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:5/3/2016)...  Neurotechnology, a provider of high-precision biometric identification ... Identification System (ABIS) , a complete system for ... can process multiple complex biometric transactions with high ... face or iris biometrics. It leverages the core ... MegaMatcher Accelerator , which have been used in ...
(Date:4/19/2016)... April 20, 2016 The new ... a compact web-based "all-in-one" system solution for all door ... reader or the door interface with integration authorization management ... control systems. The minimal dimensions of the access control ... the building installations offer considerable freedom of design with ...
(Date:3/31/2016)...   LegacyXChange, Inc. ... LegacyXChange is excited to release its first ... be launched online site for trading 100% guaranteed authentic ... also provide potential shareholders a sense of the value ... industry that is notorious for fraud. The video is ...
Breaking Biology News(10 mins):
(Date:6/24/2016)... ... 2016 , ... While the majority of commercial spectrophotometers and fluorometers use the ... models are higher end machines that use the more unconventional z-dimension of 20mm. ... the bottom of the cuvette holder. , FireflySci has developed several Agilent flow ...
(Date:6/23/2016)... 23, 2016 /PRNewswire/ - FACIT has announced the ... biotechnology company, Propellon Therapeutics Inc. ("Propellon" or ... of a portfolio of first-in-class WDR5 inhibitors for ... as WDR5 represent an exciting class of therapies, ... medicine for cancer patients. Substantial advances have been ...
(Date:6/23/2016)... , June, 23, 2016  The Biodesign Challenge (BDC), ... new ways to harness living systems and biotechnology, announced ... (MoMA) in New York City . ... participating students, showcased projects at MoMA,s Celeste Bartos Theater ... Antonelli , MoMA,s senior curator of architecture and design, ...
(Date:6/23/2016)... 2016 Apellis Pharmaceuticals, Inc. today announced ... of its complement C3 inhibitor, APL-2. The trials ... dose studies designed to assess the safety, tolerability, ... in healthy adult volunteers. Forty subjects ... single dose (ranging from 45 to 1,440mg) or ...
Breaking Biology Technology: