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A New Kind Of Genomics, With An Eye On Ecosystems

Football Betting Spread Determining the complete DNA sequence of a single species has become almost commonplace. It has been done for humans, mice, rice plants and a host of microbes, among others. Now some scientists are moving to a more audacious challenge, sequencing "metagenomes," the DNA of entire ecosystems.

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Commodity Spread Trading The new efforts seek to read all the DNA in the bacterial communities found in a patch of soil or seawater or even the lining of the human gut. Deciphering the genetic blueprint of all of the microbial species may help tell scientists which species are present and how they work together. Thousands of previously unknown micro-organisms may be unearthed, as well as new drugs, chemicals and ways of harnessing bacteria to fight pollution.

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Nfl Betting Spread "We think this is a window on biology that is really unprecedented in its implications," said Dr. Jo Handelsman, a professor of plant pathology at the University of Wisconsin, who coined the term metagenomics to refer to the new field. Others call it community genomics, environmental genomics, or microbial population genomics.

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Advanced Commodity Spread By whatever name, the task will not be easy. There can be thousands of different microbial species in a spoonful of soil. "A milliliter of seawater, in a genetic sense, has more complexity than the human genome," said Dr. Edward F. DeLong, a senior scientist at the Monterey Bay Aquarium Research Institute in California.

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Betting Exchange Spread Besides soil and seawater, scientists are trying to read all the DNA of a bacterial community that contributes to acidic runoff from a former California mine, and of another community of seabed-dwelling microbes that can be used to produce electricity. Other projects are looking at microbial communities in the guts of termites and gypsy moths, since microbes play a role in the way these pests wreak their damage.

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Stock Spread Trading Among those entering the field is Dr. J. Craig Venter, the maverick scientist whose biotech company, Celera Genomics, defied skeptics and determined the human genetic sequence in a scant three years. Dr. Venter, who now runs nonprofit research institutes in Rockville, Md., is trying to determine the genomes of all of the microbes in the Sargasso Sea, an area of the Atlantic Ocean near Bermuda known for its floating seaweed.

Online Spread Betting That area of the ocean is considered relatively devoid of life. Nevertheless, Dr. Venter said, "Just from the Sargasso Sea alone, we've discovered more new genes than in the human genome."

Complete Guide Spread Trading The project is being done by Dr. Venter's Institute for Biological Energy Alternatives, which seeks to harness microbes to make clean-burning hydrogen fuel and reduce global warning. Another of his research centers, the Institute for Genomic Research, is trying to sequence the genomes of all the organisms in the human intestinal tract. The information could lead to new ways to diagnose and treat diseases.

Betting Horse Racing Spread Until now, scientists have started with a known species, be it humans or anthrax bacteria, and sequenced the genome to learn more about it. But metagenomics works in reverse. It starts with the DNA of unknown organisms and then tries to figure out what the organisms are.

Low Spread Forex Trading More than 99 percent of bacteria cannot be grown in laboratory cultures, so scientists know almost nothing about them. But it is possible to extract DNA from a sample of soil or seawater without knowing the identities of the creatures that are the DNA sources. "We don't know what the species even look like," Dr. Venter said. "All we know of them is their genetic code."

Sport Spread Betting This DNA will consist of fragments from all the species present. The challenge is to sort out which fragments come from the same organism and then to arrange them in the correct order to determine the complete sequence of each species. Such genetic blueprints could then provide clues about what species are present and what their roles are.

Trading Spread And Seasonals The payoff could be vast. Bacteria constitute more than half the living matter on earth and play essential roles in numerous environmental cycles. They turn nitrogen in the air into a form usable by plants, produce about half the oxygen on the planet, break down minerals and clean up pollution.

Arbitrage Spread Trading "Microbes are kind of the master chemists of our planet," said Dr. DeLong of the Monterey Aquarium. Bacteria are also the source of most antibiotics and of some other drugs and industrial enzymes and of the genes that confer pest and herbicide resistance to genetically modified crops.

Betting Guide Insider Sports There have already been some discoveries from sampling environmental DNA. Dr. DeLong, sampling microscopic plankton from the surface of the Pacific Ocean, discovered certain bacteria that could convert sunlight into energy, a role normally played by plants.

Betting Spread Successful "It's a whole new class of light-driven energy generation that exists in a category of microbes that's really abundant," he said. "It remained invisible until we applied these genomics techniques."

College Football Betting Diversa, a company in San Diego, bases its business on extracting DNA from creatures that can survive in extreme environments, like super-hot deep-sea vents and the highly alkaline soda lakes of Kenya. It then searches the DNA for genes that provide the code for novel enzymes. One enzyme, found from sampling DNA in the soil of the tropics, is expected to cut in half the cost of a critical step in manufacturing the cholesterol-lowering drug Lipitor.

