Synthetic Biology: A New Engineering Discipline? 2011

Announcements MONDAY: Holiday! TUESDAY: Boston Science Museum – Meet at 8:30 am at Thayer and Charlesfield WEDNESDAY: – Wear closed gym clothes/toe shoes to class! THURSDAY: Class time will be from 1 – 4 pm. FRIDAY: Class time will be from 9 – 12 pm.

Overview What is synthetic biology? Where are the applications? Lab 1: Strawberries & DNA How to create a synthetic organism? Lab 2: Restriction enzyme mapping Undergraduate Design Competitions

What is synthetic biology? A Living Factory!

Design Hierarchies

What is Synthetic Biology? The design and construction of new biological parts, devices and systems AND The re-design of existing, natural biological systems for a useful purpose Schubert, C. Nature, 2006(441),

Review: Molecular Biology

DNA Biopolymer, a long chain of small units (A,C,T,G) Double-stranded Complementary strands

Central Dogma of Biology DNA RNA Protein Replication Transcription Translation

Gene Transcription A gene is a region of DNA, corresponding to a unit of inheritance. DNA Protein Many genes produce proteins. RNA Ribosome Binding Site Gene Y Promoter Ribosome Binding Site Gene Y Y Y Transcription Translation

Gene Transcription Some genes have the ability to regulate other genes. When placed in the same organism, these genes interact with one another to form a gene network. Gene YGene XGene Z Note that, as pictured, this network has a feedback loop

Activation Gene Transcription When one gene or factor induces creation of more of another gene, denoted with an arrow (  ) connecting the two Gene YGene X Gene X is transcribed Repression When one gene or factor prohibits creation of another gene, denoted with a perpendicular symbol (--|) connecting the two Gene YGene X Gene X is not transcribed

Genome Network Project, Nature Genetics, 2009

Engineering with Synthetic Biology

Rational Design Develop initial scheme for a gene network Test smaller circuits in the network Create mathematical model to understand theoretical behavior

Rational Design If indicated, modify theory based upon experimental results Construct and test larger network As with other engineering disciplines, this process requires standardization, modularity, and modeling Tweak as needed/desired

Standardization US Standard Screw Thread “In this country, no organized attempt has as yet been made to establish any system, each manufacturer having adopted whatever his judgment may have dictated as best, or as most convenient for himself” – William Sellers, Franklin Institute, April 21, 1864

Standard Parts Registry

Modularity Enabled by standardization Swap interchangeable parts or units in a particular category to achieve new function Groups of parts define a unique functional unit New unit, new function

Modularity Analogy: Upgrading the processor on your computer - All other parts of the computer remain the same, but the computer functions differently. Example: Modular promoters Gene Y Higher output of Y Lower output of Y Promoter 1 Promoter 2

Mathematical Modeling D Y Z β δ ρ ϒ degradation Β= rate of mRNA transcription γY= rate of mRNA degradation δ= rate of protein translation ρZ= rate of protein degradation

Modeling Transcription Same thing for translation…..

Where are the applications? Pharmaceuticals and new vaccines (shorten flu vaccine process by 99%) Biofuels Terraforming Research, NASA

According to the World Health Organization, each year nearly 500 million people become infected with malaria, and nearly three million — mostly children — die from it. Example 1: Anti-malaria Drug

Artemisinin Drug produced from plant (14 month cycle): $2.40/dose Drug produced from microbe (14 days): $0.25/dose Savings: $2.15/dose X 500 million doses = $1 Billion

What’s next? Will technology follow through on promise? Contract with Sanofi-Aventis to begin distribution of arteminisin therapeutic in 2012

Living Factories

Example 2: Biofuels Farnesene – BioFene

Biofuels $600 million deal – Exxon and J. Craig Venter Institute – Synthetic algae to output biofuel Pitfall: – Require massive amount of plant material – Land space?

Craig Venter One of the first to sequence human genome – 3 billion base pairs of DNA Created the first synthetic cell (2010) Founder of the J. Craig Venter Institute

Example 3: Terraforming

Where synthetic biology can help in space…? Green aviation and biofuels Develop new technologies to provide: – Food – Medicine – Life support

The Past: We took familiar biological organisms into space, and engineered environments to suit them. The Future: We will engineer biological systems to make them suited to extraterrestrial environments, and employ these systems in new kinds of missions.

Job Opportunities

Lab 1: Strawberries & DNA

All you wanted to know about….Strawberries Fruit of the Fragaria – genus of flowering plants from rose family An “octoploid” = 8 complete sets of chromosome in a single cell Contains fiestin – an antioxidant linked to prevention of Alzheimer’s Genome sequenced (2011): 240 million bp of DNA

How to create a synthetic organism?

Tools of the trade: Plasmids Antibiotic Selection Marker -used to select bacteria containing gene of interest Promoter -enables controlled expression of gene Gene -encodes protein of interest Multiple Cloning Sites -allows other genes to be introduced into the plasmid Units of DNA for controlled transfer of genes between organisms

Bacteria expressing green fluorescent protein from jelly fish

DNA Scissors: Restriction Enzymes GENE EcoRI XbaI SpeI PstI Vector

GENE A EcoRI XbaI SpeI PstI GENE B EcoRI XbaI SpeI PstI Mixed SpeI/XbalI Site XbaISpeI GENE A SpeI PstI GENE B EcoRI XbaISpeI/Xbal

GENE A SpeI PstI GENE B EcoRI XbaISpeI/X bal

Visualizing DNA: Agarose Gel 969 bp 3.0 kbp bp

Lab 2: Restriction enzyme mapping on DNA plasmid

International Genetically Engineered Machine competition (for undergraduates) Given a kit of biological parts Goal: design and build new biological systems and operate them in living cells

Examples of Ideas BactoBlood, UC Berkeley, 2007 – Develop cost-effective RBC substitute to safely transport O 2 in the bloodstream without inducing sepsis E. Chromi, Cambridge, 2009 – Engineer bacteria to produce different pigments in response to different concentrations of inducer

Participation Statisitics

Where is iGEM?

International Bio-molecular Design Competition Focus areas: biomolecular robotics, biomolecular logic and computing and structural bionanotechnology

DNA Origami Link DNA structures bend with radius of 6 nm Nano-car? Nanoantennae? Nanoscale circuits for drug delivery vehicles?