Category Archives: Genome

February 24, 2014

Image Caption: Boris Vinatzer has developed a naming convention based on genome sequencing to enhance the way organisms are classified. Credit: Virginia Tech

redOrbit Staff & Wire Reports Your Universe Online

A new naming system proposed by one Virginia Tech scientist proposes moving beyond the current biological naming system and supplementing it with a new classification method based on an organisms genome sequence.

The new method was developed by Boris Vinatzer, an associate professor in the College of Agriculture and Life Sciences Department of Plant Pathology, Physiology, and Weed Science, and he believes that it will create a universal language that will allow biologists to communicate about various types of life on Earth with previously unavailable specificity.

Vinatzer describes his work in the Friday edition of the open-access, peer-reviewed journal PLoS ONE, and said that switching to a taxonomy based on the genetic sequence of each individual creature will lead to the creation of a more precise, robust and informative name for animals, plants, and other forms of living organisms.

In a statement, he said that the new system builds upon the work developed by Swedish scientist Carl Linnaeus over two centuries ago, explaining that recent progress in genome sequencing technology allows researchers to distinguish between any bacteria, plant, or animal at a very low cost. The limitation of the Linnaeus system is the absence of a method to name the sequenced organisms with precision.

Vinatzer clarifies that he does not propose changing the naming conventions of the currently-used biological classification system. Instead, his new system aims only to add additional information in order to classify organisms within named species, and to more rapidly identify new ones since the process depends on the organisms DNA.

A genome-based classification system could be of great use to public health officials, given the ever-present threat posed by biological agents in this day and age. In his research, the Virginia Tech professor used the anthrax strain which surfaced following the September 11 terror attacks in order to demonstrate the limits of the Linnaeus system.

Weaponized anthrax frustrated officials as the powder found its way to offices in the United States and the ensuing investigation took months for law enforcement to identify the origin of the original pathogen as the Ames strain, the university explained. More than 1,200 strains of anthrax or Bacillus anthracis exist. Each one possesses an arbitrary name chosen by researchers that does nothing to illuminate genetic similarities.

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Virginia Tech Researcher Proposes New Genome-Based Naming System

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nanoHUB-U Nanobiosensors L5.3: Putting the pieces together - Genome Sequencer III
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nanoHUB-U Nanobiosensors L5.2: Putting the pieces together - Genome Sequencer II - Video

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February 20, 2014

Image Caption: Beagle, a Cray XE6 supercomputer at Argonne National Laboratory, supports computation, simulation and data analysis for the biomedical research community. Credit: Argonne National Laboratory

Lee Rannals for redOrbit.com Your Universe Online

Researchers writing in the journal Bioinformatics say that genome analysis can be radically accelerated.

Over the years, the cost of sequencing an entire human genome has dropped, but analyzing three billion base pairs of genetic information from a single genome can take months. A team from the University of Chicago is reporting that one of the worlds fastest supercomputers is able to analyze 240 full genomes in about two days.

This is a resource that can change patient management and, over time, add depth to our understanding of the genetic causes of risk and disease, study author Elizabeth McNally, the A. J. Carlson Professor of Medicine and Human Genetics and director of the Cardiovascular Genetics clinic at the University of Chicago Medicine, said in a statement.

Megan Puckelwartz, a graduate student in McNallys laboratory and the studys first author, said the Beagle supercomputer based at Argonne National Laboratory is able to process many genomes simultaneously rather than one at a time.

It converts whole genome sequencing, which has primarily been used as a research tool, into something that is immediately valuable for patient care, Puckelwartz said in a statement.

Scientists have been working on exome sequencing, which focuses on just two percent or less of the genome that codes for proteins. About 86 percent of disease-causing mutations are located in this coding region, but still about 15 percent of significant mutations come from the other coding regions.

Researchers used raw sequencing data from 61 human genomes and analyzed the data on Beagle. They used publicly available software packages and a quarter of the computers total capacity, finding that a supercomputer environment helped with accuracy and speed.

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Using Supercomputers To Speed Up Genome Analysis