Scientists have developed a new method for sequencing and analysis of the dark matter in life - the genomes of thousands of species of bacteria previously out of reach of scientists, from microorganisms that produce antibiotics and biofuels microbes living in the human body.
Researchers at UC San Diego, J. Craig Venter Institute, and Illumina Inc., published their findings online Sept. 18 the journal Nature Biotechnology. The discovery allows researchers to assemble a nearly complete genomic DNA extracted from a single bacterial cell. Instead of the traditional sequencing methods require at least a billion, the same cells, grown in laboratory cultures. The research opens the door for the sequencing of the bacteria, which can be cultivated - the lion's share of bacterial species that live on this planet.
"This part of life has been completely inaccessible to the genomic level," said Pavel Pevzner, a professor of computer science at the Jacobs School of Engineering at the University of California at San Diego and a pioneer of technology for sequencing algorithms of modern DNA.
Pevzner, in collaboration with UC San Diego professor of mathematics and computer TESL Glenn Hamidreza Chitsaz postdoctoral researcher, developed an algorithm that significantly improves the performance of the software used for the DNA sequence produced from a single bacterial cell. These programs traditionally covered 70 percent of the genes.
"The new assembly plant, the algorithm captures 90 percent of the genes from a single cell, however, is not 100 percent, but it is almost as good as it gets a modern sequencing technology: .. Today, biologists typically capture 95 per percent of the genes, but they need to grow billions of cells to implement, "said Tesler.
Bacteria play a vital role in human health. They represent about 10 percent of human body weight and can be found around the stomach to the mouth. Some, like E. coli, can cause havoc. Others help us to digest. Other more recent studies have shown that it is possible to change how we behave, for example, encouraging us to eat more than necessary. It is therefore essential to analyze the genomes of bacteria, which in turn help scientists understand the behavior of bacteria.
Modern DNA sequencing machines required to produce one billion bacterial cells in the whole genome. Biologists usually increases the number of bacteria in laboratory cultures. This allows them to obtain sufficient DNA sequence of E. coli. But the vast majority of bacteria - 99.9 percent according to some estimates - can not be cultured in the laboratory because they live in very specific circumstances and environments that are difficult to reproduce, for example, in symbiosis with other bacteria or skin of ' animal.
Enter multiple Displacement Amplification (MDA), developed a decade ago by Professor Roger Lasker, now at Venter Institute and coauthor of the study of Nature Biotechnology. MDA can be used on bacteria that can not be grown in the laboratory. The technology is equivalent to a copier that starts from a single cell and made copies of fragments of its genome, until it produces the equivalent of a billion cells. In 2005, Lasker and colleagues MDA DNA sequence produced from a single cell for the first time with support from the Department of Energy.
Although MDA is an ingenious copier cells, it is difficult to program sequencing. DNA copies of the MDA will lead a series of errors and is not completed by a constant: some parts of the genome is copied thousands of times, and others just once or twice. Modern sequencing algorithms are not able to address these differences. In fact, they tend to lose pieces of the genome that were repeated in only a couple of times by sequencing errors, although it could be the key to the whole genome sequencing. Pevzner algorithm, developed by a team of changes. And 'to keep these parts of the genome sequencing and use them to improve.
Researchers have sequenced a single cell of E. coli by this method to verify the accuracy of the algorithm and recycled 91 percent of his genes to do almost as well as the classic sequence from cultured cells. This gives sufficient data to answer many important biological questions, such as antibiotics of a species of bacteria produce. It is also, for the first time that researchers can conduct in-depth studies to determine which proteins and peptides, the bacteria that live with humans use to communicate with each other and with their host.
The researchers then turned to a species of marine bacteria that had never been sequenced before - part of the dark matter in life. They not only have its genome sequenced, but he analyzed and were able to obtain information on how he lives and moves. The complete annotated genome with respect, they got was the first genome available through the MDA to be deposited in GenBank, the genetic sequence database at the National Institute of Health. With the help of the new algorithm developed by Pevzner and his colleagues are thousands more expected to follow.
Pevzner team is working on a second generation version of the algorithm. Lasker and his team plan to continue their work to improve the MDA as well.
Calculating a few hundred tubes filled with the bacteria in his laboratory in sequence Venter Institute in La Jolla, Calif. Each Terra Incognita is a bacteria that scientists will soon review the method developed for the efforts of researchers at UC San Diego Jacobs School of Engineering, Venter Institute, and Illumina.
"It 'really a big step forward," said the count.
The research was supported in part by grants from the National Human Genome Research Institute and Alfred P. Sloan Foundation and a grant from the National Institutes of Health.
New Method For Sequencing And Analysis Of The Dark Matter In Life
