<body><script type="text/javascript">//<![CDATA[try{(function(a){var b="http://",c="news.mongabay.com",d="/cdn-cgi/cl/",e="img.gif",f=new a;f.src=[b,c,d,e].join("")})(Image)}catch(e){}//]]></script> --------------
Contact Us       Consulting       Projects       Our Goals       About Us
home » Archive »
Nature Blog Network



    Taiwan's Feng Chia University has succeeded in boosting the production of hydrogen from biomass to 15 liters per hour, one of the world's highest biohydrogen production rates, a researcher at the university said Friday. The research team managed to produce hydrogen and carbon dioxide (which can be captured and stored) from the fermentation of different strains of anaerobes in a sugar cane-based liquefied mixture. The highest yield was obtained by the Clostridium bacterium. Taiwan News - November 14, 2008.


Creative Commons License


Sunday, December 07, 2008

JCVI researchers streamline efficient construction of synthetic genomes - future biofuel applications

Researchers at the J. Craig Venter Institute (JCVI) have published a paper describing a significant advance in genome assembly in which the team can now assemble the whole bacterial genome, Mycoplasma genitalium, in one step from 25 fragments of DNA. The humble yeast Saccharomyces cerevisiae proves to be the ideal genetic factory for the process. Lead author Daniel G. Gibson, Ph.D. and his team published their results in the online early edition of the journal Proceedings of the National Academy of Sciences (PNAS).

The publication is another milestone in synthetic biology, a young branch of biotechnology that may one day help solve global problems like climate change, lead to new drugs, and generate hyper-efficient, 'endless' biofuels. Promising as it may be, the field is highly controversial and some civil society organisations demand a broader debate about the risks of synthetic biology (earlier post).

The new publication represents major improvements in the methods that the team developed and described in their January 2008 publication of the first synthesis of a bacterial genome, M. genitalium. That publication outlined how the team synthesized in the laboratory the 582,970 base pair M. genitalium genome using the chemical building blocks of DNA—adenine (A), guanine (G), cytosine (C) and thymine (T) (previous post).

While this was a big advance, it took several years to come to fruition and in the end was a tedious, multi- stage process in which the team had to build the genome a quarter at a time using the bacterium Escherichia coli to clone and produce the DNA segments. During this building process the team found that E. coli had difficulty reproducing the large DNA segments, so they turned to the yeast Saccharomyces cerevisiae. They were then able to finish creating the synthetic bacterial genome using a method called homologous recombination (a process that cells naturally use to repair chromosome damage).

Realizing how robustly yeast performed, the team wondered if it could be used to build the entire M. genitalium genome from multiple, smaller, overlapping segments of DNA. For this study the team used DNA fragments that ranged in size from about 17,000 base pairs to 35,000 base pairs. These relatively short segments were inserted into yeast cells in one step and through the mechanism of homologous recombination were assembled into the synthetic M. genitalium genome. Several experiments were then done to confirm that all 25 pieces of the synthetic DNA had been correctly assembled in the yeast cells, and to show that the experiment could be successfully reproduced.

The JCVI team continues to explore the capacity for DNA assembly in yeast, and the various applications of this particular method. They conjecture that a variety of combinations of DNA molecules and genetic pathways could be manufactured in yeast, in essence turning yeast into a genetic factory for specifically designed and optimized processes. This advance is being used by scientists at the company Synthetic Genomics Inc. in making next generation biofuels and biochemicals more efficiently:
:: :: :: :: :: :: :: ::
We continue to be amazed by the capacity of yeast to simultaneously take up so many DNA pieces and assemble them into genome-size molecules. This capacity begs to be further explored and extended and will help accelerate progress in applications of synthetic genomics. - Dr Gibson, lead author
Senior author Clyde Hutchison, Ph.D., adds that he is astounded by the team’s progress in assembling large DNA molecules. It remains to be seen how far they can push this yeast assembly platform but the team is hard at work exploring these methods as it works to "boot up" the synthetic chromosome.

The work was funded by the company Synthetic Genomics Inc. (SGI), which, among other things, has been active in studying the potential of synthetic genomics for applications in the biofuel sector (previous post).

