Navigation Links
Random picks better than complicated process in gene identification
Date:5/6/2009

WEST LAFAYETTE, Ind. - Researchers at Purdue University have found a way to save time, money and a little frustration in searches for specific genes that shed light on the biological processes associated with all forms of life.

Andrew DeWoody, a professor of genetics, and postdoctoral associate Matthew C. Hale have provided evidence that a step called normalization is no longer necessary with recent advances in DNA sequencing technology. Instead, they used a theoretical approach called rarefaction for gene discovery, a process developed for ecological surveys to determine the abundance of a species in an ecosystem. Their results were published in the early online release of the journal BMC Genomics.

When searching for specific genes in a tissue sample, there may be thousands of genes that perform simple housekeeping functions, whereas others expressed in smaller numbers are charged with more complex and important functions. The difficulty is sorting through thousands of genes to find the ones that have unique functions.

"These housekeeping genes are highly expressed, often hundreds or thousands of times more than other genes," DeWoody said.

Through normalization, scientists heat up DNA to a point in which its two component strands split, or denature. As it is cooled, matching strands randomly find each other and reattach. Those that reunite quickly are typically the most numerous. By adding specific enzymes, many of the overabundant genes are decreased in number, while the few that reunite slowly are amplified until the genes are equal in number, making it easier to sort through them.

DeWoody and Hale believe normalization is not necessary given the vast amount of data that can be obtained through modern DNA sequencers.

"Normalization used to be required because commonly expressed genes would swamp the signal of rare genes," DeWoody said. "But normalization also discards valuable information about the relative levels of gene expression in a tissue sample."

Another key aspect of the paper is the novel use of analytical rarefaction in gene discovery.

In rarefaction, a species is selected at random from that ecosystem. Those selections are charted, with each selection considered one unit of effort. Once selections yield only previously selected species - or in this case, genes - the amount of effort needed to find all the species or genes has been determined. Scientists then know how much effort to use when searching for other genes.

"When it plateaus, you can give up. You've put in as much effort as you need," DeWoody said.

DeWoody and Hale tested the theory on samples from the reproductive organs of lake sturgeon while trying to find the genes responsible for determining fish sex. Hale said the work is important to conserve species by understanding their biological functions.

"Few studies have been done on threatened and endangered species. They're usually done on models such as mice and Arabidopsis," Hale said. "This species, the lake sturgeon, is a perfect example of a conservation concern."

The Great Lakes Fishery Trust and the Indiana Department of Natural Resources funded the research. DeWoody said the next step is to continue the process of finding the genes responsible for determining sex in sturgeon.


'/>"/>

Contact: Brian Wallheimer
bwallhei@purdue.edu
765-496-2050
Purdue University
Source:Eurekalert

Related biology news :

1. Evolution is deterministic, not random, biologists conclude from multi-species study
2. Vitamins C and E and beta carotene again fail to reduce cancer risk in randomized controlled trial
3. USGS April 2008 science picks
4. USGS science picks -- leads, feeds and story seeds
5. USGS news: August science picks
6. NASA picks ASU research team to guide study of search for life
7. USGS Science Picks
8. New caledonian crows find 2 tools better than 1
9. Restoring sight, advances in fertility treatments and better visibility for pilots at FIO
10. New CPR promises better results by compressing abdomen, not Chest
11. City birds better than rural species in coping with human disruption
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:8/15/2017)... LLC , a medical device company focused on improving the safety ... ISO 13485 Certification, the global standard for medical device quality management ... ... for the early detection of IV infiltrations. ... "This is an important milestone for ivWatch, as it validates our ...
(Date:5/23/2017)... 23, 2017  Hunova, the first robotic gym for the rehabilitation and ... launched in Genoa, Italy . The first 30 robots ... the USA . The technology was developed and patented ... the IIT spin-off Movendo Technology thanks to a 10 million euro investment ... please click: ...
(Date:4/19/2017)... The global military biometrics market ... by the presence of several large global players. The ... major players - 3M Cogent, NEC Corporation, M2SYS Technology, ... 61% of the global military biometric market in 2016. ... military biometrics market boast global presence, which has catapulted ...
Breaking Biology News(10 mins):
(Date:10/12/2017)... ... October 12, 2017 , ... ... the pharmaceutical and biotechnology industries to improve patient outcomes and quality of life, ... in analytical testing are being attributed to new regulatory requirements for all new ...
(Date:10/11/2017)... ... October 11, 2017 , ... At its national board ... Suneel I. Sheikh, the co-founder, CEO and chief research scientist of Minnesota-based Advanced ... for membership in ARCS Alumni Hall of Fame . ASTER Labs is ...
(Date:10/11/2017)... ... ... wash is a basic first aid supply for any work environment, but most personal eye ... first if a dangerous substance enters both eyes? It’s one less decision, and likely quicker ... eye piece. , “Whether its dirt and debris, or an acid or alkali, getting anything ...
(Date:10/11/2017)... ... October 11, 2017 , ... ... today it will be hosting a Webinar titled, “Pathology is going digital. Is ... , on digital pathology adoption best practices and how Proscia improves lab economics ...
Breaking Biology Technology: