61. References Quality evaluation of databases, J. Am. Soc. Mass Spectrom., 1999, 10, 12291240 . Mendes, P., Modeling large biological systems from functional genomic http://www.noble.org/PlantBio/MS/meta.references.html

References Sumner Home Personnel Mass Spec Basics Functional Genomics ... Acknowledgments REFERENCES 1. Barker, D.G., Bianchi, S., Blondon, F., Dattée, Y., Duc, G., Essad, S., Flament, P., Gallusci, P., Génier, G., Pierre, G., Muel, X., Tourneur, J., Dénarié, J., Huguet, T., Medicago Truncatula , a model plant for studying the molecular genetics of the Rhizobium -Legume symbiosis, Plant Mol. Biol. Rep., 2. Cook, D.R., VandenBosch, K., de Bruijn, F.J., Huguet, T., Model legumes get the nod, Plant Cell, 3. Cook, D.R., Medicago truncatula - a model in the making!, Curr. Opin. Plant Biol., 4. Trieu, A.T., Burleigh, S.H., Kardailsky, I.V., Maldonado-Mendoza, I.E., Versaw, W.K., Blaylock, L.A., Shin, H., Chiou, T.-J., Katagi, H., Dewbre, G.R., Weigel, D., Harrison, M.J., Transformation of Medicago truncatula via infiltration of seedlings or flowering plants with Agrobacterium Plant J., 5. Bell, C.J., Dixon, R.A., Farmer, A.D., Flores, P., Inman, J., Gonzales, R.A., Harrison, M.J., Paiva, N.L., Scott, A.D., Weller, J.W., May, G.D., The Medicago genome initiative: A model legume database

62. The Bioinformatics.ca People Page : Region Canada tandem mass spectrometry; genome mapping; database systems Comparativegenomics. Detection of mutations responsible for human genetic disease. http://bioinformatics.ca/bioinformatics_resources/people/?region=ca

63. Publication_list Database and data manipulation for the wheat D genome physical mapping project . Dubcovsky J, Luo MC, Zhong GY, Dvorak J Comparative RFLP map of http://www.agronomy.ucdavis.edu/mcluo/publication_list.htm

Featured Links: WheatDB, A Wheat Physical Mapping Database The Harlan II Symposium mcluo@ucdavis.edu Luo, MC , Deal KR, Yang ZL and Dvorak J. Comparative genetic maps reveal extreme crossover localization in the Aegilops speltoides chromosomes. T heor. Appl. Genet. (2005) In press. Kuang H, Wei F, Marano MR, Wirtz U, Wang X, Liu J, Shum WP, Zaborsky J, Tallon L, Rensink W, Lobst SE, Zhang P, Tornqvist CE, Tek A, Bamberg J, Helgeson J, Fry W, You F, Luo MC , Jiang J, Buell CR, Baker BB. The R1 resistance cluster contains three groups of independently evolving, Type I R1 homologues and shows substantial structural variation between haplotypes of Solanum demissum. The Plant Journal. (2005) In press. Dvorak J, Yang ZL, You FM, Luo MC : Deletion Polymorphism in Wheat Chromosome Regions With Contrasting Recombination Rates. Genetics Full Text available at http://www.genetics.org/cgi/content/full/168/3/1665 Gu YQ, Crossman C, Kong X, Luo MC , You FM, Coleman-Derr D, Dubcovsky J, Anderson OD. Genomic organization of the complex

64. NABRW Conference Schedule GrainGenes The Triticeae genome Database. Victoria Carollo1, David Matthews2, Genetic Linkage Map of cv. Foster x Fusarium Resistant Line CI4196. http://www.ndsu.nodak.edu/ndsu/plant_sciences/NABRW/Conferenceschedule.htm

