Navigation Links
New tool in the fight against tuberculosis
Date:10/7/2010

Researchers at the Institute for Genomic Biology at the University of Illinois have developed a way to harness the prodigious quantities of both genomic and metabolic data being generated with high-throughput genomics and other techniques. They have developed an algorithm that automatically integrates both data sets. The model, called probabilistic regulation of metabolism (PROM), enables researchers to perturb a given regulatory gene or metabolic process and see how that affects the entire network.

"PROM provides a platform for studying the behavior of networks in a wide range of different conditions," says principal investigator Nathan Price, an associate professor of chemical and biomolecular engineering at Illinois.

Using this model the researchers have created the first genome-scale, regulatory-metabolic network of Mycobacterium tuberculosis. Their results were published online by PNAS on September 27.

Using E. Coli as a benchmark, Price and graduate student Sriram Chandrasekaran showed that PROM was more accurate and comprehensive than the previous model for E. Coli, which had been done by hand and published in 2004.

After using E. Coli as a proof of principle, they targeted tuberculosis, a bacterium that has not been as thoroughly studied as E. Coli. Price and Chandrasekaran had less than half the amount of data then they had for E. Coli and were still able to create a model that predicted knockout phenotypes 95 percent of the time, says Price.

Price and Chandrasekaran built the algorithm using microarray data, transcription-factor interactions that regulate metabolic reactions, and knock-out phenotypes. The method is both accurate and fast. PROM may prove particularly helpful to tuberculosis researchers because, although when tuberculosis is growing it can be killed, the real challenge is to target the bacterium during its dormant or quiescent stage. PROM may enable researchers to identify and target the pathways keeping the cells alive during dormancy.

PROM also represents a major advance because it successfully integrates the statistically derived transcriptional regulatory network with a biochemically derived metabolic network.

"That is the new part," says Price. "People have created regulatory models and metabolic models. But there has been nothing before that could combine them in this automated fashion. It is difficult to get these two to talk to each other in the right way."

Price and Chandrasekaran created an algorithm that makes use of probability. Earlier models used a Boolean or a binary approach, in which a gene is either on or off. PROM can account for a gene or enzyme that can also be part way on or part way off, so it acts more like a rheostat than a toggle switch.

"People were stuck here for a long time. That's why PROM is such a nice method. It's sort of Boolean but it's probabilistic Boolean. It does allow us to have a continuous variation," says Price.

"These models can guide genome-scale synthetic biology," he adds. "And understanding how the networks are put together lays the foundation for us to design genomes that encode for networks that behave in the way we want them to, such as engineering microbes to convert environmental toxins into biofuels, for example."


'/>"/>

Contact: Melissa Edwards
mme@illinois.edu
217-333-0873
Institute for Genomic Biology, University of Illinois at Urbana-Champaign
Source:Eurekalert  

Related biology news :

1. Vitiligo skin disorder could yield clues in fight against melanoma
2. Plant-eating predator to fight superweed is not magic bullet
3. UCSB study finds physical strength, fighting ability revealed in human faces
4. Scripps Florida scientists awarded $1.5M to fight major water and food parasites
5. A new weapon in the fight against obesity and diabetes
6. Researchers use chemical from medicinal plants to fight HIV
7. UNC study: Text messaging may help children fight off obesity
8. Children distressed by family fighting have higher stress hormones
9. £20 million to fight virtual crime and treat our ageing population
10. £20 million to fight virtual crime and treat our aging population
11. Feed a cold, feed a fever: Research shows calorie cut makes it harder to fight flu
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
New tool in the fight against tuberculosis
(Date:4/28/2016)... -- First quarter 2016:   , Revenues ... first quarter of 2015 The gross margin was 49% ... and the operating margin was 40% (-13) Earnings per ... from operations was SEK 249.9 M (21.2) , Outlook ... 7,000-8,500 M. The operating margin for 2016 is estimated ...
(Date:4/15/2016)...  A new partnership announced today will help ... in a fraction of the time it takes ... life insurance policies to consumers without requiring inconvenient ... Diagnostics, rapid testing (A1C, Cotinine and HIV) and ... weight, pulse, BMI, and activity data) available at ...
(Date:3/31/2016)... 2016   LegacyXChange, ... "Company") LegacyXChange is excited to release its ... to be launched online site for trading 100% guaranteed ... will also provide potential shareholders a sense of the ... an industry that is notorious for fraud. The video ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... ... 2016 , ... Supplyframe, the Industry Network for electronics hardware ... . Located in Pasadena, Calif., the Design Lab’s mission is to bring together ... built and brought to market. , The Design Lab is Supplyframe’s physical representation ...
(Date:6/23/2016)... 23, 2016  Blueprint Bio, a company dedicated to ... medical community, has closed its Series A funding round, ... "We have received a commitment from Forentis ... need to meet our current goals," stated Matthew ... runway to complete validation on the current projects in ...
(Date:6/23/2016)... WI (PRWEB) , ... June 23, 2016 , ... ... focused on quality, regulatory and technical consulting, provides a free webinar ... presented on July 13, 2016 at 12pm CT at no charge. , Incomplete ...
(Date:6/22/2016)... SAN DIEGO , June 22, 2016 /PRNewswire/ ... partnership that will allow them to produce up ... (HiPSC) from one lot within one week. These ... their time laboriously preparing cells and spend more ... made possible through a proprietary, high-volume manufacturing process ...
Breaking Biology Technology: