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RECOMB-BEDr. Laurie J. Heyer July 20, 2011
Designing and Buildinga Bacterial Computer
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Synthetic Biology
Application of engineering principles and mathematical modeling to the design and construction of biological parts, devices, and systems with applications in energy, medicine, environment, and technology.
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Hamiltonian Path Problem
Is there a path that:– Starts at node 1– Ends at node 7– Visits each node
exactly once 1
23
4
5
6
7
YES
NO
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Hamiltonian Path Problem
Is there a path that:– Starts at node 1– Ends at node 7– Visits each node
exactly once 1
23
4
5
6
7
YES
NO
✔
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A Biological Computer
Node = gene
Edge = 2 half-genes
1 2 3 4 5 6 7
GFP BLa CAT Cre cFP T7 TT
1
4
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A Biological Computer
Use hin/hix to rearrange edges:
Hin recombinase fromSalmonella typhimurium
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A Biological Computer
Use hin/hix to rearrange edges:
Hin recombinase fromSalmonella typhimurium
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Hin Recombinase
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Identify Solutions
1 4 5 2 3 6 Terminate
GFP BLa CATCre cFP T7 TT
# True Positives = (e - v + 1)! * 2(e - v + 1)
# False Positives = ?
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RBS
Promoter
ReporterDetectable Phenotype
Splitting a Gene
✔
hixCRBS
Promoter
Repo- rterDetectable Phenotype? ✔
hixCRBS
Promoter
Repo- rterDetectable Phenotype? ✖
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GFP displaying hixC insertion point
Minimize Structural Disruption
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Gene-Splitting Strategy
http://gcat.davidson.edu/iGEM07/genesplitter.html
GFP-1 GFP-2
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Gene Splitting Tool
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Note: Oligos are optimized for melting
temperatures.
Gene Splitter Output
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Embed hixC With Silent Mutations
hixC = ttatcaaaaaccatggtttttgataa
L S K T M V F D X
Y Q K P W F L I X
I K N H G F * *
Find genes with the “best” match to one of:L S K…… V F D a a t Y Q K…… F L I a
^ ^ ^ ^ ^ ^ ^ ^
t Y Q K … F L I a
L S K … V F D a a
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Conclusion
• Synthetic biology is an emerging bioinformatics playground
• Biology is more efficient with automation• Existing tools are insufficient
– Learn programming (Perl, Python, etc.)– Learn algorithms and data structures– Think and work across disciplinary boundaries
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Acknowledgements
Malcolm Campbell (Biology, Davidson College)Todd Eckdahl, Jeff Poet (Missouri Western State Univ.)iGEM ’06 team: Lance Harden, Karmella Haynes, Sabriya Rosemond, Samantha Simpson, Erin ZwackiGEM ’07 team: Oyinade Adefuye, Will DeLoache, Jim Dickson, Andrew Martens, Amber Shoecraft, and Mike Waters Karen Acker ’07 Phillip Compeau ’08 Funding from HHMI, Davidson College, Missouri Western State University, NSF UBM DMS-0733952 and -0733955