17th Triennial North American Barley Researchers Workshop Homepage TENTATIVE MEETING AGENDA Oral Presentations for the NABRW, Fargo, ND 2002 Sunday September 22 2:00 - 5:00 PM - Barley Crop Advisory Committee Meeting 6:00 - 9:00 PM - Registration 6:00-8:00 PM Poster Setup Crystal I Room 7:00 - 10:00 PM - Reception (Provided With Meeting Registration) - Bach Room Monday September 23 7:30 am - Meeting Registration 8:00 – Welcome Feed, Food and Malt Quality 8:10 Joe Hertrick, Anheuser Busch – Malting barley quality needs 8:50 William Rahr, Rahr Malting – Globalization of malting and brewing 9:20 Vern Anderson and Greg Lardy, North Dakota State University – Feed barley research and market development 9:40-10:00 Break 10:00 Walt Newman, Montana State University – Barley dietary fiber and beta-glucans: pigs and people 10:20 Christine Fastnaught, National. Barley Foods Council – Barley reduces cholesterol – an update on clinical trials and FDA petition process 10:40 Dennis Gordon, North Dakota State University – Barley as a human food and functional food 11:10 Jorge Correa, Semillas Correa Mexicana – Barley and its potential as a forage crop in dairy production in Mexico

65. 37. Construction Of A Molecular Map Of Rice And Gene Mapping Using A Double Hapl Database. All, Protein, Ontology, Mutant, Literature, Map, Marker RFLP mappingof the rice genome. In Rice Genetics II. IRRI, PO Box 933, Manila, http://www.gramene.org/newsletters/rice_genetics/rgn10/vXV37.htm

Search for: Database: All Protein Ontology Gene Literature Map Marker QTL Sequence Genome Browser BLAST CMap Markers ... Volume 10 Contents 37. Construction of a molecular map of rice and gene mapping using a double haploid population of a cross between Indica and Japonica varieties Li-Huang ZHU , Ying CHEN , Yuu-Bin XU , Ji-Chen XU , Hong-Wei CAI and Zhong-Zhuan LING 1) Institute of Genetics, Academia Sinica, Beijing, 100101 2) Agronomy Dept., Zhejiang Agric. University, Hangzhou, 310029 3) Agronomy Dept., Beijing Agric. University, Beijing, 100094 4) Institute of Crop Cultivation and Breeding, Chinese Academy of Agri. Sciences, Beijing, 100081 To construct a RFLP framework map of the DH population, the two parents were surveyed by 181 RFLP markers (provided by S.D. Tanksley) with eight restriction enzymes (EcoRI, EcoRV, HindIII, ScaI, XbaI, BamHI, BglII and DraI), and 171 markers showed polymorphism. All of the 8 isozyme markers examined in this cross also showed polymorphism. These results indicate that the polymorphism level is very high and a saturated genetic map can be con- structed from the segregating population derived from these parents. As the first step towards constructing a saturated map, 100 RFLP markers and 8 isozyme loci were scored on the DH population. Segregation data of genetic markers were analyzed, and a linkage map was constructed using MAP- MAKER software package developed by Lander et al. (1987). These 108 markers are distributed throughout the 12 chromosomes with mean map distance of 8.5 cM (Fig. 1). The number of markers on each chromosome ranges from three (chromosome 10) to 17 (chromosome 12). This map compares well with the latest RFLP map constructed in Tanksley's laboratory (personal communication) and lays down foundation for gene mapping with this DH population.

66. Pine Mapping Projects - North America Dendrome has met all obligations to the Plant genome Database genome mappingresearch has produced the first RFLP linkage map for loblolly. http://www.nal.usda.gov/pgdic/Map_proj/pine.html

67. Publications The Map Based Sequence of the Rice genome. Nature 436793800. Candidate genedatabase and transcript map for peach, a model species for fruit trees. http://www.genome.arizona.edu/information/publications/

