A Blogroll for Synthetic Biology

The emerging discipline of synthetic biology holds tremendous potential for both basic research and for delivering powerful, novel solutions to real world problems (both in medicine and in other industries). This field has grown from a handful of researchers at Princeton, MIT, Harvard, and Universities in California (with pioneers such as Dr. Drew Endy, Dr. George Church and Dr. Ron Weiss leading the way) to include laboratories all over the world. It is my belief that this field will represent the future of biology and will be a vast and critical part of the economy in the years to come.

There are several great resources on the web to learn about synthetic biology and keep abreast of the latest developments. In addition to sites such as syntheticbiology.org, I present below a blogroll of great sites to visit for anybody interested in this amazing field. (Image above is modified from synthetic biology.org; I claim no rights to this image). Of course, I haven't included my own blog, even thought I already have several posts about synthetic biology (for example, my article about DNA synthesis)

My Top Three:

Oscillator

http://blogs.scientificamerican.com/oscillator/

Part of the scientific american family of blogs, Oscillator mostly focuses on Synthetic Biology and is a great resource for interesting articles and news about the field. I especially like some of the perspectives given by the main author Chistina Agapakis (whom you can follow on Twitter).

Peccoud Lab Journal Club Page
http://peccoud.vbi.vt.edu

http://peccoud.vbi.vt.edu/category/journal-club/

For the aficionado or seasoned expert, this is a great resource where recent papers about, or related to, synthetic biology are discussed. This is a great feature to have on a laboratory group website which deserves emulation by other scientists.

Dreamer Biologist's Blog

http://dreamerbiologist.wordpress.com/blog-2/

This blog, maintained by an undergraduate with a passion for biology (and synthetic biology in particular), features articles on a range of topics. He maintains a separate section with material solely devoted to synthetic biology (http://dreamerbiologist.wordpress.com/synbio/), and the title of the biology I think captures the essence of what this field is: a call for biologists to dream up novel solutions to real world problems, and imagine new technologies based upon the power of life.

Please continue reading the article to get my full list of synthetic biology blogs and sites (Click 'Read More'). They are really worth a read! 

Do you know of a blog or site that I have missed? Please share the link and a description below by leaving a comment.

Nanopore Sequencing: Towards Reading and Writing?

Nanopore sequencing is an emerging technology that promises fast, easy and affordable way to 'read' the bases in DNA. While researchers are seeking the $1000 genome, nanopore sequencing (once refined) may be able to deliver under budget and on a time scale of minutes, not hours or days.

Other bloggers and science writers (at BiteSize Bio, among others) have done a great job covering this technology (several of which I complied at the end of this article in a short 'webibliography', or bibliography of websites). Here, I would like to speculate on the use of a nanopore for the synthesis (or writing) of a DNA sequence. 

FInding a cheaper and faster way to synthesize a DNA sequence is a big challenge, and one that with a growing urgency. I've previously highlighted the importance of meeting this challenge and some current attempts at solutions. The ideal solution may currently be residing in the realm of science fiction. As I mentioned in the previous article, solutions that employ a controllable polymerase have great potential. A recent article from the Akeson laboratory (Olasagasti, 2012; PMC3711841) shows that this may be possible. Indeed, Akeson and colleages are able to electronically control both the threading of DNA through a nanopore, as well as the synthesis of the threaded DNA. 

Select 'Read More' to see the rest of the article. What are your thoughts on nanopore sequencing? Do you think that it is feasible that this technology can be adapted in some way for a next-generation DNA sequencing solution?

Building a Better Future, One Base at a Time

Synthetic Biology holds promise to revolutionize biotechnology and many other industries. Broadly defined, it is an engineering approach that seeks to design artificial genes, gene regulatory circuits, genomes, and useful and novel cellular behaviors. This includes efforts in recent years to program bacteria to specifically invade tumor cells as well as the production of microbial derived artemisinin. In addition to these impressive feats of bio-engineering, synthetic biology also gives researchers a way to better understand the design principles by which normal cells function. After all, it is much easier to understand how a system works once you have succeed in constructing one of similar complexity.

The scale of gene construction involved in synthetic biology can be quite large. In a multi-million dollar effort by the J. Craig Venter Institute, researchers successfully synthesized an entire bacterial genome and transplanted it into a cell. While the synthetic genome contained mostly natural sequence (the genome was physically synthetic, but the information contained within was a copy of what nature and evolution has already produced), future efforts may involved rewriting of vast sections of the genome. These grand examples of synthetic biology highlight a major obstacle facing this emerging discipline: the costs involved in the actual de novo synthesis and assembly of DNA.

Over the past decade and a half, tremendous advances in DNA sequencing technology have been made. The original human genome project took years of efforts by many researchers, with a final price tag estimated at approximately 4.4 billion dollars (current dollars, adjusted for inflation) or slightly more than $1 per base pair. Due to the improved scale of sequencing coupled with several technological revolutions, scientists are rapidly approaching the coveted $1000 genome, which would be approximately a million fold improvement in terms of cost (or $0.000001 per base)

DNA synthesis technology and capabilities currently sit where DNA sequencing was a decade ago, when the completion of the final draft of the human genome was announced. As a matter of fact, synthesis technology is arguably behind even this mark. The Venter Institute's creation of Mycoplasma laboratorium (also known as Mycoplasma genitalia JCVI-1.0) is estimated to have taken a small team of researchers nearly a decade and $40 million dollars to complete. Since this genome is only half a million dollars, this represents a cost of $80 a base pair. Most smaller projects demand less intense and less iterative assembly efforts, but synthesis of even short oligos is still between $0.25 and $1.0 per base, depending on the size, scope, and quality of the synthesis efforts.

Clearly, there is room for improvement in DNA synthesis technology. This improvement will be critical to the advance of the field of synthetic biology, which hold tremendous promise for a variety of industries. Where will the improvement come from? For DNA sequencing, improved scale and efficiency of existing technology was important, but not enough for the incredible leap in capability and cost-effectiveness. Both evolution and revolution (innovative second and third generation technologies) was necessary to achieve the current level of capability. 

So far, the horizon for new, ground-breaking technology for DNA synthesis is not clear. The chemistry used in the synthesis of oligomers has remained largely unchanged for years. There are a few new approaches which may hint at how DNA synthesis can be made more reliable and affordable. Here, I'll survey a few of the newest developments. This includes the MOSIC method, the research by Dr. George Church's group at Harvard and its implementation at Gen9, as well as Cambrian Genomics and some other creative ideas. 

Select 'Read More' to learn more about emerging DNA synthesis technologies.