Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Researchers Develop Tool To Study Genes

07.07.2008
Two Texas A&M University researchers have developed a computational tool that will help scientists more accurately study complex units of clustered genes, called operons, in bacteria.

The tool, which allows scientists to analyze many bacterial genomes at once, is more accurate than previous methods because it starts from experimentally validated data instead of from statistical predictions, they say. The researchers hope their tool will lead to a better understanding of the complex genetic mechanisms involved in a cell’s functioning.

“It’s a very complicated mechanism inside a cell that makes the whole thing work, and operons are one of the important components in this process,” said Sing-Hoi Sze, Texas A&M computer science, biochemistry and biophysics researcher. “We want to understand how these genetic mechanisms work because DNA codes proteins, and proteins are what make up everything in your body. In order to understand the genetic processes in more complex organisms, we have to start with the simpler organisms like bacteria.”

Sze and his colleague, computer science researcher Qingwu Yang, detail their computational tool and its implications in their paper published in the journal Genome Research .

... more about:
»Coli »Computational »E. coli »Sze »experimentally »operon »species

An operon is a unit of genes that are clustered together and have similar functions, Sze said. Genes are controlled by a mechanism called a promoter, which turns the genes on or off. In higher organisms, like humans, there is usually a specific promoter that controls each gene separately, Sze explained. However, a bacteria’s genome has to be compact, so there are a lot of genes clustered close together that are controlled by the same promoter, and this set of genes is called an operon.

Different species of bacteria have similar genes, but their genes may not have the same layout or clustering pattern, so their operons may function differently, Sze said. Scientists want to understand how the operons in each species of bacteria are different, how the genes in the operons are organized, and how the operons function.

Because of time and resource constraints, however, researchers cannot directly study in detail the genomes of all of the thousands of species of bacteria and can only carry out experiments on some of them, Sze explained. So researchers need a computational tool to help them predict where similar clusters of genes are in different species of bacteria so they can better focus their experiments, he said.

For each level of complexity in organisms, there is a model organism that scientists center their experiments on, and for bacteria, the model organism is E. coli . Because E. coli is a model organism, scientists have studied it in great detail and have a large amount of experimentally validated data on its genome and the operons that function, Sze said.

Sze and Yang’s computational tool starts with a known and experimentally validated E. coli operon and then searches each of hundreds of separate species of bacteria for genes that are related to those in the E. coli operon. Once the tool has located related genes in a bacterium, it then checks to see if there is a strong clustering of the genes. It does this by using a statistical procedure that computes which genes are statistically very close to each other when you compare it to a random situation of genes, Sze explained.

“Imagine putting genes in a random order,” Sze said. “When placed randomly, two specific genes are likely to be located at a far distance from each other. But if there is clustering, then the genes will be much closer to each other than they would be by chance.”

So by using Sze and Yang’s tool, scientists can easily locate sub-blocks of genes in different bacteria that are arranged in a similar fashion as one of the operons in E. coli . “If biologists are interested in a particular E. coli operon, they can use our tool to find where the operon is in the different bacteria,” Sze said. “They can then analyze the differences in the operon in the different bacteria and see if there are any interesting relationships.”

Sze said his and Yang’s tool is an improvement on previous methods because it is a new way to analyze many bacterial genomes at the same time. It is also more accurate than previous methods in which scientists start by simply using a statistical method to predict the location of an operon in a bacterial genome. Sze and Yang, however, show that it is more accurate to start from a known and experimentally validated E. coli operon to find similar operons in other bacteria.

“Eventually, we want to try to improve our tool to make it better and more accurate,” Sze said. “Although our tool can analyze a lot of bacteria at the same time, it compares each bacterium to E. coli separately. So the ultimate goal would be to develop a tool that will analyze them all together.”

Contact: Sing-Hoi Sze at (979) 845-5009, email shsze@tamu.edu , or Keith Randall at (979) 845-4644, email keith-randall@tamu.edu

Sing-Hoi Sze | EurekAlert!
Further information:
http://www.tamu.edu

Further reports about: Coli Computational E. coli Sze experimentally operon species

More articles from Life Sciences:

nachricht The Secret of the Rock Drawings
24.05.2019 | Max-Planck-Institut für Chemie

nachricht Chemical juggling with three particles
24.05.2019 | Rheinische Friedrich-Wilhelms-Universität Bonn

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: New studies increase confidence in NASA's measure of Earth's temperature

A new assessment of NASA's record of global temperatures revealed that the agency's estimate of Earth's long-term temperature rise in recent decades is accurate to within less than a tenth of a degree Fahrenheit, providing confidence that past and future research is correctly capturing rising surface temperatures.

The most complete assessment ever of statistical uncertainty within the GISS Surface Temperature Analysis (GISTEMP) data product shows that the annual values...

Im Focus: The geometry of an electron determined for the first time

Physicists at the University of Basel are able to show for the first time how a single electron looks in an artificial atom. A newly developed method enables them to show the probability of an electron being present in a space. This allows improved control of electron spins, which could serve as the smallest information unit in a future quantum computer. The experiments were published in Physical Review Letters and the related theory in Physical Review B.

The spin of an electron is a promising candidate for use as the smallest information unit (qubit) of a quantum computer. Controlling and switching this spin or...

Im Focus: Self-repairing batteries

UTokyo engineers develop a way to create high-capacity long-life batteries

Engineers at the University of Tokyo continually pioneer new ways to improve battery technology. Professor Atsuo Yamada and his team recently developed a...

Im Focus: Quantum Cloud Computing with Self-Check

With a quantum coprocessor in the cloud, physicists from Innsbruck, Austria, open the door to the simulation of previously unsolvable problems in chemistry, materials research or high-energy physics. The research groups led by Rainer Blatt and Peter Zoller report in the journal Nature how they simulated particle physics phenomena on 20 quantum bits and how the quantum simulator self-verified the result for the first time.

Many scientists are currently working on investigating how quantum advantage can be exploited on hardware already available today. Three years ago, physicists...

Im Focus: Accelerating quantum technologies with materials processing at the atomic scale

'Quantum technologies' utilise the unique phenomena of quantum superposition and entanglement to encode and process information, with potentially profound benefits to a wide range of information technologies from communications to sensing and computing.

However a major challenge in developing these technologies is that the quantum phenomena are very fragile, and only a handful of physical systems have been...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

SEMANTiCS 2019 brings together industry leaders and data scientists in Karlsruhe

29.04.2019 | Event News

Revered mathematicians and computer scientists converge with 200 young researchers in Heidelberg!

17.04.2019 | Event News

First dust conference in the Central Asian part of the earth’s dust belt

15.04.2019 | Event News

 
Latest News

On Mars, sands shift to a different drum

24.05.2019 | Physics and Astronomy

Piedmont Atlanta first in Georgia to offer new minimally invasive treatment for emphysema

24.05.2019 | Medical Engineering

Chemical juggling with three particles

24.05.2019 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>