Synthetic biology

Dr.T.V.Rao MD

Dr.T.V.Rao MD 1

(also known as Synbio, Synthetic Genomics,

Constructive Biology or Systems Biology) – the design and construction of new biological parts, devices and systems that do not exist in the natural world and also the redesign of existing biological systems to perform specific tasks. Advances in Nano scale technologies – manipulation of matter at the level of atoms and molecules – are contributing to advances in synthetic biology.

Definition: Synthetic Biology

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The title ‗synthetic biology‘ appeared in the

literature in 1980, when it was used by Barbara Hobom to describe bacteria that had been genetically engineered using recombinant DNA technology. These bacteria are living systems (therefore biological) that have been altered by human intervention (that is, synthetically). In this respect, synthetic biology was largely synonymous with „bioengineering‟.

What is Synthetic Biology

Dr.T.V.Rao MD 3

Bio-Informatics enters Synthetic Biology

Looking at life as an

information system

DNA as a database

RNA as a decision

network

Proteins and genes as

runtime DLLs

Modeling gene regulatory

networks

Simulating life as a

computer program

Using silicon to validate

biological models

Synthetic Biology Means ?

It is an emerging field of biology that aims at designing and building novel biological systems.

The final goal is to be able to design biological systems in the same way engineers design electronic or mechanical systems.

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Synthetic biology is a new area of biological

research that combines science and engineering. Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature.

Synthetic Biology – A new Biological Research

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Subfields of contemporary SB

2. DNA based bio-circuits

3. Minimal genome

4. Protocells

5. Chemical SB/Xenobiology

1. DNA Synthesis

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Components of Synthetic Biology

Genetic Manipulation?

Genetic selection carried out for millennia (domestication of animals)

Mendelian selection ‗rationalized‘ process.

Recombinant DNA

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Synthetic Biology becomes part of living system

In 2000, the term ‗synthetic biology‘ was again introduced by Eric Kool and other speakers at the annual meeting of the American Chemical Society in San Francisco. Here, the term was used to describe the synthesis of unnatural organic molecules that function in living systems

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Synthetic Biology Redefines Life

Broadly the term has been

used with reference to efforts to ‗redesign life‘

This use of the term is an extension of the concept of ‗biomimetic chemistry‘, in which organic synthesis is used to create artificial molecules that recapitulate the behavior of parts of biology, typically enzymes

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Synthetic biology has a broader scope, however, in

that it attempts to recreate in unnatural chemical systems the emergent properties of living systems, including inheritance, genetics and evolution Synthetic biologists seek to assemble components that are not natural (therefore synthetic) to generate chemical systems that support Darwinian evolution

The motivation is similar in biomimetic chemistry, where synthetic enzyme models are important for understanding natural enzymes.

Scope of Synthetic Biology

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Potential applications of synthetic biology range very

widely across scientific and engineering disciplines, from medicine to energy generation. For example, designed microorganisms might be capable of producing pharmaceutical compounds that are extremely challenging for existing methods of chemical or biological synthesis. While several pharmaceuticals are already produced biotechnologically using genetically engineered organisms, the capacity to design complex synthesis pathways into such organisms could greatly expand the repertoire of products that can be made this way.

What can synthetic biology achieve?

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Engineered biological ‗devices‘ based on modular

assemblies of genes and proteins might also be able to act within the body to detect and respond to changes in the state of health – a kind of autonomous, molecular-scale ‗physician‘ that can combat disease at a very early stage in its development. Such devices could also be used for tissue repair and cell regeneration. Such means, synthetic biology might provide the tools for medical intervention at the molecular level, obviating the rather crude surgical or pharmaceutical tools currently at our disposal

What are the applications of Synthetic Biology ?

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Synthetic Biology is an emerging technology that

hopes to further develop biology as a substrate for engineering by adapting concepts developed in other fields of engineering. Foundational tools to meet this challenge include: ready access to off-the-shelf standardized biological parts and devices; a reliable and defined cellular chassis in which engineers can assemble and power DNA programs; and computational tools as well as measurement standards that enable the ready integration of simpler devices into many-component functional systems

Synthetic Biology as Emerging Science

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Goals in Synthetic Engineering

Engineering Goal:

To build components that can be reliably and predictably assembled into ever more complicated systems

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Synthetic Biology Adopts Many Techniques

Nanotechnology is emulating biology

Molecular assemblers, molecular sensors

‘Bots’ that deliver medicine to specific cells

Biotechnology is helping out

Genetic ‘reengineering’ of e-coli, phages

Nano-Bio or Bio-Nano?