Betting Financial Risk Spread Community genomics got its start in the 1980's, when scientists began sampling microbial DNA from the environment and studying a single gene that coded for part of the ribosome, the cell's protein-making machinery.

Betting Point Spread On Nfl Virtually every creature on earth is thought to have this gene, though it has changed through evolution. So looking at it could tell scientists how many different types of microbes were present and into what broad categories they fell. But it did not tell them more about the way the bacteria functioned.

Betting Point Spread In the 1990's, scientists began to analyze larger fragments of DNA, looking for genes of interest. This was how Dr. DeLong found the photosynthetic bacteria and Diversa the enzyme to be used in making Lipitor.

Super Bowl Betting Spread Now, to get even more information, scientists are trying to determine the complete genome sequences of all the bacterial denizens of a community.

Betting Fan Football Guide The technique they use is called shotgun sequencing, which was used by Celera in sequencing the human genome. Because gene-sequencing machines can handle only small stretches of DNA, the DNA to be sequenced is broken into random fragments. After the sequence of each fragment is determined, powerful computers assemble the pieces in the correct order by looking at overlapping sequences.

Spread Betting Uk It is like shredding multiple copies of a book into tiny pieces and then trying to figure out the text.

Betting Betting Fan Football But while this has been done for individual species, doing it for hundreds or thousands is expected to be much harder, like shredding and reconstructing multiple copies of multiple books. Dr. Venter says computer simulations indicate that it should be possible, at least for the Sargasso Sea.

Betting Company Germany In Many scientists still doubt that. But success is already being seen on more narrow communities. Dr. Jill Banfield, professor of earth and planetary science at the University of California at Berkeley, is studying the microbes found 400 feet underground at Iron Mountain, an abandoned mine in Northern California. The microbes contribute to the highly acidic runoff that has made the mine a major hazardous waste site under the federal Superfund program.

Ig Index Spread Betting Dr. Banfield, who is working with the Department of Energy's Joint Genome Institute in nearby Walnut Creek, says there are probably just seven different species in the sample, either bacteria or archaea, another type of microbe that tends to inhabit extreme environments. The full genomes of the two organisms have already been determined. "As far as I know, it's the first time a genome has been recovered from a truly environmental sample," she said.

Betting Guide Practical There are some obstacles to overcome before even trying to put the DNA fragments together into the correct order. Extracting DNA fragments from the environment can be difficult, particularly from soil, which contains acids that break down the genetic material. And one or two species may dominate in an environment, outnumbering other species by as much as 100,000 to 1. So the DNA fragments will be mainly from the dominant species.

Betting Blogspot Com Site "When somebody says they are going to sequence all the bacteria in a soil sample, well, that's rubbish," said Dr. Julian Davies, an emeritus professor of microbiology and immunology at the University of British Columbia.

Learn Spread Betting Dr. Davies started a company to find new antibiotics by extracting genes from soil bacteria that could not be cultured in the laboratory. But antibiotic production is often governed by many genes, not just one, and it was impossible to extract DNA fragments large enough to contain all the necessary genes, he said.

Financial Spread Trading Still, sampling techniques are improving. Diversa has a method, based on the relative density of DNA's chemical units, to prevent rarer species in a sample from being overlooked.

Football Betting Spread There is still debate about how valuable it will be to reconstruct the genomes of all members of a community. That alone will not necessarily tell which genes are active or how the bacteria interact with one another. "What you get is a catalog," Dr. Davies said. "You get unnamed organisms. The question is how can you tell what they do."

Commodity Spread Trading But Dr. Steven R. Gill, a microbiologist at the Institute for Genomic Research, countered that if a creature's genetic blueprint was known, "we can go back and reconstruct its metabolism."

Nfl Betting Spread Besides providing clues about the roles organisms play, such information may pinpoint nutrients they need, allowing previously unculturable organisms to be grown in the laboratory. And once all the genes in an organism or community are known, it will be possible to make gene chips to study which genes are turned on or off as environmental conditions change.

Advanced Commodity Spread Some scientists think ecosystem genome sequencing may eventually be used to monitor the health of environments or to predict environmental impacts. That could apply not only to the external environment but also to the ones inside people.

Betting Exchange Spread Dr. David A. Relman, an associate professor of medicine and microbiology at Stanford who is collaborating on the project to read the DNA of the bacteria in the human digestive tract, said changes in those bacterial communities contributed to diseases like colitis.

Stock Spread Trading It may be possible to find patterns in the bacterial population that will predict when someone is about to get sick. The human gut metagenome project "will be the first step in identifying these patterns," Dr. Relman said.

Online Spread Betting By Andrew Pollack
New York Times - 10/21/2003

Topic: Biodiversity

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