Featured Research

from universities, journals, and other organizations

Random Picks Better Than Complicated Process In Gene Identification

Date:
May 11, 2009
Source:
Purdue University
Summary:
Researchers 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.

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.

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.


Story Source:

The above story is based on materials provided by Purdue University. Note: Materials may be edited for content and length.


Journal Reference:

  1. Hale et al. Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics, 2009; 10 (1): 203 DOI: 10.1186/1471-2164-10-203

Cite This Page:

Purdue University. "Random Picks Better Than Complicated Process In Gene Identification." ScienceDaily. ScienceDaily, 11 May 2009. <www.sciencedaily.com/releases/2009/05/090506110158.htm>.
Purdue University. (2009, May 11). Random Picks Better Than Complicated Process In Gene Identification. ScienceDaily. Retrieved July 25, 2014 from www.sciencedaily.com/releases/2009/05/090506110158.htm
Purdue University. "Random Picks Better Than Complicated Process In Gene Identification." ScienceDaily. www.sciencedaily.com/releases/2009/05/090506110158.htm (accessed July 25, 2014).

Share This




More Plants & Animals News

Friday, July 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

How to Make Single Serving Smoothies: Howdini Hacks

How to Make Single Serving Smoothies: Howdini Hacks

Howdini (July 24, 2014) Smoothies are a great way to get in lots of healthy ingredients, plus they taste great! Howdini has a trick for making the perfect single-size smoothie that will save you time on cleanup too! All you need is a blender and a mason jar. Video provided by Howdini
Powered by NewsLook.com
Boy Attacked by Shark in Florida

Boy Attacked by Shark in Florida

Reuters - US Online Video (July 24, 2014) An 8-year-old boy is bitten in the leg by a shark while vacationing at a Florida beach. Linda So reports. Video provided by Reuters
Powered by NewsLook.com
Goma Cheese Brings Whiff of New Hope to DRC

Goma Cheese Brings Whiff of New Hope to DRC

Reuters - Business Video Online (July 24, 2014) The eastern region of the Democratic Republic of Congo, mainly known for conflict and instability, is an unlikely place for the production of fine cheese. But a farm in the village of Masisi, in North Kivu is slowly transforming perceptions of the area. Known simply as Goma cheese, the Congolese version of Dutch gouda has gained popularity through out the region. Ciara Sutton reports. Video provided by Reuters
Powered by NewsLook.com
Tyrannosaur Pack-Hunting Theory Aided By New Footprints

Tyrannosaur Pack-Hunting Theory Aided By New Footprints

Newsy (July 24, 2014) A new study claims a set of prehistoric T-Rex footprints supports the theory that the giant predators hunted in packs instead of alone. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins