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Synthetic Biology

Microbes in the Media Seminar
by

Anna Clements

on 5 March 2014

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Transcript of Synthetic Biology

Synthetic
Biology

Anna Clements
What is Synthetic Biology?
New
, innovative field in which technology and
engineering
are applied to
biology
Construct biological systems from computer-generated,
synthetic DNA

“Synthetic biology is an emerging area of research that can broadly be described as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems.”
-UK Royal Society

“Synthetic biology is an emerging form of science and engineering that aims at the design and construction of (new) biological systems.”
-3rd International Conference on Synthetic Biology

“Synthetic biology aims to design and build new biological parts and systems or to modify existing ones to carry out novel tasks.”
-UK Parliamentary Office of Science and Technology

Progression throughout history...
Methods Used in Synthetic Biology
For thousands of years, humans have selectively chosen which livestock or crops to reproduce for the next year based on desirable characteristics.
(Artificial selection/selective breeding)
More recent decades, genetic engineering has allowed scientists to transfer a gene from one organism and insert it into another organism to express certain traits.
Goals: engineer microbial genomes for the use of synthesizing products (ex. biofuels, renewable chemicals), construct an entire genome for a microorganism.
Synthetic biology involves the synthesis of long strands of DNA and assembly of genomic codes with access to large DNA data banks. Essentially this field aims to construct natural biological systems from the ground up.
How did synthetic biology evolve?
Work Cited
http://syntheticbiology.org
http://www.foe.org/projects/food-and-technology/synthetic-biology
http://www.nytimes.com/2007/07/08/weekinreview/08wade.html?_r=0
http://www.synbioproject.org/topics/synbio101/definition/
http://archives.nbclearn.com/portal/site/k-12/flatview?cuecard=41482
http://www.bio.org/articles/synthetic-biology-explained
http://syntheticbiology.arc.nasa.gov
http://www.youtube.com/watch?v=Fv0hV-gWwGY
http://www.dnalc.org/resources/animations/pcr.html
http://www.sciencedirect.com/science/article/pii/B9780123851208000127
http://www.stanford.edu/~maureenh/quals/html/synbio/node18.html
http://www.crchudequebec.ulaval.ca/ronyweb/DOWNLOADS/Chemical_Synthesis_of_Oligonucleotides.pdf
http://www.jcvi.org/cms/research/projects/first-self-replicating-synthetic-bacterial-cell/overview/
http://www.genomeweb.com/blog/night-living-dead-pigeon
http://synbio.berkeley.edu/index.php?page=research-themes
http://longnow.org/revive/what-we-do/passenger-pigeon/
http://libcloud.s3.amazonaws.com/93/59/9/529/1/SynBio-Biofuels_Report_Web.pdf
Best way to learn about biological systems is by building them
"Bioeconomy" that yields products made by synthetic organisms (ex. biofuels, food, medicine, industrial chemicals)
As technology becomes more readily available, the cost of creating synthetic DNA will decrease
1. Recombinant DNA
2. PCR (Polymerase chain reaction)
3. DNA sequencing
Basic Tools for Genetic Engineering
DNA Synthesis: Phosphoramidite Chemistry
Major Synthetic Biology
Institutions and Achievements
NASA: interest in expanding technology to allow for extraterrestrial explorations
Creating biofuels, food, medicine, spacecraft materials from synthetic organisms
In 2003, the J. Craig Venter Institute created a synthetic version of the bacteriophage PhiX 174, a virus that infects bacteria.
>1 million base pairs and almost 1,000 genes
In 2006, the Berkeley Center for Synthetic Biology engineered a yeast with bacterial & wormwood genes, changing it into a "chemical factory" that could produce a precursor to artemisinin.
In 2010, JCVI completed the first self-replicating synthetic bacterial cell (
Mycoplama mycoides JCV-syn1.0
) with 1.08 million base pairs.
Four "watermarks" inserted into the DNA as indicators that the DNA is synthetic, as well as to identify which laboratory it came from
Oligonucleotides: small, single-stranded synthetic molecules of DNA, usually no more than 20 nitrogen bases
Phosphoramidite chemistry synthesizes oligonucleotides in the opposite direction as the natural biological process, from 3' to 5' (as opposed to 5' to 3')
Synthetic oligonucleotides can be used for PCR, DNA sequencing, probes for detecting DNA
DNA Databases
Public databases of DNA sequences are more readily available, given the ease by which DNA can be sequenced now.
Data is stored by recording the sequenced A, T, G, and C bases as 0's and 1's (binary code) on the computer.
In order to synthesize DNA, the code is first written on the computer and then translated into base sequences.
Bacteriophage PhiX 174
Mycoplasma mycoides JCVI-syn1.0
Passenger Pigeon Revival?
Led by Ben Novak of The Long Now Foundation: an effort to bring back the extinct species of the Passenger Pigeon using DNA from museum specimens.
DNA sequencing of a passenger pigeon from 1871 was completed in Oct. 2013, sequencing of a band-tailed pigeon for reference was completed in February 2014.
20 other specimens chosen for studying population genetics sequencing.
Next step: a "first draft" of a passenger pigeon genome with the help of references from the band-tailed and rock pigeons.
Passenger Pigeon
Band-Tailed Pigeon
Rock Pigeon
PROS
Synthetic organisms' assimilation into the natural environment could negatively impact ecosystems as invasive species
Synthetic organisms would be created ready to reproduce or replicate, which is a variable that is harder to control
Contamination of natural DNA with synthetic DNA
Overuse of resources and biomass to supply the construction and growth of the synthetic organisms
Ethical implications of recreating organisms
CONS
Do you think Synthetic Biology will be harmful or helpful to society?
In what direction do you think the field will go in 10 years? 20 years? 50?
Full transcript