Download Minimal Genome

Designer Biology
&
Minimal Genome
‘OM’ICS
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Genomics
Transcriptomics
Proteomics
Metablomics
Cellomics
Nutriomics
Phenomics
Pharmacogenomics
Multidisciplinary
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Artists
engineering,
chemistry,
computer science, and
molecular biology
How does a Gene work?
Adventures in Synthetic Biology
Synthetic Biology is
A) the design and construction of new biological parts,
devices, and systems, and
B) the re-design of existing, natural biological systems
for useful purposes.
Vision
• rational assembly/ design of complex biologic
systems by providing the foundations for
classic engineering strategies
Strategies
• to limit the impact of manipulation of selected parts on the
rest of the system,
• strategies and parts to control complex system assemblies,
such as genetic circuits;
• providing the functional parts to implement artificial
designs, e.g., obtained from freely re-assembling protein
domains such as in polyketide synthesis
• research to provide the technology for the implementation
of complex system designs in the laboratory,
• such as large scale de novo DNA design and the integration
of complex protocols on microfluidic chips.
Tools
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manipulating genes for decades;
inserting,
deleting,
and changing them in various microbes
Scissors- Restriction Enzymes
Joining- Ligases
Most Important Tools
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RNA
Regulation of gene expression
Protein
Ability to interact with small molecules
Antisense technologies
Plasmids
E.coli- Favourite organism to manipulate
Challenges for Synthetic Biology
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sustainable energy,
protecting human health,
creating new materials,
and revealing the origin & fate of the universe
Scope – Is it really defined for SB?
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Designing and constructing novel organisms
biologically-inspired systems – or
redesigning existing organisms and systems –
to solve problems that natural systems
cannot.
Potential Scope
BIODESIGN INDIA 1.0; October 8, 2010
Genetic Circuits
An engineered cell
Initiatives
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OpenWetWare
Synthetic Genomics Study
BioBricks
The BioBricks Foundation
Registry of Standard Biological Parts
SynBERC
Standard Part Registry
• gene expression-based devices
• i.e., PoPS, or polymerase per second (a term
for quantifying the input/output signals in
genetic circuits);
• specifications for hierarchies for the
Protein:DNA Parts (PDP)
• Post-Translational Parts (PTP) families;
• the first specification datasheet for a
biological device.
Projects
• E. coli Automatic Directed Evolution Machine
(E.ADEM) project
• Engineering the Host/System Interface
• Minimal Cell Project (MCP)
• Rebuilding T7
• Synthetic E. coli genome project
• Synthetic Mycoplasma genome project
• Synthetic yeast genome project
www.synbio.org
Evolution is greater than God
• automatically created,
• from promoters, regulators, receptors, binding
partners, enzymes and ribozymes, to sensors,
logic devices, reporters, metabolic pathways,
entire genomes,
• and even solutions of mathematic problems.
BIODESIGN INDIA 1.0; October 8, 2010
USA
Source: www.synbioproject.org
BIODESIGN INDIA 1.0; October 8, 2010
Source: www.synbioproject.org
BIODESIGN INDIA 1.0; October 8, 2010
BIODESIGN INDIA 1.0; October 8, 2010
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Biodream machines
Synthetic Biology
Designer Genome
Computational Designs
Playing God
Hand made Biology
Extreme Engineering
Complexity of simplicity
Custom made
Tailor made
Various Facets
Information Reductionist Approach
BIODESIGN INDIA 1.0; October 8, 2010
Craig Venter
• Cynthia/Synthia
• Mycoplasma laboratorium
• I plan to show that we understand the
software of life by creating true artificial life.
And in this way I want to discover whether a
life decoded is truly a life understood.
• – A Life Decoded
Craig Venter’s Synthia
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Mycoplasma mycoides JCV1-syn1.0
"the first species.... to have its parents be a computer”
Introduced in Mycoplasma capricolum
Mycoplasma genitalium
482 genes comprising 582,970 base pairs
382 genes
Single Cell
Minimal Genome
1.8 Mbp
Huge Financial Investments
Bio-Energy and Drug Production
Patent Application
US 2007/0122826 and WO/2007/047148
BIODESIGN INDIA 1.0; October 8, 2010
Story of Cynthia/Synthia
• http://www.youtube.com/watch?v=cXQhJPdlE
lY
Other Important Areas
• Biofuels
• Marine Biology
-Natural Products
-Biomimicking
-Evolutionary Aspects
Patterns
Clean Technologies
Other Areas
• Creating genes from Junk DNA
• Clipperton Project
• Parsi Genome Project
Synthetic Biology and Art
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BioART
Synthetic Aesthetics
Univ Edinburgh and Stanford University
Art and Design- Science by Design
Smell of earth after rain
Srishsti Media Arts
NCBS
Algae tasting like beef
Pattern studies and graphical designing
Cheese smell
Drug Discovery
• Biofactories
Artemisinin Case
(Wormwood Tree)
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Call for International Justice
Artemisinic acid
Artemisia annua
Jay Keasling UC Berkley
Commercialization Issues
Dependence on developed countries
Generic Drugs
BIODESIGN INDIA 1.0; October 8, 2010
Open Access
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Tools
the analytical methods,
design software,
data
will be available to the NON-profit research
community
• To Companies (that are members of the
Center’s industrial consortium)
Softwares available
• Bio SPICE(Biological Simulation Program for
Intra- and Inter-Cellular Evaluation),
• a framework and software toolset for modeling &
simulation of spatio-temporal processes in living
cells
• tools for the comparison of genome structure
(operon, regulon, etc.) across sequenced
microbes
• Systems Biology Markup Language (SBML), a
computer-readable format for representing
models of biological processes.
Drew Endy
• Chassis Engineering
• Interaction between Chassis and System
• engineering of biological systems with
predictable behavior – Biggest Challenge
• Design of standard interface between
biological systems and host cell (chassis)
Minimal Genome
• Chemical Self Assembly
• reconstitution of DNA, RNA and protein
syntheses from pure components
• self-assembly occurs in a definite sequence and is
generally energetically favored, obviating the
need for enzymes and an energy source.
Assembling some type of cell (i.e. a selfreplicating, membrane-encapsulated collection of
biomolecules)
• Core is cellular replication machinery
• Forster and Church
• initially define the components sufficient for each
subsystem,
• allow detailed kinetic analyses
• lead to improved in vitro methods for synthesis of
biopolymers, therapeutics and biosensors.
• Completion would yield a functionally and
structurally understood self-replicating biosystem
• 113 kbp
• 151 genes
http://www.nature.com/msb/journal/v2/n1/fig_tab/msb4100090_F1.html
Issues
• Do I Understand What I Can Create?
Biosafety Issues in Synthetic Biology
• IPRs
• Socio-ethical
• Dual Use
• Use- Misuse
• Bioterrorism
• Biosafety
• Risk/impact Assessment
• Should we learn from GM crops
Facts and Forward looking
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Current Market $600 M
May rise to $3.5 B
Chemical Industry 1.8T (1/5th)
Public Awareness 9 to 26%
Security Concerns 27%
Moral Concerns 25%
Health Consequence (-ve) 25%
Damage to Environment (13%)
Source: www.synbioproject.org
The Pros and Cons
BIODESIGN INDIA 1.0; October 8, 2010