum). Genome 50:954-962.
- Barnes, C.W. and L.J. Szabo. 2007. Detection and identification of four common rust pathogens of cereals and grasses using real-time polymerase chain reaction. Phytopathology 97:717-727.
- Barnes, C.W. and L.J. Szabo. 2007. Long distance dispersal of Phakopsora pachyrhizi spores in rain, comparing data from 2005 and 2006. Phytopathology 97:S8-S8.
- Baumgarten, A.M., J. Suresh, G. May, and R.L. Phillips. 2007. Mapping QTLs contributing to Ustilago maydis resistance in specific plant tissues of maize. Theoretical and Applied Genetics 114:1229-1238.
- Bhattacharyya, S., M.T. Stankovich, D.G. Truhlar, and J.L. Gao. 2007. Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase. Journal of Physical Chemistry A 111:5729-5742.
- Chang, W.S., W.L. Franck, E. Cytryn, S. Jeong, T. Joshi, D.W. Emerich, M.J. Sadowsky, D. Xu, and G. Gary Stacey. 2007. An oligonucleotide microarray resource for transcriptional profiling of Bradyrhizobium japonicum. Molec. Plant Microbe Interact. 20:12981307.
- Chen, Y.Q., J.H. Staddon, and G.M. Dunny. 2007. Genetic analysis of conjugative DNA processing and virulence functions of Enterococcus faecalis pheromone-inducible plasmid pCF10. Plasmid 57:216-216.
- Chen, Y.Q., J.H. Staddon, and G.M. Dunny. 2007. Specificity determinants of conjugative DNA processing in the Enterococcus faecalis plasmid pCF10 and the Lactococcus lactis plasmid pRS01. Molecular Microbiology 63:1549-1564.
- Choi, I.Y., D.L. Hyten, J.E. Specht, L.K. Matukumalli, Q. Song, C.V. Quigley, M.S. Lee, K. Chase, K.G. Lark, R.S. Reiter, M.S. Yoon, E.Y. Hwang, S.I. Yi, N.D. Young, R.C. Shoemaker, C.P. van Tassell, P.B. Cregan. 2007. A soybean transcript map: Discovery and mapping of single nucleotide polymorphisms in soybean genes. Genetics 176: 685-696.
- Coste, A., A. Selmecki, A. Forche, D. Diogo, M. E. Bougnoux, C. dEnfert, J. Berman, and D. Sanglard. 2007. Genotypic evolution of azole resistance mechanisms in sequential Candida albicans isolates. Eukaryotic Cell 6:1889-1904.
- Cuomo, C, UGueldener, JXu, FTrail, BTurgeon, ADi Pietro, JWalton, LMa, SBaker, MRep, GAdam, JAntoniw, TBaldwin, SCalvo, YChang, DDeCaprio, LGale, SGnerre, RGoswami, KHammond-Kosack, LHarris, KHilburn, JKennell, SKroken, JMagnuson, GMannhaupt, EMauceli, HMewes, RMitterbauer, GMuehlbauer, MMunsterkotter, DNelson, KO'Donnell, TOuellet, WQi, HQuesneville, MRoncero, KSeong, ITetko, MUrban, CWaalwijk, TWard, JYao, BBirren, and HCKistler. 2007. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317:1400-1402.
- Cytryn, E.J., D.P. Sangurdekar, J.G. Streeter, W.L. Franck, W.S. Chang, G. Stacey, D.W. Emerich, T. Joshi, D. Xu, and M.J. Sadowsky. 2007. Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. J. of Bacteriology 189:6751-6762.
- Dahlke, E.E. and D.G. Truhlar. 2007. Electrostatically embedded many-body correlation energy, with applications to the calculation of accurate second-order Moller-Plesset perturbation theory energies for large water clusters. Journal of Chemical Theory and Computation 3:1342-1348.
- Dahlke, E.E. and D.G. Truhlar. 2007. Electrostatically embedded many-body expansion for large systems, with applications to water clusters. Journal of Chemical Theory and Computation 3:46-53.
- De Villena, F.A., V.A. Fritz, J.D. Cohen, and W.D. Hutchison. 2007. Changes in gluconasturtiin concentration in Chinese cabbage with increasing cabbage looper density. Hortscience 42:1337-1340.
- Dean, A.M. 2007. The selective cause of an ancient adaptation. Faseb Journal 21:A210-A210. Dean, A.M. and J.W. Thornton. 2007. Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics 8:675-688.
- DeBruin, D.A., Scholder, S.L., Kahn, J.P., Mastroianni, A.C., Marshall, M.F., Lantos, J., Sugarman, J. 2007. Educational Approaches to the Responsible Conduct of Clinical Research: An Exploratory Study. Academic Medicine, 82(1):32-39. De Leon Gatti, M., K.F. Wlaschin, P.M. Nissom, M.Yap, W.S. Hu. 2007. Comparative Transcriptional analysis of mouse hybridoma and recombinant Chinese hamster ovary cells undergoing butyrate treatment. J. Biosci. Eng. 103:82-91.
- Dunny, G. M. 2007. The peptide pheromone-inducible conjugation system of Enterococcus faecalis plasmid pCF10: cell-cell signalling, gene transfer, complexity and evolution. Philosophical Transactions of the Royal Society B-Biological Sciences 362:1185-1193.
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Progress 01/01/06 to 12/31/06
Outputs
The Microbial and Plant Genomics Institute, formed from the merger of the Plant Molecular Genetics Institute (PMGI) and the Center for Microbial and Plant Genomics (CMPG), promotes advances in microbial and plant genomics, genomics-enabled sciences, and molecular genetics. The Institute strives through research, educational, and outreach activities to foster a multi-disciplinary interchange of ideas and applications of cutting-edge technologies to research. Institute activities contribute to basic science and the translation of genomics for applications to the environment, agriculture, and human health. MPGI is composed of 66 faculty members representing four Colleges at the U of MN: Food, Agricultural, and Natural Resource Sciences (CFANS), Biological Sciences (CBS), Institute of Technology (IT), and Academic Health Center (AHC). In 2006, MPGI funds were used to partially support the salaries of faculty member M. David Marks, Prin. Admin. Spec. Odette Holter, and two
students. MPGI awards enabled 18 graduate students and 17 postdoctoral researchers from 24 university-wide labs to attend meetings to present their research and interact with scientists. With contributions from CFANS and the Graduate School, MPGI continues sponsorship of two graduate integrative fellowships: one for the second of a two-year stipend to Anna Selmecki (J Berman, advisor), and one for a single year's stipend to Carrie Eberle (A Smith & N Anderson, co-advisors). MPGI coordinated and sponsored a one-credit graduate course (PBIO5960-001) on the topic of Natural Variation which brought renowned scientists to campus for each of five weeks to lecture and interact. Each scientist chose a paper for students to read and critique, then after giving a seminar, the speaker met with students for discussion. It was an excellent opportunity for students to learn about exciting fields of science and interact with prominent researchers. The scientists participating in the short course
were: Devaki Bhaya, Stanford U; Ed Buckler, USDA-ARS, Cornell U; Justin Borevitz, U of Chicago; Jennifer Hughes Martiny, Brown U; Eric Richards, Washington U. MPGI sponsors several seminar series throughout the academic year: (A) The NAS Lectureship Series features research by National Academy of Sciences members. Prominent scientists, particularly in the field of microbial and/or plant science, are invited to campus to give seminars, discuss research, and interact with students, faculty, and the public. NAS scientists in 2006 were: 1) Prof E. Peter Greenberg, U of Washington; 2) Prof James Tiedje, Mich State U; 3) Prof Marc Van Montagu, Ghent U, Belgium. (B) The Leading-Edge Technologies Seminars highlight advanced techniques or their applications in the fields of microbial and plant genomics. Researchers who have developed or significantly adapted a technique are invited to give a seminar, meet with faculty, staff, and students, and provide the theoretical principles underlying the
technique. (C) At Bi-Weekly Seminars, MPGI faculty present information concerning their current research. These seminars have expanded opportunities for interdisciplinary connections with other University researchers.
Impacts
With the merger of PMGI and CMPG in 2005, the Microbial and Plant Genomics Institute (MPGI) has continued to expand its mission to contribute to basic science and the translation of genomics for applications in the environment, agriculture, and human health. The combined resources have allowed MPGI to allocate even more support for a greater number of students and postdoctoral scientists to travel to meetings to present their research and interact with current and future scientists in their fields. The combined 25-year history of PMGI and CMPG, along with the supported seminar series, the fellowships, the travel awards, the annual retreat, and the spring course, have all succeeded in creating opportunities for productive interactions for faculty, staff, and students. MPGI supports its members by promoting genetics and genomics research which can advance innovations in agriculture, the environment, and human health. The cooperative efforts of MPGI scientists enhance
their individual projects and assure a strong basis for education of students in the disciplines of the basic agricultural, environmental, and health sciences. MPGI seeks to establish the University of Minnesota as a center of innovation in microbial and plant genomics. Through research, education and outreach activities, MPGI promotes understanding of and access to microbial and plant genomics and genomics-related technologies.
Publications
- Korochkina S, Barreau C, Pradel G, Jeffery E, Li J, Natarajan R, Shabanowitz J, Hunt D, Frevert U, Vernick KD. 2006. A mosquito-specific protein family includes candidate receptors for malaria sporozoite invasion of salivary glands. Cellular Microbiology 8 (1): 163-175.
- Kazlauskas RJ. 2006. Engineering a multipurpose catalyst. Nature Chemical Biology 2 (10): 514-515.
- Kaznessis YN. 2006. Multi-scale models for gene network engineering. Chemical Engineering Science 61 (3): 940-953.
- Keifenheim DL, Smith AG, Tong CBS. 2006. Cloning and accumulation of anthocyanin biosynthesis genes in developing tubers. American Journal of Potato Research 83 (3): 233-239.
- Kelly CP, Cramer CJ, Truhlar DG. 2006. Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants. Journal of Physical Chemistry A 110 (7): 2493-2499.
- Kelly CP, Cramer CJ, Truhlar DG. 2006. Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton. Journal of Physical Chemistry B 110 (32): 16066-16081.
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- Ellis LBM, Roe D, Wackett LP. 2006. The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. Nucleic Acids Research 34: D517-D521 Sp. Iss. SI.
- Engelen-Eigles G, Holden G, Cohen JD, Gardner G. 2006. The effect of temperature, photoperiod, and light quality on gluconasturtiin concentration in watercress (Nasturtium officinale R. Br.) Journal of Agricultural and Food Chemistry 54 (2): 328-334.
- Estes JD, Li QS, Reynolds MR, Wietgrefe S, Duan LJ, Schacker T, Picker LJ, Watkins DI, Lifson JD, Reilly C, Carlis J, Haase AT. 2006. Premature induction of an immunosuppressive regulatory T cell response during acute simian immunodeficiency virus infection. Journal of Infectious Diseases 193 (5): 703-712.
- Fernandez-Ramos A, Miller JA, Klippenstein SJ, Truhlar DG. 2006. Modeling the kinetics of bimolecular reactions. Chemical Reviews 106 (11): 4518-4584.
- Fidaleo M, Charaniya S, Solheid C, Diel U, Laudon M, Ge H, Scriven LE, Flickinger MC. 2006. A model system for increasing the intensity of whole-cell biocatalysis: Investigation of the rate of oxidation of D-sorbitol to L-sorbose by thin bi-layer latex coatings of non-growing Gluconobacter oxydans. Biotechnology and Bioengineering 95 (3): 446-458.
- Abd-Alla MD, Jackson TFGH, Rogers T, Reddy S, Ravdin JI. 2006. Mucosal immunity to asymptomatic Entamoeba histolytica and Entamoeba dispar infection is associated with a peak intestinal anti-lectin immunoglobulin A antibody response. Infection and Immunity 74 (7): 3897-3903.
- Accinelli C, Koskinen WC, Sadowsky MJ. 2006. Influence of Cry1Ac toxin on mineralization and bioavailability of glyphosate in soil. Journal of Agricultural and Food Chemistry 54 (1): 164-169.
- Anastas P, Kazlauskas R, Sheldrake G. 2006. Ten years of green chemistry at the Gordon Research Conferences: frontiers of science. Green Chemistry 8 (8): 677-678.
- Anderson JA, Busch RH, McVey DV, Kolmer JA, Jin Y, Linkert GL, Wiersma JV, Dill-Macky R, Wiersma JJ, Hareland GA. 2006. Registration of 'Ulen' wheat. Crop Science 46 (2): 979-980.
- Banerji N, Kanjilal S. 2006. Somatic alterations of the p53 tumor suppressor gene in vaccine-associated feline sarcoma. American Journal of Veterinary Research 67 (10): 1766-1772.
- Bentley, SD and Ishimaru, CA. 2006. The genome of the potato ring rot pathogen, Clavibacter michiganensis subsp. sepedonicus (Cms) suggests recent niche adaptation. Phytopathology 96:S134. Berman, J. 2006. Morphogenesis and cell cycle progression in Candida albicans. Curr. Opin. Microbiol. 9:595-601.
- Bhatt D, Jasper AW, Schultz NE, Siepmann JI, Truhlar DG. 2006. Critical properties of aluminum. Journal of the American Chemical Society 128 (13): 4224-4225.
- Blazquez J, Gomez-Gomez JM, Oliver A, Juan C, Kapur V, Martin S. 2006. PBP3 inhibition elicits adaptive responses in Pseudomonas aeruginosa. Molecular Microbiology 62 (1): 84-99.
- Bock KW, Honys D, Ward JM, Padmanaban S, Nawrocki EP, Hirschi KD, Twell D, Sze H. 2006. Integrating membrane transport with male gametophyte development and function through transcriptomics. Plant Physiology 140 (4): 1151-1168.
- Boddu J, Cho S, Kruger WM, Muehlbauer GJ. 2006. Transcriptome analysis of the barley-Fusarium graminearum interaction. Molecular Plant-Microbe Interactions 19 (4): 407-417.
- Boisson B, Jacques JC, Choumet V, Martin E, Xu JN, Vernick K, Bourgouin C. 2006. Gene silencing in mosquito salivary glands by RNAi. Febs Letters 580 (8): 1988-1992.
- Hossler P, Goh LT, Lee MM, Hu WS. 2006. GlycoVis: Visualizing glycan distribution in the protein N-glycosylation pathway in mammalian cells. Biotechnology and Bioengineering 95 (5): 946-960.
- Hong SB, Peebles CAM, Shanks JV, San KY, Gibson SI. 2006. Expression of the Arabidopsis feedback-insensitive anthranilate synthase holoenzyme and tryptophan decarboxylase genes in Catharanthus roseus hairy roots. Journal of Biotechnology 122 (1): 28-38.
- Hong SB, Peebles CAM, Shanks JV, San KY, Gibson SI. 2006. Terpenoid indole alkaloid production by Catharanthus roseus hairy roots induced by Agrobacterium tumefaciens harboring rol ABC genes. Biotechnology and Bioengineering 93 (2): 386-390.
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Progress 01/01/05 to 12/31/05
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics in plant biology and agriculture. PMGI is composed of 29 faculty members and their lab personnel in eight departments of the College of Agricultural, Food and Environmental Sciences and the College of Biological Sciences at the University of Minnesota. PMGI supports research and organizes educational opportunities. In 2005, faculty member M. David Marks, Principal Administrative Specialist Odette Holter, Ph.D. candidate Ryoko Oono, and two undergraduates were supported in part by PMGI funds. PMGI support also enabled 13 graduate students or postdoctoral scientists to attend scientific meetings to present their research. In 2005, PMGI coordinated and sponsored a graduate course on Plant Signaling that featured five internationally known speakers who interacted extensively with PMGI students, faculty, and staff: Sheila McCormick (USDA Plant Gene
Expression Center, Albany, CA); Steve Clark (Molecular, Cellular and Developmental Biology, U. of Michigan, Ann Arbor); Judy Callis ( Molecular and Cellular Biology, UC-Davis); Shuqun Zhang (Biochemistry, U. of MO-Columbia); and Jeff Harper (Biochemistry, U of Nevada-Reno). This year, PMGI and the Center for Microbial and Plant Genomics (CMPG) voted to merge, becoming the Microbial and Plant Genomics Institute (MPGI) in response to a charge from the Deans of CBS and COAFES. There are 65 full members of CMPG and 24 associate members; all but one of the 29 PMGI members were also members of CMPG. The consensus was that the memberships and goals of the groups overlapped extensively, so the merger seemed appropriate and would combine the strengths of both. Throughout 2005, PMGI and CMPG had many joint activities: Members of PMGI labs, together with members of the Center for Microbial and Plant Genomics, presented biweekly informal research seminars throughout the academic year. CMPG
originally initiated a National Academy of Sciences Lecturer Seminar Series, a Leading-Edge Technologies Seminar Series, and a seminar series featuring presentations of research carried out in the Cargill Building for Microbial and Plant Genomics. These activities were continued jointly by PMGI and CMPG in 2005. PMGI and CMPG hosted an annual retreat in November at the University of Minnesota Humphrey Institute, which was attended by about 80 institute researchers. Speakers included: Carol Ishimaru (Plant Pathology, U of MN); Mark Johnston (Genetics, Washington University Medical School); Neil Olszewski (Plant Biology, U of MN); Lai-Wa Tam, Post Doctoral Research Associate (Lefebvre lab); and PMGI-funded graduate students, Anna Selmecki (Berman lab) and David Schladt (May lab). A poster session featuring a dozen research posters from PMGI and CMPG labs was also held during the retreat. Contributions from the College of Agricultural, Food and Environmental Sciences and the Graduate
School have allowed CMPG to award two 2-year ($25,000/yr) graduate integrative fellowships in 2005 to recipients, Anna Selmecki (Berman lab) and Garrett Olson (Kapur lab).