Publications Home Search 2005 Publications The International Rice Genome Sequencing Project Project. (2005). The Map Based Sequence of the Rice Genome. Nature 436:793-800. Wang, W., M. Tanurdzic, M. Luo, N. Sisneros, H.R. Kim, J.K. Weng, D. Kudrna, C. Mueller, K. Arumuganathan, J. Carlson, C. Chapple, C. de Pamphilis, D. Mandoli, J. Tomkins, R.A. Wing, and J.A. Banks. 2005. Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics. BMC Plant Biol 5: 10. Yang, T.-J., S. Lee, S.-B. Chang, Y. Yu, H.d. Jong, and R.A. Wing. (2005). In-depth sequence analysis of the tomato chromosome 12 centromere: identification of a large CAA block and characterization of a species-specific pericentromere retrotranposons. Chromosoma 114: 103-117. Horn, R., A.C. Lecouls, A. Callahan, A. Dandekar, L. Garay, P. McCord, W. Howad, H. Chan, I. Verde, D. Main, S. Jung, L. Georgi, S. Forrest, J. Mook, T. Zhebentyayeva, Y. Yu, H.R. Kim, C. Jesudurai, B. Sosinski, P. Arus, V. Baird, D. Parfitt, G. Reighard, R. Scorza, J. Tomkins, R. Wing, and A.G. Abbott. (2005). Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110: 1419-1428.

68. Biochem. J. (2003) 370, 35-46 - L. Trabalzini And Others - Proteome Changes Due Proteomic studies can help to relate the genome and proteome to cell functions, Nterminal microsequence analysis and database searching http://www.biochemj.org/bj/370/0035/bj3700035.htm

About the journal Subscriptions Authors Users ... Download to Citation Matcher Biochem. J. (2003) Proteomic response to physiological fermentation stresses in a wild-type wine strain of Saccharomyces cerevisiae Key words: ethanol, glucose, oenology, two-dimensional electrophoresis, yeast. Abbreviations used: 2D, two-dimensional; Hsp26 (etc.), heat-shock protein 26 (etc.); YPD, yeast peptone dextrose. We report a study on the adaptive response of a wild-type wine Saccharomyces cerevisiae strain, isolated from natural spontaneous grape must, to mild and progressive physiological stresses due to fermentation. We observed by two-dimensional electrophoresis how the yeast proteome changes during glucose exhaustion, before the cell enters its complete stationary phase. On the basis of their identification, the proteins representing the S. cerevisiae proteomic response to fermentation stresses were divided into three classes: repressed proteins, induced proteins and autoproteolysed proteins. In an overall view, the proteome adaptation of S. cerevisiae

69. Relnotes.35.txt DATABASE NAME=Text; NOTE=Text; WWW= Address ; FTP= Address . Sequence features in the 1 Mb RT region from map positions 64% to 92% of the genome. http://www.expasy.org/txt/old-rel/relnotes.35.txt

ExPASy Home page Site Map Search ExPASy Contact us Hosted by CBR Canada Mirror sites: Australia Brazil Korea Switzerland ... USA Search Swiss-Prot/TrEMBL Swiss-Prot/TrEMBL (full text) PROSITE SWISS-2DPAGE ENZYME NEWT Taxonomy HAMAP families ExPASy web site for The ExPASy Server requires Javascript to be fully functional. You may not see all the information available for this page (More information) ExPASy Home page Site Map Search ExPASy Contact us Hosted by CBR Canada Mirror sites: Australia Brazil Korea Switzerland ... USA The ExPASy Server requires Javascript to be fully functional. You may not see all the information available for this page (More information)

70. Relnotes.32.txt PAGE 3.2 TREMBL a supplement to SWISS-PROT The ongoing genome sequencing andmapping Prom * - * Sequence Database * * ECDC E.coli map http://www.expasy.org/txt/old-rel/relnotes.32.txt

