“So you’ve made a synthetic cell….”

Summer@Brown2011

Who has heard of…..

The Minimal Cell?

The Minimal Cell is …

Recipient cell: M. capricolumGenome: 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/doseSavings:

$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

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 Y Gene X Gene 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 Y Gene 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 Y Gene 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

http://partsregistry.org/Main_Page

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

Gene Y Higher output of Y

Lower output of YPromoter 1

Promoter 2

Modularity

D

Y

Z

β

δ

ρ

ϒ

degradation

degradation

Β= rate of mRNA transcriptionγY= rate of mRNA degradation

δ= rate of protein translationρZ= rate of protein degradation

Modeling of Genetic Networks

Y (t t)Y(t)t Y (t)t

Y(t t) Y(t)t

Yt

Y (t)

t 0,dY

dt(t) Y(t)

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

VectorPlasmid

GENE A

EcoRI

XbaI

SpeI

PstI

GENE B

EcoRI

XbaI

SpeI

PstI

Mixed SpeI/XbalI Site

XbaISpeI

GENE A

SpeI

PstI

GENE B

EcoRI

XbaI SpeI/Xbal

GENE A

SpeI

PstI

GENE B

EcoRI

XbaI SpeI/Xbal

Plasmid

Visualizing DNA: Agarose Gel

3.0

kbp

1.0

254 bp = MCSNo Gene Insert

969 bp = GFPGene Inserted

2.01.5

Individual Bacterial Colonies

http://ung.igem.org/Main_Page

• 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 O2 in the bloodstream without inducing sepsis

• E. Chromi, Cambridge, 2009– Engineer bacteria to produce different pigments in

response to different concentrations of inducer

2003 2004 2005 2006 2007 2008 2009 20100

20

40

60

80

100

120

140

Year

Num

ber o

f Tea

ms

Participation Statisitics

Where is iGEM?

http://biomod.net

• 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