Impacts
PMGI has a rich 20-year history: the bi-weekly seminars, the annual retreat, the spring course have all succeeded in bringing faculty, staff, and students together very productively. PMGI supports its members by promoting genetics and genomics research which can advance innovations in agriculture. The cooperative efforts of the PMGI scientists vitalizes their individual projects and assures a strong basis for education of students in the discipline of the basic agricultural sciences. The CMPG seeks to establish the University of Minnesota as a center of innovation in Microbial and Plant Genomics. Through research, education and outreach activities, CMPG promotes understanding of and access to microbial and plant genomics and genomics-related technologies. CMPGs membership in the Consortium on Law and Values in Health, Environment & the Life Sciences provides campus-wide recognition, and has allowed development of two national symposia (one on GMOs and one on
Intellectual Property). With the merger of PMGI and CMPG, The Microbial and Plant Genomics Institute will be even better able to contribute to basic science and the translation of genomics for applications in the environment, agriculture, and human health.
Publications
- Cannon, S.B., Crow, J.A., Heuer, M.L., Wang, X.H., Cannon, E.K.S., Dwan, C., Lamblin, A.F., Vasdewani, J., Mudge, J., Cook, A., Gish, J., Cheung, F., Kenton, S., Kunau, T.M., Brown, D., May, G.D., Kim, D., Cook, D.R., Roe, B.A., Town, C.D., Young, N.D. and Retzel, E.F. 2005. Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiology 138 (1) 38-46.
- Cheng, G., Shapir, N., Sadowsky, M.J. and Wackett, L.P. 2005. Allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism. Appl. Environ. Microbiol. 71 (8): 4437-4445.
- Kynast, R.G., Okagaki, R.J., Galatowitsch, M.W., Huettl, P.A., Jacobs, M.S., Stec, A.O., Walch, M.D., Cabral, C.B., Odland, W.E., Rines, H.W. and Phillips, R.L. 2005. Development of the first fertile plants with an addition of the whole maize chromosome to the oat genome. Maize Genetics Coop. Newsletter 79:45.
- Leonard, K.J. and Szabo, L.J. 2005. Stem rust of small grains and grasses caused by Puccinia graminis. Molecular Plant Path. 6 (2) 99-111. [Correction pub. Molecular Plant Path. 6 (4): 489.]
- Lin, J.Y., Jacobus, B.H., SanMiguel, P., Walling, J.G., Yuan, Y., Shoemaker, R.C., Young, N.D. and Jackson, S.A. 2005. Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile. Genetics 170 (3): 1121-1230.
- Crampin, H., Finley, K., Gerami-Nejad, M., Court, H., Gale, C., Berman, J.and Sudbery, P. 2005. Candida albicans hyphae have a Spitzenkorper that is distinct from the polarisome found in yeast and pseudohyphae. J. Cell Science 118 (13): 2935-2947.
- Emerson, J.P., Wagner, M.L., Reynolds, M.F., Que, L., Sadowsky, M.J. and Wackett, L.P. 2005. The role of histidine 200 in MndD, the Mn(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis CM-2, a site-directed mutagenesis study. J. Biol. Inorg. Chem. 10 (7): 751-760.
- Finley, K.R.and Berman, J. 2005. Microtubules in Candida albicans hyphae drive nuclear dynamics and connect cell cycle progression to morphogenesis. Eukaryotic Cell 4 (10): 1697-1711.
- Foley, J. W., Hass, N.A. and Silflow, C.D. 2005. Positional cloning of the APM1 gene in Chlamydomonas. Amer.Soc. for Plant Biol. Mtg Abstr.
- Gepts, P., Beavis, W.D., Brummer, E.C., Shoemaker, R.C., Stalker, H.T., Weeden, N.F. and Young, N.D. 2005. Legumes as a model plant family. Genomics for food and feed report of the cross-legume advances through genomics conference. Plant Physiology 137 (4): 1228-1235.
- Gibson, S.I. 2005. Control of plant development and gene expression by sugar signaling. Curr. Opinion in Plant Biol. 8 (1): 93-102.
- Henderson, D.C., Muehlbauer, G.J. and Scanlon, M.J. 2005. Radial leaves of the maize mutant ragged seedling2 retain dorsiventral anatomy. Develop. Biology 282 (2): 455-466.
- Ibrahim, A.F.M., Hedley, P.E., Cardle, L., Kruger, W., Marshall, D.F., Muehlbauer, G.J. and Waugh, R. 2005. A comparative analysis of transcript abundance using SAGE and closed Affymetrix arrays. Funct. Integ. Gen. 5:163-174.
- Ihmels, J., Bergmann, S., Berman, J., and Barkai, N. 2005. The Differential Clustering for comparative gene expression analysis: application to the Candida albicans transcription program. PloS Genetics 1 (3): e39;0380-0393.
- Shapir, N., Rosendahl, C., Johnson, G., Andreina, M., Sadowsky, M.J. and Wackett L.P. 2005. Substrate specificity and colorimetric assay for recombinant TrzN derived from Arthrobacter aurescens TC1. Appl. Environ. Microbiol. 71 (5): 2214-2220.
- Shapir, N., Sadowsky, M.J. and Wackett, L.P. 2005. Purification and characterization of allophanate hydrolase (AtzF) from Pseudomonas sp strain ADP. J. Bacteriol. 187 (11): 3731-3738.
- Sherrier, D.J., Taylor, G.S., Silverstein, K.A.T., Gonzales, M.B. and VandenBosch, K.A. 2005. Accumulation of extracellular proteins bearing unique proline-rich motifs in intercellular spaces of the legume nodule parenchyma. Protoplasma 225 (1-2): 43-55.
- Shigaki, T., Kole, M., Ward, J.M., Sze, H. and Hirschi, K.D. 2005. Cre-IoxP recombination vectors for the expression of Riken Arabidopsis full-length cDNAs in plants. Biotechniques 39 (3): 301-+.
- Shigaki, T., Vyzasatya, R.R., Sivitz, A.B., Ward, J.M., Sze, H. and Hirschi, K.D. 2005. The Cre-loxP recombination-based reporter system for plant transcriptional expression studies. Plant Molec. Biol. 58 (1): 65-73.
- Peebles, C.A.M., Hong, S-B, Gibson, S.I., Shanks, J.V. and San, K-Y. 2005. Transient effects of overexpressing anthranilate synthase alpha and beta subunits in Catharanthus roseus hairy roots. Biotech. Prog. 21: (5): 1572-1576.
- Phillips, R.L. 2004. Intellectual property rights for the public good: Obligations of U.S. universities to developing countries. MN J. Law, Sci. & Tech. 6: 177-185.
- Phillips, R.L. 2005. Genetic tools from nature and the nature of genetic tools. Crop Sci. Soc. Am. Abstr. 151-2.
- Phillips, R.L., Odland, W.O. and Kahler, A.L. 2005. Rice as a reference genome and more. 5th Intl. Rice Genetics Symposium Abstr. p. 1.
- Piasecki, B., Wu, W., LsVoie, M., Tam, L-W., Lefebvre, P.A. and Silflow, C.D. 2005. A biochemical and genetic approach to understand the function of UNI2, a gene encoding a novel basal body protein in Chlamydomonas reinhardtii. Amer. Soc. for Cell Biol. Mtg. Abstr.
- Pongsilp, N., Triplett, E.W. and Sadowsky, M.J. 2005. Detection of homoserine lactone-like quorum sensing molecules in Bradyrhizobium strains. Curr. Microbiol. 51 (4): 250-254.
- Porter R., Kahler, A., Carey, L., Braeten, D., Schumer, H. and Phillips, R.L. 2005. Variety Trial Data and Request for Increase of K2EF-C4.
- Kahler, A.L., Porter, R.A. and Phillips, R.L. 2005. Expanding the molecular genetic map of American wildrice (Zizania palustris) through addition of SSR markers from rice (Oryza sativa). Plant and Animal Genome Conf. XIII. Abstr. p. 137.
- Kahler, A.L., Porter, R.A. and Phillips, R.L. 2005. Marker-assisted selection for non-shattering wildrice (Zizania palustris). Crop Sci. Soc. Am., Abstr. 11
- Kahler, A.L., Porter, R.A., and Phillips, R.L. 2005. Adapting SSR markers from rice (Oryza sativa) for molecular mapping and marker-assisted selection in wildrice (Zizania palustris). Plant and Animal Genome Conf. XIII Abstr. p. 137.
- Kang, X.J., Chong, J. and Ni, M. 2005. Hypersensitive to red and blue 1, a ZZ-type zinc finger protein, regulates phytochrome B-Mediated red and cryptochrome-mediated blue light responses. Plant Cell 17 (3): 822-835.
- Liu, J.Q., Samac, D.A., Bucciarelli, B., Allan, D.L. and Vance, C.P. 2005. Signaling of phosphorus deficiency-induced gene expression in white lupin requires sugar and phloem transport. Plant J. 41 (2): 257-268.
- Lohar, D.P. and VandenBosch, K.A. 2005. Grafting between model legumes demonstrates roles for roots and shoots in determining nodule type and host/rhizobia specificity. J. Expt. Botany 56 (416): 1643-1650.
- Ludwig-Muller, J., Walz, A., Slovin, J.P., Epstein, E., Cohen, J.D., Dong, W.Q. and Town, C.D. 2005. Overexpression of maize IAGLU in Arabidopsis thaliana alters plant growth and sensitivity to IAA but not IBA and 2,4-D. J. Plant Growth Regulation 24 (2): 127-141.
- Monjardino, P., Smith, A.G. and Jones, R.J. 2005. Heat stress effects on protein accumulation of maize endosperm. Crop Science 45 (4): 1203-1210.
- Mudge, J., Cannon, S.B., Kalo, P., Oldroyd, G.E.D., Roe, B.A., Town, C.D. and Young, N.D. 2005. Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biology 5:15.
- Nagpal, P., Ellis, C.M., Weber, H., Ploense, S.E., Barkawi, L.S., Guilfoyle, T.J., Hagen, G., Alonso, J.M., Cohen, J.D., Farmer, E.E., Ecker, J.R. and Reed, J.W. 2005. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development 132 (18): 4107-4118.
- Nguyen, R.L., Tam, L.W. and Lefebvre, P.A. 2005. The LF1 gene of Chlamydomonas reinhardtii encodes a novel protein required for flagellar length control. Genetics 169 (3): 1415-1424.
- Ni, M. 2005. Integration of light signaling with photoperiodic flowering circadian rhythm. Cell Research 15 (8): 559-566.
- Normanly, J., Slovin, J.P. and Cohen, J.D. 2004. Auxin biosynthesis and metabolism. In: Plant Hormones: Biosynthess, Signal Transduction, Action! (3rd edition). P.J. Davies, ed. Kluwer Academic Publ., Dordrecht, pp. 36-62.
- Odland, W., Baumgarten, A., Schmidt, C., Rines, H. and R. Phillips. 2005. Simplifying the grass genome to evaluate the maize genome. 47th Annual Maize Genet. Conf. Abstr. p. 34.
- Odland, W., Yu, H., Rines, H.W. and Phillips, R.L. 2005. Genic and repetitive sequence similarities between maize chromosomes. Plant & Animal Genome Conf. XIII. Abstr. p. 168.
- Okagaki, R., Baumgarten, A. and Phillips, R. 2005. Junction-linked primers for mapping repetitive elements. 47th Maize Genet. Conf. Abstr. p. 122.
- Okagaki, R., Baumgarten, A., and Phillips, R. 2005. Mapping individual repetitive element insertions. Plant and Animal Genome Conf. XIII Abstr. p. 107.
- Reinders, A., Panshyshyn, J.A. and Ward, J.M. 2005. Analysis of transport activity of Arabidopsis sugar alcohol permease homolog AtPLT5. J. Biol. Chem. 280: 1594-1602.
- Rines, H.W., Phillips, R.L., Kynast, R.G., Okagaki, R.J., Odland, W.E., Stec, A.O., Jacobs, M.S. and Granath, S.R. 2005. Maize chromosome additions and radiation hybrids in oat and their use in dissecting the maize genome. In: In the wake of the double helix: from the green revolution to the gene revolution. Eds. Tuberosa, R., R.L. Phillips, and M. Gale, Avenue Media, Bologna, Italy, pp. 427-442.
- Salvi, S., Sponza, G., Morgante, M., Fengler, K., Meeley, R., Ananiev, E., Svitashev, S., Bruggemenn, E., Niu, A., Li, B., Hainey, C., Rafalski, A., Tingey, S., Tomes, D., Miao, G-H., Phillips, R. and Tuberosa, R. 2005. The maize QTL Vgt1 corresponds to a ca. 2.7-kb non-coding region upstream of an Ap2-like gene. 47th Maize Genet. Conf. Abstr. p. 24.
- Silverstein, K.A.T., Graham, M.A., Paape, T.D. and VandenBosch, K.A. 2005. Genome organization of more than 300 defensin-like genes in arabidopsis. Plant Physiol. 138 (2): 600-610.
- Sivitz, A.B., Reinders, A. and Ward, J.M. 2005. Analysis of the transport activity of barley sucrose transporter HvSUT1. Plant and Cell Physiol. 46 (10): 1666-1673.
- Snustad, D.P., and Simmons, M.J. (Publ. 2005, Copyright 2006) Principles of Genetics, 4th edition. John Wiley & Sons, Hoboken, NJ.
- Stacey, G. and VandenBosch, K. 2005. Translational legume biology. Models to crops. Plant Physiol. 137 (4): 1173.
- Tesfaye, M., Denton, M.D., Samac, D.A. and Vance, C.P. 2005. Transgenic alfalfa secretes a fungal endochitinase protein to the rhizosphere. Plant and Soil 269 (1-2) 233-243.
- Tuberosa, R., Phillips, R.L., and Gale, M., (eds.) 2005. In the wake of the double helix: From the green revolution to the gene revolution. Avenue Media, Bologna, Italy. 772 pp.
- Uhde-Stone, C., Liu, J.Q., Zinn, K.E., Allan, D.L. and Vance, C.P. 2005. Transgenic proteoid roots of white lupin: a vehicle for characterizing and silencing root genes involved in adaptation to P stress. Plant J. 44 (5): 840-853.
- Vales, M.I., Riera-Lizarazu, O., Rines, H.W. and Phillips, R.L. 2004. Transmission of maize chromosome 9 rearrangements in oat-maize radiation hybrids. Genome 47: 1202-1210.
- Okagaki, R., Kynast, R., Stec, A., Schmidt, C., Jacobs, M., Odland, W., Cabral, C., Walch, M., Galatowitsch, M., Huettl, P., Suresh, J., Dosdall, A., Ninkovic, J., Gillen, J., Yoon, C., Retzel, E., Rines, H.W. and Phillips, R.L. 2005. Studying repetitive sequences using oat-maize radiation hybrid lines. Plant & Animal Genome Conf. XIII, Abstr. p. 171.
- Okagaki, R., Kynast, R., Stec, A., Schmidt, C., Jacobs, M., Odland, W., Cabral, C., Walch, M., Galatowitsch, M., Huettl, P., Suresh, J., Retzel, E., Rines, H. and Phillips, R. 2005. A radiation hybrid system for the genetic and physical mapping of the maize genome. 47th Maize Genet. Conf. Abstr. p. 109.
- Peebles, C.A.M., Gibson, S.I., Shanks, J.V. and San, K-Y. 2005. Metabolic engineering of the terpenoid indole alkaloid pathways in Catharanthus roseus hairy roots. ACS Abstr. 229: U222.
- Peebles, C.A.M., Gibson, S.I., Shanks, J.V. and San, K-Y. 2005. Effect of overexpressing AS alpha and DXS in Catharanthus roseus hairy roots on the terpenoid indole alkaloid pathway. ACS Abstr. 229: U180.
- Peebles, C.A.M., Hong, S.B., Hughes, E.H., Gibson, S.I., Shanks, J.V. and San, K.Y. 2005. Metabolic engineering of the terpenoid indole alkaloid pathways in Catharanthus roseus hairy roots: The effects of terpenoid precursor feeding on transgenic as alpha beta hairy roots. ACS Abstr. 227: U226-227.
- Portyanko, V.A., Chen, G., Rines, H.W., Phillip,s R.L., Leonard, K.J., Ochock,i G.E. and Stuthman, D.D. 2005. Quantitative trait loci for partial resistance to crown rust, Puccinia coronata, in cultivated oat, Avena sativa L. Theor. Appl. Gen.111 (2): 313-324. [Correction pub 2005: Theor. Appl. Gen. 112 (1): 195-197.]
- Ramirez, M., Graham, M.A., Blanco-Lopez, L., Silvente, S., Medrano-Soto, A., Blair, M.W., Hernandez, G., Vance, C.P. and Lara, M. 2005. Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol. 137 (4): 1211-1227.
- Ihmels, J., Bergmann, S., Gerami-Nejad, M., Yanai, I., McClellan, M., Berman, J. and Barkai, N. 2005. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309 (5736): 938-940.
- Ihmels, J., Bergmann, S., Berman, J. and Barkai, N. 2005. Comparative Gene Expression Analysis by a Differential Clustering Approach: Application to the Candida albicans Transcription Program. PLoS Genetics 1 (3) e39.
- Ilic, N., Habus, I., Barkawi, L.S., Park, S., Stefanic, Z., Kojic-Prodic, B. and Cohen, J.D. 2005. Magnus V Aminoethyl-substituted indole-3-acetic acids for the preparation of tagged and carrier-linked auxin. Bioorganic and Medicinal Chem.13:3229-3240.
- Ivashuta, S., Liu, J.Y., Liu, J.Q., Lohar, D.P., Haridas, S., Bucciarelli, B., VandenBosch, K.A., Vance, C.P., Harrison, M.J. and Gantt, J.S. 2005. RNA interference identifies a calcium-dependent protein kinase involved in Medicago truncatula root development. Plant Cell 17 (11): 2911-2921.
- Iyer, M., Slovin, J.P., Epstein, E. and Cohen, J.D. 2005. Transgenic tomato plants with a modified ability to synthesize indole-3-acetyl-beta-1-O-D-glucose. J. Plant Growth Regulation 24 (2): 142-152.
