“So you’ve made a synthetic cell….” 2011

Who has heard of….. The Minimal Cell?

The Minimal Cell is … Recipient cell: M. capricolum Genome: M. mycoides JCVI-syn1.0 First synthetic self-replicative cell (May 2010) Mother: computer Function of every gene is known (1.8 Mbp) 15 years 24 scientists ~$40 million Chassis for biological devices

A Living Factory! What is synthetic biology?

Design Hierarchies

Arteminisin Project: Anti-malaria drug BioFene: biofuels Terraforming Research: NASA Sensors Bioremediation Applications

According to the World Health Organization, each year nearly 500 million people become infected with malaria, and nearly 3 million — mostly children — die from it. Malaria Crisis

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 Arteminisin

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

Living Factories

Farnesene – BioFene BioFene: Biofuels

$600 million deal – Exxon and J. Craig Venter Institute – Synthetic algae to output biofuel Biofuels

Terra-forming Research

Green aviation and biofuels Develop new technologies to provide: – Food – Medicine – Life support Emerging technologies?

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

Analogies

Review: Molecular Biology

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

DNA RNA Protein Replication Transcription Translation Central Dogma of Biology

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 Gene Transcription

Activation 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 Gene Transcription

Genome Network Project, Nature Genetics, 2009

Engineering with Synthetic Biology

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 Rational Design

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 Standardization

Standard Registry

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 Modularity

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 of Genetic Networks

Same thing for translation….. Model Transcription

Manipulating DNA to engineer organisms

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 Plasmid

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 Plasmid

Visualizing DNA: Agarose Gel 3.0 kbp bp = MCS No Gene Insert 969 bp = GFP Gene Inserted Individual Bacterial Colonies

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?

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