Two very interesting approaches…

The answer might be ‘synthetic biology’

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Nature as a Nano Toolbox

http://www.cse.ucsc.edu/~hongwang/ATP_synthase.html Dr.T.V.Rao MD 17

Synthetic Proteins

Synthesis New polymers

Biochemistry

Structural studies Structure / function

Functional studies New properties

New applications Cell structure adapts

well to environments Dr.T.V.Rao MD 18

DNA 2.0

DNA 2.0 Inc. is a leading provider for synthetic biology. With our gene synthesis process you can get synthetic DNA that conforms exactly to your needs, quickly and cost effectively. Applications of custom gene synthesis include codon optimization for increased protein expression, synthetic biology, gene variants, RNAi trans-complementation and much more.

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Bio-Nano Convergence

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Bio-Nano Machinery

Using protein / viral

complexes and DNA to

self-assemble devices,

and novel function, into

biomechanical systems

Earth’s early nanostructures ~ 2 billion years ago Dr.T.V.Rao MD 21

Molecular Self Assembly

Figure1: 3D diagram of a lipid bilayer membrane - water molecules not represented for clarity

http://www.shu.ac.uk/schools/research/mri/model/micelles/micelles.htm

Figure 2: Different lipid model

-top : multi-particles lipid molecule

-bottom: single-particle lipid molecule

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Goal of Digital Cells

Simulate a Gene Regulatory Network Goal of e-cell, CellML,

and SBML projects

Test microarray data for biological model Run expression data

through GRN functions

Create biological cells with new functions Splice in promoters to

control expression

Create oscillating networks using operons

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Biology from Laptops

Biological engineers of the future will start with their laptops, not in the laboratory.”

— Drew Endy, MIT

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How computer Helps in Designing Life

While computers store and process information in binary strings – coded as the numbers 0 and 1 – DNA operates in (mathematical) base four.

Its information is coded by the sequence of the four nucleotide bases, A, C, T and G. The bases are spaced every 0.35 nm along the DNA molecule, giving DNA a data density of over one-half million gigabits per square centimeter, many thousands of times more dense than a typical hard drive.

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How Technology helps to create Life

It would take more than a trillion music CDs to hold the amount of information that DNA can hold in a cubic centimeter. Moreover, different strands of DNA can all be working on computational problems at the same time – and are a lot cheaper than buying multiple PowerBooks

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DNA synthesis speeds Science ?

The increasing speed and decreasing cost of DNA synthesis will assist the progress of experimental research in the biological sciences (Endy 2005). For these reasons, the discussion of applications and their opportunities is rather speculative.

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Environmental Applications

Bioremediation. Another area with potential environmental benefits is bioremediation. Microorganisms or even plants could be engineered to degrade pesticides and remove pollutants (Tucker and Zilinskas 2006).

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Environmental Applications

Biosensors. The area of biosensors also has potential environmental benefits. Although biosensors have a broad range of uses (including the production of photographic bacteria, see Levskaya et al. 2005), they can also be developed to detect toxic chemicals, such as arsenic (Chu 2007).

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In vivo applications. There are a range of potential

applications of synthetic biology which could monitor and respond to conditions in the human body. For example, regulatory circuits could be designed which trigger insulin production in diabetes (ITI Life Sciences 2007). Bacteria or viruses could be programmed to identify malignant cancer cells and deliver therapeutic agents (Serrano 2007). Viruses have also been engineered to interact with HIV-infected cells, which could prevent the development of AIDS (De Vriend 2006).

Medical Applications

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Synthetic Biology Creates New Drug Development

New drug development pathways. One of the avenues

of synthetic biology that has wide application is the development of alternative production routes for useful compounds, and one of the most discussed of these is the construction of an artificial metabolic pathway in E. coli and yeast to produce a precursor (arteminisin) for an antimalarial drug (Martin et al. 2003, Ro et al. 2006).

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Solutions for HIV and Cancer

Can be used for development of other therapeutically useful compounds for cancer and HIV treatment (Voigt 2005). Polyketides are another important class of drugs which could potentially be produced using synthetic biology (Heinemann and Panke 2006).

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Helps development of Synthetic Vaccines

Synthetic vaccines. The fact that synthetic biology can ‗start from scratch‘ means that new synthetic vaccines could be produced in response to viruses that themselves evolve rapidly, such as those that cause severe acute respiratory syndrome (SARS) and hepatitis C (Garfinkel et al. 2007).

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Industrial Applications

Biofuels. One of the most

widely discussed areas of future application of synthetic biology research is biofuels. There are many ways of engineering microorganisms to produce carbon-neutral (or more environmentally friendly) sources of energy. For example, bacteria could be engineered to synthesize hydrogen or ethanol by degrading cellulose, although further work is needed to overcome technical barriers.