Key Milestones
The JCVI builds on a portfolio of major scientific breakthroughs which gradually built up to the current status - a series of applications that may soon make the creation of artificial organisms possible:
Mid-1990’s: After sequencing the M. genitalium genome, Dr. Venter and colleagues begin work on the minimal genome project. This area of research, trying to understand the minimal genetic components necessary to sustain life, started with M. genitalium because it is a bacterium with the smallest genome known that can be grown in pure culture. This work was published in the journal Science in 1995.

2003: Drs. Venter, Smith and Hutchison (along with JCVI's Cynthia Andrews-Pfannkoch) made the first significant strides in the development of a synthetic genome by assembling the 5,386 base pair genome of bacteriophage ΦX174 (phi X). They did so using short, single strands of synthetically produced, commercially available DNA (known as oligonucleotides) and using an adaptation of polymerase chain reaction (PCR), known as polymerase cycle assembly (PCA), to build the phi X genome. The team produced the synthetic phi X in just 14 days.

2007: JCVI researchers led by Carole Lartigue, Ph.D., announced the results of work published in the journal Science, which outlined the methods and techniques used to change one bacterial species, Mycoplasma capricolum, into another, Mycoplasma mycoides Large Colony (LC), by replacing one organism’s genome with the other one’s genome. Genome transplantation was the first essential enabling step in the field of synthetic genomics as it is a key mechanism by which chemically synthesized chromosomes can be activated into viable living cells.

January 2008: The second successful step in the JCVI teams’ journey to create a cell controlled by synthetic DNA was completed when Gibson et al published in the journal Science, the synthetic M. genitalium genome. The team is still working on experiments to install a fully synthetic bacterial chromosome into a recipient cell and thus “boot up” a synthetic chromosome.
Ethical Considerations
Since the beginning of the quest to understand and build a synthetic genome, Dr. Venter and his team have been concerned with the societal issues surrounding the work. In 1995 while the team was doing the research on the minimal genome, the work underwent significant ethical review by a panel of experts at the University of Pennsylvania (Cho et al, Science December 1999:Vol. 286. no. 5447, pp. 2087 – 2090). The bioethical group's independent deliberations, published at the same time as the scientific minimal genome research, resulted in a unanimous decision that there were no strong ethical reasons why the work should not continue as long as the scientists involved continued to engage public discussion.

Dr. Venter and the team at JCVI continue to work with bioethicists, outside policy groups, legislative members and staff, and the public to encourage discussion and understanding about the societal implications of their work and the field of synthetic genomics generally. As such, the JCVI’s policy team, along with the Center for Strategic & International Studies (CSIS), and the Massachusetts Institute of Technology (MIT), were funded by a grant from the Alfred P. Sloan Foundation for a 20-month study that explored the risks and benefits of this emerging technology, as well as possible safeguards to prevent abuse, including bioterrorism. After several workshops and public sessions the group published a report in October 2007 outlining options for the field and its researchers.

This report was criticized by a number of organisations, who demand a far broader debate about the potential benefits and risks of synthetic biology (previous post).


Illustration: Assembly of the synthetic M. genitalium genome in yeast from 25 overlapping DNA fragments. Credit: J. Craig Venter Institute.

References:

Biopact: Scientists create first synthetic bacterial genome - importance for biofuels - January 25, 2008

Biopact: Civil society organizations respond to report on synthetic biology governance - October 18, 2007


Biopact: Scientists take major step towards 'synthetic life': first bacterial genome transplantation changing one species to another - June 29, 2007

Biopact: Breakthrough in synthetic biology: scientists synthesize DNA-based memory in yeast cells, guided by mathematical model - September 17, 2007

Biopact: Scientists call for global push to advance synthetic biology - biofuels to benefit - June 25, 2007

Biopact: Scientists patent synthetic life - promise for 'endless' biofuels - June 09, 2007

Biopact: Synthetic Genomics and Asiatic Centre for Genome Technology to sequence oil palm genome - July 11, 2007

Biopact: Agrivida and Codon Devices to partner on third-generation biofuels - August 03, 2007

0 Comments:

Post a Comment

Links to this post:

Create a Link

<< Home