Navigation Links
Fleshing out the genome

Genomics, the study of all the genetic sequences in living organisms, has leaned heavily on the blueprint metaphor. A large part of the blueprint, unfortunately, has been unintelligible, with no good way to distinguish a bathroom from a boardroom, to link genomic features to cell function.

A national consortium of scientists led by BIATECH, a Seattle based non-profit research center, and Pacific Northwest National Laboratory (PNNL), a Department of Energy research institution in Richland, Wash., now suggests a way to put this house in order. They offer a powerful new method that integrates experimental and computational analyses to ascribe function to genes that had been termed "hypothetical" -- sequences that appear in the genome but whose biological purposes were previously unknown.


The method not only portends a way to fill in the blanks in any organism's genome but also to compare the genomes of different organisms and their evolutionary relationship.

The new tools and approaches offer the most-comprehensive-to-date "functional annotation," a way of assigning the mystery sequences biological function and ranking them based on their similarity to genes known to encode proteins. Proteins are the workhorses of the cell, playing a role in everything from energy transport and metabolism to cellular communication.

This new ability to rank hypothetical sequences according to their likelihood to encode proteins "will be vital for any further experimentation and, eventually, for predicting biological function," said Eugene Kolker, president and director of BIATECH, an affiliate scientist at PNNL and lead author of a study in the Feb. 8 Proceedings of the National Academy of Sciences that applies the new annotation method to a strain of the metal-detoxifying bacterium Shewanella oneidensis.

"In a lot of cases," said James K. Fredrickson, a co-author and PNNL chief scientist, "it was not known from the gene sequence if a protei n was even expressed. Now that we have high confidence that many of these hypothetical genes are expressing proteins, we can look for what role these proteins play."

Before this study, nearly 40 percent of the genetic sequences in Shewanella oneidensis--of key interest to DOE for its potential in nuclear and heavy metal waste remediation--were considered as hypothetical. This work identified 538 of these genes that expressed functional proteins and messenger RNA, accounting for a third of the hypothetical genes. They enlisted analytic software to scour public databases and applied expression data to improve gene annotation, identifying similarities to known proteins for 97 percent of these hypothetical proteins. All told, computational and experimental evidence provided functional information for 256 more genes, or 48 percent, but they could confidently assign exact biochemical functions for only 16 proteins, or 3 percent. Finally, they introduced a seven-category system for annotating genomic proteins, ranked according to a functional assignment's precision and confidence.

Kolker said that "a big part of this was the proteomics"-- a systematic screening and identification of proteins, in this case those which were expressed in the microbe when subjected to stress. The proteomic analyses were done by four teams led by Kolker, Carol S. Giometti, Argonne National Laboratory (ANL); John R. Yates III; The Scripps Research Institute (TSRI); and Richard D. Smith, W.R. Wiley Environmental Molecular Sciences Laboratory, based at PNNL. BIATECH's analysis of this data included dealing with more than 2 million files.


'"/>

Source:DOE/Pacific Northwest National Laboratory


Related biology news :

1. Program finds lost genes in nematode genome
2. Punctuated evolution in the human genome
3. US/African project deciphers deadly parasite genome
4. University of Arizona plant scientists to unravel maize genome
5. Mining for gems in the fungal genome
6. Illinois pig to make history as source of first complete swine genome
7. MBL leads effort to update E. coli genome
8. In a technical tour de force, Salk scientists take a global view of the epigenome
9. DOE JGI finishes 100th microbial genome
10. Gut reaction: Researchers define the colons genome
11. New technology used to construct the first map of structural variation in the human genome
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:5/12/2016)... 2016 WearablesResearch.com , a brand of ... results from the Q1 wave of its quarterly wearables ... consumers, receptivity to a program where they would receive ... insurance company. "We were surprised to see ... Michael LaColla , CEO of Troubadour Research, "primarily because ...
(Date:4/28/2016)... , April 28, 2016 Infosys ... (NYSE: INFY ), and Samsung SDS, a global ... that will provide end customers with a more secure, fast ...      (Logo: http://photos.prnewswire.com/prnh/20130122/589162 ) , ... but it also plays a fundamental part in enabling and ...
(Date:4/26/2016)... -- Research and Markets has announced the ...  report to their offering.  , ,     (Logo: ... forecast the global multimodal biometrics market to grow ... 2016-2020.  Multimodal biometrics is being implemented ... healthcare, BFSI, transportation, automotive, and government for controlling ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... , June 27, 2016  Sequenom, Inc. (NASDAQ: ... enabling healthier lives through the development of innovative products ... the United States denied its ... the claims of Sequenom,s U.S. Patent No. 6,258,540 (",540 ... criteria established by the Supreme Court,s Mayo Collaborative Services ...
(Date:6/27/2016)... 2016  Liquid Biotech USA ... a Sponsored Research Agreement with The University of ... from cancer patients.  The funding will be used ... with clinical outcomes in cancer patients undergoing a ... be employed to support the design of a ...
(Date:6/24/2016)... ... 24, 2016 , ... Researchers at the Universita Politecnica delle Marche in Ancona ... or pleural mesothelioma. Their findings are the subject of a new article on the ... are signposts in the blood, lung fluid or tissue of mesothelioma patients that can ...
(Date:6/23/2016)... , June 23, 2016 A person commits a ... crime scene to track the criminal down. An ... Food and Drug Administration (FDA) uses DNA evidence to track ... Sound far-fetched? It,s not. The FDA has increasingly ... support investigations of foodborne illnesses. Put as simply as possible, ...
Breaking Biology Technology: