Open-source software designed to minimize synthetic biology risks

Rigorous bioinformatic analysis of the strengths, limitations published in Nature Biotechnology

2011-03-22

(Press-News.org) A software package designed to minimize the potential risks of synthetic biology for the nation's defense and security is now available to the gene synthesis industry and synthetic biology community in an open-source format.

Virginia Tech has licensed GenoTHREAT, a software tool that helps detect the use of synthetic DNA as bioterrorism agents. Developed as an open-source project by a team led by Jean Peccoud, associate professor at Virginia Bioinformatics Institute at Virginia Tech, it is being released using the Apache License Version 2.0 to ensure broad accessibility.

GenoTHREAT implements the "best match" screening protocol method recommended by the federal government to minimize the risk that unauthorized individuals or those with malicious intent will obtain toxins and other potentially dangerous materials from DNA synthesis providers. The process of developing GenoTHREAT allowed Peccoud's team to conduct a rigorous bioinformatic analysis of the strengths and limitations of the best match method which was published in the March issue of Nature Biotechnology .

"It was natural to start developing GenoTHREAT around the federal guidance on synthetic DNA," said Peccoud. "Since this regulation is only one of many regulations and policies that providers of synthetic DNA need to comply with, our current efforts aim at developing a more comprehensive biosecurity solution that can be customized for a variety of users."

Five of the report's co-authors – Arunima Srivastava of Delhi, India, a sophomore majoring in computer science in the College of Science; Michael Kozar of Harwich, Mass., a junior majoring in biology in the College of Science and French in the College of Liberal Arts and Human Sciences; Tyler Stewart of Springfield, Va., a junior majoring in biological sciences in the College of Science and biochemistry in the College of Agriculture and Life Sciences; and Gaelle Letort and Olivier Mirat, visiting students from ENSIMAG, an engineering school in Grenoble, France – are undergraduate students who worked with Peccoud and were part of a team of undergraduate students enrolled in the 2010 International Genetically Engineered Machines (iGEM) competition. The other two authors are Laura Adam, graduate research assistant, and Mandy Wilson, database administrator with Peccoud's group

"This project exemplifies how it is possible to train students to use interdisciplinary strategies to confront today's most important scientific problems," said Virginia Tech Vice President and Dean for Undergraduate Education Daniel Wubah. "By breaking down the separation of basic and applied research, and by combining engineering and life science expertise, this team has made a valuable contribution to a real-world problem directly related to the security of our nation."

Since the first synthetic cell in May 2010, the security and ethical aspects of synthetic biology have been debated in congressional hearings and by the Presidential Commission for the Study of Bioethical Issues and the National Academy of Science, among others.

"While the U.S. government does not endorse any particular tools, as stated in the Guidance, the U.S. government is supportive of efforts to develop new and improved methods to screen double-stranded DNA sequences for biosecurity purposes," explained Capt. Theresa Lawrence of the U.S. Department of Health and Human Services. "We applaud efforts to advance this important field of science and enhance security."

### About the Virginia Bioinformatics Institute The Virginia Bioinformatics Institute (http://www.vbi.vt.edu) at Virginia Tech is a premier bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches to science combining information technology, biology, and medicine. These approaches are used to interpret and apply vast amounts of biological data generated from basic research to some of today's key challenges in the biomedical, environmental, and agricultural sciences. With more than 240 highly trained multidisciplinary, international personnel, research at the institute involves collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology, and medicine. The large amounts of data generated by this approach are analyzed and interpreted to create new knowledge that is disseminated to the world's scientific, governmental, and wider communities.

Learn more about Jean Peccoud at https://www.vbi.vt.edu/vbi_faculty/vbi_persons/dev_vbi_faculty?personId=98

Learn more about biosecurity Adam L et al, Strengths and limitations of the federal guidance on synthetic DNA, Nature Biotechnology (2011) 29, 208� doi:10.1038/nbt.1802 http://bit.ly/hMEmXQ

US Department of Health and Human Services voluntary guidelines "Screening Framework Guidance for Synthetic Double-Stranded DNA Providers" November 2009. http://bit.ly/cwkcpb

Minimizing the Risks of Synthetic DNA: Scientists' Views on the US Governments Guidance on Synthetic Genomics. American Association for the Advancement of Science workshop: http://bit.ly/98o0kO

The Presidential Commission for the Study of Bioethical Issues: http://bit.ly/dys4rs

For a taste of the iGEM competition, watch this video: http://bit.ly/9mqOIG

ELSE PRESS RELEASES FROM THIS DATE:

Study suggests alternative treatment for bacteria in oysters

2011-03-22

A joint study by local oyster growers and researchers at the Virginia Institute of Marine Science shows that moving farmed oysters into saltier waters just prior to harvest nearly eliminates the presence of a bacterium that can sicken humans. The findings—reported by VIMS professors Kim Reece and Howard Kator, and local oyster growers Thomas Gallivan, A.J. Erskine, and Tommy Leggett—may offer a relatively low-cost solution to a controversial change in FDA regulations that many growers believe will eventually affect the oyster industry in Chesapeake Bay. The Food and ...

