Researchers at Virginia Tech and the Massachusetts Institute of Technology have used a computer-aided design tool to create genetic languages to guide the design of biological systems.
Known as GenoCAD, the open-source software was developed by researchers at the Virginia Bioinformatics Institute at Virginia Tech to help synthetic biologists capture biological rules to engineer organisms that produce useful products or health-care solutions from inexpensive, renewable materials.
GenoCAD helps researchers in the design of protein expression vectors, artificial gene networks, and other genetic constructs, essentially combining engineering approaches with biology.
Synthetic biologists have an increasingly large library of naturally derived and synthetic parts at their disposal to design and build living systems. These parts are the words of a DNA language and the “grammar” a set of design rules governing the language.
It has to be expressive enough to allow scientists to generate a broad range of constructs, but it has to be focused enough to limit the possibilities of designing faulty constructs.
MIT’s Oliver Purcell, a postdoctoral associate, and Timothy Lu, an associate professor in the Department of Electrical Engineering and Computer Science, have developed a language detailed in ACS Synthetic Biology describing how to design a broad range of synthetic transcription factors for animals, plants, and other organisms with cells that contain a nucleus.
Meanwhile, Sakiko Okumoto, an assistant professor of plant pathology, physiology, and weed science at the Virginia Tech College of Agriculture and Life Sciences, and Amanda Wilson, a software engineer with the Synthetic Biology Group at the Virginia Bioinformatics Institute, developed a language describing design rules for expressing genes in the chloroplast of microalgae Their work was published in the Jan. 15 issue of Bioinformatics.
“Just like software engineers need different languages like HTML, SQL, or Java to develop different kinds of software applications, synthetic biologists need languages for different biological applications,” said Jean Peccoud, an associate professor at the Virginia Bioinformatics Institute, and principal investigator of the GenoCAD project. “From its inception, we envisioned GenoCAD as a framework allowing users to capture their expertise of a particular domain in languages that they could use themselves or share with others.”
The researchers said encapsulating current knowledge by defining standards will become increasingly important as the number and complexity of components engineered by synthetic biologists increases.
They propose that grammars are a first step toward the standardization of a broad range of synthetic genetic parts that could be combined to develop innovative products.
“Developing a grammar in GenoCAD is a little like writing a review paper,” Purcell said. “You start with the headings and you progressively dig deeper in the details. At the end of the process, you have a much better appreciation for what you know and what you don’t know about a particular domain.”
Lu added, “Our group has a recognized expertise in synthetic transcription factors. We hope that this work will help a broad range of scientists use our results in their own projects.”
“GenoCAD exemplifies the kind of cyberinfrastructure the institute is known for,” said Dennis Dean, the director of the Virginia Bioinformatics Institute. “This type of portal can enable collaborations across disciplines and institutions to foster a team approach to today’s most pressing scientific challenges.”
This work was supported by the Defense Advanced Research Projects Agency, the National Institutes of Health New Innovator Award (1DP2OD008435), the National Science Foundation (1124247 to T.K.L. and 0850100 to J.P.), and the Office of Naval Research (N00014-13-1-0424). Peccoud is Chief Scientific Officer of GenoFAB LLC, a company providing products and services derived from GenoCAD.
Written by Emily Kale.
Tiffany L Trent
Tiffany Trent | EurekAlert!
Gene switch may repair DNA and prevent cancer
12.02.2016 | Institute for Integrated Cell-Material Sciences at Kyoto University
New method opens crystal clear views of biomolecules
11.02.2016 | Deutsches Elektronen-Synchrotron DESY
Today, plants and microorganisms are heavily used for the production of medicinal products. The production of biopharmaceuticals in plants, also referred to as “Molecular Pharming”, represents a continuously growing field of plant biotechnology. Preferred host organisms include yeast and crop plants, such as maize and potato – plants with high demands. With the help of a special algal strain, the research team of Prof. Ralph Bock at the Max Planck Institute of Molecular Plant Physiology in Potsdam strives to develop a more efficient and resource-saving system for the production of medicines and vaccines. They tested its practicality by synthesizing a component of a potential AIDS vaccine.
The use of plants and microorganisms to produce pharmaceuticals is nothing new. In 1982, bacteria were genetically modified to produce human insulin, a drug...
Atomic clock experts from the Physikalisch-Technische Bundesanstalt (PTB) are the first research group in the world to have built an optical single-ion clock which attains an accuracy which had only been predicted theoretically so far. Their optical ytterbium clock achieved a relative systematic measurement uncertainty of 3 E-18. The results have been published in the current issue of the scientific journal "Physical Review Letters".
Atomic clock experts from the Physikalisch-Technische Bundesanstalt (PTB) are the first research group in the world to have built an optical single-ion clock...
The University of Würzburg has two new space projects in the pipeline which are concerned with the observation of planets and autonomous fault correction aboard satellites. The German Federal Ministry of Economic Affairs and Energy funds the projects with around 1.6 million euros.
Detecting tornadoes that sweep across Mars. Discovering meteors that fall to Earth. Investigating strange lightning that flashes from Earth's atmosphere into...
Physicists from Saarland University and the ESPCI in Paris have shown how liquids on solid surfaces can be made to slide over the surface a bit like a bobsleigh on ice. The key is to apply a coating at the boundary between the liquid and the surface that induces the liquid to slip. This results in an increase in the average flow velocity of the liquid and its throughput. This was demonstrated by studying the behaviour of droplets on surfaces with different coatings as they evolved into the equilibrium state. The results could prove useful in optimizing industrial processes, such as the extrusion of plastics.
The study has been published in the respected academic journal PNAS (Proceedings of the National Academy of Sciences of the United States of America).
Exceeding critical temperature limits in the Southern Ocean may cause the collapse of ice sheets and a sharp rise in sea levels
A future warming of the Southern Ocean caused by rising greenhouse gas concentrations in the atmosphere may severely disrupt the stability of the West...
12.02.2016 | Event News
09.02.2016 | Event News
02.02.2016 | Event News
12.02.2016 | Physics and Astronomy
12.02.2016 | Life Sciences
12.02.2016 | Medical Engineering