ExPASy Home page Site Map Search ExPASy Contact us Hosted by CBR Canada Mirror sites: Australia Brazil Korea Switzerland ... USA Search Swiss-Prot/TrEMBL Swiss-Prot/TrEMBL (full text) PROSITE SWISS-2DPAGE ENZYME NEWT Taxonomy HAMAP families ExPASy web site for The ExPASy Server requires Javascript to be fully functional. You may not see all the information available for this page (More information) ExPASy Home page Site Map Search ExPASy Contact us Hosted by CBR Canada Mirror sites: Australia Brazil Korea Switzerland ... USA The ExPASy Server requires Javascript to be fully functional. You may not see all the information available for this page (More information)

71. Honeybee - RIRDC Completed Projects In 1999-2000 & Research In Progress As At Ju A genetic map of the honeybee genome (25 linkage groups, a total map Project Title, Natural resource database for the South Australian apiary industry http://www.rirdc.gov.au/comp01/hb2.html

Rural Industries Home Search Contact Free Publications ... BACK TO INDEX 3.3 Honeybee - continued (return to first Honeybee page Project Title Production of a publication on honeybee nutrition in Australia - 'Fat bees/skinny bees' RIRDC Project No.: DAN-186A Start Date: Finish Date: Researcher: Mr. Doug Somerville Organisation: NSW Department of Agriculture PO Box 389 GOULBURN NSW 2580 Phone: Fax: Email: doug.somerville@agric.nsw.gov.au Objectives To produce an extension publication on honey bee nutrition, incorporating research findings from past RIRDC projects, literature searches and anecdotal examples of applications in the Australian context in a format that will be readily understood and adopted by beekeepers. Current Progress Information on the use of carbohydrate supplements to increase pollination efficiency has been gathered and was presented to a Crop Pollination field day in South Australia on the 16 February 2001. The field day focus was on lucerne pollination, yet the published evidence would indicate that there is a strong role for the use of sugar feeding to stimulate colonies to increase foraging flights in general, increasing visits to blossom and thus increasing the pollination benefit from honey bees in a range of crops. There are some strong cases for the use of sugar feeding in the provision of a pollination service, particularly for kiwifruit, some lucerne crops and perhaps avocados. Other horticultural or agronomic crops may also benefit, particularly via the stimulation effect of regular small amounts of sugar syrup (1 to 2 litres) every one to three days per hive. Open or bulk feeding next to, or feeders distributed throughout the crop may also have benefit, and this was demonstrated at the SA field day on lucerne.

72. Botany Agric Biochemistry - Barrington A map of endemic centers in Polystichum and our latest twosequence tree for the I maintain a virtually complete nomenclatural database for the genus, http://www.uvm.edu/~plantbio/faculty/barrington.html

David Barrington Professor of Botany Ph. D. 1975, Harvard University Email: David.Barrington@uvm.edu Phone: Office: 225 Marsh Life Science Building Research Area: Plant Systematics and Evolution Courses Taught: Mailing Address: Botany Department Marsh Life Science Building 109 Carrigan Drive University of Vermont Burlington, VT 05405-0086 USA Barrington lab procedures, primers, and the like Barrington course syllabi and related matters. THE BARRINGTON LAB AT THE UNIVERSITY OF VERMONT Summary of Research Program My graduate students Julie Dragon, Heather Driscoll, Sonja Schmitz, Cathy Paris, who is also in the systematics research group at UVM, portrays her research activities here. Polystichum tripteron in Japan SYSTEMATICS OF FERNS: POLYSTICHUM For some years I have been interested in the fern genus Polystichum , which includes well-known ferns such as the sword fern of the American northwestern forests and Christmas fern, widely distributed in the eastern United States. The European holly fern Polystichum aculeatum is a well-known species, and the Eastern Asian

73. Vitisrupestris The references listed below are from the Biological Abstracts database (19882000) A molecular marker based linkage map of Vitis. genome 38(4) 786-794. http://www.newcrops.uq.edu.au/listing/vitisrupestris.htm