Adolescent offspring of women who drank alcohol during first trimester

2011-03-22

Washington, D.C., 21 March, 2011 – Alcohol use during pregnancy is common and is associated with significant threats to the health and development of exposed offspring. Despite warnings from the Surgeon General to limit alcohol use if pregnant or contemplating pregnancy, a recent survey by the National Birth Defects Prevention Study(1) found that nearly one-third of women drank alcohol at some time during their pregnancy, with one-fourth of the women surveyed having drunk during the first trimester. Heavy use of alcohol during pregnancy may lead to fetal alcohol syndrome ...

Study shows Native Americans modified American landscape years prior to arrival of Europeans

2011-03-22

A new study by Baylor University geology researchers shows that Native Americans' land use nearly a century ago produced a widespread impact on the eastern North American landscape and floodplain development several hundred years prior to the arrival of major European settlements. The study appears on-line in the journal Geology. Researchers attribute early colonial land-use practices, such as deforestation, plowing and damming with influencing present-day hydrological systems across eastern North America. Previous studies suggest that Native Americans' land use in ...

Jimmie Lee aka The Jersey Outlaw's New Song "I'm All IN" is Sweeping the Country

2011-03-22

Jimmie Lee aka The Jersey Outlaw's new explosive single "I'm All In" is capturing the emotion of poker players across the country. The newest tune from the Jersey Outlaw channels the emotions of what poker players feel when they're waiting for that crucial card. The song is unique in the fact that it combines rock with crossover country and just a dash of rap. Insiders say that I'm All In will chart soon and become an anthem for the world of poker. Super Model Cindy Margolis commented, "The only thing hotter than Jimmie's song...is Jimmie himself!" The airplay of the ...

Princeton engineers make breakthrough in ultra-sensitive sensor technology

2011-03-22

Princeton researchers have invented an extremely sensitive sensor that opens up new ways to detect a wide range of substances, from tell-tale signs of cancer to hidden explosives. The sensor, which is the most sensitive of its kind to date, relies on a completely new architecture and fabrication technique developed by the Princeton researchers. The device boosts faint signals generated by the scattering of laser light from a material placed on it, allowing the identification of various substances based on the color of light they reflect. The sample could be as small ...

OAI: Check With Auto Insurance Provider Before Renting a Moving Van

2011-03-22

The U.S. Census Bureau estimated that between 2002 and 2003, more than 40 million people changed residences. That's a lot of furniture being moved and a lot of moving vans and trucks being rented to transport it all. Even though changing residences can, for many, be an incredible hassle that couldn't be over soon enough, there are many administrative tasks that need to be given proper attention. When it comes time to rent a vehicle to move all of one's belongings, the person moving should know whether they have or need insurance for it before they reach the rental counter. ...

Time lived with obesity linked with mortality

2011-03-22

Monash University researchers have found the number of years individuals live with obesity is directly associated with the risk of mortality. The research shows that the duration of obesity is a strong predictor of mortality, independent of the actual level of Body Mass Index (BMI). As the onset of obesity occurs earlier and the number of years lived with obesity increases, the risk of mortality associated with adult obesity in contemporary populations is expected to increase compared with previous decades. Using data from the Framingham Heart Study, 5209 participants ...

Teenagers, parents and teachers unaware of social networking risks

2011-03-22

A report into the legal risks associated with the use of social networking sites (eg. Facebook, myspace) has found that while 95 per cent of Victorian students in years 7 to 10 use social networking sites, nearly 30 per cent did not consider social networking held any risks. The project was established to investigate the legal risks of social networking as experienced by Victorian secondary school students, teachers and parents. Survey and interview data was gathered from over 1000 Victorian middle school students (years 7-10), 200 teachers and 49 parents. The report, ...

When it comes to the environment, education affects our actions

2011-03-22

The first set of findings from the survey are based on data from more than 22,000 individuals and show that people with degrees are 25% more likely, on average, than people with no education qualifications to adopt pro-environmental behaviours, at least in terms of paying more for environmentally-friendly products. However, they are less likely to turn off the TV overnight or to use public transport. Overall the survey, which will follow 40,000 UK households over many years, found that 60% of people believed that a major environmental disaster is pending if things continue ...

NYC Transcription Offers High Quality, Fast Turnaround, and the Lowest Prices in the Transcription Services Industry to Clients Across the United States

2011-03-22

NYC Transcription offers many great services, including: general transcription, corporate transcription, financial transcription, audio tape transcription and focus group transcription. But the chief services that are utilized by customers are medical transcription and legal transcription. The legal transcription service at NYC Transcription is overseen with long-standing project management experience. The staff of legal transcribers has been proven to deliver quality and timeliness of service that is unrivaled in the industry. A primary consideration with legal ...

LAST 30 PRESS RELEASES:

The American Society of Tropical Medicine and Hygiene and the Bill & Melinda Gates Foundation announce new research fellowship in malaria genomics in honor of professor Dominic Kwiatkowski