Earth Science News  





. Evolutionary Comparison Finds New Human Genes

Over millions of years, individual bases can be swapped -- C to G, T to A, for example -- by damage or miscopying. Changes that alter the structure of a protein can kill the organism or send it down a dead-end evolutionary path. But conserved genes contain only minor changes that leave the protein able to do its job. The computer looked for regions with those sorts of changes by creating a mathematical model of how the gene might have changed, then looking for matches to this model.
by Staff Writers
Ithaca NY (SPX) Nov 26, 2007
Using supercomputers to compare portions of the human genome with those of other mammals, researchers at Cornell have discovered some 300 previously unidentified human genes, and found extensions of several hundred genes already known. The discovery is based on the idea that as organisms evolve, sections of genetic code that do something useful for the organism change in different ways.

The research is reported by Adam Siepel, Cornell assistant professor of biological statistics and computational biology, Cornell postdoctoral researcher Brona Brejova and colleagues at several other institutions in the online version of the journal Genome Research, and it will appear in the December print edition.

The complete human genome was sequenced several years ago, but that simply means that the order of the 3 billion or so chemical units, called bases, that make up the genetic code is known. What remains is the identification of the exact location of all the short sections that code for proteins or perform regulatory or other functions.

More than 20,000 protein-coding genes have been identified, so the Cornell contribution, while significant, doesn't dramatically change the number of known genes. What's important, the researchers say, is that their discovery shows there still could be many more genes that have been missed using current biological methods. These methods are very effective at finding genes that are widely expressed but may miss those that are expressed only in certain tissues or at early stages of embryonic development, Siepel said.

"What's exciting is using evolution to identify these genes," Siepel said. "Evolution has been doing this experiment for millions of years. The computer is our microscope to observe the results."

Four different bases -- commonly referred to by the letters G, C, A and T -- make up DNA. Three bases in a row can code for an amino acid (the building blocks of proteins), and a string of these three-letter codes can be a gene, coding for a string of amino acids that a cell can make into a protein.

Siepel and colleagues set out to find genes that have been "conserved" -- that are fundamental to all life and that have stayed the same, or nearly so, over millions of years of evolution.

The researchers started with "alignments" discovered by other workers -- stretches up to several thousand bases long that are mostly alike across two or more species. Using large-scale computer clusters, including an 850-node cluster at the Cornell Center for Advanced Computing, the researchers ran three different algorithms, or computing designs -- one of which Siepel created -- to compare these alignments between human, mouse, rat and chicken in various combinations.

Over millions of years, individual bases can be swapped -- C to G, T to A, for example -- by damage or miscopying. Changes that alter the structure of a protein can kill the organism or send it down a dead-end evolutionary path. But conserved genes contain only minor changes that leave the protein able to do its job. The computer looked for regions with those sorts of changes by creating a mathematical model of how the gene might have changed, then looking for matches to this model.

After eliminating predictions that matched already known genes, the researchers tested the remainder in the laboratory, proving that many of the genes could in fact be found in samples of human tissue and could code for proteins. The researchers were sometimes able to identify the proteins by comparison with databases of known proteins. The discovered genes mainly have to do with motor activity, cell adhesion, connective tissue and central nervous system development, functions that might be expected to be common to many different creatures.

The entire project, from building and testing the mathematical models to running final laboratory tests, took about three years, Siepel said. The work was supported by the National Cancer Institute, a National Science Foundation Early Career Development Grant and a University of California graduate research fellowship.

Community
Email This Article
Comment On This Article

Related Links
Cornell University
All About Human Beings and How We Got To Be Here




Tempur-Pedic Mattress Comparison

Newsletters :: SpaceDaily Express :: SpaceWar Express :: TerraDaily Express :: Energy Daily
XML Feeds :: Space News :: Earth News :: War News :: Solar Energy News
Mapping The Selective Brain
Washington DC (SPX) Nov 22, 2007
Researchers have added a new piece to the puzzle of how the brain selectively amplifies those distinctions that matter most from the continuous cascade of sights, sounds, and other sensory input. Whether recognizing a glowering face among smiling ones or the unmistakable sound of a spouse calling one's name, such "categorical perception" is central to sensory function.

.
Get Our Free Newsletters Via Email
  



  • US marines assist stepped up relief effort in Bangladesh
  • LSU Helps Bangladesh Save Lives By Providing Storm Surge Models 24 Hours In Advance Of Cyclone Sidr
  • Tsunami-Recording In The Deep Sea
  • Bangladesh cyclone an 'ecological disaster': experts

  • Then there was one: US now alone as Kyoto holdout
  • Indonesia's peatlands: a little-known culprit in climate change
  • Scientists warn of agrarian crisis from climate change
  • New Australian leader works on climate change

  • Rosetta: Earth's True Colours
  • Northrop Grumman-Built Hyperion Imager Celebrates Seventh Anniversary On-Orbit
  • TRMM Turns Ten - Studying Precipitation From Space
  • Rosetta: OSIRIS' View Of Earth By Night

  • Analysis: U.S. irked by Turkmen gas policy
  • Analysis: Delta funding not just for arms
  • Analysis: KazMunayGaz's prosperity rises
  • Britain launches its first sugar-fuel plant

  • UN cuts AIDS infection estimate: report
  • Repellents Between Dusk And Bedtime Make Insecticide-Treated Bednets More Effective
  • Global Fund approves over 1 bln dlrs in new grants to fight disease
  • Bug-Zapper: A Dose Of Radiation May Help Knock Out Malaria

  • Liquid Crystal Phases Of Tiny DNA Molecules Point Up New Scenario For First Life On Earth
  • Illuminating Study Reveals How Plants Respond To Light
  • Are Current Projections Of Climate Change-Impacts On Biodiversity Misleading
  • 390-Million-Year-Old Scorpion Fossil Is The Biggest Known Bug

  • Atmospheric Measuring Device For Understanding Smog Formation
  • China pollution costs 5.8 pct of GDP: report
  • Local Sources Major Cause Of US Near-Ground Aerosol Pollution
  • Brazilian CO2 pollution outstripping economic growth: study

  • Evolutionary Comparison Finds New Human Genes
  • Mapping The Selective Brain
  • How Do We Make Sense Of What We See
  • New Antarctica Research Season Kicks Off

  • The content herein, unless otherwise known to be public domain, are Copyright 1995-2007 - SpaceDaily.AFP and UPI Wire Stories are copyright Agence France-Presse and United Press International. ESA Portal Reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement,agreement or approval of any opinions, statements or information provided by SpaceDaily on any Web page published or hosted by SpaceDaily. Privacy Statement