Listing of Useful Plants of the World [formerly Listing of Potential New Crops for Australia] NOTICE: Information on the background to this Listing is available. The analysis of numbers of papers/mentions over time was completed in 1997, using the Agricola database (1970-1996). Hard copies of the Listing (553 pages; over 4200 new crops listed with the analyses of numbers of papers over time included) are available from the publisher, Dr Rob Fletcher; see Advice on Publications Available The references listed below are from the Biological Abstracts database (1988-2000) and are courtesy of SilverPlatter Information. For more information re Silverplatter, go to www.silverplatter.com Vitis rupestris Analysis of numbers of papers/mentions over time (Agricola database 1970-1996): Source: AGRICOLA database (1970-1996) Common Name(s): bush grape syn mountain grape syn rock grape syn sand grape syn sugar grape Crop Use(s): fruit Reference Source(s): sturtevant Number of Papers/Mentions: References Biological Abstracts 1988-2000 [These references are from the Biological Abstracts database and are courtesy of SilverPlatter Information. For more information re SilverPlatter, go to

74. The GP Problem: Quantifying Gene-to-phenotype Relationships Figure 1 Concept map for modeling biophysical systems. With the increasingavailability of the complete genome sequences of a number of prokaryotic and http://www.bioinfo.de/isb/2002/02/0013/main.html

In Silico Dagstuhl Seminar "Functional Genomics" The GP problem: Quantifying gene-to-phenotype relationships Mark Cooper , Scott C. Chapman , Dean W. Podlich and Graeme L. Hammer School of Land and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia Current Address: Pioneer Hi-Bred International Inc., 7300 N.W. 62 nd Avenue, P.O. Box 1004, Johnston, Iowa 50131, USA CSIRO Plant Industry, 120 Meiers Road, Indooroopilly, Queensland 4068, Australia Agricultural and Production Systems Research Unit (APSRU), Queensland Department of Primary Industries, Tor Street, Toowoomba, Queensland, Australia *Corresponding author: Email: mark.cooper@pioneer.com Edited by E. Wingender; received September 26, 2001; revised and accepted December 21, 2001; published January 24, 2002 Abstract In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis

75. The January Issue Of The Computing Service Newsletter Contains The David Robey (University of Manchester) o The Classical Chinese Database Project, model of disablement. ecolagric This list is intended for academics, http://www.sussex.ac.uk/USCS/Archive/Publications/Newsletters/9501.txt

76. Science -- Sign In Arabidopsis Microarray Database and Analysis Toolbox. Plant Physiol. genomeWide Analysis of the Cyclin Family in Arabidopsis and Comparative http://www.sciencemag.org/cgi/content/full/302/5652/1956?ijkey=icyCVsvtQV.SU&key

77. Toward Integration Of Comparative Genetic, Physical, Diversity, And Cytomolecula The sorghum genomic clone pSB1742 detects RFLPs that map to LGs B (allele pairindicated by Ming et al., 1998 ), maize (Zea mays; Maize genome Database, http://www.plantphysiol.org/cgi/content/full/125/3/1325

HOME HELP FEEDBACK SUBSCRIPTIONS ... TABLE OF CONTENTS QUICK SEARCH: [advanced] Author: Keyword(s): Year: Vol: Page: This Article Abstract Full Text (PDF) Alert me when this article is cited ... Alert me if a correction is posted Services Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal ... Cited by other online articles Search for citing articles in: ISI Web of Science (21) PubMed PubMed Citation Articles by Draye, X. Articles by Paterson, A. H. Agricola Articles by Draye, X. Articles by Paterson, A. H. Plant Physiol, March 2001, Vol. 125, pp. 1325-1341 Toward Integration of Comparative Genetic, Physical, Diversity, and Cytomolecular Maps for Grasses and Grains, Using the Sorghum Genome as a Foundation Xavier Draye, Yann-Rong Lin, Xiao-yin Qian, John E. Bowers, Gloria B. Burow, Peter L. Morrell, Daniel G. Peterson, Gernot G. Presting, Shu-xin Ren, Rod A. Wing, and Andrew H. Paterson

