Dr.T.V.

Rao MD

Dr.T.V.Rao MD 1
Definition: Synthetic Biology

 (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.
Dr.T.V.Rao MD 2
What is Synthetic Biology

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‟.
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.

Dr.T.V.Rao MD 5
 Synthetic Biology –
A new Biological Research

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.
Dr.T.V.Rao MD 6
Subfields of contemporary SB
1. DNA Synthesis

2. DNA based bio-circuits

3. Minimal genome

4. Protocells

5. Chemical SB/Xenobiology
Dr.T.V.Rao MD 7
 Components of Synthetic Biology

 Genetic Manipulation?

 Genetic selection
carried out for
millennia
(domestication of
animals)
 Mendelian selection
‗rationalized‘ process.
 Recombinant DNA

Dr.T.V.Rao MD
8
 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

Dr.T.V.Rao MD 9
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

Dr.T.V.Rao MD 10
Scope of Synthetic Biology

 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.
Dr.T.V.Rao MD 11
What can synthetic biology achieve?

 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.
Dr.T.V.Rao MD 12
 What are the applications of
Synthetic Biology ?

 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
Dr.T.V.Rao MD 13
Synthetic Biology as Emerging
Science

 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
Dr.T.V.Rao MD 14
Goals in Synthetic Engineering

Engineering Goal:

To build
components that
can be reliably
and predictably
assembled into
ever more
complicated
systems Dr.T.V.Rao MD 15
 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’
Dr.T.V.Rao MD 16
Nature as a Nano Toolbox


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

Dr.T.V.Rao MD 19
Bio-Nano Convergence

Dr.T.V.Rao MD 20
 Bio-Nano Machinery
Using protein / viral
complexes and DNA to
self-assemble devices,
and novel function, into
biomechanical systems

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

Figure1: 3D diagram of a lipid bilayer membrane - water molecules not represented for clarity
Dr.T.V.Rao MD Figure 2: Different lipid model 22
-top : multi-particles lipid molecule
http://www.shu.ac.uk/schools/research/mri/model/micelles/micelles.htm -bottom: single-particle lipid molecule
 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

Dr.T.V.Rao MD 23
 Biology from Laptops

Biological
engineers of the
future will start
with their laptops,
not in the
laboratory.”
— Drew Endy, MIT
Dr.T.V.Rao MD 24
 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.
Dr.T.V.Rao MD 25
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
Dr.T.V.Rao MD 26
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.
Dr.T.V.Rao MD 27
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).
Dr.T.V.Rao MD 28
 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).

Dr.T.V.Rao MD 29
 Medical Applications

 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).
Dr.T.V.Rao MD 30
 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).
Dr.T.V.Rao MD 31
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
Dr.T.V.Rao MD
(Heinemann and Panke 32

2006).
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).

Dr.T.V.Rao MD 33
 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.
Dr.T.V.Rao MD 34
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
Dr.T.V.Rao MD 35
 Risks related to synthetic
biology

 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).

Dr.T.V.Rao MD 36
 Environmental risks:
biosafety

 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
Dr.T.V.Rao MD 37
 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).

Dr.T.V.Rao MD 38
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
Dr.T.V.Rao MDnature and our place in it. 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
Dr.T.V.Rao MD 40
 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?

Dr.T.V.Rao MD 41
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
 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”?
Dr.T.V.Rao MD 43
 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
Dr.T.V.Rao MD 44
―nanotechnology revolution‖.
 First Self-Replicating Synthetic
Bacterial Cell

 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.
Dr.T.V.Rao MD 45
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
Dr.T.V.Rao MDcloned it in a yeast cell 46
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?

Dr.T.V.Rao MD 47
 Follow me for Articles of
Interest on Microbiology ..


Dr.T.V.Rao MD 48
 
Created by Dr.T.V.Rao MD for „e‟
learning resources for Biologists
in the Developing world
 Email
 doctortvrao@gmail.com

Dr.T.V.Rao MD 49