- Jacobs, J.L., Diez-Gonzalez, F. and Phillips, R.L. 2005. Colicinogenic maize: transgenic analysis and effectiveness against pathogenic E. coli O157:H7. Crop Sci. Soc. Amer. Abstr. 70-5.
- Jacobs, J.L., Diez-Gonzalez, F. and Phillips, R.L. 2005. Development of colicinogenic maize to inhibit Escherichia coli O157:H7. Plant and Animal Genome XIII, Abstr p. 232.
- Jacobs, J.L., Diez-Gonzalez, F. and Phillips, R.L. 2005. Inhibition of pathogenic E. coli O157:H7: analysis of transgenic maize expressing colicin E7. 47th Maize Genetics Conf., Abstr. p. 142.
- Jacobs, J.L., Diez-Gonzalez, F., Stern, M.D. and Phillips, R.L. 2005. Detection of transgenic maize Cry1Ab protein subjected to ruminal digestion. J. Animal and Feed Sciences 14 (4): 655-664.
- Judd, P.K., Kumar, R.B. and Das, A. 2005. Spatial location and requirements for the assembly of the Agrobacterium tumefaciens type IV secretion apparatus. PNAS 102 (32): 11498-11503.
- Kelley, J.L., Stinchcombe, J.R., Weinig, C. and Schmitt, J. 2005. Soft and hard selection on plant defence traits in Arabidopsis thaliana. Evol. Ecology Res. 7 (2): 287-302.
- Kowles, R.V., Minnerath, J.M., Phillips, R.L. and Rines, H.W. 2005. Expression of C4 photosynthetic characteristics in oat-maize addition lines. 47th Maize Genetics Conf. Abstr. p. 21.
- Kunkel, B.N., Agnew, J., Collins, J., Cohen, J.D. and Chen, Z. 2005. Molecular genetic analysis of AvrRpt2 activity in promoting virulence of Pseudomonas syringae. In: Genomic and Genetic Analysis of Plant Parasitism and Defense, S. Tsuyumu, T. Shiraishi, T. Wolpert, J.E. Leach, eds., APS Press, pp 92-102.
- Kynast, R.G., Galatowitsch, M.W., Huettl, P.A., Cabral, C.B., Walch, M.D., Phillips, R.L. and Rines, H.W. 2005. Sexual transfer of B-chromosomes from maize, Zea mays L. into oat, Avena sativa L. 47th Maize Genetics Conf. Abstr. p. 58.
- Wang, L., Samac, D.A., Shapir, N., Wackett, L.P., Vance, C.P., Olszewski, N.E. and Sadowsky, M.J. 2005. Biodegradation of atrazine in transgenic plants expressing a modified bacterial atrazine chlorohydrolase (atzA) gene. Plant Biotech. J. 3 (5): 475-486.
- Webb, C. A., Szabo, L. J., Bakkeren, G. Garry, C., Staples, R. C., Eversmeyer, M. and Fellers, J. P. 2005. Transient expression and insertional mutagenesis of Puccinia triticina using biolistics. Functional and Integrative Genomics (online).
- Weinig, C. 2005. Rapid evolutionary responses to selection in heterogeneous environments among agricultural and nonagricultural weeds. Internatl. J. Plant Sciences 166 (4): 641-647.
- Yamagishi, M., Liu, J.Q., Uhde-Stone, C., Bucciarelli, B., Allan, D., Osaki, M. and Vance, C. 2005. Expressional analysis of a novel R2R3-MYB gene in white lupin roots. Plant and Cell Physiology Mtg Abstr. 46: S197.
- Young, N.D., Cannon, S.B., Sato, S., Kim, D., Cook, D.R., Town, C.D., Roe, B.A. and Tabata, S. 2005. Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiology 137 (4): 1174-1181.
- Yun, S.J., Gyenis, L., Hayes, P.M., Matus, I., Smith, K.P., Steffenson, B.J. and Muehlbauer G.J. 2005. Quantitative trait loci for multiple disease resistance in wild barley. Crop Science 45 (6): 2563-2572.
- Accinelli, C., Koskinen, W.C., Seebinger, J.D., Vicari, A.and Sadowsky, M.J. 2005. Effects of incorporated corn residues on glyphosate mineralization and sorption in soil. J. Agric. and Food Chem. 53 (10): 4110-4117.
- Bensen, E.S., Clemente-Blanco, A., Finley, K.R., Correa-Bordes, J. and Berman, J. 2005. The mitotic Cyclins Clb2p and Clb4p affect morphogenesis in Candida albicans. Mol. Biol. of the Cell 16 (7): 3387-3400.
- Braun, B, vanhet Hoog, M, dEnfert, C, Martchenko, M, Dungan, J, Kuo, A, Inglis, D, Uhl, M, Hogues, H, Berriman, M, Lorenz, M, Levitin, A, Oberholzer, U, Bachewich, C, Harcus, D, Marcil, A, Dignard, D, Iouk, T., Zito, R, Frangeul, L, Tekaia, F, Rutherford, K, Wang, E, Munro, C, Bates, S, Gow, N, Hoyer, L, Kohler, G, Morschhauser, J, Newport, G, Znaidi, S, Raymond, M, Turcotte, B, Sherlock, G, Costanzo, M, Ihmels, J, Berman, J, Sanglard, D, Agabian, N, Mitchell, A, Johnson, A, Whiteway, M and Nantel, A. 2005. A Human-Curated Annotation of the Candida albicans Genome. PLoS Genetics, 1:36-57.
- Brock, M.T., Weinig, C. and Galen, C. 2005. A comparison of phenotypic plasticity in the native dandelion Taraxacum ceratophorum and its invasive congener T-officinale. New Phytologist 166 (1): 173-183.
- Buhinicek, I., Pejic, I., Suresh, J., Vragolovic, A. and Phillips, R.L. 2004. Genetic divergence of elite maize inbred lines comparing to Illinois high oil source. Austrian J. Agric. Res. 55: 29-35.
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Progress 01/01/04 to 12/31/04
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics in plant biology and agriculture. PMGI is composed of 35 faculty members and their lab personnel in eight departments of the College of Agricultural, Food and Environmental Sciences and the College of Biological Sciences at the University of Minnesota. PMGI supports research, often including joint research projects, and organizes educational opportunities. Faculty member M. David Marks, Ph.D. candidates Kavitha Kuppusamy and Margaret Chen, and graduate students Jenny Dechaine, Keunsub Lee, and David Schladt were supported in part by PMGI funds. PMGI provided funds to enable 10 graduate students or postdoctoral scientists to attend scientific meetings to present their research and partially supported travel of two graduate students to obtain specialized training in labs outside the University. Members of PMGI labs, along with members of the Center for
Microbial and Plant Genomics (CMPG), presented biweekly informal research seminars throughout the academic year. The PMGI spring course on molecular plant-microbe interactions featured five internationally known speakers who interacted extensively with PMGI students, faculty and staff scientists. Over 90 members of PMGI and CMPG attended the annual retreat, held at Coffman Union on the Minneapolis campus of the University of Minnesota. Speakers at the retreat included: Perry Hackett (Genetics, Cell Biology and Development), Corby Kistler (USDA-ARS and Plant Pathology), Tom Michaels (Horticultural Science), Wei-Shou Hu (Chemical Engineering and Materials Science) and PMGI graduate students Jenny Dechaine, Kavitha Kuppusamy, Keunsub Lee and Margaret Chen. A poster session with over 30 research posters from PMGI and CMPG labs was held during the retreat. The Institute provided matching funds for the purchase of a digital camera that is to be shared by several PMGI labs and a laptop
computer to be used primarily for seminars. PMGI was a supporter of the annual meeting of the International Triticeae Mapping Initiative, organized and attended by PMGI members, and provided partial bridging funds to cover a temporary grant shortfall in a PMGI lab.
Impacts
The PMGI fosters cooperation among its members and other to strengthen projects in plant molecular genetic research and applications in agriculture, food, and environmental sciences. PMGI encourages the development of innovative methods in agriculture based on recent developments in biology, and the education of future scientists about how to implement genomic, molecular, and cellular techniques in agriculture.
Publications
- Chuang, H.W., Zhang, W., and Gray, W.M. 2004. Arabidopsis ETA2, an apparent ortholog of the human cullin-interacting protein CAND1, is required for auxin responses mediated by the SCF(TIR1) ubiquitin ligase. Plant Cell 16(7):1883-1897.
- Close, T.J., Wanamaker, S.I., Caldo, R.A., Turner, S.M., Ashlock, D.A., Dickerson, J.A., Wing ,R.A., Muehlbauer, G.J., Kleinhofs, A., and Wise, R.P. 2004. A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol. 134(3):960-968.
- Davelos, A.L., Kinkel, L.L., and Samac, D.A. 2004. Spatial variation in frequency and intensity of antibiotic interactions among Streptomycetes from prairie soil. Appl. Environ. Microbiol. 70(2):1051-1058.
- Dinu, I., Hayes, R.J., Kynast, R.G., Phillips, R.L., and Thill, C.A. 2004. Novel inter-series hybrids in Solanum, section Petota. Theor. Appl. Genet. In press.
- Dietrich, D., Hammes, U., Thor, K., Suter-Grotemeyer, M., Fluckiger, R., Slusarenko, A.J., Ward, J.M., and Rentsch, D. 2004. AtPTR1, a plasma membrane peptide transporter expressed during seed germination and in vascular tissue of Arabidopsis. Plant J. 40:488-499.
- Dyer, A.T., Szabo, L.J. and Windels, C.E. 2004. Characterization and spatial distribution of Aphanomyces in sugarbeet fields. Journal of Sugar Beet Research 41:1-16.
- Dymek, E.E., Lefebvre, P.A., and Smith, E.F. 2004. PF15p is the Chlamydomonas homologue of the Katanin p80 subunit and is required for assembly of flagellar central microtubules. Eukaryot. Cell. 3(4):870-879.
- Enomoto, S., Glowczewski, L., Lew-Smith, J., and Berman, J. G. 2004. Telomere cap components influence the rate of senescence in telomerase-deficient yeast cells. Mol Cell Biol. 24(2):837-45.
- Esch, J. J., Chen, M. A., Hillestad, M., and Marks, M.D. 2004. Comparison of TRY and the closely related At1g01380 gene in controlling Arabidopsis trichome patterning. Plant J. 40:860-869.
- Eulgem, T., Weigman, V.J., Chang, H.S., McDowell, J.M., Holub, E.B., Glazebrook, J., Zhu, T., and Dangl, J.L. 2004. Gene expression signatures from three genetically separable resistance gene signaling pathways for downy mildew resistance. Plant Physiol. 135(2):1129-1144.
- Johnson, L.K., Brown, M.B., Carruthers, E.A., Ferguson, J.A, Dombek, P.E., and Sadowsky, M.J. 2004. Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl. Environ. Microbiol. 70(8):4478-4485.
- Judd, P.K., Kumar, R.B. and Das, A. 2004. The type IV secretion apparatus protein VirB6 of Agrobacterium tumefaciens localizes to a cell pole. Mol. Microbiol. in press.
- Kang, X., Chong, J., and Ni, M. 2004. HYPERSENSITIVE TO RED AND BLUE 1, a ZZ-type zinc finger protein, regulates phyB-mediated red and cry-mediated blue light Responses. Plant Cell in press.
- Katagiri, F. 2004. A global view of defense gene expression regulation--a highly interconnected signaling network. Curr. Opin. Plant Biol. 7(5):506-511.
- Katagiri, F. 2004. Disease resistance genes and pathogen recognition mechanisms in Plant Disease resistance at the Molecular Level, 2nd edition (in Japanese), Eds. Shimamoto, K. et al. (Shujunsha Co., Tokyo, Japan), pp. 88-95.
- Katagiri, F. and Glazebrook, J. 2004. Overview of mRNA Expression Profiling Using Microarrays. In: Current Protocols in Molecular Biology, Eds. Ausubel et al., (John Wiley & Sons, New York, NY), unit 22.4.
- Keller, C.P., Stahlberg, R., Barkawi, L.S., and Cohen, J.D. 2004. Long-term inhibition by auxin of leaf blade expansion in bean and Arabidopsis. Plant Physiol. 134(3):1217-1226.
- Kosman, E., Pardes, E., Anikster, Y., Manisterski, J., Yehuda, P.B., Szabo, L.J. and Sharon, A. 2004. Genetic variation and virulence on Lr26 in Puccinia triticina. Phytopathology 94:632-640.
- Kuppusamy, K.T., Endre, G., Prabhu, R. Penmetsa, R.V., Veereshlingam, H., Cook, D.R., Dickstein, R., VandenBosch, K.A. 2004. LIN, a Medicago truncatula gene required for nodule differentiation and persistence of rhizobial infections. Plant Physiol. 136(3):3682-3691.
- Kynast, R.G., Okagaki, R.J., Galatowitsch, M.W., Granath, S.R., Jacobs, M.S., Stec, A.O., Rines, H.W., and Phillips, R.L. 2004. Dissecting the maize genome by using chromosome addition and radiation hybrid lines. Proc. Natl. Acad. Sci. USA 101(26):9921-9926.
- Lee, C.C., Wood, M.D., Ng, K., Andersen, C.B., Liu, Y., Luginbuhl, P., Spraggon, G., and Katagiri, F. 2004. Crystal structure of the type III effector AvrB from Pseudomonas syringae. Structure 12(3):487-494.
- Martin, D.J., and Somers, D.A. 2004. A 1,3-beta-glucanase expressed during oat endosperm development. J. Cereal Sci. 39:265-272.
- Matsuura, K., Lefebvre, P.A., Kamiya, R., and Hirono, M. 2004. Bld10p, a novel protein essential for basal body assembly in Chlamydomonas: localization to the cartwheel, the first ninefold symmetrical structure appearing during assembly. J. Cell. Biol. 165(5):663-671.
- McLaughlin, D.J., Hanson, Jr, R.W., Frieders, E.M., Swann, E.C. and Szabo, L.J. 2004. Mitosis in the yeast phase of the basidiomycetes Bensingtonia yuccicola and Stilbum vulgare and its phylogenetic implications. American Journal of Botany 91:808-815.
- McNeil, K.J., E. and Smith, A.G. 2004. An anther-specific cysteine-rich protein of tomato localized to the tapetum and microspores. J. Plant Physiol. In press.
- Monjardino, P., Smith, A.G. and Jones, R.J. 2004. Effects of heat stress on protein accumulation of maize (Zea mays L.) kernels. Crop Sci. in press.
- Moyle, L.C., Olson, M.S., and Tiffin, P. 2004. Patterns of reproductive isolation in three angiosperm genera. Evolution 58(6):1195-1208.
- Mudge, J., Huihuang, Y., Denny, R.L., Howe, D.K., Danesh, D., Marek, L.F., Retzel, E., Shoemaker, R.C., and Young, N.D. 2004. Soybean bacterial artificial chromosome contigs anchored with RFLPs: insights into genome duplication and gene clustering. Genome 47(2):361-372.
- Ni, M. 2004. Downstream integrators of red, far-red, and blue light signaling for photomorphogenesis. In: Light Sensing in Plants, M. Wada, K. Shimazaki, and M. Iino eds. (Sringer-Verlag, Tokyo) In press.
- Okagaki, R.J., and Phillips, R.L. 2004. Maize DNA-sequencing strategies and genome organization. Genome Biol. 5(5):223.
- Olhoft, P.M., Flagel, LE., and Somers, D. A. 2004. T-DNA locus structure in a large population of soybean plants transformed using the Agrobacterium-mediated cotyledonary-node method. Plant Biotechnology Journal 2:289-300.
- Olsen, K.M., Halldorsdottir, S.S., Stinchcombe, J.R., Weinig, C., Schmitt, J., Purugganan, M.D. 2004. Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167(3):1361-1369.
- Pagel, J., Walling, J.G., Young, N.D., Shoemaker, R.C., and Jackson, S.A. 2004. Segmental duplications within the Glycine max genome revealed by fluorescence in situ hybridization of bacterial artificial chromosomes. Genome 47(4):764-768.
- Rahman, F.A., Allan, D.L., Rosen, C.J., and Sadowsky, M.J. 2004. Arsenic availability from chromated copper arsenate (CCA)-treated wood. J. Environ. Qual. 33(1):173-180.
- Rines, H.W., Molnar, S.J., Tinker, N. A., and Phillips, R.L. 2004. Genome mapping and molecular breeding: oat. In: Genome Mapping and Molecular Breeding, Vol. 1, Cereals and Millets. Ed. Kole, C., Oxford Press.
- Bensen, E., Martin, S., Berman, J. and Davis, D.A. 2004. Transcriptional profiling in C. albicans reveals new adaptive responses to extracellular pH and functions for Rim101p. Mol. Microbiol. 54(5):1335-1351.
- Berman, J. and Gow, N. A. R. 2004. Cell cycle in Human Fungal Pathogens. In: Pathogenic Fungi: Structural Biology and Taxonomy, SanBlas, G. & R. Calderone, eds., Horizon press. Norfolk,UK, pp. 101-127.
- Brambl, R. 2004. Regulation of expression of mitochondrial genes. Pp. 129-140. In: The Mycota III. Biochemistry and Molecular Biology, 2nd ed. (R. Brambl and G. Marzluf, eds.) Springer-Verlag, Berlin.
- Brambl, R. and Marzluf, G. A. 2004. The Mycota III. Biochemistry and Molecular Biology, 2nd ed. Springer-Verlag, Berlin (447 p.).
- Bryan, A., Shapir, N., and Sadowsky, M.J. 2004. Frequency and distribution of tetracycline resistance genes in genetically diverse, nonselected, and nonclinical Escherichia coli strains isolated from diverse human and animal sources. Appl. Environ. Microbiol. 70(4):2503-2507.
- Caldwell, D.G., McCallum, N., Shaw, P., Muehlbauer, G.J., Marshall, D.F., and Waugh, R. 2004. A structured mutant population for forward and reverse genetics in barley (Hordeum vulgare L.). Plant J. 40(1):143-150.
