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NMSU home to genetic testing instrument with statewide benefits

New Mexico State University biologists have begun work using a genetic analysis instrument that has the potential to increase advantages for the university, the region and the state.



02/25/2010: Haofeng Chen operates a 454 Life Sciences genome sequencing machine in his laboratory in Foster Hall. (Photo by Darren Phillips)

The pyrosequencer is capable of testing applications for health, agricultural and economical issues, but it also puts NMSU on the map as the only Hispanic-serving institution to house this type of instrument.

"While most universities have the capability to sequence small pieces of DNA, it is generally only big medical schools or national genome sequencing centers that possess the costly infrastructure required to sequence the entire genomes of organisms," said Brook Milligan, professor of biology. "We're the first and only minority-serving institution to have this instrumentation."

The pyrosequencer's basic capabilities include obtaining ultra-deep sampling of large populations of DNA sequences and finding variations that may be present. The data allow biologists to further research what happens to cell function when people become ill either by inherited or environmental mutations. The instrument can also reveal how organisms originated and how they are related to each other.

Currently researchers are using the pyrosequencer to test the different strains of staphylococcus. By taking oral samples and running the genome sequencing, researchers can see the differences between the individual strains and how they may be related to drug resistance. This includes the origins and transmission of the infection.

The testing applications can be used on infections in humans and animals. Milligan said bovine tuberculosis is closely related to human tuberculosis.

"Testing for the presence of bovine tuberculosis is a project the university has identified as a high priority in order to help out the livestock board," Milligan said. "Genetic testing would allow us to detect the presence of diseases before the animal starts showing symptoms. This is the goal."

By using these types of genetic testing applications, cattle ranchers would be able to curb the cost of losing an entire herd to a disease or infection that could have been detected early. This makes investing in the technology and developing the expertise economical and practical in solving statewide problems.

The pyrosequencer testing has other practical applications such as determining the origins of contraband like ivory or illegal fish. Milligan said the genotype, or genetic markers, of these types of items are difficult to find and characterize, but the pyrosequencer has the ability to rapidly identify vast numbers of these at a significantly reduced cost.

Milligan said researchers are spending time making sure they can do the test and analyze the data thoroughly. Helping out with the analysis beyond the sequencing service would be an integral part of the NMSU process.

"There's a lot of software to organize and support that," Milligan said. "We're dealing with tons of data."

In fact, the pyrosequencer can characterize more than one million genetic samples in the same period of time that older technology processed 96 samples, and for about one percent of the cost.

Peter Houde, professor of biology, said other entities outside of the university are starting to take notice of NMSU and the work being done with the pyrosequencer. Researchers at the University of Maryland enlisted NMSU's help on a project dealing with fungus on chestnut trees.

Other projects NMSU biologists are working on include testing the genomes of parasites and mosquitoes. Changes in genetic materials occur when an organism becomes diseased, which causes the host to modify its DNA products. The machine evaluates those products and can determine the phylogenetics, or relation between organisms.

In the evaluation process, a door has been opened to do cutting-edge work, made possible by a cost-share grant from the National Science Foundation. The NSF funded the Major Research Instrumentation grant for the pyrosequencer, but NMSU also put money toward the $1.8 million effort. Houde acted as principal investigator on the grant and Milligan as a co-principal investigator.

"This has the potential for other areas of biology," Houde said. "It'll open up opportunities for research on campus. That's how we presented it to the university and to the NSF."

Houde also mentioned receiving strong support from Vimal Chaitanya, NMSU vice president for research, graduate studies and international programs, and Robert Czerniak, associate dean of research in the College of Arts and Sciences.

The biology department received the instrument in January 2009 and was able to get it up and running a few months later. It is housed in Foster Hall and staffed with two graduate students, laboratory manager Haofeng Chen and Director of Bioinformatics Alexander Tchourbanov performing the test operations and analyses. The name pyrosequencer has to do with how the DNA sequence emits light as it is read

Video and sound bites are available under the slug Pyrosequencer at the following ftp site: ftp://aggievision:goaggies@aggievision.nmsu.edu If you are downloading through Filezilla or other download client use the following information: Host: aggievision.nmsu.edu Username: aggievision Password: goaggies. For questions on problems with downloading, please contact Minerva Baumann (575) 646-7566.