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Welcome to BOT 6516 Plant Metabolism Section #: 4222 Spring 2005 Instructor: Charles Guy

Welcome to BOT 6516 Plant Metabolism Section #: 4222 Spring 2005 Instructor: Charles Guy PMCB/Department of Environmental Horticulture Rm 107 Building 68 Phone: 392-1831x222; Email: clguy@ufl.edu Website: http://hort.ifas.ufl.edu/teach/guyweb/bot6516/index.html. Course Format:

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Welcome to BOT 6516 Plant Metabolism Section #: 4222 Spring 2005 Instructor: Charles Guy

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  1. Welcome to BOT 6516 Plant Metabolism Section #: 4222 Spring 2005 Instructor: Charles Guy PMCB/Department of Environmental Horticulture Rm 107 Building 68 Phone: 392-1831x222; Email: clguy@ufl.edu Website: http://hort.ifas.ufl.edu/teach/guyweb/bot6516/index.html

  2. Course Format: • Plant Metabolism is designed to focus on themes of current interest in plant metabolism and biochemistry. Since this is exclusively a graduate level course, a dialogue between the instructor and class members is not only desirable, but required. There will not be formal lectures, but instead we will have discussion sessions focused around two major metabolic/bioinformatics projects. I will lead all class discussions. The material to be discussed will be assigned in advance and will come from either the primary text or from supplemental materials. My role will be to provide general background information, when necessary, to make the reading material more understandable and useful.

  3. Course Format: • There will be only the two class projects (100 points each) and a final exam (100 points). Class participation will constitute 1/4 (100 points) of the grade.

  4. Major metabolic/bioinformatics project: • We are going to check and verify the annotations of the gene sequences that encode enzymes of intermediary metabolism at the KEGG and TAIR databases. We are going to use our knowledge of plant metabolism to correct and extend the annotations of these two critically important and key databases and current research working websites. In order to do this, we will need to be come knowledgeable about plant metabolism. I will provide reference materials for each of the pathways and cycles that will give you the fundamental information you will need to begin the annotation work.

  5. Major metabolic/bioinformatics project: • You will keep a research notebook that will allow me to validate the annotation work that you have done. You should keep a record of everything you do. It must be organized and easy for me to follow. • The annotation work, verification, correction, and extension will be done as a group effort. I will leave it up to each group as to how you will divide up the work and compile the group report on the assigned pathway. However, the work should be divided equally. If any member of the group fails to equally participate, I should be informed immediately.

  6. Major metabolic/bioinformatics project URLs: KEGG:http://www.genome.jp/kegg/ TAIR: http://arabidopsis.org/index.jsp TAIR/Metabolism: http://arabidopsis.org/tools/aracyc/ PubChem: http://pubchem.ncbi.nlm.nih.gov/ Brenda: http://www.brenda.uni-koeln.de/ NCBI: http://www.ncbi.nlm.nih.gov/ NCBI/Nucleotide: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&itool=toolbar NCBI/Blast: http://www.ncbi.nlm.nih.gov/BLAST/

  7. Major metabolic/bioinformatics project: Initial Group Assignments: Group I (Glycolysis from Glc or Glc-1-P to Pyruvate) Karla Addesso, Christopher Cerveny, Rebecca Schnelle Group II (Pentose Phosphate Pathway cytosolic) Nicacio Cruz-Huerta, Ji-Young Hong, Karthik-Joseph John Group III (Calvin Cycle) Charles Hunter, Yingnan Jiang, Thelma Madzima Group IV (TCA Cycle) Stefanie Maruhnich, Scott Morris, Wei Pan

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