- Canci, P.C., Nduulu, L.M., Muehlbauer, G.J., Dill-Macky, R., Rasmusson, D.C. and Smith, K.P. 2004. Validation of quantitative trait loci for Fusarium head blight and kernel discoloration resistance in barley. Mol. Breed. 14:91-104.
- Cannon, S.B., Mitra, A., Baumgarten, A., Young, N.D., May, G. 2004. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 4(1):10.
- Choi, H.K., Mun, J.H., Kim, D.J., Zhu, H., Baek ,J.M., Mudge, J., Roe, B., Ellis, N., Doyle, J., Kiss, G.B., Young, N.D., and Cook, D.R. 2004. Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci. USA. 101(43):15289-15294.
- Chou, J.C., Welch, W.H., and Cohen, J.D. 2004. His-404 and His-405 are essential for enzyme catalytic activities of a bacterial indole-3-acetyl-L-aspartic acid hydrolase. Plant Cell Physiol. 45(9):1335-1341.
- Selmecki, A., Bergmann, S., and Berman, J. 2004. Comparative Genome Hybridization reveals widespread aneuploidy in Candida albicans laboratory strains. Mol. Microbiol. In press.
- Snustad, D.P. 2004. Genetics, Molecular Basis of. In: Encyclopedia of Molecular Cell Biology and Molecular Medicine, (R.A. Meyers, ed.). VCH Verlagsgesellschaft, Weinheim, Germany 5:369-411.
- Somers, D.A., and Makarevitch, I. 2004. Transgene integration in plants: poking or patching holes in promiscuous genomes? Curr. Opin. Biotechnol. 15(2):126-131.
- Springer, N.M., Xu, X., and Barbazuk, W.B. 2004. Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space. Plant Physiol. 136(2):3023-3033.
- Stinchcombe, J.R., Weinig, C., Ungerer, M., Olsen, K.M., Mays, C., Halldorsdottir, S.S., Purugganan, M.D., and Schmitt, J. 2004. A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA. Proc. Natl. Acad. Sci. USA 101(13):4712-7.
- Stombaugh, S.K., Orf, J.H., Jung H.G., Chase, K., Lark, K.G., and Somers, D.A. 2004. QTL associated with cell wall polysaccharides in soybean seed. Crop Sci. 44:2101-2106.
- Tseng, T.S,. Salome, P.A., McClung, C.R., and Olszewski, N.E. 2004. SPINDLY and GIGANTEA interact and act in Arabidopsis thaliana pathways involved in light responses, flowering, and rhythms in cotyledon movements. Plant Cell 16(6):1550-1563.
- Verhagen, B.W., Glazebrook, J., Zhu, T., Chang, H.S., van Loon, L.C., and Pieterse, C.M. 2004. The transcriptome of rhizobacteria-induced systemic resistance in Arabidopsis. Mol. Plant Microbe Interact. 17(8):895-908.
- Weinig, C., and Schmitt, J. 2004. Environmental effects on the expression of quantitative trait loci and implications for phenotypic evolution. BioScience 54(7): 627-636.
- Fedorova, M., Denton, M., Schultz, J., Liu, J., Graham, M., Allan, D., Samac, D. and Vance, C.P. 2004. Improving the legume-Rhizobium symbiosis: can genomics and molecular genetics help. In Biology of Plant-Microbe Interactions, Volume 4 (eds. I. Tokhonovich, B. Lugtenberg, and N. Provolov). APS Press, St. Paul, MN.
- Forche, A., Magee, P.T., Magee, B.B., and May, G. 2004. Genome-wide single-nucleotide polymorphism map for Candida albicans. Eukaryot Cell. 3(3):705-714.
- Gerami-Nejad, M., Berman, J., and Gale, C.A. 2004. Cassettes for the PCR-mediated construction of regulatable alleles in C. albicans. Yeast 21:429-436.
- Gibson, S.I. 2004. Sugar and phytohormone response pathways: navigating a signalling network. J. Exp. Bot. 55:253-264.
- Glowczewski, L., Waterborg, J.H., and Berman, J. G. 2004. Yeast chromatin assembly complex 1 protein excludes nonacetylatable forms of histone H4 from chromatin and the nucleus. Mol. Cell Biol. 24(23):10180-10192.
- Graham, M.A., Silverstein, K.A., Cannon, S.B., VandenBosch, K.A. 2004. Computational identification and characterization of novel genes from legumes. Plant Physiol. 135(3):1179-1197.
- Hagen, G., T.J. Guilfoyle, and W.M. Gray. 2004. Auxin Signal Transduction. In Plant Hormones: Biosynthesis, Signal Transduction, Action!, P.J. Davies, ed. Kluwer Academic Publishers, Dordrecht, The Netherlands.
- Hughes, E.H., Hong, S.B., Gibson, S.I., Shanks, J.V., and San, K.Y. 2004. Metabolic engineering of the indole pathway in Catharanthus roseus hairy roots and increased accumulation of tryptamine and serpentine. Metab. Eng. 6(4):268-276.
- Hughes, E.H., Hong, S.B., Gibson, S.I., Shanks, J.V., and San, K.Y. 2004. Expression of a feedback-resistant anthranilate synthase in Catharanthus roseus hairy roots provides evidence for tight regulation of terpenoid indole alkaloid levels. Biotechnol. Bioeng. 86(6):718-727.
- Ilic, N. and Cohen, J.D. 2004. Synthesis of [13C]-isotopomers of indole and tryptophan for use in the analysis of indole-3-acetic acid biosynthesis. J. Labelled Compd. Radiopharm. 47:635-646.
- Ivashuta, S., Gantt, J.S. and Vance, C.P. 2004. Medicago truncatula as a model legume. p. 143-162. In Legume Crop Genomics (eds. R.F. Wilson, H.T. Stalker, E.C. Brummer). AOCS Press, Champaign, IL.
- Sudbery, P.E., Gow, N.A.R., and Berman, J. 2004. The distinct morphological states of Candida albicans. Trends in Microbiology 12:317-324.
- Sullivan, M.L., Hatfield, R.D., Thoma, S.L., and Samac, D.A. 2004. Cloning and characterization of red clover polyphenol oxidase cDNAs and expression of active protein in Escherichia coli and transgenic Alfalfa. Plant Physiol. 136(2):3234-3244.
- Sze, H., Padmanaban, S., Cellier, F., Honys, D., Cheng, N.H., Bock, K.W., Conejero, G., Li, X., Twell, D., Ward, J.M., Hirschi, K.D. 2004. Expression patterns of a novel AtCHX gene family highlight potential roles in osmotic adjustment and K+ homeostasis in pollen development. Plant Physiol.136:2532-2547.
- Tesfaye, M., Denton, M.D., Samac, D.A., and Vance, C.P. 2004. Transgenic alfalfa secretes a fungal endochitinase to the rhizosphere. Plant Soil. In press.
- Tiffin, P. 2004. Comparative evolutionary histories of chitinase genes in the genus Zea and family Poaceae. Genetics 167(3):1331-1340.
- Tiffin, P., Hacker, R., and Gaut, B.S. 2004. Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea. Genetics 168(1):425-434.
- Till, B.J., Reynolds, S.H., Weil, C., Springer, N., Burtner, C., Young, K., Bowers, E., Codomo, C.A., Enns, L.C., Odden, A.R., Greene, E.A., Comai, L., and Henikoff, S. 2004. Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol. 28;4(1):12.
- Rubio, M.C., James, E.K., Clemente, M.R., Bucciarelli, B., Fedorova, M., Vance, C.P., and Becana, M. 2004. Localization of superoxide dismutases and hydrogen peroxide in legume root nodules. Mol. Plant Microbe Interact. 17:1294-1305.
- Ryan, A.D., Kinkel, L.L. and Schottel, J.L. 2004. Effect of pathogen isolate, potato cultivar, and antagonist strain on potato scab severity and biological control. Biocontrol Sci. Technol. 14:301-311.
- Sajjaphan, K., Shapir, N., Wackett, L.P., Palmer, M., Blackmon, B., Tomkins, J., and Sadowsky, M.J. 2004. Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli. Appl. Environ. Microbiol. 70(7):4402-4407.
- Samac, D.A., Litterer, L., Temple, G., Jung, H.J., and Somers, D.A. 2004. Expression of UDP-glucose dehydrogenase reduces cell-wall polysaccharide concentration and increases xylose content in alfalfa stems. Appl. Biochem. Biotechnol. 116:1167-1182.
- Samac, D.A. and Temple, S.J. 2004. Development and utilization of transformation in Medicago species. In: Genetically Modified Crops: Their development, uses, and risks. G. H. Liang, D. Z. Skinner, eds. p. 165-202. Haworth Press, New York.
- Samac, D.A., Tesfaye, M., Dornbusch, M., Saruul, P., and Temple, S.J. 2004. A comparison of constitutive promoters for expression of transgenes in alfalfa (Medicago sativa). Transgenic Res. 13(4):349-361.
- Weinig, C., Gravuer, K., Kane, N.C. and Schmitt, J. 2004. Testing adaptive plasticity to UV: costs and benefits of stem elongation and light-induced phenolics. Evolution in press.
- Wilson, N.F., and Lefebvre, P.A. 2004. Regulation of flagellar assembly by glycogen synthase kinase 3 in Chlamydomonas reinhardtii. Eukaryot Cell. 3(5):1307-1319.
- Yan, H.H., Mudge, J., Kim, D.J., Shoemaker, R.C., Cook, D.R., and Young, N.D. 2004. Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome 47(1):141-155.
- Al-Saady, N.A., Torbert, K.A., Smith, L., Makarevitch, I., Baldridge, G., Zeyen, R.J., Muehlbauer, G. J., Olszewski, N. E., and Somers, D. A. 2004. Tissue specificity of the sugarcane bacilliform virus promoter in oat, barley and wheat. Mol. Breed. 13:331-338.
- Anikster, Y., Szabo, L.J., Eilam, T., Manisterski, J., Koike, S.T., and Bushnell, W.R. 2004. Morphology, life cycle biology and DNA sequence analysis of rust fungi on garlic and chives from California. Phytopathology 94:569-577.
- Barriuso, E., Koskinen, W.C., and Sadowsky, M.J. 2004. Solvent extraction characterization of bioavailability of atrazine residues in soils. J. Agric. Food Chem. 52(21):6552-6556.
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Progress 01/01/03 to 12/31/03
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics in plant biology and agriculture. PMGI is composed of 33 faculty members and their lab personnel in eight departments of the College of Agriculture, Food and Environmental Sciences and the College of Biological Sciences at the University of Minnesota. PMGI supports research, often including joint research projects, and organizes educational opportunities. Faculty member M. David Marks, Ph.D. candidates Steve Cannon and Dan Griffin, and incoming graduate student Brendan Mattingly were supported in part by PMGI funds. PMGI provided funds to send six postdoctoral or research fellows to scientific meetings to present posters of their work. Members of PMGI laboratories presented biweekly seminars throughout the academic year; starting in September, members of the Center for Plant and Microbial Genomics (CMPG) were also involved in these informal seminars.
The PMGI annual retreat, held at the Minnesota Landscape Arboretum, was attended by about 75 members. Speakers included Dr. Brad Barbazuk of the Donald Danforth Plant Science Center, St. Louis, MO, University of MN scientists Ann Rougvie (Genetics, Cell Biology and Development) and Vivek Kapur (Microbiology), and Sue Gibson (Plant Biology) and PMGI graduate students Dan Griffin and Steve Cannon. The Institute also provided matching funds for the purchase of an incubator to be shared by several PMGI laboratories and allocated $1000 towards the expenses of the 2003 Plant Pathology Graduate Student Symposium on the future of plant health.
Impacts
The PMGI fosters cooperation among its members and other to strengthen projects in plant molecular genetic research and applications in agriculture, food, and environmental sciences. PMGI encourages the development of innovative methods in agriculture based on recent developments in biology, and educating future scientists about how to implement genomic, molecular, and cellular techniques in agriculture.
Publications
- van Wees SCM. Glazebrook J. 2003. Loss of non-host resistance of Arabidopsis NahG to Pseudomonas syringae pv. phaseolicola is due to degradation products of salicylic acid. Plant Journal. 33(4):733-742
- Ward JM. Hirschi KD. Sze H. 2003. Plants pass the salt Trends in Plant Science. 8(5):200-201
- Weinig C. Dorn LA. Kane NC. German ZM. Hahdorsdottir SS. Ungerer MC. Toyonaga Y. Mackay TFC. Purugganan MD. Schmitt J. 2003. Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana. Genetics. 165(1):321-329
- Weinig C. Stinchcombe JR. Schmitt J. 2003. QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments. Molecular Ecology. 12(5):1153-1163
- Weinig C. Stinchcombe JR. Schmitt J. 2003. Evolutionary genetics of resistance and tolerance to natural herbivory in Arabidopsis thaliana. Evolution. 57(6):1270-1280
- Wick S. 2003. Plant microtubule nucleation sites: moving right along. Nature Cell Biology. 5(11):954
- Wight CP. Tinker NA. Kianian SF. Sorrells ME. O'Donoughue LS. Hoffman DL. Groh S. Scoles GJ. Li CD. Webster FH. Phillips RL. Rines HW. Livingston SM. Armstrong KC. Fedak G. Molnar SJ. 2003. A molecular marker map in 'Kanota' x 'Ogle' hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework. Genome. 46(1):28-47
- Wu Y. Wood MD. Tao Y. Katagiri F. 2003. Direct delivery of bacterial avirulence proteins into resistant Arabidopsis protoplasts leads to hypersensitive cell death. Plant Journal. 33(1):131-137
- Katagiri F. 2003. Attacking complex problems with the power of systems biology. Plant Physiology. 132(2):417-419
- Katagiri F. Glazebrook J. 2003. Local Context Finder (LCF) reveals multidimensional relationships among mRNA expression profiles of Arabidopsis responding to pathogen infection. Proc. National Academy of Sciences USA. 100(19):10842-10847
- Kathir P. LaVoie M. Brazelton WJ. Haas NA. Lefebvre PA. Silflow CD. 2003. Molecular map of the Chlamydomonas reinhardtii nuclear genome Eukaryotic Cell. 2(2):362-379
- Kleidon J. Plesofsky N. Brambl R. 2003. Transcripts and transcript-binding proteins in mitochondria of Neurospora crassa. Mitochondrion. 2(5):345-360
- Lahner B. Gong JM. Mahmoudian M. Smith EL. Abid KB. Rogers EE. Guerinot ML. Harper JF. Ward JM. McIntyre L. Schroeder JI. Salt DE. 2003. Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana. Nature Biotechnology. 21(10):1215-1221
- Tao Y. Xie ZY. Chen WQ. Glazebrook J. Chang HS. Han B. Zhu T. Zou GZ. Katagiri F. 2003. Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae. Plant Cell. 15(2):317-330
- Tesfaye M. Dufault NS. Dornbusch MR. Allan DL. Vance CP. Samac DA. 2003. Influence of enhanced malate dehydrogenase expression by alfalfa on diversity of rhizobacteria and soil nutrient availability. Soil Biology & Biochemistry. 35(8):1103-1113
- To JPC. Reiter WD. Gibson SI. 2003. Chloroplast biogenesis by Arabidopsis seedlings is impaired in the presence of exogenous glucose. Physiologia Plantarum. 118(3):456-463
- Tseng-Rogenski SSI. Chong JL. Thomas CB. Enomoto S. Berman J. Chang TH. 2003. Functional conservation of Dhh1p, a cytoplasmic DExD/H-box protein present in large complexes. Nucleic Acids Research. 31(17):4995-5002
- Uhde-Stone C. Gilbert G. Johnson JMF. Litjens R. Zinn KE. Temple SJ. Vance CP. Allan DL. 2003. Acclimation of white lupin to phosphorus deficiency involves enhanced expression of genes related to organic acid metabolism. PLANT AND SOIL. 248(1-2):99-116
- Uhde-Stone C. Zinn KE. Ramirez-Yanez M. Li AG. Vance CP. Allan DL. 2003. Nylon filter arrays reveal differential gene expression in proteoid roots of white lupin in response to phosphorus deficiency. Plant Physiology. 131(3):1064-1079
- Vance CP. Uhde-Stone C. Allan DL. 2003. Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource New Phytologist. 157(3):423-447
- VandenBosch K. Stacey G. 2003. Advances in legume biology. Plant Physiology. 131(3):839
- VandenBosch KA. Stacey G. 2003. Summaries of legume genomics projects from around the globe. Community resources for crops and models Plant Physiology. 131(3):840-865
- van Wees SCM. Chang HS. Zhu T. Glazebrook J. 2003. Characterization of the early response of Arabidopsis to Alternaria brassicicola infection using expression profiling. Plant Physiology. 132(2):606-617
- Yan HH. Mudge J. Kim DJ. Larsen D. Shoemaker RC. Cook DR. Young ND. 2003. Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. Theoretical & Applied Genetics. 106(7):1256-1265
- Young ND. Mudge J. Ellis THN. 2003. Legume genomes: more than peas in a pod. Current Opinion in Plant Biology. 6(2):199-204
- Zhu YL. Song QJ. Hyten DL. Van Tassell CP. Matukumalli LK. Grimm DR. Hyatt SM. Fickus EW. Young ND. Cregan PB. 2003. Single-nucleotide polymorphisms in soybean. Genetics. 163(3):1123-1134
- Lamb JFS. Sheaffer CC. Samac DA. 2003. Population density and harvest maturity effects on leaf and stem yield in alfalfa. Agronomy Journal. 95(3):635-641
- Lamblin AFJ. Crow JA. Johnson JE. Silverstein KAT. Kunau TM. Kilian A. Benz D. Stromvik M. Endre G. VandenBosch KA. Cook DR. Young ND. Retzel EF. 2003. MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome. Nucleic Acids Research. 31(1):196-201
- Ashfield T. Bocian A. Held D. Henk AD. Marek LF. Danesh D. Penuela S. Meksem K. Lightfoot DA. Young ND. Shoemaker RC. Innes RW. 2003. Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of NBS-LRR genes. Molecular Plant-Microbe Interactions. 16(9):817-826
