SynBioFromLeukipposInstitute

by
James M. Carothers

"Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commercially-important applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems."
http://bit.ly/14AoPHk

Accelerate your Synthetic Biology vision!
Design, Build and Launch http://bit.ly/1aCKgHv

"UC Berkeley's top-ranked Bioengineering Department announced the creation of a Synthetic Biology concentration in Bioengineering. The concentration represents one of the few US degree specializations in synthetic biology. It also represents an important step toward SynBERC's strategic educational goal to spawn a national synthetic biology curriculum.

 The concentration program was developed in consultation with SynBERC Principal Investigators Adam Arkin and Christopher Anderson, SynBERC Affiliate Investigator +John Dueber  and Department Lecturer Terry Johnson, all from UC Berkeley's Bioengineering Department. (In April, Johnson received the 2010 Golden Apple, UC Berkeley 's student award for most outstanding teacher.) The course listing can be found here: http://bioeng.berkeley.edu/program/synbio.php

...."

http://bit.ly/123B8eP

by
Byron Spice-

"Gene expression goes better in tight quarters, especially when other conditions are less than ideal, say researchers.

As the researchers report in an advance online publication in Nature Nanotechnology, these findings may help explain how cells have adapted to the phenomenon of molecular crowding, which has been preserved through evolution.And this understanding may guide synthetic biologists as they develop artificial cells that might someday be used for drug delivery, biofuel production, and biosensors.“These are baby steps we’re taking in learning how to make artificial cells,” says study leader Cheemeng Tan, a postdoctoral fellow in the Lane Center for Computational Biology at Carnegie Mellon University...."

http://bit.ly/1dFxEz8

*Podcast with Alok Jha

"Imperial College London hosts a meeting of scientists working at the cutting edge of bio-engineering and synthetic biology.

Synthetic biology is likely to have a profound impact on our future health, the environment and how scientists relate to society – and Imperial College London is at the forefront of this exciting new field in Europe. In this week's show Alok Jha attends the sixth international meeting on synthetic biology, which took place at Imperial. Prof Paul Freemont and Professor Richard Kitney, co-directors of the EPSRC Centre for Synthetic Biology and Innovation at Imperial, explained why synthetic biology has become so important for industry in such a short time. The conference hosted a diverse range of scientists, academics and artists. Alok interviewed designer Alexandra Daisy Ginsberg about collaborating with bio-engineers and scientists in imagining future applications and consequences of this emerging technology; Dr Tom Ellis, of Imperial College London, and Dr Leslie Mitchell, of Johns Hopkins University, about their work creating a synthetic yeast; Prof Farren Issacs from Yale University about new tools he is designing for biomedical research; and biological conservationist and consultant Kent Redford on using synthetic biology to preserve the world's biodiversity. Subscribe for free via iTunes to ensure every episode gets delivered. (Here is the non-iTunes URL feed). Follow the podcast on our Science Weekly Twitter feed and receive updates on all breaking science news stories from Guardian Science."

 http://bit.ly/10X93mF

by
Cheemeng Tan,Saumya Saurabh,Marcel P. Bruchez,Russell Schwartz& Philip LeDuc

"The integration of synthetic and cell-free biology has made tremendous strides towards creating artificial cellular nanosystems using concepts from solution-based chemistry, where only the concentrations of reacting species modulate gene expression rates. However, it is known that macromolecular crowding, a key feature in natural cells, can dramatically influence biochemical kinetics via volume exclusion effects, which reduce diffusion rates and enhance binding rates of macromolecules. Here, we demonstrate that macromolecular crowding can increase the robustness of gene expression by integrating synthetic cellular components of biological circuits and artificial cellular nanosystems. Furthermore, we reveal how ubiquitous cellular modules, including genetic components, a negative feedback loop and the size of the crowding molecules can fine-tune gene circuit response to molecular crowding. By bridging a key gap between artificial and living cells, our work has implications for efficient and robust control of both synthetic and natural cellular circuits."


http://bit.ly/12BDMac

by
Di Liu, Allison Hoynes-O’Connor and Fuzhong Zhang

"Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics and metabolomics, aiming to fill the gap between systems and synthetic biology."

http://bit.ly/15DHpNd

by
Bernd Giese, Stefan Koenigstein, Henning Wigger, Jan C. Schmidt, Arnim von Gleich

"The term “synthetic biology” is a popular label of an emerging biotechnological field with strong claims to robustness, modularity, and controlled construction, finally enabling the creation of new organisms. Although the research community is heterogeneous, it advocates a common denominator that seems to define this field: the principles of rational engineering. However, it still remains unclear to what extent rational engineering—rather than “tinkering” or the usage of random based or non-rational processes—actually constitutes the basis for the techniques of synthetic biology. In this article, we present the results of a quantitative bibliometric analysis of the realized extent of rational engineering in synthetic biology. In our analysis, we examine three issues: (1) We evaluate whether work at three levels of synthetic biology (parts, devices, and systems) is consistent with the principles of rational engineering. (2) We estimate the extent of rational engineering in synthetic biology laboratory practice by an evaluation of publications in synthetic biology. (3) We examine the methodological specialization in rational engineering of authors in synthetic biology. Our analysis demonstrates that rational engineering is prevalent in about half of the articles related to synthetic biology. Interestingly, in recent years the relative number of respective publications has decreased. Despite its prominent role among the claims of synthetic biology, rational engineering has not yet entirely replaced biotechnological methods based on “tinkering” and non-rational principles."


http://bit.ly/1dLTXmI

The impact of synthetic biology 

by
Gi Na Lee and Jonguk Na 

"Synthetic biology has recently been at the center of the world’s attention as a new scientific and engineering discipline. It allows us to design and construct finely controllable metabolic and regulatory pathways, circuits, and networks, as well as create new enzymes, pathways, and even whole cells. With this great power of synthetic biology, we can develop new organisms that can efficiently produce new drugs to benefit human healthcare and superperforming microorganisms capable of producing chemicals, fuels, and materials from renewable biomass, without the use of fossil oil. Based on several successful examples reported, this commentary aims at peeking into the potential of synthetic biology."

http://bit.ly/130SYtW

by
rpshetty 

"Stencil corresponding to symbols from SBOL Visual 1.0.0. Useful for creating diagrams of synthetic biology pathways and circuits.

