Mdoyle Week 9

Assignment Page
BIOL367/F10:GenMAPP and MAPPFinder Protocols

Electronic Lab Notebook
Top 10 GO Terms: Compare with a buddy: Salomon's terms were different from mine, because of the changes made to the newer version of the gene database that I was using.
 * 1) hexose catabolic process
 * 2) glucose catabolic process
 * 3) glycolysis
 * 4) monosaccharide catabolic process
 * 5) cytoplasm
 * 6) alcohol catabolic process
 * 7) cellular carbohydrate catabloic process
 * 8) glucose metabolic process
 * 9) protein folding
 * 10) hexose metabolic process

VC0028
 * 1) branched chain family amino acid biosynthetic process
 * 2) cellular amino acid biosynthetic process
 * 3) metabolic process
 * 4) metal ion binding
 * 5) iron-sulfur cluster binding
 * 6) 4 iron, 4 sulfur cluster binding
 * 7) catalytic activity
 * 8) lyase activity
 * 9) dihydroxy-acid dehydratase activity

VC0941
 * 1) glycine metabolic process
 * 2) L-serine metabolic process
 * 3) one-carbon metabolic process
 * 4) cytoplasm
 * 5) pyridoxal phosphate binding
 * 6) transferase activity
 * 7) glycine hydroxymethyltransferase activity

VC0869
 * 1) glutamine metabolic process
 * 2) purine nucleotide biosynthetic process
 * 3) 'de novo' IMP biosynthetic process
 * 4) cytoplasm
 * 5) nucleotide binding
 * 6) ATP binding
 * 7) catalytic activity
 * 8) ligase activity
 * 9) phosphoribosylformylglycinamidine synthase activity

VC0051
 * 1) purine nucleotide biosynthetic process
 * 2) 'de novo' IMP biosynthetic process
 * 3) nucleotide binding
 * 4) ATP binding
 * 5) catalytic activity
 * 6) lyase activity
 * 7) carboxy-lyase activity
 * 8) phosophoribosylaminoimidazole carboxylase activity

VC0647
 * 1) mRNA catabolic process
 * 2) RNA processing
 * 3) cytoplasm
 * 4) mitochondrion
 * 5) RNA binding
 * 6) 3'-5'-exoribonuclease activity
 * 7) transferase activity
 * 8) nucleotidyltransferase activity
 * 9) polyribonucleotide nucleotidyltransferase activity

VC0468
 * 1) glutathione biosynthetic process
 * 2) metal ion binding
 * 3) nucleotide binding
 * 4) ATP binding
 * 5) catalytic activity
 * 6) ligase activity
 * 7) glutathione synthase activity

VC2350
 * 1) deoxyribonucleotide catabolic process
 * 2) metabolic process
 * 3) cytoplasm
 * 4) catalytic activity
 * 5) lyase activity
 * 6) deoxyribose-phosphate aldolase activity

VCA0583
 * 1) transport
 * 2) outer membrane-bound periplasmic space
 * 3) transporter activity

Compare with buddy: My partner got different terms again, I assume due to the fact that several changes have been made between the old and new versions of the gene database.

Questions

The GO term I chose was VCA0583, and the expression of the gene appeared to have increased fairly significantly. The function of the gene is that it is involved in the storage or transport of lipids necessary for membrane maintenance under stressful conditions. It also displays a binding preference for lysophospholipids

Pretty much all of the numbers were different, given that there was such a marked difference between the old database that Salomon used and the newer version that I used. It appears that a lot of genomic data was added between the release of the old database, and the new one.

The results from this analysis suggest that each of the GO terms I ended up with play a large role in the pathogenecity of Vibrio cholerae. These are the major players that allow the bacterium to survive and flourish. The terms I ended up with being top hits in my ranked list include quite a few catabolic processes, genomic regulation and growth, and, of course, glycolysis. By comparing the changes made in these key players between the laboratory and patient-derived bacterium, scientists can narrow down what specific changes result in increased or decreased pathogenecity. For example, because we know that colonization of the bacteria in a human creates a hyperinfectious strain, we can infer that posssibly the effect of the human gastrointestinal environment is a favorable one on catabolic processes, maybe making them more efficient due to the availibilty of certain nutrients. I can't think of a way in which the human stomach would be beneficial to the DNA processes referenced by my GO terms, except possibly that the exposure to human defense systems and the growth of the bacteria in its presence creates an immunity or resistance to human tactics of getting rid of the bacteria, again, creating a hyperinfectious strain.

Margie Doyle 13:47, 29 October 2010 (EDT)

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