- Babb S. Muehlbauer GJ. 2003. Genetic and morphological characterization of the barley uniculm2 (cul2) mutant. Theoretical & Applied Genetics. 106(5):846-857
- Baumgarten A. Cannon S. Spangler R. May G. 2003. Genome-level evolution of resistance genes in Arabidopsis thaliana. Genetics. 165(1):309-319
- Berman SA. Wilson NF. Haas NA. Lefebvre PA. 2003. A novel MAP kinase regulates flagellar length in Chlamydomonas. Current Biology. 12(13):1145-1149
- Bucciaglia PA. Zimmermann E. Smith AG. 2003. Functional analysis of a beta-1,3-glucanase gene (Tag 1) with anther-specific RNA and protein accumulation using antisense RNA inhibition. Journal of Plant Physiology. 160(11):1367-1373
- Byappanahalli MN. Shively DA. Nevers MB. Sadowsky MJ. Whitman RL. 2003. Growth and survival of Escherichia coli and enterococci populations in the macro-alga Cladophora (Chlorophyta). FEMS Microbiology Ecology. 46(2):203-211
- Canci PC. Nduulu LM. Dill-Macky R. Muehlbauer GJ. Rasmusson DC. Smith KP. 2003. Genetic relationship between kernel discoloration and grain protein concentration in barley. Crop Science. 43(5):1671-1679
- Cannon SB. McCombie WR. Sato S. Tabata S. Denny R. Palmer L. Katari M. Young ND. Stacey G. 2003. Evolution and microsynteny of the apyrase gene family in three legume genomes. Molecular Genetics & Genomics: MGG. 270(4):347-361
- Cannon SB. Young ND. 2003. Genomic architecture and evolution of NBS-LRRs. PLANT-MICROBE INTERACTIONS, VOL 6. 6 PG. 81-95
- Chandran D. Reinders A. Ward JM. 2003. Substrate specificity of the Arabidopsis thaliana sucrose transporter AtSUC2. Journal of Biological Chemistry. 278(45):44320-44325
- Cohen JD, Slovin JP and Hendrickson AM 2003. Two genetically discrete pathways convert tryptophan to auxin: more redundancy in auxin biosynthesis. Trends in Plant Science 8:197-199
- Cooper B. Clarke JD. Budworth P. Kreps J. Hutchison D. Park S. Guimil S. Dunn M. Luginbuhl P. Ellero C. Goff SA. Glazebrook J. 2003. A network of rice genes associated with stress response and seed development. Proc National Academy of Sciences USA. 100(8):4945-4950
- Cooper B. Hutchison D. Park S. Guimil S. Luginbuhl P. Ellero C. Goff SA. Glazebrook J. 2003. Identification of rice (Oryza sativa) proteins linked to the cyclin-mediated regulation of the cell cycle. Plant Molecular Biology. 53(3):273-279
- Cordoba E. Shishkova S. Vance CP. Hernandez G. 2003. Antisense inhibition of NADH glutamate synthase impairs carbon/nitrogen assimilation in nodules of alfalfa (Medicago sativa L.). Plant Journal. 33(6):1037-1049
- Dahlseid JN. Lew-Smith J. Lelivelt MJ. Enomoto S. Ford A. Desruisseaux M. McClellan M. Lue N. Culbertson MR. Berman J. 2003. mRNAs encoding telomerase components and regulators are controlled by UPF genes in Saccharomyces cerevisiae. Eukaryotic Cell. 2(1):134-142
- de Araujo MRA. Coulman B. Somers D. Ferdinandez Y. 2003. Random amplified polymorphic DNA variation within and among meadow bromegrass progeny types. Plant Breeding. 122(5):416-420 DeHaan LR. Ehlke NJ. Sheaffer CC. Muehlbauer GJ. Wyse DL. 2003. Illinois bundleflower genetic diversity determined by AFLP analysis. Crop Science. 43(1):402-408
- Filardo FF. Swain SM. 2003. SPYing on GA signaling and plant development. Journal of Plant Growth Regulation. 22(2):163-175
- Forche A. May G. Beckerman J. Kauffman S. Becker J. Magee PT. 2003. A system for studying genetic changes in Candida albicans during infection. Fungal Genetics & Biology. 39(1):38-50
- Fruchey I. Shapir N. Sadowsky MJ. Wackett LP. 2003. On the origins of cyanuric acid hydrolase: Purification, substrates, and prevalence of AtzD from Pseudomonas sp strain ADP. Applied & Environmental Microbiology. 69(6):3653-3657
- Gibson, S.I. 2003. Sugar and phytohormone response pathways: navigating a signaling network. J. Exp. Bot., accepted pending revision
- Graham PH. Vance CP. 2003. Legumes: Importance and constraints to greater use. Plant Physiology. 131(3):872-877
- Glazebrook J. Chen WJ. Estes B. Chang HS. Nawrath C. Metraux JP. Zhu T. Katagiri F. 2003. Topology of the network integrating salicylate and jasmonate signal transduction derived from global expression phenotyping. Plant Journal. 34(2):217-228
- Gray WM. Muskett PR. Chuang HW. Parker JE. 2003. Arabidopsis SGT1b is required for SCFTIR1-mediated auxin response. Plant Cell. 15(6):1310-1319
- Hass BL. Pires JC. Porter R. Phillips RL. Jackson SA. 2003. Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris). Theoretical & Applied Genetics. 107(5):773-782
- Halverson KM. Barry BA. 2003. Evidence for spontaneous structural changes in a dark-adapted state of photosystem II. Biophysical Journal. 85(4):2581-2585
- Halverson KM. Barry BA. 2003. Sucrose and glycerol effects on photosystem II. [Article] Biophysical Journal. 85(2):1317-1325
- Hong SB. Hughes EH. Shanks JV. San KY. Gibson SI. 2003. Role of the non-mevalonate pathway in indole alkaloid production by Catharanthus roseus hairy roots. Biotechnology Progress. 19(3):1105-1108
- Jin P. Wood MD. Wu Y. Xie ZY. Katagiri F. 2003. Cleavage of the Pseudomonas syringae type III effector AvrRpt2 requires a host factor(s) common among eukaryotes and is important for AvrRpt2 localization in the host cell. Plant Physiology. 133(3):1072-1082
- Liu JY. Blaylock LA. Endre G. Cho J. Town CD. VandenBosch KA. Harrison MJ. 2003. Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis. Plant Cell. 15(9):2106-2123
- Lovas A. Bimbo A. Szabo L. Banfalvi Z. 2003. Antisense repression of StubGAL83 affects root and tuber development in potato. Plant Journal. 33(1):139-147
- Magee PT. Gale C. Berman J. Davis D. 2003. Molecular genetic and genomic approaches to the study of medically important fungi. Infection & Immunity. 71(5):2299-2309
- Samac DA. Tesfaye M. 2003. Plant improvement for tolerance to aluminum in acid soils - a review. Plant Cell Tissue & Organ Culture. 75(3):189-207
- Samac DA. Willert AM. McBride MJ. Kinkel LL. 2003. Effect of antibiotic-producing Streptomyces on nodulation and leaf spot in alfalfa. Applied Soil Ecology. 22(1):55-66
- Sameshima R. Isawa T. Sadowsky MJ. Hamada T. Kasai H. Shutsrirung A. Mitsui H. Minamisawa K. 2003. Phylogeny and distribution of extra-slow-growing Bradyrhizobium japonicum harboring high copy numbers of RS alpha, RS beta and IS1631. FEMS Microbiology Ecology. 44(2):191-202
- Somers DA. Samac DA. Olhoft PM. 2003. Recent advances in legume transformation. Plant Physiology. 131(3):892-899
- Springer NM. Napoli CA. Selinger DA. Pandey R. Cone KC. Chandler VL. Kaeppler HF. Kaeppler SM. 2003. Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiology. 132(2):907-925
- Stombaugh SK. Orf JH. Jung HG. Somers DA. 2003. Relationships between soybean seed cell wall polysaccharides, yield, and seed traits. Crop Science. 43(2):571-576
- Tam LW. Dentler WL. Lefebvre PA. 2003. Defective flagellar assembly and length regulation in LF3 null mutants in Chlamydomonas. [Article] Journal of Cell Biology. 163(3):597-607
- Makarevitch I. Svitashev SK. Somers DA. 2003. Complete sequence analysis of transgene loci from plants transformed via microprojectile bombardment. Plant Molecular Biology. 52(2):421-432
- Marks MD. Esch JJ. 2003. Initiating inhibition - Control of epidermal cell patterning in plants [Review]. EMBO Reports. 4(1):24-25
- Mesfin A. Smith KP. Dill-Macky R. Evans CK. Waugh R. Gustus CD. Muehlbauer GJ. 2003. Quantitative trait loci for fusarium head blight resistance in barley detected in a two-rowed by six-rowed population. Crop Science. 43(1):307-318
- Muehlbauer GJ. Bushnell WR. 2003. Transgenic approaches to Fusarium head blight resistance. FUSARIUM HEAD BLIGHT OF WHEAT & BARLEY. PG. 318-362
- Neuhauser C. Andow DA. Heimpel GE. May G. Shaw RG. Wagenius S. 2003. Community genetics: Expanding the synthesis of ecology and genetics Ecology. 84(3):545-558
- Olhoft PM. Flagel LE. Donovan CM. Somers DA. 2003. Efficient soybean transformation using hygromycin B selection in the cotyledonary-node method. Planta. 216(5):723-735
- O'Neill NR. Bauchan GR. Samac DA. 2003. Reactions in the annual Medicago spp. core germ plasm collection to Phoma medicaginis. Plant Disease. 87(5):557-562
- Pujols-Ayala I. Sacksteder CA. Barry BA. 2003. Redox-active tyrosine residues: Role for the peptide bond in electron transfer. Journal of the American Chemical Society. 125(25):7536-7538
- Sachs RK. Halverson KM. Barry BA. 2003. Specific isotopic labeling and photooxidation-linked structural changes in the manganese-stabilizing subunit of photosystem II. Journal of Biological Chemistry. 278(45):44222-44229
- Samac DA. Smigocki AC. 2003. Expression of oryzacystatin I and II in alfalfa increases resistance to the root-lesion nematode. Phytopathology. 93(7):799-804
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Progress 01/01/02 to 12/31/02
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics in plant biology and agriculture. PMGI is composed of 27 faculty members and their lab personnel in seven departments of the College of Agriculture, Food and Environmental Sciences and the College of Biological Sciences at the University of Minnesota. PMGI supports research, often including joint research projects, and organizes educational opportunities. Faculty member M. David Marks, Ph.D. candidates Rachel Nguyen and Andy Baumgarten, and incoming graduate student Divya Chandran were supported in part by PMGI funds. PMGI provided funds to send six postdoctoral fellows and graduate students to scientific meetings to present posters of their work, and to partially cover the cost of a specialized course off-campus for one postdoctoral fellow. Members of PMGI laboratories presented biweekly seminars throughout the academic year. The PMGI spring course
featured five internationally known speakers in the area of plant development who interacted extensively with PMGI students. The PMGI annual retreat, attended by about 50 members, included talks by Dr. Bonnie Bartell (Dept. Biochemistry & Cell Biology, Rice University), University of MN scientists Ann Fallon (Entomology) and Claudia Schmidt-Dannert (Biochemistry, Molecular Biology and Biophysics), and PMGI graduate student Divya Chandran. The Institute also purchased a service agreement for a piece of shared equipment, the purchase of which had been funded in part by PMGI.
Impacts
The PMGI fosters cooperation among its members and other to strengthen projects in plant molecular genetic research and applications in agriculture, food, and environmental sciences. PMGI encourages the development of innovative methods in agriculture based on recent developments in biology, and educating future scientists about how to implement genomic, molecular, and cellular techniques in agriculture.
Publications
- Shapir N, Osborne JP, Johnson G, Sadowsky MJ, Wackett LP. 2002. Purification, substrate range, and metal center of AtzC: the N-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism. Journal of Bacteriology 184:5376-5384. Springer NM, Danilevskaya ON, Hermon P, Helentjaris TG, Phillips RL, Kaeppler HF, Kaeppler SM. 2002. Sequence relationships, conserved domains and expression patterns for maize homologs of the polycomb group genes E(z), esc, and E(Pc). Plant Physiology 128:1332-1345.
- Strong LC, Rosendahl C, Johnson G, Sadowsky MJ, Wackett LP. 2002. Arthrobacter aurescens TC1 metabolizes diverse s-triazine ring compounds. Applied & Environmental Microbiology 68:5973-5980. Svensson B, Tiede DM, Barry BA. 2002. Small-angle X-ray scattering studies of the manganese stabilizing subunit in photosystem II. Journal of Physical Chemistry B. 106:8485-8488.
- Svitashev SK, Pawlowski WP, Makarevitch I, Plank DW, Somers DA. 2002. Complex transgene locus structures implicate multiple mechanisms for plant transgene rearrangement. Plant Journal 32:433-445.
- Svitashev SK, Somers DA. 2002. Characterization of transgene loci in plants using FISH: A picture is worth a 1000 words. Plant Cell Tissue & Organ Culture 69:205-214. Swain SM, Tseng TS, Thornton TM, Gopalraj M, Olszewski NE. 2002. SPINDLY is a nuclear-localized repressor of gibberellin signal transduction expressed throughout the plant. Plant Physiology 129:605-615. Sztein AE, Ilic N, Cohen JD, Cooke TJ. 2002. Indole-3-acetic acid biosynthesis in isolated axes from germinating bean seeds: The effect of wounding on the biosynthetic pathway. Plant Growth Regulation 36:201-207.
- Tam LW, Lefebvre PA. 2002. The Chlamydomonas MBO2 locus encodes a conserved coiled-coil protein important for flagellar waveform conversion. Cell Motility & the Cytoskeleton 51:197-212.
- Wackett LP, Sadowsky MJ, Martinez B, Shapir N. 2002. Biodegradation of atrazine and related s-triazine compounds: from enzymes to field studies. Applied Microbiology & Biotechnology 58:39-45. Walz A, Park S, Slovin JP, Ludwig-Muller J, Momonoki YS, Cohen JD. 2002. A gene encoding a protein modified by the phytohormone indoleacetic acid. Proc. National Academy of Sciences USA 99:1718-1723. Xiao K, Kinkel LL, Samac DA. 2002. Biological control of Phytophthora root rots on alfalfa and soybean with Streptomyces. Biological Control 23(3):285-295, 2002.
- Zhu HY, Cannon SB, Young ND, Cook DR. 2002. Phylogeny and genomic organization of the TIR and non-TIR NBS-LRR resistance gene family in Medicago truncatula. Molecular Plant-Microbe Interactions 15:529-539.
- Ludwig-Muller J, Cohen JD. 2002. Identification and quantification of three active auxins in different tissues of Tropaeolum majus. Physiologia Plantarum 115:320-329. Matsuura K, Lefebvre PA, Kamiya R, Hirono M. 2002. Kinesin-II is not essential for mitosis and cell growth in Chlamydomonas. Cell Motility & the Cytoskeleton 52:195-201. Milach SCK. Rines HW, Phillips RL. 2002. Plant height components and gibberellic acid response of oat dwarf lines. Crop Science 42:1147-1154.
- Montealegre CM, van Kessel C, Russelle MP, Sadowsky MJ. 2002. Changes in microbial activity and composition in a pasture ecosystem exposed to elevated atmospheric carbon dioxide. Plant & Soil 243:197-207.
- Olszewski N, Sun TP, Gubler F. 2002. Gibberellin signaling: Biosynthesis, catabolism, and response pathways. Plant Cell 14:S61-S80. Ouelette AJA, Barry BA. 2002. Tandem mass spectrometric identification of spinach Photosystem II light-harvesting components. Photosynthesis Research 72:159-173.
- Patzlaff JS, Zhang JY, Brooker RJ, Barry BA. 2002. An isotope-edited FT-IR study of a symporter, the lactose permease. Biochemistry 41:7366-7372.
- Hartweck LM, Scott CL, Olszewski NE. 2002. Two O-linked N-acetylglucosamine transferase genes of Arabidopsis thaliana L. Heynh. Have overlapping functions necessary for gamete and seed development. Genetics 161:1279-1291.
- Kruger WM, Pritsch C, Chao SM, Muehlbauer GJ. 2002. Functional and comparative bioinformatic analysis of expressed genes from wheat spikes infected with Fusarium graminearum. Molecular Plant-Microbe Interactions 15:445-455.
- Kuchitsu K, Ward JM, Allen GJ, Schelle I, Schroeder JI. 2002. Loading acetoxymethyl ester fluorescent dyes into the cytoplasm of Arabidopsis and Commelina guard cells. New Phytologist 153:527-533.
- Ljung K, Hull AK, Kowalczyk M, Marchant A, Celenza J, Cohen JD, Sandberg G. 2002. Biosynthesis, conjugation, catabolism and homeostasis of indole-3-acetic acid in Arabidopsis thaliana. Plant Molecular Biology 50:309-332.
- Penuela S, Danesh D, Young ND. 2002. Targeted isolation, sequence analysis, and physical mapping of nonTIR NBS-LRR genes in soybean. Theoretical & Applied Genetics 104:261-272.
- Pongsilp N, Teaumroong N, Nuntagij A, Boonkerd N, Sadowsky MJ. 2002. Genetic structure of indigenous non-nodulating and nodulating populations of Bradyrhizobium in soils from Thailand. Symbiosis 33:39-58. Pujols-Ayala I, Barry BA. 2002. Histidine 190-D1 and glutamate 189-D1 provide structural stabilization in photosystem II. Biochemistry 41:11456-11465.
- Qiu JL, Jilk R, Marks MD, Szymanski DB. 2002. The Arabidopsis SPIKE1 gene is required for normal cell shape control and tissue development. Plant Cell 14:101-118.
