SynBioFromLeukipposInstitute

Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves [George M. Church,Ed Regis] on Amazon.com. *FREE* super saver shipping on qualifying offers.

Caltech scientists have created an ultra-sensitive device that can weigh an individual molecule for the first time...

by

Xavier Rios, Adrian W. Briggs, Danos Christodoulou, Josh M. Gorham, Jonathan G. Seidman, George M. Church

"Recent advances allow multiplexed genome engineering in E. coli, employing easily designed oligonucleotides to edit multiple loci simultaneously. A similar technology in human cells would greatly expedite functional genomics, both by enhancing our ability to test how individual variants such as single nucleotide polymorphisms (SNPs) are related to specific phenotypes, and potentially allowing simultaneous mutation of multiple loci. However, oligo-mediated targeting of human cells is currently limited by low targeting efficiencies and low survival of modified cells. Using a HeLa-based EGFP-rescue reporter system we show that use of modified base analogs can increase targeting efficiency, in part by avoiding the mismatch repair machinery. We investigate the effects of oligonucleotide toxicity and find a strong correlation between the number of phosphorothioate bonds and toxicity. Stably EGFP-corrected cells were generated at a frequency of ~0.05% with an optimized oligonucleotide design combining modified bases and reduced number of phosphorothioate bonds. We provide evidence from comparative RNA-seq analysis suggesting cellular immunity induced by the oligonucleotides might contribute to the low viability of oligo-corrected cells. Further optimization of this method should allow rapid and scalable genome engineering in human cells."

http://1.usa.gov/OjtrVK

http://bit.ly/RbvfQR

by

Pasotti L, Politi N, Zucca S, Cusella De Angelis MG, Magni P.

"Modularity is a crucial issue in the engineering world, as it enables engineers to achieve predictable outcomes when different components are interconnected. Synthetic Biology aims to apply key concepts of engineering to design and construct new biological systems that exhibit a predictable behaviour. Even if physical and measurement standards have been recently proposed to facilitate the assembly and characterization of biological components, real modularity is still a major research issue. The success of the bottom-up approach strictly depends on the clear definition of the limits in which biological functions can be predictable.
RESULTS:
The modularity of transcription-based biological components has been investigated in several conditions. First, the activity of a set of promoters was quantified in Escherichia coli via different measurement systems (i.e., different plasmids, reporter genes, ribosome binding sites) relative to an in vivo reference promoter. Second, promoter activity variation was measured when two independent gene expression cassettes were assembled in the same system. Third, the interchangeability of input modules (a set of constitutive promoters and two regulated promoters) connected to a fixed output device (a logic inverter) expressing GFP was evaluated. The three input modules provide tunable transcriptional signals that drive the output device. If modularity persists, identical transcriptional signals trigger identical GFP outputs. To verify this, all the input devices were individually characterized and then the input-output characteristic of the logic inverter was derived in the different configurations.
CONCLUSIONS:
Promoters activities (referred to a standard promoter) can vary when they are measured via different reporter devices (up to 22%), when they are used within a two-expression-cassette system (up to 35%) and when they drive another device in a functionally interconnected circuit (up to 44%). This paper provides a significant contribution to the study of modularity limitations in building biological systems by providing useful data on context-dependent variability of biological components."
http://bit.ly/PfwK0X

In the year 2000, conceiving of a device that worked simultaneously as a handheld computer, portable MP3 player, satellite radio, GPS, and phone seemed like...

by

Eric Sawyer

"Synthetic biology is in the midst of branching out from bacterial to eukaryotic systems. With the increased complexity of the eukaryotic cell come new challenges, but more importantly new opportunities, for the biological engineer. The typical synthetic biology device in bacteria is a promoter, ribosome binding site (RBS), and one or more genes. The amount of protein product can be adjusted by tuning promoter strength (affinity for RNA polymerase binding) and RBS strength (closeness to the consensus sequence recognized by the ribosome). Additional control can be obtained from tuning mRNA folding, protein tags, and codon optimization.

Eukaryotic devices can be controlled with a whole host of other tools. Proteins can be localized to organelles (as well as the cell membrane, as in bacteria), and introns allow for the regulation of RNA processing, including producing alternative splicing products. The mRNA sequence can be tinkered to adjust transcript half-life. Regulation at the DNA level is possible through engineering chromatin folding and methylation patterns, and enhancers distant in the genome can modulate gene expression. Most intriguingly, transcription factors (TFs) can be used to regulate gene expression, and networks of any size can be created through the sharing of particular TFs.

Eukaryotic cells use a large collection of TFs to control patterns of native gene expression. There are plenty of TFs in any model eukaryote to choose from, but using them means cross-talk between the synthetic construct and the genome. We want to be able to create designer TFs de novo, not only to avoid cross-talk, but to allow customizable function...."
http://bit.ly/PjIgs1