Synthetic Biology
Synthetic biology is a new area of biological research that
combines science and engineering in order to design and
build ("synthesize") novel biological functions and systems.
Wikipedia, 2010
Synthetic Biology
Potential Application Areas
Or: looking ahead to the next 50 years
• Understanding Biological and Complex Systems
Synthetic Biology
Potential Application Areas
Or: looking ahead to the next 50 years
• Health:
• Diagnostics
• Microbial Sensors
• Health Monitors
• Disease Management
• Inherited Diseases
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Smart Drugs
Synthetic Biology
• Chemical Engineering
• Natural Product Synthesis
• Novel Chemical Feeds Stuffs
• New Computational Technologies
• Liquid Based Computers
• Parallel Processing
• Self repairing systems
• Analog computers at the molecular level
Synthetic Biology
• New Materials
• Living/Non-Living Interfacing Materials
• Neural Implants
• New Enhanced Tissues (Stronger bone)
• Novel Materials, Wood++ (Smart materials)
• Programmed Development, complex structures
• Nano Assembly (DNA Origami)
• New BioMechno-devices
Caltech
Synthetic Biology
• Whole Genome Design and Construction
• New Life Forms
• Fully Customized Organisms
• Environment
• Bioremediation (clean up our mess)
• Advanced GMOs (maybe?)
• Energy: Solar based Biofuel Production
• “Steak in a vat”
• Terraforming
Existing Applications
1. Genetic Logic Circuits
2. Binary Logic Decoder
3. Natural Drug Production
4. Pipe Repair
5. Breast Cancer Targeting Phage
6. Alarm clocks
7. Bacterial Powered Battery
8. Arsenic Detector
9. Cadmium Detector
10. Nitrate Detector
11. Bioplastic Production
12. Landmine Detection
13. Heavy Meta Scavengers
14. Interspecies Optical Communication
Existing Applications
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Pattern Formation
Pesticide Degrader
Detect Multiple Heavy Metals
E. coli Fragrance Factory
Fast Acting Wound Dressing
Multi-Wavelength Color Detector
Random Number Generator
All-in-one Protein Expression and Purification System
Etc etc
Key Technologies
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Basic Genetic Engineering
Protein Engineering
Fabrication
Modeling
Measurement
Standards
Abstraction
Genetic Engineering
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Cut and ligate (Join) DNA (Restriction enzymes)
Transform Cells
Polymerase Chain Reaction (PCR)
Automated Sequencing
Fabrication
• DNA Synthesis
• Standard Assembly Methods
– Tom Knight’s BioBrick Assembly
– Freiburg Fusion
– In-Fusion Biobrick Assembly
http://openwetware.org/wiki/In-fusion_biobrick_assembly
http://bbf.openwetware.org/Standards/Technical/Formats.html
Standard BioBrick Assembly
B0034 = RBS Brick
C0010 = Terminator
Standard BioBrick Assembly
University of Virginia iGEM Team
Modeling
TinkerCell.com : Deepak Chandran Bioeng, UW
Modeling
TinkerCell.com : Deepak Chandran Bioeng, UW
Modeling
TinkerCell.com : Deepak Chandran Bioeng, UW
Why do Modeling?
What is a model:
A simplified piece of reality, a work of fiction.
Purpose:
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To obtain answers about what will happen in the physical world
To influence further experimentation
To foster conceptual progress and understanding
To assist in the axiomization of a physical situation
Why do Modeling?
Models should be able to satisfy the following two requirements:
1. Be able to describe current knowledge
2. Be able to make non-trivial predictions
A good model should be:
1. Salient – should not represent everything!
2. Parsimonious - be as simple as possible
3. Predictive
4. Falsifiable
5. Understandable and explanatory
Type of Models
1. Discrete or Continuous
2. Deterministic or Stochastic
3. Linear of Nonlinear
Common models in synthetic biology include all of them!
Measurement
GFP: Green Fluorescent
Protein
And lots of other colors
Measurement
Simpson, Nature 439, 608 (2006)
DNA
Abstraction in biology
Metabolic
reactions
Systems
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Lac Repressor
Tet Repressor
Devices
Plac Op
Parts
tetR