- Rapparini F, Tam YY, Cohen JD, Slovin JP. 2002. Indole-3-acetic acid metabolism in Lemna gibba undergoes dynamic changes in response to growth temperature. Plant Physiology 128:1410-1416.
- Reinders A, Schulze W, Kuhn C, Barker L, Schulz A, Ward JM, Frommer WB. 2002. Protein-protein interactions between sucrose transporters of different affinities colocalized in the same enucleate sieve element. Plant Cell 14:1567-1577.
- Reinders A, Schulze W, Thaminy S, Stagljar I, Frommer WB, Ward JM. 2002. Intra- and intermolecular interactions in sucrose transporters at the plasma membrane detected by the split-ubiquitin system and functional assays. Structure 10:763-772. Ribnicky DM, Cohen JD, Hu WS, Cooke TJ. 2002. An auxin surge following fertilization in carrots: a mechanism for regulating plant totipotency. Planta 214:505-509.
- Sajjaphan K, Shapir N, Judd AK, Wackett LP, Sadowsky MJ. 2002. Novel psbA1 gene from a naturally occurring atrazine- resistant cyanobacterial isolate. Applied & Environmental Microbiology 68:1358-1366.
- Saruul P, Srienc F, Somers DA, Samac DA. 2002. Production of a biodegradable plastic polymer, poly-beta-hydroxybutyrate, in transgenic alfalfa. Crop Science 42:919-927.
- Salvi S, Tuberosa R, Chiapparino E, Maccaferri M, Veillet S, van Beuningen L, Isaac P, Edwards K, Phillips RL. 2002. Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize. Plant Molecular Biology 48:601-613. Schulze J, Tesfaye M, Litjens RHMG, Bucciarelli B, Trepp G, Miller S, Samac D, Allan D, Vance CP. 2002. Malate plays a central role in plant nutrition. Plant & Soil 247:133-139.
- Seffernick JL, McTavish H, Osborne JP, de Souza M, Sadowsky MJ, Wackett LP. 2002. Atrazine chlorohydrolase from Pseudomonas sp strain ADP is a metalloenzyme. Biochemistry 41:14430-14437.
- Seffernick JL, Shapir N, Schoeb M, Johnson G, Sadowsky MJ, Wackett LP. 2002. Enzymatic degradation of chlorodiamino-s-triazine Applied & Environmental Microbiology 68:4672-4675.
- Ananiev EV, Vales MI, Phillips RL, Rines HW. 2002. Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa. Genome 45:431-441.
- Anderson LB, Maderia M, Ouellette AJA, Putnam-Evans C, Higgins L, Krick T, MacCoss MJ, Lim H, Yates JR, Barry BA. 2002. Posttranslational modifications in the CP43 subunit of photosystem II. Proc. National Academy of Sciences USA 99:14676-14681.
- Ayala I, Range K, York D, Barry BA. 2002.Spectroscopic properties of tyrosyl radicals in dipeptides. Journal of the American Chemical Society 124:5496-5505.
- Bean GJ, Marks MD, Hulskamp M, Clayton M, Croxdale JL. 2002. Tissue patterning of Arabidopsis cotyledons. New Phytologist 153:461-467.
- Benson ES, Filler SC, Berman J, 2002. A forkhead transcription factor is important for true hyphal as well as yeast morphogenesis in Candida albicans. Eukaryotic Cell 1:787-798.
- Cannon SB, Zhu HY, Baumgarten AM, Spangler R, May G, Cook DR, Young ND. 2002. Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies. Journal of Molecular Evolution 54:548-562.
- Cappuccio JA, Ayala I, Elliott GI, Szundi I, Lewis J, Konopelski JP, Barry BA, Einarsdottir O. 2002. Modeling the active site of cytochrorne oxidase: Synthesis and characterization of a cross-linked histidine-phenol. Journal American Chemical Society 124:1750-1760.
- Charnock SJ, Bolam DN, Nurizzo D, Szabo L, McKie VA, Gilbert HJ, Davies GJ. 2002. Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello-and mannohexaose. Proc National Academy of Sciences USA 99:14077-14082.
- Chou JC, Mulbry WW, Cohen JD. 2002. N-carbobenzyloxy-D-aspartic acid as a competitive inhibitor of indole-3-acetyl-L-aspartic acid hydrolase of Enterobacter agglomerans. Plant Growth Regulation 37:241-248.
- Cooke TJ, Poli D, Sztein AE, Cohen JD. 2002. Evolutionary patterns in auxin action. Plant Molecular Biology 49:319-338.
- Enomoto S, Glowczewski L, Berman J. 2002. MEC3, MEC1, and DDC2 are essential components of a telomere checkpoint pathway required for cell cycle arrest during senescence in Saccharomyces cerevisiae. Molecular Biology of the Cell 13:2626-2638.
- Epstein E, Cohen JD, Slovin JP. 2002. The biosynthetic pathway for indole-3-acetic acid changes during tomato fruit development. Plant Growth Regulation 38:16-21A.
- Erwin JE, Warner RM, Smith AG. 2002. Vernalization, photoperiod and GA(3) interact to affect flowering of Japanese radish (Raphanus sativus Chinese Radish Jumbo Scarlet). Physiologia Plantarum 115:298-302.
- Fedorova M, van de Mortel J, Matsumoto PA, Cho J, Town CD, VandenBosch KA, Gantt JS, Vance CP. 2002. Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula. Plant Physiology 130:519-537.
- Foster-Hartnett D, Mudge J, Larsen D, Danesh D, Yan HH, Denny R, Penuela S, Young ND. 2002. Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G. Genome 45:634-645.
- Gleason FK, Olszewski NE. 2002. Isolation of the gene for the B-12-dependent ribonucleotide reductase from Anabaena sp strain PCC 7120 and expression in Escherichia coli. Journal of Bacteriology 184:6544-6550.
- Harper G, Hull R, Lockhart B, Olszewski N. 2002. Viral sequences integrated into plant genomes. Annual Review of Phytopathology 40:119-136.
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Progress 01/01/01 to 12/31/01
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics in plant biology and agriculture. PMGI is composed of 27 faculty members and their lab personnel in seven departments of the College of Agriculture, Food and Environmental Sciences and the College of Biological Sciences at the University of Minnesota. PMGI supports research, often including joint research projects, and organizes educational opportunities. Faculty member M. David Marks, Ph.D. candidates Rachel Nguyen, Andrew Baumgarten, and incoming graduate student Divya Chandran were supported in part by PMGI funds. PMGI provided funds to support the travel of 11 postdocs and graduate students to national and international meetings to present talks or posters of their work, and the 2-month visit and seminar series by virologist Roger Hull of the John Innes Research Centre, Norwich, England. Members of PMGI presented biweekly seminars, and PMGI also
co-sponsored several seminars in departments housing PMGI members. The PMGI annual retreat included talks by Dr. Rick Amasino (Dept. Biochemistry, University of Wisconsin), University of MN scientists Jeff Simon (Genetics, Cell Biology and Development) and Arkady Khodursky (Biochemistry, Molecular Biology and Biophysics), and the two advanced graduate students supported by PMGI.
Impacts
The PMGI fosters cooperation among its members and other to strengthen projects in plant molecular genetic research and applications in agriculture, food, and environmental sciences. PMGI encourages the development of innovative methods in agriculture based on recent developments in biology, and educating future scientists about how to implement genomic, molecular, and cellular techniques in agriculture.
Publications
- Publications submitted separately due to large number of publications for this group project. 2001
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Progress 01/01/00 to 12/31/00
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics in plant biology and agriculture. PMGI is composed of 23 faculty members and their lab personnel in six departments of the College of Agriculture, Food and Environmental Sciences and the College of Biological Sciences at the University of Minnesota. PMGI supports faculty research, including joint research projects, and organizes educational opportunities. PMGI funds support part of the salary for Dr. M. David Marks (Associate Professor, Plant Biology), as well as one incoming graduate student and two Ph.D. candidates in the process of thesis writing. PMGI assisted 16 graduate students and postdocs to travel to national and international meetings. Partial funding for the purchase of a Lightcycler Thermocycler and Deconvolution software was also provided by PMGI. Members of PMGI presented biweekly seminars throughout the year and held an annual retreat,
including presentations by Dr. Jeffery Kahn (Center for Bioethics), Dr. Gary Nelsestuen (Biochemistry, Molecular Biology, and Biophysics).
Impacts
The PMGI fosters cooperation among its members and others to strengthen projects in plant molecular genetic research and applications in agriculture, food, and environmental sciences by encouraging the development of innovative methods in agriculture based on recent developments in biology, and educating future scientists with skills to implement genomic, molecular, and cellular techniques in agriculture.
Publications
- Smith EF. Lefebvre PA. Defining functional domains within PF16: A central apparatus component required for flagellar motility. Cell Motility & the Cytoskeleton. 46(3):157-165, 2000.
- Stombaugh SK. Jung HG. Orf JH. Somers DA. Genotypic and environmental variation in soybean seed cell wall polysaccharides. Crop Science. 40(2):408-412, 2000.
- Strong LC. McTavish H. Sadowsky MJ. Wackett LP. Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase. Environmental Microbiology. 2(1):91-98, 2000.
- Svitashev S. Ananiev E. Pawlowski WP. Somers DA. Association of transgene integration sites with chromosome rearrangements in hexaploid oat. Theoretical & Applied Genetics. 100(6): 872-880, 2000.
- Szymanski DB. Lloyd AM. Marks MD. Progress in the molecular genetic analysis of trichome initiation and morphogenesis in Arabidopsis. Tends in Plant Science. 5(5):214-219, 2000.
- Vance CP. Amide biosynthesis in root nodules of temperate legumes. prokaryotic Nitrogen Fixation: A Model System for the Analysis of a biological Process. Pg. 589-607, 2000.
- Walker AR. Marks MD. Trichome initiation in Arabidopsis. Advance in Botanical Research Incorporating Advances In Plant Pathology, Vol 31 2000 : Plant Trichomes. 31 pg. 219-236. 2000
- Young, N.D. The genetic architecture of resistance. Current Opinion in Plant Biology 3: 285-290, 2000.
- Yu Y. Tomkins JP. Waugh R. Frisch DA. Kudma D. Kleinhofs A. Brueggeman RS. Muehlbauer GJ. Wise RP. Wing RA. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theoretical & applied Genetics. 101(7):1093-1099, 2000.
- Zambino PJ. Kubelik AR. Szabo LJ. Gene action and linkage of avirulence genes to DNA markers in he rust fungus Puccinia graminis. Phytopathology. 90(8):819-826, 2000.
- Engelen-Eigles G. Jones RJ. Phillips RL. DNA endoreduplication in maize endosperm cells: the effect of exposure to short-term high temperature. Plant, Cell & Environment. 23(6):657-663, 2000.
- Anderson LB. Ouellette AJA. Barry BA. Probing the structure of photosystem II with amines and phenylhydrazine. Journal of Biological Chemistry. 275(7):4920-4927, 2000.
- Asleson CM. Asleson JC. Malandra E. Johnston S. Berman J. Filamentous growth of Saccharomyces cerevisiae is regulated by manganese. Fungal Genetics & Biology. 30(2):155-162, 2000.
- Baird V. Blume YB. Wick SM. Microtubular and cytoskeletal mutants. Plant Microtubules: Potential For Biotechnology. Pg. 159-191, 2000.
- Bass HW. Riers-Lizarazu O. Ananisv EV. Bordoli SJ. Rines HW. Phillips RL. Sedat JW. Agard DA. Cande WZ. Evidence for the coincident initiation of homologue pairing and synapses during the telomere-clustering (bouquet) sage of meiotic prophase. Journal of Cell Science. 113(6):1033-1042, 2000.
- Cao XF. Springer NM. Muszynski MG. Phillips RL. Kaeppler S. Jacobsen SE. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proceedings of the National Academy of Sciences of the United States of America. 97(9):4979-4984, 2000.
- Day, R.B., McAlvin, C.B., Loh, J.T., Denny, R.L., Wood, T.C., Young, N.D., Stacey, G. Differential expression of two soybean apyrases; one of which is an early nodulin. Molecular Plant-Microbe Interactions 13:1053-1070, 2000.
- Dombek PE. Johnson LK. Zimmerley ST. Sadowsky MJ. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Applied & Environmental Microbiology. 66(6):2572-2577, 2000.
- Plesofsky N. Gardner N. Videira A. Brambl R. NADH dehydrogenase in Neurospora crassa contains myristic acid covalently linked to the ND5 subunit peptide. Biochimica et Biophysica Acta - Molecular Cell Research. 1495(3):223-230, 2000.
- Pritsch C. Muehlbauer GJ. Bushnell WR. Somers DA. Vance CP. Fungal development and induction of defense response genes during early infection of wheat spikes by Fusarium graminearum. Molecular Plant-Microbe Interactions. 13(2):159-169, 2000.
- Riera-Lizarazu O. Vales MI. Ananiev EV. Rines HW. Phillips RL. Production and characterization of maize chromosome 9 radiation hybrids derived from an oat-maize addition line. Genetics. 156(1):327-339, 2000.
- Sadowsky MJ> Competition for nodulation in the soybean/Bradyrhizobium symbiosis. Prokaryotic Nitrogen Fixation: A Model System For The Analysis of a Biological Process. Pg. 279-293, 2000.
- Schoenbeck MA. Temple SJ. Trepp GB. Blumenthal JM. Samac DA. Gantt JS. Hernandez G. Vance CP. Decreased NADH glutamate synthase activity in nodules and flowers of alfalfa (Medicago sativa L.) transformed with an antisense glutamate synthase transgene. Journal of Experimental Botany. 51(342): 29-39, 2000.
- Seffernick JL. Johnson G. Sadowsky MJ. Wackett LP. Substrate specificity of atrazine chlorohydrolase and atrazine-catabolizing bacteria. Applied & Environmental Microbiology. 66(10):4247-4252, 2000.
- Espinosa-Victoria D. Vance CP. Graham PH. Host variation in traits associated with crown nodule senescence in soybean. Crop Science, 40(1):103-109, 2000.
- Gilbert GA. Knight JD. Vance CP. Allan DL. Proteoid root development of phosphorus deficient lupin is mimicked by auxin and phosphonate. Annals of Botany. 85(6):921-928, 2000.
- Graham PH. Vance CP. Nitrogen fixation in perspective : an overview of research and extension needs. Field Crops Research. 65(2-3):93-106, 2000.
- Kennard WC. Phillips RL. Porter RA. Grombacher AW. A comparative map of wild ice (Zizania palustris L. 2n=2x=3-). Theoretical & Applied Genetics. 101(5-6):677-684, 2000.
- Kim S. Barry BA. Identification of carbonyl modes of P-700 and P-700(+) by in situ chlorophyll labeling in photosystem I. Journal of the American Chemical Society. 122(20):4980-4981, 2000 May 24.
- Kianian SF. Phillips RL. Rines HW. Fulcher RG. Webster FH. Stuthman DD. Quantitative trait loci influencing bet-glucan content in oat (Avena sativa, 2n=6x=42). Theoretical & Applied Genetics. 101(7):1039-1048, 2000.
- Lockhart BE. Menke J. Dahal G. Olszewski NE. Characterization and genomic analysis of tobacco vein clearing virus, a plant pararetrovirus that is transmitted vertically and related to sequences integrated in the host genome. Journal of General Virology. 81(Part 6):1579-1585, 2000.
- Lohrke SM. Madrzak CJ. Hur HG. Judd AD. Orf JH. Sadowsky MF. Short communication - Inoculum density - dependent restriction of nodulation in the soy bean-bradyrizobium japonicum symbiosis. Symbiosis. 29(1):59-70, 2000.
- Patzlaff JS. Brooker RJ. Barry BA. A reaction-induced Fourier transform-infrared spectroscopic study of the lactose permease - A transmembrane potential perturbs carboxylic acid residues. Journal of biological Chemistry. 275(37): 28695-28700, 2000.
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Progress 01/01/99 to 12/31/99
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics in plant biology and agriculture. PMGI is composed of 23 faculty members and their lab personnel in six departments of the College of Agriculture, Food and Environmental Sciences and the College of Biological Sciences at the University of Minnesota. PMGI supports faculty research, often including joint research projects, and organizes educational opportunities. Dr. M. David Marks (Plant Biology)and one postdoc (Dr. Lynn Hartweck) were supported, in part, by PMGI funds. Funds for 20 graduate students and postdocs to travel to national and international meetings and give presentations or posters were also provided by PMGI. Members of PMGI presented biweekly seminars throughout the year and held an annual retreat, including presentations by Dr. Vic Bloomfield (Biochemistry, Molecular Biology and Biophysics), Dr. Tony Dean (Ecology and Evolutionary
Biology, and Dr. Georgiana May (Plant Biology). A special topics course on "Bioinformatics and Proteomics" was sponsored by PMGI, in which five outstanding scientists were invited to campus to give presentations and lead discussion with graduate students and postdocs.
Impacts
The PMGI fosters cooperation among its members and others to strengthen projects in plant molecular genetic research and applications in agriculture, food, and environmental sciences by encouraging the development of innovative methods in agriculture based on recent developments in biology, and educating future scientists with skills to implement genomic, molecular, and cellular techniques in agriculture.
Publications
- Yoshioka H. Gregerson RG. Samac DA. Hoevens KCM. Trepp G. Gantt JS. Vance CP. Aspartate aminotransferase in alfalfa nodules: Localization of mRNA during effective and ineffective nodule development and promoter analysis. Molecular Plant-Microbe Interactions. 12(4):263-274, 1999 Apr.
- Bucciarelli B. Ostry ME. Fulcher RG. Anderson NA. Vance CP. Histochemical and microspectrophotometric analyses of early wound responses of resistant and susceptible Populus tremuloides inoculated with Entoleuca mammata ( Hypoxylon mammatum). Canadian Journal of Botany-Revue Canadienne de Botanique. 77(4):548-555, 1999
- Cregan PB. Mudge J. Fickus EW. Danesh D. Denny R. Young ND. Two simple sequence repeat markers to select for soybean cyst nematode resistance coditioned by the rhg1 locus. Theoretical & Applied Genetics. 99(5):811-818, 1999 Sep.
