CISBIC: Sub-project 1: Stephen Muggleton CISBIC, Flowers Building, Imperial College London. www.imperial.ac.uk/cisbic Modeling genotype-phenotype relations Modeling genotype-phenotype relations in Campylobacter: an update and in Campylobacter: an update and future plans future plans
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CISBIC: Sub-project 1: Stephen Muggleton CISBIC, Flowers Building, Imperial College London. Modeling genotype-phenotype relations.
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CISBIC:Sub-project 1:
Stephen MuggletonCISBIC, Flowers Building, Imperial College London.www.imperial.ac.uk/cisbic
Modeling genotype-phenotype Modeling genotype-phenotype relations in Campylobacter: an relations in Campylobacter: an update and future plansupdate and future plans
Aim. Model effects of changes to pathogen genome of expression of glycosolated surface molecules involved in triggering of innate immune response of host.
Mycobacterium bovis Campylobacter jejuni
Initial focus
• Synthetic pathways for capsule in C. jejuni• 38 genes involved. Full set of knock-outs.• Functions - 1/3 known,1/3 suspected, 1/3 unknown. • Microarray and metabonomic experiments.
Polysaccharide capsule
Pathway database
Prolog database
Machine learning
Visualisation
KEGG BioCyc
ONDEXONDEX
Brendan/papers
Hypotheses for capsule pathway (in red)
cj1432c
cj1416c / cj1417c / cj1418c
Hypotheses predict
• Cj1416, Cj1417, Cj1418 involved in OMePN synthesis. Wren group has verified this by mutagenesis and structural analysis. Fairly obvious from BLAST analysis.
• Cj1432, a protein of unknown function, is central to capsule synthesis. Not predictable from amino acid similarity and BLAST analysis.
Experiments to test cj1432 hypothesis
1.Immunoassay.2.Alcian Blue dye staining of
Campylobacter.3.Electron microscopy – direct visual
inspection.4.Complementation – reintroduce cj1432
to chromosome of mutant5.Structural analysis of capsule glycan.6.Protein purification and enzyme assays.
Hypotheses/experiments
E1: A E2: B E3: C E4: D E5: E E6: AB E7: BC E8: BE E9: AD E10: ABC E11: ABCD E12: ABCEH1: codes(geneX,rA) 0 1 1 1 1 0 1 1 0 0 0 0H2: codes(geneX,rB) 1 0 1 1 1 0 0 0 1 0 0 0H3: codes(geneX,rC) 1 1 0 1 1 1 0 1 1 0 0 0H4: codes(geneX,rD) 1 1 1 0 1 1 1 1 0 1 0 1H5: codes(geneX,rE) 1 1 1 1 0 1 1 0 1 1 1 0
E
C B A
Pre-E
Pre-C
Pre-B
rB
rC
rD E
E10
E9 E11
H4H1
0
00
1
11
H5E8
H2 H3
Conclusions
•Integration of diverse background knowledge
•ILP produces readable rules
•Gap-filling in networks
•Ongoing NMR/MS experimental testing of hypotheses