Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Using combinatorial libraries to engineer genetic circuits advances synthetic biology

24.04.2009
Streamlining the construction of synthetic gene networks has led a team of Boston University researchers to develop a technique that couples libraries of diversified components with computer modeling to guide predictable gene network construction without the back and forth tweaking.

By applying engineering principles to biological systems where a set of components can evolve into networks that display desired behaviors – known as synthetic biology -- , has led to new opportunities for biofabrication, drug manufacturing -- even potential biofuels.

And while there have been notable successes, the basic process of building and assembling a predictable gene network from bio-molecular parts remains a major challenge that is often frustrating. The time-consuming tweaking phase often requires many months of swapping out different chemical inputs, RNA regulators and promotors before the sought -after network is realized.

In a paper published online this week in Nature Biotechnology, the research team, led by James J. Collins, BU professor of biomedical engineering, focused on ways to speed up the construction process by assembling a library of 20 versions of two gene promotors and a simple synthesis technique to create component libraries for synthetic biology. Each version covered a wide range gene expression. With the activity levels calculated from the component libraries, the scientists turned to a computer model and designed and built a basic gene circuit to predict how fluorescent protein expression varied with levels of promoter-inhibiting chemicals.

Using the same simulation, for the simple gene circuit the researchers went the next step with a genetic timer, a more complicated circuit. However, computer simulation, on its own, was unable to predict the behavior of this timing circuit. They then built a representative genetic timer using a promoter from each of their libraries and, over time, tracked its behavior. Based on information from one network, the research team was able to calibrate their model and achieve accurate predictions from all the other possible network combinations. These timers, the study notes, are effectively genetic toggle switches.

One last test of these genetic timers was to assemble and test one in yeast, which could accurately time yeast sedimentation -- a process that can be applied to biotechnology and some popular brewed beverages.

"The phenotype is crucial in industrial beer, wine and bioethanol fermentation, as it allows for easy removal of yeast sediments after all the sugars have been converted to ethanol," the paper noted.

The researchers concluded that their method using combinatorial libraries to engineer genetic circuits moves the "tweaking" from the back-end of gene network engineering to the front-end.

"Projects undertaken with this approach will help accelerate synthetic biology by yielding many more components for the community," the paper concludes, noting the need for extensive characterization of each component is eliminated or substantially reduced.

"Our work also provides an accessible method for introducing predictable, controlled variability to networks, a feature that is increasingly becoming desirable as synthetic biology enters its second decade."

The research paper, "Diversity-based, Model-Guided Construction of Synthetic Gene Networks with Predicted Functions, "was authored by Tom Ellis and Xiao Wang, both post doctoral students at Boston University's Center for BioDynamics and Center for Advanced Biotechnology and Collins.

Founded in 1839, Boston University is an internationally recognized institution of higher education and research. With more than 30,000 students, it is the fourth largest independent university in the United States. BU consists of 17 colleges and schools along with a number of multi-disciplinary centers and institutes which are central to the school's research and teaching mission.

Ronald Rosenberg | EurekAlert!
Further information:
http://www.bu.edu

More articles from Life Sciences:

nachricht Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory

nachricht How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>