Newsflash:

ISS2011The 9th International Student Seminar was held at the University of Kyoto. Students from all over the world attended to present their work, and promote international communication and collaboration.

For me, one of the highlights was presentation of work from the Kyoto lab of Takayuki Kohchi, and his colleague Kimitsune Ishizake. The work here has provided a lead for the development of Marchantia polymorpha as a new system for plant development and physiology, and Synthetic Biology. Takayuki worked on Marchantia plastid gene expression in his early career, and the Kohchi lab is now contributing a raft of new methods for plant culture, high throughput transformation, mutagenesis and developmental analysis in Marchantia.

The labs of Takayuki Kohchi and  John Bowman are coordinating in the sequencing of the 280 Mb M. polymorpha genome. Liverworts like M. polymorpha are descendants of the first terrestrial plants. The work in these labs is demonstrating that Marchantia retains an extraordinarily simple genetic architecture, compared to higher plants - where genetic redundancy is pared to a minimum.  

MrMrsMarchantiaMarchantia have a number of advantages for basic studies in developmental biology - there is more information available at:
Marchan Genomics, Kyoto lab pages (Japanese language, registration required)
Marchantia Exchange, for information about Marchantia 

Importantly, the same characteristics that make Marchantia an ideal system for plant developemnt studies - make it a potential chassis of choice for Synthetic Biology experiments in plants. For more information see:
Haseloff Lab pages, outlining benefits of the Marchantia system for Synthetic Biology

right: The fabulous Mrs and Mr Marchantia by Kentaro Ide, Kohchi Lab.

synbio.org.uk

SynBio news

Classifying DNA assembly protocols for devising cellular architectures.

Biotechnol Adv. 2011 Jan-Feb;29(1):156-63 Authors: Wang X, Sa N, Tian PF, Tan TW DNA assembly is one of the most fundamental techniques in synthetic biology. Efficient methods can turn traditional DNA cloning into time-saving and higher efficiency practice, which is a foundation to accomplish the dreams of synthetic biologists for devising cellular architectures, reprogramming cellular behaviors, or creating synthetic cells. In this review, typical strategies of DNA assembly are discussed with special emphasis on the assembly of long and multiple DNA fragments into intact plasmids or assembled...
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Supporting the synthetic revolution

Nature Reviews Microbiology 9, 2 (2011). doi:10.1038/nrmicro2498 Recommendations on the regulation of synthetic biology in the United States provide important lessons on how to foster a nascent field of research while promoting public awareness and support. (Via Nature Reviews Microbiology.)
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Model Annotation for Synthetic Biology: Automating Model to Nucleotide Sequence Conversion.

Bioinformatics. 2011 Feb 4; Authors: Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A MOTIVATION: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts...
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Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms.

Nat Rev Microbiol. 2011 Feb;9(2):131-7 Authors: Medema MH, Breitling R, Bovenberg R, Takano E One of the most promising applications of synthetic biology is the biosynthesis of new drugs from secondary metabolites. Here, we survey a wide range of strategies that control the activity of biosynthetic modules in the cell in space and time, and illustrate how these strategies can be used to design efficient cellular synthetic production systems. Re-engineered versions of secondary metabolite biosynthetic pathways identified from any genomic sequence can then be inserted into these systems in a plug-and-play...
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Opportunities for yeast metabolic engineering: Lessons from synthetic biology.

Biotechnol J. 2011 Feb 16; Authors: Krivoruchko A, Siewers V, Nielsen J Constant progress in genetic engineering has given rise to a number of promising areas of research that facilitated the expansion of industrial biotechnology. The field of metabolic engineering, which utilizes genetic tools to manipulate microbial metabolism to enhance the production of compounds of interest, has had a particularly strong impact by providing new platforms for chemical production. Recent developments in synthetic biology promise to expand the metabolic engineering toolbox further by creating novel biological...
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Synthetic Toxicology: Where engineering meets biology and toxicology.

Toxicol Sci. 2010 Nov 10; Authors: Schmidt M, Pei L This article examines the implications of synthetic biology (SB) for toxicological sciences. Starting with a working definition of SB, we describe its current subfields, namely DNA synthesis, the engineering of DNA-based biological circuits, minimal genome research, attempts to construct protocells and synthetic cells, and efforts to diversify the biochemistry of life through xenobiology. Based on the most important techniques, tools and expected applications in SB, we describe the ramifications of SB for toxicology under the label of synthetic...
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Contrasts: Craig Venter and NSABB on synthetic biology

  Two rather contrasting videos on synthetic biology this month. In the first videocast, released by TED, Craig Venter exposes his grand vision of synthetic genomics. He insists on the notion of 'combinatorial genomics', that will combine the power of large scale DNA synthesis ('robots that can make a million chromosomes a day') with a database of 20 million genes, 'the design components of the future'. This approach, a pragmatic mixture of rational function-oriented...
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Model Annotation for Synthetic Biology: Automating Model to Nucleotide Sequence Conversion.

Model Annotation for Synthetic Biology: Automating Model to Nucleotide Sequence Conversion.: Bioinformatics. 2011 Feb 4; Authors: Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A MOTIVATION: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the...
Read More...
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