 See description provided in BBF RFC 93 (DOI: 1721.1/78249). Please note that all credit for this stencil goes to the authors of BBF RFC 93. I've simply uploaded this stencil for convenienc"

http://bit.ly/1bMgkdB

by

Calviello L, Stano P, Mavelli F, Luisi PL, Marangoni R.

"BACKGROUND:

The wet-lab synthesis of the simplest forms of life (minimal cells) is a challenging aspect in modern synthetic biology. Quasi-cellular systems able to produce proteins directly from DNA can be obtained by encapsulating the cell-free transcription/translation system PURESYSTEM™(PS) in liposomes. It is possible to detect the intra-vesicle protein production using DNA encoding for GFP and monitoring the fluorescence emission over time. The entrapment of solutes in small-volume liposomes is a fundamental open problem. Stochastic simulation is a valuable tool in the study of biochemical reaction at nanoscale range. QDC (Quick Direct-Method Controlled), a stochastic simulation software based on the well-known Gillespie's SSA algorithm, was used. A suitable model formally describing the PS reactions network was developed, to predict, from inner species concentrations (very difficult to measure in small-volumes), the resulting fluorescence signal (experimentally observable).RESULTS:Thanks to suitable features specific of QDC, we successfully formalized the dynamical coupling between the transcription and translation processes that occurs in the real PS, thus bypassing the concurrent-only environment of Gillespie's algorithm. Simulations were firstly performed for large liposomes (2.67µm of diameter) entrapping the PS to synthetize GFP. By varying the initial concentrations of the three main classes of molecules involved in the PS (DNA, enzymes, consumables), we were able to stochastically simulate the time-course of GFP-production. The sigmoid fit of the GFP-production curves allowed us to extract three quantitative parameters which are significantly dependent on the various initial states. Then we extended this study for small-volume liposomes (575 nm of diameter), where it is more complex to infer the intra-vesicle composition, due to the expected anomalous entrapment phenomena. We identified almost two extreme states that are forecasted to give rise to significantly different experimental observables.CONCLUSIONS:The present work is the first one describing in the detail the stochastic behavior of the PS. Thanks to our results, an experimental approach is now possible, aimed at recording the GFP production kinetics in very small micro-emulsion droplets or liposomes, and inferring, by using the simulation as a reverse-engineering procedure, the internal solutes distribution, and shed light on the still unknown forces driving the entrapment phenomenon."

http://bit.ly/16JZzKq

by
Narjeskhatoon Habibia, Siti Zaiton Mohd Hashima, Cesar A. Rodriguez, Mohd Razip Samian

"ynthetic biology is to apply engineering standards to the biology. It has two main aims; first to design and construct biological systems in order to extend the understanding of how they work, and second, to design biological systems for performing valuable tasks like medications synthesis and biofuels production. Due to the complex nature of the biological systems, and similar to the engineering fields, computational methods and computer aided design (CAD) tools, are required to handle this complexity. In this review, existing CADs, languages and data models for synthetic biology are explored. The goal is to provide an insight for the synthetic biologists to take advantage of the available computational tools and to find out the gaps to work on."


 http://bit.ly/18mnOVO

by
Herbert M. Huttanusa, Elton Graugnarda, Bernard Yurkea,, William B. Knowltona, Wan Kuangb, William L. Hughesa, Jeunghoon Leec


"Highlights

•Gold nanoparticle-based colorimetric sensing scheme using a DNA reaction network was devised.•In the catalytic aggregation design, a target strand induces multiple inter-particle linkages.•Catalytic aggregation show greater extent of absorption spectrum change.•This work provides a path for applying DNA reaction networks on colorimetric detection.AbstractA catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkage from only ones target DNA strand, the catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gel electrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules..."

http://bit.ly/15IE2ou

by
anonymous

"- A UK team is building an “artificial” chromosome to be inserted into the world’s first synthetic yeast.

 Teams worldwide are making the other parts of its genome, which will be assembled to make the yeast strain Saccharomyces cerevisiae. Once complete, new strains of synthetic yeast could help make products such as vaccines, biofuels and chemicals. The UK government has announced a grant of almost £1m towards the project, which aims to be complete by 2017. Synthetic biology involves assembling artificial genes to create new materials in a similar way that engineers build machines using many parts. Some even think it can form the basis of a new industrial revolution. Teams worldwide are making the other parts of its genome, which will be assembled to make the yeast strain Saccharomyces cerevisiae. Once complete, new strains of synthetic yeast could help make products such as vaccines, biofuels and chemicals. The UK government has announced a grant of almost £1m towards the project, which aims to be complete by 2017. Synthetic biology involves assembling artificial genes to create new materials in a similar way that engineers build machines using many parts. Some even think it can form the basis of a new industrial revolution."

http://bit.ly/18iiWRv