Evolutionary comparison finds new human genes

November 16, 2007
Evolutionary comparison finds new human genes

Enlarge

Over millions of years of evolution, a gene called GRIA2 has continued to do it's job of making a receptor for neurotransmitters. The portions of the gene that code for amino acids that make up a protein change in different ways from other parts of the genome, so computer algorithms can use these distinctive patterns of evolutionary change to identify new genes that have been missed by other methods. A portion of GRIA2 is shown here in an alignment of the genomes of several species, beneath a graph of the computer analysis. Peaks in the graph identify exons (regions that are expressed), separated by introns (non-coding regions). When a cell reads the gene to make a protein the introns are edited out. Credit: Provided/Siepel

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.

Source: Cornell University

4.6 /5 (34 votes)  

Filter


Move the slider to adjust rank threshold, so that you can hide some of the comments.


Display comments: newest first

docatomic
Nov 17, 2007

Rank: 1 / 5 (1)
It would be interesting to sequence some DNA from human remains of some centuries ago, in order to run the comparison again. Would this action provide sufficient proof of human evolution to finally dispell the myths of the Creationists? I personally doubt it would - yet I would surely wish to see some of the arguements they may attempt to pose as "counter-proofs"! ;-))
HeRoze
Mar 31, 2008

Rank: not rated yet
What makes you think creationists don't believe in evolution within a species?
Rank 4.6 /5 (34 votes)
Tags

Relevant PhysicsForums posts

More news stories

Ultraviolet protection molecule in plants yields its secrets

Lying around in the sun all day is hazardous not just for humans but also for plants, which have no means of escape. Ultraviolet (UV) radiation from the sun can damage proteins and DNA inside cells, leading ...

Biology / Plants & Animals

created 12 hours ago | popularity 5 / 5 (5) | comments 0 | with audio podcast

Deadly bird parasite evolves at exceptionally fast rate

A new study of a devastating bird disease that spread from poultry to house finches in the mid-1990s reveals that the bacteria responsible for the disease evolves at an exceptionally fast rate. What's more, ...

Biology / Biotechnology

created 10 hours ago | popularity 5 / 5 (2) | comments 0 | with audio podcast

Decoding the molecular machine behind E. coli and cholera

Scientists from Queen Mary, University of London have discovered the workings behind some of the bacteria that kill hundreds of thousands every year, possibly paving the way for new antibiotics that could treat infections ...

Biology / Cell & Microbiology

created 10 hours ago | popularity not rated yet | comments 0 | with audio podcast

Deciding to go left or right: Researchers use device to determine that lower animals can navigate too

For decades, scientists have associated binary decision making — opting to go left or right — with higher-ranking animals, including humans. A team of Harvard researchers, however, is rewriting that ...

Biology / Plants & Animals

created 18 hours ago | popularity not rated yet | comments 2 | with audio podcast

5-10 percent corn yield jump using erosion-slowing cover crops shown in new study

The most recent annual results from a four-year Iowa State University study on using cover crops between rows of corn reveals that higher yields – by as much as 10 percent – are possible using the ...

Biology / Other

created 14 hours ago | popularity not rated yet | comments 2


'Dark plasmons' transmit energy

Microscopic channels of gold nanoparticles have the ability to transmit electromagnetic energy that starts as light and propagates via "dark plasmons," according to researchers at Rice University.

FDA-approved drug rapidly clears amyloid from the brain, reverses Alzheimer's symptoms in mice

Neuroscientists at Case Western Reserve University School of Medicine have made a dramatic breakthrough in their efforts to find a cure for Alzheimer's disease. The researchers' findings, published in the journal Science, show t ...

Hydrogen from acidic water: Researchers develop potential low cost alternative to platinum for splitting water

A technique for creating a new molecule that structurally and chemically replicates the active part of the widely used industrial catalyst molybdenite has been developed by researchers with the Lawrence Berkeley ...

Soraa LED light may dim 50-watt halogen rivals

(PhysOrg.com) -- Soraa, a Fremont, California company founded in 2008, this week launched its first product, a light that uses LEDS (light emitting diodes). The "Soraa LED MR16 lamp" is the "perfect" replacement ...

Anyone can learn to be more inventive, cognitive researcher says

There will always be a wild and unpredictable quality to creativity and invention, says Anthony McCaffrey, a cognitive psychology researcher at the University of Massachusetts Amherst, because an "Aha moment" is rare and ...

Engineers find inspiration for new materials in Piranha-proof armor

(PhysOrg.com) -- It’s a matchup worthy of a late-night cable movie: put a school of starving piranha and a 300-pound fish together, and who comes out the winner?