RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer...

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RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer [email protected]

Transcript of RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer...

Page 1: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

RECOMB-BEDr. Laurie J. Heyer July 20, 2011

Designing and Buildinga Bacterial Computer

[email protected]

Page 2: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

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.

Page 3: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

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

Page 4: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

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

Page 5: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

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

Page 6: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

A Biological Computer

Use hin/hix to rearrange edges:

Hin recombinase fromSalmonella typhimurium

Page 7: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

A Biological Computer

Use hin/hix to rearrange edges:

Hin recombinase fromSalmonella typhimurium

Page 8: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

Hin Recombinase

Page 9: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

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 = ?

Page 10: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

RBS

Promoter

ReporterDetectable Phenotype

Splitting a Gene

hixCRBS

Promoter

Repo- rterDetectable Phenotype? ✔

hixCRBS

Promoter

Repo- rterDetectable Phenotype? ✖

Page 11: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

GFP displaying hixC insertion point

Minimize Structural Disruption

Page 12: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

Gene-Splitting Strategy

http://gcat.davidson.edu/iGEM07/genesplitter.html

GFP-1 GFP-2

Page 13: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

Gene Splitting Tool

Page 14: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

Note: Oligos are optimized for melting

temperatures.

Gene Splitter Output

Page 15: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

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

Page 16: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

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

Page 17: RECOMB-BE Dr. Laurie J. Heyer July 20, 2011 Designing and Building a Bacterial Computer laheyer@davidson.edu.

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