- Anikster Y. Eilam T. Mittelman L. Szabo LJ. Bushnell WR. 1999, Sep-Oct. Pycnial nectar of rust fungi induces cap formation on pycniospores of opposite mating type. Mycologia. 91(5):858-870.
- Ascenzi R. Gantt JS. 1999 Sep. Molecular genetic analysis of the drought-inducible linker histone variant in Arabidopsis thaliana. Plant Molecular Biology. 41(2):159-169.
- Ascenzi R. Gantt JS. 1999, Nov. Subnuclear distribution of the entire complement of linker histone variants in Arabidopsis thaliana. Chromosoma. 108(6):345-355.
- Ayala I. Kim S. Barry BA. A difference fourier transform infrared study of tyrosyl radical Z center dot decay in photosystem II. Biophysical Journal. 77(4):2137-2144, 1999 Oct.
- Badrane H. May G. The divergence-homogenization duality in the evolution of the b1 mating type gene of Coprinus cinereus. Molecular Biology & Evolution. 1999.
- Cregan PB. Mudge J. Fickus EW. Marek LF. Danesh D. Denny R. Shoemaker RC. Matthews BF. Jarvik T. Young ND. Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theoretical & Applied Genetics. 98(6-7):919-928, 1999 May.
- De Koyer DL. Phillips RL. Stuthman DD. Changes in genetic diversity during seven cycles of recurrent selection for grain yield in oat, Avena sativa L.. Plant Breeding. 118(1):37-43, 1999 Mar.
- de la Pena RC. Smith KP. Capettini F. Muehlbauer GJ. Gallo-Meagher M. Dill-Macky R. Somers DA. Rasmusson DC. Quantitative trait loci associated with resistance to Fusarium head blight and kernel discoloration in barley. Theoretical & Applied Genetics. 99(3-4):561-569, 1999 Aug.
- de Souza ML. Sadowsky MJ. Wackett LP. Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: Gene sequence, enzyme purification, and protein characterization (vol 178, pg 4894, 1996).
- El Maghraby GMM. Williams AC. Barry BW. Skin delivery of oestradiol from deformable and traditional liposomes: Mechanistic studies. Journal of Pharmacy & Pharmacology. 51(10):1123-1134, 1999 Oct.
- Fedorova M. Tikhonovich IA. Vance CP. Expression of C-assimilating enzymes in pea (Pisum sativum L.) root nodules. In situ localization in effective nodules. Plant, Cell & Environment. 22(10):1249-1262, 1999 Oct.
- Silflow CD. Liu B. LaVoie M. Richardson EA. Palevitz BA. gamma-tubulin in Chlamydomonas: Characterization of the gene and localization of the gene product in cells. Cell Motility & the Cytoskeleton. 42(4):285-297, 1999.
- Hutchison RS. Steenhuis JJ. Yocum CF. Razeghifard MR. Barry BA. Deprotonation of the 33-kDa, extrinsic, manganese-stabilizing subunit accompanies photooxidation of manganese in photosystem II. Journal of Biological Chemistry. 274(45):31987-31995, 1999 Nov 5.
- Gengenbach BG. VanDee KL. Egli MA. Hildebrandt KM. Yun SJ. Lutz SM. Marshall LC. Wyse DL. Somers DA. Genetic relationships of alleles for tolerance to sethoxydim herbicide in maize. Crop Science. 39(3):812-818, 1999 May-Jun.
- Gilbert GA. Knight JD. Vance CP. Allan DL. Acid phosphatase activity in phosphorus-deficient white lupin roots. Plant, Cell & Environment. 22(7):801-810, 1999 Jul.
- Hahn JJ. Eschenlauer AC. Sleytr UB. Somers DA. Srienc F. Peroxisomes as sites for synthesis of polyhydroxyalkanoates in transgenic plants. Biotechnology Progress. 15(6):1053-1057, 1999 Nov-Dec.
- Johnston SD. Lew JE. Berman J. 1999. Gbp1p, a protein with RNA recognition motifs, binds single-stranded telomeric DNA and changes its binding specificity upon dimerization.
- Kianian SF. Egli MA. Phillips RL. Rines HW. Somers DA. Gengenbach BG. Webster FH. Livingston SM. Groh S. O'Donoughue LS. Sorrells ME. Wesenberg DM. Stuthman DD. Fulcher RG. 1999. Association of a major groat oil content QTL and an acetyl-CoA carboxylase gene in oat. Theoretical & Applied Genetics. 98(6-7):884-894.
- Lefebvre PA. Silflow CD. Chlamydomonas: The cell and its genomes. Genetics. 151(1):9-14, 1999 Jan.
- Loh J. Stacey MG. Sadowsky MJ. Stacey G. The Bradyrhizobium japonicum nolA gene encodes three functionally distinct proteins. Journal of Bacteriology. 181(5):1544-1554, 1999 Mar.
- Lynberg OK. Thiagarajan V. Stemke DJ. Schottel JL. Scriven LE. Flickinger MC. A Patch Coating Method For Preparing Biocatalytic Films Of Escherichia coli. Biotechnology & Bioengineering. 62(1):44-55, 1999 Jan 5.
- Lyngberg OK. Stemke DJ. Schottel JL. Flickinger MC. A single-use luciferase-based mercury biosensor using Escherichia coli HB101 immobilized in a latex copolymer film. Journal of Industrial Microbiology & Biotechnology. 23(1):668-676, 1999 Jul.
- May G. Shaw F. Badrane H. Vekemans X. The signature of balancing selection: Fungal mating compatibility gene evolution. Proceedings of the National Academy of Sciences of the United States of America. 96(16):9172-9177, 1999 Aug 3.
- McCallum BD. Roelfs AP. Szabo LJ. Groth JV. Comparison of Puccinia graminis f.sp tritici from South America and Europe. Plant Pathology. 48(5):574-581, 1999
- Meyers BC. Dickerman AW. Michelmore RW. Sivaramakrishnan S. Sobral BW. Young ND. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant Journal. 20(3):317-332, 1999.
- Muehlbauer GJ. Fowler JE. Girard L. Tyers R. Harper L. Freeling M. Ectopic expression of the maize homeobox gene Liguleless3 alters cell fates in the leaf. Plant Physiology. 119(2):651-662, 1999 Feb.
- Ndowora T. Dahal G. LaFleur D. Harper G. Hull R. Olszewski NE. Lockhart B. Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences. Virology. 255(2):214-220, 1999 Mar 15.
- Neeno-Eckwall EC. Schottel JL. Occurrence of antibiotic resistance in the biological control of potato scab disease. Biological Control. 16(2):199-208, 1999 Oct.
- Plesofsky N. Brambl R. Glucose metabolism in Neurospora is altered by heat shock and by disruption of HSP30. Biochimica et Biophysica Acta - Molecular Cell Research. 1449(1):73-82, 1999 Feb 4.
- Plesofsky N. Gardner N. Lill R. Brambl R. Disruption of the gene for Hsp30, an alpha-crystallin-related heat shock protein of Neurospora crassa, causes defects in import of proteins into mitochondria. Biological Chemistry. 380(10):1231-1236, 1999 Oct.
- Razeghifard MR. Kim S. Patzlaff JS. Hutchison RS. Krick T. Ayala I. Steenhuis JJ. Boesch SE. Wheeler RA. Barry BA. In vivo, in vitro, and calculated vibrational spectra ofplastoquinone and the plastosemiquinone anion radical. Journal of Physical Chemistry B. 103(44):9790-9800, 1999 Nov 4.
- Sadowsky M. Obituary - Dr. Edwin L. Schmidt. Symbiosis. 26(1):91-92, 1999. Table of Contents Complete Reference
- Schoenbeck MA. Samac DA. Fedorova M. Gregerson RG. Gantt JS. Vance CP. The alfalfa (Medicago sativa) TDY1 gene encodes a mitogen-activated protein kinase homolog. Molecular Plant-Microbe Interactions. 12(10):882-893, 1999 Oct.
- Steenhuis JJ. Hutchison RS. Barry BA. Alterations in carboxylate ligation at the active site of photosystem II. Journal of Biological Chemistry. 274(21):14609-14616, 1999 May 21.
- Stewart EL. Liu ZW. Crous PW. Szabo LJ. Phylogenetic relationships among some cercosporoid anamorphs of Mycosphaerella based on rDNA sequence analysis. Mycological Research. 103(Part 11):1491-1499, 1999 Nov.
- Thiagarajan VS. Huang ZS. Scriven LE. Schottel JL. Flickinger MC. Microstructure of a biocatalytic latex coating containing viable Escherichia coli cells. Journal of Colloid & Interface Science. 215(2):244-257, 1999 Jul 15.
- Thornton TM. Swain SM. Olszewski NE. Gibberellin signal transduction presents ... the SPY who O-GlcNAc'd me . Trends in Plant Science. 4(11):424-428, 1999 Nov.
- Trepp GB. Plank DW. Gantt JS. Vance CP. 1999, Mar. NADH-glutamate synthase in alfalfa root nodules. Immunocytochemical localization. Plant Physiology. 119(3):829-837.
- Trepp GB. Temple SJ. Bucciarelli B. Shi LF. Vance CP. Expression map for genes involved in nitrogen and carbon metabolism in alfalfa root nodules. Molecular Plant-Microbe Interactions. 12(6):526-535, 1999 Jun.
- Trepp GB. van de Mortel M. Yoshioka H. Miller SS. Samac DA. Gantt JS. Vance CP. NADH-glutamate synthase in alfalfa root nodules. Genetic regulation and cellular expression. Plant Physiology. 119(3):817-828, 1999 Mar.
- Vladutu C. McLaughlin J. Phillips RL. Fine mapping and characterization of linked quantitative trait loci involved in the transition of the maize apical meristem from vegetative to generative structures. Genetics. 153(2):993-1007, 1999 Oct.
- Walker AR. Davison PA. Bolognesi-Winfield AC. James CM. Srinivasan N. Blundell TL. Esch JJ. Marks MD. Gray JC. The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein. Plant Cell. 11(7):1337-1349, 1999 Jul.
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Progress 01/01/98 to 12/31/98
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics in plant biology and agriculture. PMGI is composed of 23 faculty members and their lab personnel in six departments of the College of Agricultural, Food and Environmental Sciences and the College of Biological Sciences at the University of Minnesota. PMGI supports faculty research, often including joint research projects, and organizes educational opportunities. Dr. M. David Marks (Genetics and Cell Biology), three postdoctorals (Dr. Lynn Harteck, Dr. Rong-Lin Wang, and Dr. Ron Hutchinson) and one graduate student (Joann Mudge) were supported, in part, by PMGI funds. Funds for 20 graduate students and postdocs to travel to national and international meetings and give presentations or posters were also provided by PMGI. Members of PMGI presented biweekly seminars throughout the year and held an annual retreat, including presentations by Dr. Vivek Kapur
(Advanced Genetic Analysis Center), Dr. Gary Muehlbauer (Agronomy and Plant Genetics), and Dr. Alan Smith (Horticulture). A special topics course in "Functional Genomics" was sponsored by PMGI, in which five outstanding scientists were invited to campus to give presentations and lead discussion with graduate students and postdocs.
Impacts
(N/A)
Publications
- Szymanski, D.B., R.A. Jilk, S.M. Pollock, and M.D. Marks (1998) Control of GL2 expression in Arabidopsis leaves and trichomes. Development 125:1161-1171.
- Szymanski, D.B., D.A. Klis, J.C. Larkin, and M.D. Marks (1998) cot1: A regulator of Arabidopsis trichome initiation. Genetics 149:565-577.
- Szymanski, D.B., and M.D. Marks (1998) GLABROUS1 overexpression and TRIPTYCHON alter the cell cycle and trichome cell fate in Arabidopsis. Plant Cell 10:2047-2062.
- Torbert, K.A., H.W. Rines and D.A. Somers. (1998). Transformation of oat using mature embryo-derived tissue cultures. Crop Sci. 38:226-231.
- Torbert, K.A., Gopalraj, M., Medberry, S.L., Olszewski, N.E. and Somers, D.A. (1998) Vascular-specific expression of the Commelina yellowmottle virus promoter in transgenic oat. Plant Cell Reports 17: 284-287.
- Cheng, C.-P., Lockhart, B.E. and Olszewski, N.E. (1998) Tubules containing virus particles are present in plant tissues infected with commelina yellow mottle badnavirus. Journal of General Virology 79: 925-929.
- Robertson, M., Swain, S.M., Chandler, P.M. and Olszewski, N.E. (1998) Identification of a negative regulator of gibberellin action, HvSPY, in barley. Plant Cell 10: 995-1007.
- Tzafrir, I., Torbert, K.A., Lockhart, B.E.L., Somers, D.A. and Olszewski, N.E. (1998) The sugarcane bacilliform virus promoter is active in both monocots and dicots. Plant Molecular Biology 347-356.
- Shi, L. and Olszewski, N.E. (1998) Gibberellin and abscisic acid regulate GAST1 Expression at the level of transcription. Plant Mol. Biol. 38:1053-1060.
- Koev, G., B.R. Mohan, S.P. Dinesh-Kumar, K.A. Torbert, D.A. Somers, and W.A. Miller. 1998. Extreme reduction of disease in oats transformed with the 5' half of the barley yellow dwarf virus-PAV genome. Phytopathology 88:1013-1019.
- McGrath, P.F., J.R. Vincent, C.-H-. Lei, W.P. Pawlowski, K.A. Torbert, W. Gu, H.F. Kaeppler, Y. Wan, P.G. Lemaux, H.R. Rines, D.A. Somers, B.A. Larkins and R.M. Lister. (1998). Coat protein-mediated resistance to barley yellow dwarf in oats and barley. European Journal of Plant Pathology. 103:695-710.
- Pawlowski, W.P. and D.A. Somers.(1998) Transgenic DNA integrated into the oat genome is frequently interspersed by host DNA. Proc. Natl. Acad. Sci. USA 95:12106-12110.
- Pawlowski, W.P., K.A. Torbert, H.W. Rines, and D.A. Somers. (1998). Irregular patterns of transgene silencing in allohexaploid oat. Plant Molec. Biol. 38:597-607.
- Torbert, K.A., H.W. Rines, H.F. Kaeppler, G.R. Menon, and D.A. Somers. (1998). Genetically engineering elite oat cultivars. Crop Sci. 38:1685-1687.
- Torbert, K.A., M. Gopalraj, S.L. Medberry, N.E. Olszewski and D.A. Somers. (1998). Expression of the Commelina yellow mottle virus promoter in transgenic oat. Plant Cell Rep. 17:284-287.
- Tzafrir, I., K.A. Torbert, B.E.L. Lockhart, D.A. Somers, and N.E. Olszewski. (1998). The sugarcane bacilliform badnavirus promoter is active in both monocots and dicots. Plant Molec. Biol. 38:347-356.
- Ananiev, E.V., R.L. Phillips, and H.W. Rines, (1998). A knob-associated tandem repeat in maize capable of forming fold-back DNA segments: Are chromosome knobs megatransposons? Proc. Natl. Acad. Sci. USA 95: 10785-10790.
- Ananiev, E.V., R.L. Phillips, and H.W. Rines, (1998). Complex structure of knob DNA on maize chromosome 9: Retrotransposon invasion into heterochromatin. Genetics 149: 2025-2037.
- Chen, Z.J., R.L. Phillips, and H.W. Rines, (1998). Maize DNA enrichment by representational difference analysis. Theor. Appl. Genet. 97:337-344.
- Jellen, E.N., H.W. Rines, S.L. Fox, D.W. Davis. R.L. Phillips, and B.S. Gill. (1998). Characterization of "Sun II" oat monosomics through C-banding and identification of eight new "Sun II" monosomics. Theor. Appl. Genet. 95:1190-1195.
- Milach, S.C.K., H.W. Rines, R.L. Phillips, D.D. Stuthman, and J. Morikawa. (1998). Inheritance of a new dwarfing gene in oat. Crop Sci. 38:356-360.
- Olhoft, P.M. and R.L. Phillips. (1998). Genetic and epigenetic instability in tissue culture and regenerated progenies. In Plant Response to Environmental Stresses: From phytohormones to genomic reorganization. Ed. H.R. Lerner, M. Dekker Inc., New York.
- Phillips, R.L. and M. Freeling, (1998). Plant genomics and our food supply: An introduction. Proc. Natl. Acad. Sci. USA 95: 1969-1970.
- Chu,B., T.J. Wilson, C. McCune-Zierath, D.P. Snustad, and J.V. Carter (1998) Two beta(symbol)-tubulin genes, TUB1 and TUB8, of Arabidopsis exhibit largely nonoverlapping patterns of expression. Plant Mol. Biol. 37:785-790.
- Vance, C.P. (1998) Legume symbiotic nitrogen fixation: agronomic aspects. p. 509 -530. In The Rhizobiaceae (eds. H.P. Spaink, A. Kondorosi, P.J.J. Hooykas) Kluwer Academic Publishers, Dordrecht, The Netherlands.
- Zhu, Y., C.C. Sheaffer, M.P. Russelle, and C.P. Vance. (1998) Dry matter accumulation and dinitrogen fixation of annual Medicago species. Agron. J. 90:103-108. 1998.
- Miller, S.S., B.T. Driscoll, R.G. Gregerson, J.S. Gantt, and C.P. Vance. Alfalfa malate dehydrogenase (MDH): molecular cloning and characterization of five different forms reveals a unique nodule-enhanced MDH. Plant J. 15:173-184.
- Schulze, J., L. Shi, J. Blumenthal, D.A. Samac, J.S. Gantt, and C.P. Vance. (1998) Inhibition of root nodule phosphoenolpyruvate carboxylase through antisense strategy impacts nitrogen fixation and plant growth. Phytochemistry 49:341-346.
