Chasing a Virus Through Mathematical Models

Viruses mutate often and because their life spans are on the order of minutes or hours, a tremendous amount of change can occur in a short amount of time.

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A Triangle of Collaboration

A Triangle of Collaboration: Core Lab Increases Efficiency

Institute for Bioinformatics and Evolutionary Studies (IBEST) | Visit IBEST

Following the University of Idaho’s spirit of collaboration and enterprise, the Genomics Resources Core Lab in the Institute for Bioinformatics and Evolutionary Studies (IBEST) is hitting the mark on both accounts.

Through a unique collaboration, known as “the triangle of collaboration,” an investigator, genomics scientist and bioinformatics scientist meet as a team to talk about the goals and best method to generate the data.

“It’s extremely uncommon for a core facility to have both (physical lab work and data analysis) aspects together,” says Matt Settles, lab director. “It really helps improve the success rate of the work we do, and it’s absolutely critical.”
In a rare meeting of the wet lab -- where samples are run through machines -- and the dry lab -- where bioinformatics and data analysis occurs -- Idaho’s core lab is not only at the forefront of collaboration, but it is providing a better research experience for all involved.

Settles says when he worked in a previous bioinformatics core facility, he never talked to the researcher prior to the analysis, which didn’t always yield results. He says that Idaho’s triangle of collaboration strategy ensures productive experiments.

“We’re excited about the Core’s capabilities and our collaborative process,” says Settles. “We have a lot of services that we can offer researchers at the University of Idaho and across the United States in the area of DNA sequencing, microarrays and bioinformatic analysis.”

The “wet” lab focuses on three functions: DNA sequencing, DNA microarrays, and genotyping.

SEQUENCING

Gone are the days of sequencing one piece of DNA at a time; with the Roche 454 Genome Sequencer, the Core can process a million pieces of DNA at a time in roughly 22 hours. This allows investigators to sequence whole genomes and look at the species composition of bacterial communities by meta-genomic sequencing.

Roughly half the lab’s sequencing projects have been for research projects that examined soils, ocean water and swabs from various sites in and on the human body to try to determine the make-up of the microbial community that is present in each of these environments.

Specifically, the Core has worked in collaboration with investigators to improve women’s reproductive health by increasing understanding about normal vaginal microbiota – or bacteria – and physicians can better identify conditions that make women prone to infections and other diseases, and avoid the development of health problems.

DNA MICROARRAYS

By affixing millions of artificial DNA fragment to a glass slide --a DNA microarray---scientists can measure the changes in gene expression across treatments. Having both sequencing technology and Roche Nimblegen DNA microarrays in the same lab allows scientists to sequence all the genes in previously unknown organisms and build custom microarrays to test for differences in gene levels between treatments.

Studies performed through the Core include seeking an answer to a global frog die-off. Using microarrays of genes from different frog species, scientists are trying to discover why some frogs are susceptible to the fungus responsible for the die-off while other frogs remain relatively healthy.

After sequencing all the genes in different frog species that respond differently to the fungus. The Core designed a custom microarrays to assay gene expression differences between the different species when they are infected with the fungus. Those differences will help gain insights into the response of the frog to the fungus. In addition the Core has sequenced the fungal genome with antibiotic resistance to help researchers determine how resistance develops.

GENOTYPING

One of the lab’s newer capabilities is genotyping. Through this capability, researchers can simultaneously analyze single nucleotide differences (SNPs) in genomes for up to 384 distinct loci in several hundred or even thousands of different samples.

With a researcher at neighboring Washington State University, the Core is performing genotyping studies to examine the effect of temperature on the resistance of E. coli to infection by a bacterial virus. Strains of E. coli grown under different environmental conditions are compared in order to identify the single base differences in the genes between strains that may be responsible for resistance or susceptibility to viral infection.

Settles said the when the Core first began two years ago, it included $200,000 worth of equipment; now, that it includes $1.5 million in capital equipment.

For more information about the lab: http://cores.ibest.uidaho.edu/section/grc