Computer Aided Design of Synthetic Biological Systems Using Standardized Parts
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1 Computer Aided Design of Synthetic Biological Systems Using Standardized Parts Douglas Densmore* CHESS Seminar 11/18/08 *in cooperation with Prof. J. Christopher Anderson and Prof. Chris Voigt
2 Outline Synthetic Biology Overview Abstractions Automated Assembly Standards Platform-based Design in Synthetic Biology Clotho Overview Demo
3 What is Synthetic Biology? Adding multi-gene DNAs into well-characterized organisms to understand biological behavior or perform useful functions in diverse areas including therapeutics, biosensors, bioenergy, bioremediation, chemicals, and materials production. Putting the Engineering back in Genetic Engineering 3. Standards 2. Automated Assembly 1. Abstractions Automatic Sequencing PCR Recombinant DNA *Drew Endy
4 Synthetic Biology Examples Bactoblood UC Berkeley A cost-effective red blood cell substitute constructed from engineered E. coli bacteria. Bactricity - Harvard Bacterial biosensors with electrical output. BacToKidney NYMU-Tapei Bacteria to replace a hemodialysis machine to remove toxic waste for treating kidney failure.
5 Abstraction Overview Biological Engineering? Protein Engineering Promoter Engineering Synthetic Biology bases parts devices A T C G 1bp 1-20kb 0.1-3kb genomes Mb
6 Parts Terminators Abstractions Parts and Devices Ribosome Binding Site Devices Regulatory Reporters Registry of Standard Biological Parts: Sensors: Circuits: Light Sensor (Levskaya, 2005) Touch Sensor (Materi, 2007) Memory Actuators: Movement (Cirino, 2006) Secretion (Widmaier, 2007) Adhesion (Falkow et al., 1987) One instance of an inverter (Ham, 2006) AND (Anderson, 2007) NOT (Weiss, 2001)
7 Abstractions Difficulties
8 Abstraction - Potential
9 Standardized Parts BioBricks (Tom Knight, MIT) one of the most prevalent standards. 2ab Layered assembly (J. Christopher Anderson) is another proposal Look to reduce reactions required, increase productivity, aid in reliability, and increase reuse. Assembly Vector Cloning Site Replication Origin Antibiotic Resistance
10 Standard Assembly EcoRI and XbaI SpeI and PstI XbaI and SpeI have the same sticky ends, CTAG
11 Automated Assembly A B C D Primitive parts A B C D Assembly Step Compound parts A.B C.D Assembly Stage A.B.C.D Goal part A.B.C.D
12 Automated Assembly Opportunities b [C/K] c [K/A] b [K/C] c [C/A] c [A/K] d [K/C] b [K/C] c [C/A] b [K/C] c [C/A] a [K/C] b.c [C/A] a [C/K] b.c [K/A] b [K/A] c.d [A/C] b.c [K/A] d [A/C] a [C/K] b.c [K/A] d [A/C] a.b.c [K/A] a.b.c [C/A] b.c.d [K/C] b.c.d [K/C] a.b.c [C/A] b.c.d [K/C] *work in progress with Chris Batten, Tim Hsiau, and Will DeLoache
13 Automated Assembly Complete Flow Designed Assembly Goal Set Optimal Assembly Algorithm Assembly Tree Automated Layered Assembly
14 Interchange Standards How do we store and exchange part data electronically? More and more parts are being created. MIT parts registry, JBEI registry, etc More and more tools are being created. Clotho, BioMortar, BioJADE, Tinkercell, etc. Raw data is not the only concern Scalability Privacy Quality control
15 Interchange Example
16 Outline Synthetic Biology Overview Abstractions Automated Assembly Standards Platform-based Design in Synthetic Biology Clotho Overview Demo
17 IF (dark) MAKE pigment Photographic Bacteria Biological Function Space Image Bacterial Lawn SER no inducer no attractant or wrong lock / key pair x = 0 LOOP IF (ara) x = 1 SWITCH x CASE 0: IF (ser) SWIM CASE 1: IF (asp) SWIM Remote Control of Bacteria ASP + inducer
18 Biological Architecture Space Plasmid Backbone Standard Assembly Parallel Assembly BioBrick Design Instance Rules and procedures for part assembly i.e. Prefix rules: gaattcgcggccgcttctagatg... gaattcgcggccgcttctagagca.. Suffix rules:...actactagtagcggccgctgcag
19 SER PBD & Bio: Putting it all together Remote Control of Bacteria ASP x = 0 LOOP IF (ara) x = 1 SWITCH x CASE 0: IF (ser) SWIM CASE 1: IF (asp) SWIM ara inducible Key Switch Lock Key Asp sensor Lock Ser sensor (Ham, 2006) Inducer (ara) ASP SER t0 t0 arac rbs P c c P BAD BAD rbs FimE T1 T1 T1 T1 T1 T1 T1 T1 chew* rbs2 P TRC TRC rbs2 chew T1 T1 P J23113 rbs0 tar tar rbs0 tsr* T1 T1
20 Lab 1 Tool 1 Tool N Manual Multiple Tools Communication Issues Iterative Lab Computer Exists? Proprietary? Need: An integrated design environment with flexible database support and a data model with a meaningful semantic Data Model Support? Starting Design Multiple Files Lab Database Lab N Standards? Access Issues? Global Repository
21 Tools: What do we need?
22 Tools: What do we need?
23 Clotho Design Environment
24 Database Interaction Needs
25 Clotho Database Flexibility
26
27 More information and thanks Thanks to CHESS, SynBERC J.Christopher Anderson, Chris Voigt, Matthew Johnson, Nade Sritanyaratana, Anne Van Devender Synthetic Biology Workshop at DAC??
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