- Temple, S.J., C.P. Vance, and J.S. Gantt. (1998) Glutamate synthase and nitrogen assimilation. Trends Plant Sci. 3:51-56. 1998.
- Danesh, D., Pe=F1uela, S., Mudge, J., Denny, R.L., Nordstrom, H., Martinez, J.P., Young, N.D. (1998). A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene. Theoretical and Applied Genetics 96: 196-206.
- Lange, D.A., Pe=F1uela, S., Denny, R.L., Mudge, J., Orf, J.H., Young, N.D. (1998) A plant DNA isolation protocol suitable for polymerase chain reaction marker-assisted selection. Crop Science 38: 217-220.
- Schnell, J.R., Berman, J. and V.A. Bloomfield. (1998) Insertion of telomere repeat sequence decreases plasmid DNA condensation by cobalt (III) hexaammine. Biophys. J., 74: 1484-91.
- Kim, S., I. Ayala, J. J. Steenhuis, E. T. Gonzalez, M. R. Razeghifard, and B. A. Barry. (1998) Infrared spectroscopic identification of the C-O stretching vibration associated with the tyrosyl Z and D radicals in photosystem II. Biochimica et Biophysica Acta. 1366, 330-354.
- Kim. S. and B. A. Barry. (1998) The protein environment surrounding tyrosyl radicals D and Z in photosystem II: a difference FT-IR study. Biophysical Journal 74, 2588-2600.
- Hutchison, R., S. D. Betts, C. F. Yocum, B.A. Barry. (1998) Conformational changes can occur in the manganese stabilizing protein of photosystem II: an isotope editing and FT-IR study. Biochemistry 37, 5643-5653.
- Ouellette, A. J. A., L. B. Anderson, and B. A. Barry. (1998) Amine binding and oxidation at the catalytic site for photosynthetic water oxidation. Proc. Nat. Acad. Sci. U.S.A. 95, 2204-2209.
- Steenhuis, J. J. and B. A. Barry. (1998) An FT-IR study of photoassembly in the manganese catalytic site of photosystem II. Journal of Physical Chemistry B 102, 4-8. (Letter)
- Patzlaff, J.S., J. A. Moeller, B. A. Barry, and R. J. Brooker. (1998) 46T-IR analysis of purified lactose permease: A mono-disperse lactose permease preparation is stably folded, a helical, and highly accessible to deuterium exchange. Biochemistry 37, 15363-15375.
- Kim, S. and B. A. Barry. (1998) The vibrational spectrum associated with the reduction of tyrosyl radical D: a comparative biochemical and kinetic study. Biochemistry 37, 13882-13992.
- Gale, C., Bendel, C., Berman, J., McClellan, M., Hauser, M., Becker, J.M, Berman, J and Hostetter, M (1998). Linkage of adhesion, filamentous growth, and virulence in Candida albicans to a single gene, INT1 Science 279: 1355-58.
- Enomoto, S., Chen, G. and Berman, (1998). J. Vectors for expressing T7 epitope- and His6-affinity tagged fusion proteins in S. cerevisiae. BioTechniques, 24:782-788.
- Qian, Z, Huang, H., Hong, J. Y., Burck, C.L., Johnston, S.D., Berman, J., Carol, A., and S.W. Liebman. (1998). Yeast Ty1 retrotransposition is stimulated by aynergistic interaction between mutations in Chromatin Assembly Factor-I and histone regulator (Hir) proteins. Mol. Cell. Biol. 18:4783-4792.
- Lew, J., Enomoto, S. and Berman, J. (1998). Telomere length regulation and telomeric chromatin require the nonsense-mediated mRNA decay pathway. Mol. Cell. Biol. 18: 6121-6130.
- Johnston, S.D., Lew, J. and J. Berman. (1998). Gbp1p, a protein with RNA recognition motifs, binds single-stranded telomeric DNA and changes its binding specificity upon dimerization. Mol Cell Biol. 19 (1) 923-933.
- Das, A. and Xie, Y.-H. (1998) Construction of transposon tn3::phoA: Its application in the analysis of the membrane topology of the Agrobacterium tumefaciens VirB proteins. Mol. Microbiol. 27:405-414.
- Das, A. (1998) DNA transfer from Agrobacterium to plant cells in crown gall tumor disease, In Subcellular Biochemistry, Vol. 29: Plant Microbe Interactions, Biswas, B. B. and Das, H. K., eds., Plenum Publishing Corp., London pp. 343-363.
- Johnson, T. and Das, A. (1998) Organization and expression of the Agrobacterium tumefaciens virulence genes, In 'The Rhizobiaceae', Spaink, H., Kondorosi, A. and Hooykaas, P., eds., Kluwer Academic Press, Dordrecht, The Netherlands 267-279.
- Kinkel, L.L., J.H. Bowers, K. Shimizu, E.C. Neeno-Eckwall and J.L.Schottel. 1998. Quantitative relationships among thaxtomin A production, potato scab severity, and fatty acid composition in Streptomyces. Can. J. Microbiol. 44:768-776.
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Progress 01/01/97 to 12/31/97
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics to biological and agricultural problems. PMGI is composed of 23 members and their lab personnel in 6 departments of the COAFES and CBS. PMGI supports faculty research, often including joint research with others not in the institute, and organizes a variety of educational opportunities. Two graduate students were supported for one quarter each. Two postdocs, Lynn Hartweck and Rong-Lin Wang, were also supported. Biweekly seminars presented by PMGI researchers were held throughout the year. Travel grants were awarded to 18 graduate students and postdocs to attend national and international meetings and make an oral report or serve as the senior author of a poster presentation. A PMGI-funded course, PBIO 5960 'Plant Development', was offered. Five prominent US scientists participated in this course and also presented research seminars that were open to
all. Planning was initiated for a course in 'Genomics' which will be offered in the spring of 1998. A retreat was held at the University's Landscape Arboretum. There were research talks or posters by faculty, postdocs, and students. Two faculty members, Michael Sadowsky and Gary Muehlbauer, were elected to PMGI.
Impacts
(N/A)
Publications
- Publications submitted separately for 1997.
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Progress 01/01/96 to 12/30/96
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics to biological and agricultural problems. PMGI is composed of 22 members and their lab personnel in 6 departments of the COAFES and CBS. PMGI supports faculty research, often including joint research with others not in the institute, and organizes a variety of educational opportunities. Four graduate students were supported for one quarter each. Two postdocs, Eugueni Ananiev and Rong-Lin Wang, were also supported. Eugueni Ananiev recently became supported on a research grant and a search for a new postdoc is underway. Biweekly seminars presented by PMGI researchers were held throughout the year. Travel grants were awarded to 13 grad students and postdocs to attend scientific meetings and make an oral report or serve as the senior author of a poster presentation. A PMGI-funded course, PB70 5960 "Molecular Plant Microbe Interaction", was offered. Five
prominent US scientists participated in this course and also presented research seminars that were open to all. Funds were committed for the purchase of several items of common equipment and software that are maintained by PMGI for use by all university faculty and staff. A retreat was held at the Landscape Arboretum. There were research talks or posters by faculty, postdocs, students and two non-PMGI faculty, Drs. Peter Ascher and Michael Sadowsky. A new faculty member, Dr. Bridgette Barry, was elected to PMGI membership.
Impacts
(N/A)
Publications
- STEENHUIS, J. J., BARRY, B.A.. 1996. A difference infrared study of protein structural changes in the photosynthetic water-oxidizing complex. Journal of theAmerican Chemical Society 118; pp. 11927-11932.
- MA, C., and BARRY, B.A.. 1996. EPR characterization of tyrosine radical, M+, insite directed mutants of photosystem II. Biophysical Journal 71; pp. 1961-1972.
- PATZLAFF, J.S. and BARRY, B.A.. 1996. Pigment quantitation and analysis by HPLC reverse phase chromatography: a characterization of antenna size in oxygen-evolving photosystem II preparations from cyanobacteria and plants. Biochemistry 35;.
- ROBINSON, D.L., PATHIRANA, S. M., GANTT, J.S. and VANCE, C.P. 1996. Immunogold Localization of Nodule-Enhanced Phosphoenolpyravate Carboxylase in Alfalfa. Plant Cell Environ. 19; pp. 602-608.
- LIN, K-C., BUSHNELL, W.R., SZABO, L. J., and SMITH, A.G.. 1996. Isolation and expression of a host response gene family encoding thaumatin-like proteins in incompatible oat-stem rust fungus interactions. Molec. Plant-Microbe Interact. 9; pp.
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Progress 01/01/95 to 12/30/95
Outputs
The Plant Molecular Genetics Institute (PMGI) fosters interdisciplinary applications of molecular biology and genetics to biological and agricultural problems. PMGI is composed of 22 members and their lab personnel in 6 departments of the Colleges of Agriculture and Biological Sciences. PMGI supports the faculty research, often including joint research with others not in the institute, and organizes a variety of educational opportunities. One grad student, Lewis Lukens, and one postdoc, Eugueni Ananieu, were supported by PMGI. A second postdoc, Shawn White, received her own support from NSF and did not accept PMGI support. A National search to identify an additional postdoc was commenced. Biweekly seminars presented by PMGI researchers were held throughout the year. Seminars in grad programs related to institute activities were sponsored by PMGI. Travel grants were awarded to 19 grad students and postdocs to attend national meetings and present an oral report or serve
as the senior author of a poster presentation. Emergency bridging funding was provided to two labs. Funds were committed toward the purchase of several items of common equipment and software for the Advanced Biosciences Computing Center. A retreat was held at the University's Landscape Arboretum; research talks were given by faculty, postdocs, two non-PMGI faculty, Drs. Ernest Retzel and Deborah Samac. Planning was initiated for a PMGI sponsored course. A new faculty member, Dr. Georgiana May, was elected to PMGI membership.
Impacts
(N/A)
Publications
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Progress 01/01/93 to 12/30/93
Outputs
The Plant Molecular Genetics Institute (PMGI) is an interdisciplinary program tofacilitate the discovery and application of plant molecular biology and genetics. Interactions occur among the 20 professors in 6 departments (College of Agriculture and College of Biological Sciences) their undergraduate, graduate, and postdoctoral students, and others. Biweekly seminars were presented by members of each of the 20 laboratories. The institute sponsored seminars by non-University of Minnesota researchers in 6 different graduate programs. A retreat was sponsored at the Southern Agricultural Experiment Station at Waseca for exchange of scientific information and to discuss genetic engineering regulatory issues. A tour of the Northrup King Co. Research Center at Stanton followed by a discussion with their scientists identified research areas of mutual interest. A new faculty member in plant developmental biology, Dr. David Marks, was successfully recruited by PMGI. The
institute also sponsored two graduate students and two postdoctorals. Partial travel grants were awarded to 15 graduate and postdoctoral students to make presentations of their work at national meetings. A national symposium entitled "Cloning Plant Genes Known Only By Phenotype" is planned. A grant proposal was submitted to USDA and private sponsors are being solicited.
Impacts
(N/A)
Publications
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Progress 01/01/92 to 12/30/92
Outputs
The Plant Molecular Genetics Institute (PMGI) at the University of Minnesota coordinates and promotes research and graduate education in this important area of the biological and agricultural sciences. The Institute consists of 19 faculty dispersed among and housed within six departments. PMGI sponsored seminar speakers in six graduate programs, held 17 bi-monthly research discussions led by faculty, graduate students, and postdoctorates, provided partial travel support for 16 graduate students and postdoctorates to make oral reports or poster presentations at national or international meetings, held an off-campus retreat to discuss research results, reviewed new University documents on the proper conduct of research, and planned the next PMGI-sponsored national symposium on identifying and cloning useful plant genes. A review session was held on the State of Minnesota Environmental Quality Board guidelines for the release of genetically engineered organisms into the
environment. PMGI co-organized a campus-wide symposium on "Genetically Engineered Organisms: Policies and Guidelines for Introduction into the Environment". Three graduate students, five postdoctorates, and a visiting scientist were at least partly supported by PMGI. A search committee is in the process of filling the vacated PMGI-funded faculty position. The oligonucleotide synthesizer and other jointly used equipment continues to benefit the program.
Impacts
(N/A)
Publications
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Progress 01/01/91 to 12/30/91
Outputs
Three additional plant biologists joined PMGI for a total of 20 faculty members. PMGI sponsored quest speakers in six graduate program seminar series, held 17 bi-monthly research discussions led by faculty, students and postdoctorals during the academic year, organized and sponsored a well-attended workshop on the molecular basis of heterosis, co-sponsored a regional meeting on Agrobacterium, and provided partial support for 33 graduate students and postdoctorals to present research at national or international meetings. Two graduate students currently are funded by PMGI. Posters advertising PMGI and related graduate programs were sent to over 500 colleges in the US and Canada, PMGI brochures were sent in response to requests from more than 380 prospective applicants, and their names were given to specific graduate programs for follow up. PMGI support of the plant Biological Sciences graduate program helped secure a National Needs Fellowship grant awarded for three
doctoral students in Plant Biotechnology. Ads for Postdoctoral Associate positions were placed nationally and two positions were filled bringing the total to six that PMGI has supported. A proposal concerning the University of Minnesota's procedures for research relating to introduction of genetically engineered plants and plant-associated microorganisms was drafted and discussed by PMGI faculty and presented to administrators and the Institutional Biosafety Committee for consideration.
Impacts
(N/A)
Publications
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Progress 01/01/90 to 12/30/90
Outputs
PMGI sponsored guest speakers in six graduate program seminar series, held bi-monthly, current research discussions led by faculty, students and postdoctorals during the academic year, organized in 1991 workshop on the molecular basis of heterosis, and provided partial support for 22 graduate students and postdoctorals to present research at national or international meetings. One graduate student was recruited and one completed a Ph.D. degree keeping the current total funded by PMGI at three students. One of the undergraduate interns funded by PMGI in 1989 was successfully recruited to the Genetics graduate program. Graduate program information was sent in response to requests from more than 250 prospective applicants. PMGI assisted in preparation of a National Needs Fellowship grant application for Doctoral Students in Plant Biotechnology. Ads for Postdoctoral Associate positions were placed nationally; one position was filled and another will be in early 1991
bringing the total to five that PMGI has supported. A revised draft of a document concerning release of genetically engineered plants and microbes was discussed by PMGI faculty for further modification and presentation to the University's Institutional Biosafety Committee. Research capabilities of PMGI were enhanced by purchase of jointly used equipment for gene expression assays of engineering plants; numerous oligonucleotides were synthesized at cost on PGMI equipment for members' research.
Impacts
(N/A)
Publications
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Progress 01/01/89 to 12/30/89
Outputs
PMGI sponsored guest speakers in six graduate program seminar series, co-sponsored the annual Plant Biology Symposium in conjunction with the Plant Biology Department centennial celebration, held bimonthly discussions of current research led by faculty, students and postdoctorals, and provided partial support for seven graduate students and postdoctorals to present research at national or international meetings. Dr. Nevin Young, Department of Plant Pathology, joined the PMGI faculty bringing the current total to 17. One graduate student was recruited bringing the total to three funded by PMGI. Three postdoctoral associates were recruited; two started in 1989 and the third will start in 1990. Two undergraduate interns were recruited; one worked on heat-induced gene expression in corn pollen and the other assisted in preparation of a draft document concerning local guidelines for environmental release of genetically engineered plants and microbes. Research capabilities
of PMGI were enhanced by purchase of jointly used equipment for oligonucleotide synthesis, DNA amplification, scanning and recording data for 2D gels and DNA sequencing gels, and for protein purification and characterization. A subgroup of PMGI received $200,000 in funding from the Midwest Plant Biotechnology Consortium for transformation of oats and corn.
Impacts
(N/A)
Publications
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Progress 01/01/87 to 12/30/87
Outputs
The Institute currently has 15 members. They are Judith Berman, Robert Brambl, Mark L. Brenner, Anath Das, J. Stephen Gantt, Burle G. Gengenbach, Paul A. Lefebvre, Neil Olszewski, Ronald L. Phillips, Robert Pruitt, Janet L. Schottel, Carolyn D. Silflow, D. Peter Snustad, and David A. Somers. Irwin Rubenstein is Director and Mark Brenner, Ronald L. Phillips, and Carolyn D. Silflow serve on the Institute's steering committee. The Institute has successfully recruited a new faculty member, Robert Pruitt; been awarded two USDA National Needs Graduate Student Fellowships; and submtited two major center grants. One of these is under the Midwest Plant Biotechnology Consortium and the other the NSF Biological Centers Program. The Consortium proposal was favorably reviewed and is one of ten (out of about 60) that will be sent to USDA early in 1988 for possible funding. The Institute has rewarded two graduate fellowships and a number of seed grants to Institute faculty,
sponsored a three day symposium on Plant Biochemistry, held a one day retreat this fall, supported outside speakers in plant molecular biology in established seminar programs, instituted a twice a month noontime plant molecular biology discussion group, and aided in the recruitment of faculty in plant molecular biology in various departments.
Impacts
(N/A)
Publications
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Progress 07/01/85 to 12/30/86
Outputs
The Institute has been organized and has begun its activities. There are presently 12 members of the Institute. They are Robert Brambl, Mark L. Brenner, Anath Das, J. Stephen Gantt, Burle G. Gengenbach, Paul A. Lefebvre, Ronald L. Phillips, Janet L. Schottel, Carolyn D. Silflow, D. Peter Snustad, and David A. Somers. Irwin Rubenstein was elected by the members to the the Institute director for the next three years. Robert Brambl, Ronald L. Phillips, and Carolyn D. Silflow were elected to the Institute's steering committee. The following goals of the Institute were adopted: conduct interdisciplinary research in molecular biology and genetics of economic plants and relevant model systems; develop genetic engineering methodologies for application to plant improvement; educate future plant biology researchers and teachers; coordinate planning and development of facilities for research in molecular biology; and provide a mechanism for exchange of information, ideas,
and research technology through seminars, journal clubs, and the Plant Biology Symposium.
Impacts
(N/A)
Publications
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