Synthetic Biology

1. Synthetic Biology (The Cell as a Nanosystem) ARC Bioinformatics UC Davis Summer 2006

8. Bio-Nano Convergence

12. Affymetrix GeneChip™

15. Viral Self-Assembly http://www.virology.net/Big_Virology/BVunassignplant.html

16. Self-Assembled Algorithms --------------------------- 1010110001011010 ATGCCAGTACTGG TACGGTCATGACC 0101001110100101 ---------------------------

18. Nano-Bio-Info-Tech Nano Bio Info Self assembly Microarrays, BioMEMS Quantum computing nanoelectronic devices Digital cells DNA computing insilico biology Concept by Robert Cormia

22. Digital Cell Basics http://www.ee.princeton.edu/people/Weiss.php

23. Digital Cell Circuit (1) INVERSE LOGIC. A digital inverter that consists of a gene encoding the instructions for protein B and containing a region (P) to which protein A binds. When A is absent (left)—a situation representing the input bit 0—the gene is active. and B is formed—corresponding to an output bit 1. When A is produced (right)—making the input bit 1—it binds to P and blocks the action of the gene—preventing B from being formed and making the output bit 0. Weiss http://www.ee.princeton.edu/people/Weiss.php

24. Digital Cell Circuit (2) In this biological AND gate, the input proteins X and Y bind to and deactivate different copies of the gene that encodes protein R. This protein, in turn, deactivates the gene for protein Z, the output protein. If X and Y are both present, making both input bits 1, then R is not built but Z is, making the output bit 1. In the absence of X or Y or both, at least one of the genes on the left actively builds R, which goes on to block the construction of Z, making the output bit 0. Weiss http://www.ee.princeton.edu/people/Weiss.php

25. Digital Cells – Bio Informatics http://www.ee.princeton.edu/people/Weiss.php Modeling life as an information system

26. Gene Regulatory Network

27. Basic GRN Circuit Flow Gross anatomy of a minimal gene regulatory network (GRN) embedded in a regulatory network. A regulatory network can be viewed as a cellular input-output device. http://doegenomestolife.org/

28. http://doegenomestolife.org/ Gene regulatory networks ‘interface’ with cellular processes

29. Information vs. Processing Just as in a computer, data bits and processing bits are made from the same material, 0 or 1, or A, T, C, G, or U in biology

39. Green Algae at Work Making H 2 Algal cell suspension / cells Thylakoid membrane  These little critters are very happy just to be working!

40. Proposed Engineered H 2 Bacterium http://gcep.stanford.edu/pdfs/tr_hydrogen_prod_utilization.pdf

41. In Vitro Photo-Production of H 2 Yellow arrow marks insertion of hydrogenase promoter. Right side data cell optimized for continuous H 2 production .

44. Global Gene Expression Gene expression tells you how the machine is working Bioinformatics shows you where the control points are

46. Synthetic Proteins All proteins are ‘synthetic’ – peptides => polymers

48. Nature as a NanoToolbox http://www.cse.ucsc.edu/~hongwang/ATP_synthase.html