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Bio based manufacturing and chemical synthesis

The development of alternative production routes (as in the arteminisin case above) does not have to be limited to health-related applications, but could also be used for the production of other useful compounds

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These potential applications of synthetic biology have to

be viewed in the light of the possible risks. There are two factors which make the risk governance of synthetic biology potentially problematic. The first is that synthetic biology (like genetic engineering) involves the production of living organisms, which by definition are self-propagating. The second is that with the growth of the Internet and the routinisation of many biotechnological procedures, the tools for doing synthetic biology are readily accessible (Garfinkel et al. 2007).

Risks related to synthetic biology

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The major biosafety risk of synthetic biology is the

accidental release of synthetic organisms, which could have unintended detrimental effects on the environment or on human health (De Vriend 2006). This could be a particular in the case of bioremediation, where synthetic organisms would be purposely released into the environment, for example to remove toxins from the soil. Not only are microorganisms living and self-propagating, but they also evolve rapidly, and they can exchange genetic material with each other across species boundaries

Environmental risks: biosafety

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Creations of Unpredictable Microbes

Additionally, the flexibility of synthetic biology means that microorganisms could be created which are radically different from existing ones, and these microorganisms might have unpredictable and emergent properties (Tucker and Zilinskas 2006), making the risks of accidental release very difficult to assess in advance (De Vriend 2006).

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Ethical Issues – A certain Concern

It is the perceived unnaturalness of synthetic biology which is most likely to give rise to ethical alarm. Statements to the effect that the next 50 years of DNA evolution will take place ―not in Nature but in the laboratory and clinic‖ (Benner 2004:785), accompanied by inventions such as plants that produce spider silk, clearly challenge everyday understandings of nature and our place in it. Dr.T.V.Rao MD 39

Synthetic Biology can create New Pathogens

The major advantage of our approach is putting together well characterized components.

Creating new pathogens would require a full scale research effort

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SYNBIOSAFE: Safety and Ethical aspects of Synthetic Biology

Ethics Related to its applications (e.g. human enhancement)

Related to its distribution (e.g. biofuel production)

Related to the procedure as such (e.g. status of living

machines)

Biosafety How to assess risks from new SB products, functions and

systems? How can we improve safety through SB biosafety

engineering? What happens if non-professionals (amateurs, hackers) start

using SB?

Schmidt M, Ganguli-Mitra A, Torgersen H, Kelle A, Deplazes A & Biller-Andorno N. 2009. A Priority Paper for the

Societal and Ethical Aspects of Synthetic Biology. Systems and Synthic Biology Vol.3(1-4):1-2

Dr.T.V.Rao MD

Rebooting Life

A new report looks at the challenges of regulating first generation products of synthetic biology. At the J. Craig Venter Institute, scientists are on the verge of creating a living organism from ―dead‖ chemicals, by rebooting a microbe with a new—and completely artificially constructed—genome. At the University of California Berkeley, researchers are modifying microbes to Dr.T.V.Rao MD 42

Synthetic biology and Nanotechnology

The popular computer game ―SimLife‖ allows users to create and manipulate virtual people. But what are the chances of us one day being able to do the same with real organisms: building new life-forms out of basic chemicals, so “SimLife” becomes “SynLife”?

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Craig venter creates revolution in Synthetic Biology

Craig Venter‘s team (and the associated paper in Science) that they have successfully synthesized the complete genome of the bacterium Mycoplasma genitalium is an important step towards achieving what is becoming known as ―synthetic biology‖. By constructing complete DNA sequences from scratch, the door is being opened to transforming common laboratory chemicals into new living organisms; that are engineered with specific purposes in mind. And perhaps not surprisingly, this manipulation of DNA at the nan scale is increasingly being seen as part of the ―nanotechnology revolution‖.

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The complete synthetic M. mycoides genome was isolated

from the yeast cell and transplanted into Mycoplasma capricolum recipient cells that have had the genes for its restriction enzyme removed. The synthetic genome DNA was transcribed into messenger RNA, which in turn was translated into new proteins. The M. capricolum genome was either destroyed by M. mycoides restriction enzymes or was lost during cell replication. After two days viable M. mycoides cells, which contained only synthetic DNA, were clearly visible on petri dishes containing bacterial growth medium.

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First Self-Replicating Synthetic Bacterial Cell

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Breakthrough in creating Synthetic Cell

Creating a 'synthetic cell', as described in a report published online in Science, meant putting together a series of previously developed steps. First, the team established a method for transplanting natural DNA from M. mycoides into M. capricolum . Then, working with Mycoplasma genitalium, a species whose genome is about half the length of that of M. mycoides, the group stitched together a synthetic donor genome and cloned it in a yeast cell

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New Hope in Science

It is hoped that this discovery will lead to the development of many important applications and products including biofuels, vaccines, pharmaceuticals, clean water and food products. Cleaning up oil spills maybe?

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