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May 10, 2010

New detection technology identifies All Genetically Sequenced bacteria and viruses and Other Organisms within 24 hours

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Shown is the one-inch wide by three-inch long Lawrence Livermore Microbial Detection Array that contains 388,000 probes that are used to detect viruses and bacteria. Photos by Jacqueline McBride/LLNL
The Lawrence Livermore Microbial Detection Array (LLMDA), could enable law enforcement, medical professionals and others to detect within 24 hours any virus or bacteria that has been sequenced and included among the array’s probes.

Developed between October 2007 and February 2008, the LLMDA detects viruses and bacteria with the use of 388,000 probes that fit in a checkerboard pattern in the middle of a one-inch wide, three-inch long glass slide. The current operational version of the LLMDA contains probes that can detect more than 2,000 viruses and about 900 bacteria.

Currently, Slezak’s team is testing a next-generation LLMDA that boasts 2.1 million probes. This version contains probes representing about 178,000 viral sequences from some 5,700 viruses, and about 785,000 bacterial sequences from thousands of bacteria.

The latest LLMDA version also encompasses fungi and protozoa – with probes representing about 237,000 fungal sequences from thousands of fungi and about 202,000 protozoa sequences from 75 protozoa.


“The LLMDA allows us to not only identify the biological pathogens on a priority screening list, but also any other already-sequenced bacteria or virus in a sample that you might not have been expecting to find, including possible novel or emerging pathogens,” Slezak said.

Current plans call for the detection array to be evaluated for operational bioforensic use at the Frederick, Md.-based National Biodefense Analysis and Countermeasures Center of the U.S. Department of Homeland Security.

As the cost of the array is reduced, the LLMDA technology could be used to improve public health diagnostics, Slezak said, adding that dozens of bacteria and viruses can be detected in a single test from the entire spectrum of sequenced organisms. One advantage of the Livermore array is that it provides researchers with the capability of detecting pathogens over the entire range of known viruses and bacteria. Current multiplex polymerase chain reaction (PCR) techniques can at most offer detection from among 50 organisms in one test.

As a screening tool, Slezak sees the LLMDA as occupying niche roles between PCR machines and sequencing.

The LLMDA process starts with the purification of DNA or RNA from a sample, such as sputum or blood. The sample is next labeled with a fluorescent dye and hybridized on the microarray at 42 degrees C or about 107.6 degrees Fahrenheit. In turn, a fluorescent scanner and analysis software are used to detect the probes that have lit up, identifying the presence of viral or bacterial sequences.

The Livermore team plans to update probes on the array with new sequences of bacteria, viruses and other microorganisms from GenBank and other public databases about once per year, in addition to using sequences obtained from collaborators for their probes.


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