Welcome to BOT 6516 Plant Metabolism

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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_at_ufl.edu Website
http//hort.ifas.ufl.edu/teach/guyweb/bot6516/inde
x.html
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• 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.

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• 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.

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• 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.

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• 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.

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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?dbN
ucleotideitooltoolbar NCBI/Blast
http//www.ncbi.nlm.nih.gov/BLAST/
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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