Featured Research

from universities, journals, and other organizations

Discovery allows scientists for the first time to annotate genomes experimentally

Date:
November 26, 2009
Source:
University of California - San Diego
Summary:
Bioengineers have made a breakthrough development that will now allow scientists to perform full delineation of the location and use of genomic elements.

From left to right, UCSD bioengineering professor Bernhard Palsson and project scientist Byung-Kwan Cho have made a breakthrough discovery for genome sequencing.
Credit: UC San Diego

Over the last 20 years, the sequencing of the human genome, along with related organisms, has represented one of the largest scientific endeavors in the history of humankind. The information collected from genome sequencing will provide the raw data for the field of bioinformatics, where computer science and biology meet.

Related Articles


Since the publication of the first full genome sequence in the mid-1990s, scientists have been working to identify the genomic location of all the gene products involved in the complex biological processes in a single organism. However, they have only been able to identify a fraction of those locations. Until now.

Bioengineers at UC San Diego have made a breakthrough development that will now allow scientists to perform full delineation of the location and use of genomic elements. The researchers have discovered that multiple simultaneous genome-scale measurements are needed to identify all gene products, and to determine their cellular locations and interactions with the genome.

In a recent Nature Biotechnology paper, the researchers describe a four-step systems approach that integrates multiple genome-scale measurements on the basis of genetic information flow to identify the organizational elements and map them onto the genome sequence. The bioengineers have applied this approach to the E. coli genome to generate a detailed description of its transcrip¬tion unit architecture.

"What's important about this paper is it now enables us to experimentally annotate genomes," said Bernard Palsson, a UCSD bioengineering professor and co-author of the paper. "All this information gives us a fine resolution of the contents of a genome and location of its elements. This is a fine blueprint of a genetic makeup of the genome. We have been able to use genome scale computational models that have been developed at UCSD under the systems biology program, which have enabled us to compute organism designs with higher resolution or better accuracy, which has not been possible before. It takes a lot of the guesswork out of making an organism. Currently there is extensive trial and error in gene sequencing procedures. Hopefully this 'metastucture' of a genome that we have developed will eliminate that trial and error and will enable us to reach new metabolic designs faster with lower failure rates."

Palsson said there are many significant implications of this new finding, such as enhancing metabolic engineering (such as the engineering of microorganisms to make fuels and commodity chemicals).

The UCSD bionengineers combined several computation methods with information mapping in this research. "There are several high throughput methods developed recently like deep sequencing and micro array systems that we used," said Byung-Kwan Cho, a project scientist in the UCSD bioengineering department and the lead author of the Nature Biotechnology paper. "We wanted to integrate all the information into one format to describe the genome. We have genome sequences but we don't know what all of them are. When we sequenced the Human Genome we thought we knew everything but actually we don't know everything. There are lots of data generation techniques and a huge amount of data available. So we were able to map all of this information into one genome sequence.

"So far, scientists have been able to make chemicals to kill pathogenic strains but we haven't been as successful as we have wanted to be," Cho added. "By using this newly discovered information we may be able to design better drugs or medicines to kill pathogenic strains. That's the important point of this research -- there is a huge amount of applications for this. The E. coli bacteria is just the beginning."


Story Source:

The above story is based on materials provided by University of California - San Diego. Note: Materials may be edited for content and length.


Journal Reference:

  1. Byung-Kwan Cho, Karsten Zengler, Yu Qiu, Young Seoub Park, Eric M Knight, Christian L Barrett, Yuan Gao & Bernhard Ψ Palsson. The transcription unit architecture of the Escherichia coli genome. Nature Biotechnology, 2009; 27 (11): 1043 DOI: 10.1038/nbt.1582

Cite This Page:

University of California - San Diego. "Discovery allows scientists for the first time to annotate genomes experimentally." ScienceDaily. ScienceDaily, 26 November 2009. <www.sciencedaily.com/releases/2009/11/091109174343.htm>.
University of California - San Diego. (2009, November 26). Discovery allows scientists for the first time to annotate genomes experimentally. ScienceDaily. Retrieved March 2, 2015 from www.sciencedaily.com/releases/2009/11/091109174343.htm
University of California - San Diego. "Discovery allows scientists for the first time to annotate genomes experimentally." ScienceDaily. www.sciencedaily.com/releases/2009/11/091109174343.htm (accessed March 2, 2015).

Share This


More From ScienceDaily



More Health & Medicine News

Monday, March 2, 2015

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Treadmill Test Can Predict Chance Of Death Within A Decade

Treadmill Test Can Predict Chance Of Death Within A Decade

Newsy (Mar. 2, 2015) — Johns Hopkins researchers analyzed 58,000 heart stress tests to come up with a formula that predicts a person&apos;s chances of dying in the next decade. Video provided by Newsy
Powered by NewsLook.com
Going Gluten-Free Could Get You A Tax Break

Going Gluten-Free Could Get You A Tax Break

Newsy (Mar. 2, 2015) — If a doctor advises you to remove gluten from your diet, you could get a tax deduction on the amount you spend on gluten-free foods. Video provided by Newsy
Powered by NewsLook.com
GlaxoSmithKline and Novartis Try Swapping Success

GlaxoSmithKline and Novartis Try Swapping Success

Reuters - Business Video Online (Mar. 2, 2015) — GlaxoSmithKline and Novartis have completed a series of asset swaps worth more than $20 billion. As Grace Pascoe reports they say the deal will reshape both drugmakers. Video provided by Reuters
Powered by NewsLook.com
How Can West Africa Rebuild After Ebola?

How Can West Africa Rebuild After Ebola?

Reuters - Business Video Online (Mar. 2, 2015) — How best to rebuild the three West African countries struggling with Ebola will be discussed in Brussels this week. As Hayley Platt reports Sierra Leone has the toughest job ahead - its once thriving economy has been ravaged by the disease. Video provided by Reuters
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:

Strange & Offbeat Stories

 

Health & Medicine

Mind & Brain

Living & Well

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