78. Mapping Maize Sequences To Chromosomes Using Oat-Maize Chromosome Addition Mater It is unfortunate that a public sequence database adequate to identify large These bands reflect the duplicated nature of the maize genome and/or the http://www.plantphysiol.org/cgi/content/full/125/3/1228

HOME HELP FEEDBACK SUBSCRIPTIONS ... TABLE OF CONTENTS QUICK SEARCH: [advanced] Author: Keyword(s): Year: Vol: Page: This Article Abstract Full Text (PDF) Data Supplement ... Alert me if a correction is posted Services Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal ... Cited by other online articles Search for citing articles in: ISI Web of Science (6) PubMed PubMed Citation Articles by Okagaki, R. J. Articles by Phillips, R. L. Agricola Articles by Okagaki, R. J. Articles by Phillips, R. L. Plant Physiol, March 2001, Vol. 125, pp. 1228-1235 Mapping Maize Sequences to Chromosomes Using Oat-Maize Chromosome Addition Materials [w] Ron J. Okagaki, Ralf G. Kynast, Suzanne M. Livingston, Charles D. Russell, Howard W. Rines, and Ronald L. Phillips Department of Agronomy and Plant Genetics (R.J.O., R.G.K., S.M.L., C.D.R., H.W.R., R.L.P.), Plant Molecular Genetics Institute (R.J.O., R.G.K., S.M.L., C.D.R., R.L.P.), and Plant Sciences Research Unit, United States Department of Agriculture, Agricultural Research Service, and Department of Agronomy and Plant Genetics (H.W.R.), University of Minnesota, St. Paul, Minnesota 55108 ABSTRACT TOP ABSTRACT INTRODUCTION RESULTS AND DISCUSSION MATERIALS AND METHODS LITERATURE CITED Oat- ( Avena sativa ) maize ( Zea mays ) chromosome additions are produced by crossing maize and oat. During early embryo development

79. Genome-scale Reconstruction Of The Metabolic Network In Staphylococcus Aureus N3 Results We reconstructed a genomescale metabolic network of S. aureus Each key metabolic pathway present in map form on the Kyoto Encyclopedia of Genes http://bmc.ub.uni-potsdam.de/cgi-bin/show.pl?1471-2180-5-8

80. GDR Conference GDR A comparative genomics database for Rosaceae We are constructing acomplete physical map for peach, a Rosaceae genome model species, http://www.mainlab.clemson.edu/gdr/conference/abstractList.html

PRESENTATION ABSTRACTS Sunday, May 23, 2004 Email: pere.arus@irta.es Prunus Genetics and Genomics Email: dirlewan@bordeaux.inra.fr Genetic analysis of major fruit quality components in peach -Comparison with apricot E. Dirlewanger, INRA-UREFV;M Claverie, INRA-UIPMSV; N. P. Cosson, INRA-UIPMSV; B. Lafargue, INRA-UREFV; R. Voisin, INRA-UREFV; M. Kleinhentz, INRA-UIPMSV; P. Arus, IRTA; B. Chalhoub, INRA-URGV; D. Esmenjaud, INRA-UIPMSV Email: dirlewan@bordeaux.inra.fr Plum genetic and physical map of the RKN Ma locus region C. E. Durel, F. Calenge; INRA - GenHort Email: durel@angers.inra.fr Genomic organization of disease resistance factors in apple Susan Gardiner, Rachel Rusholme, Andrew Allan, Heather Bassett, Vincent Bus, Wendy Legg, Erik Rikkerink, Andrew Gleave, Paul Austin , Ross Crowhurst; HortResearch, New Zealand. Email: SGardiner@hortresearch.co.nz Gene mapping in Malus harnessing an EST database Email: mbadenes@ivia.es

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