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July 15, 2015

This summer, in collaboration with the UNM Sevilleta Field Station, CARC supported the Ecological and Evolutionary Genomics Biology 402/502 class taught by Don Natvig, Miriam Hutchinson, and Dan Colman of the UNM Department of Biology.

The participants, eight advanced undergraduates and two graduate students, toured the Sevilleta National Wildlife Refuge in the Chihuahuan desert, 20 miles north of Socorro, New Mexico. There they collected pond water, grass, and samples of herbivore droppings for DNA isolation, cloning, and sequencing. Utilizing CARC computational resources on the Center's new Ulam supercomputer, they were introduced to Linux commands and job submission in a supercomputing environment, and ran through a series of computational exercises using the QIIME (Quantitative Insights Into Microbial Ecology) analysis code.

The first exercise employed a 454 sequence dataset of 16S rRNA (ribosomal RNA) sequences from the Antarctic, an analysis which was previously published by a group directed by UNM’s Prof. Cristina Takacs-Vesbach, also of the Department of Biology. The second exercise employed a similar QIIME bioinformatics pipeline, but used fungal ITS sequences from creosote shrubs and grasses, data which had not been analyzed previously. In addition to the two QIIME exercises, the group analyzed Sanger sequence data from the samples collected from the Wildlife Refuge. Utilizing a combination of online and Windows programs, the sequences were employed in alignment and BLAST (Basic Local Alignment Search Tool) exercises, as well as phylogenetic analysis.

"The students appreciated participating in every step of a real metagenomics research project, from sample collection to data analysis,” said Prof. Natvig. “Several of the students were especially interested in the opportunity to learn about the physical structure and to engage in data analysis on a supercomputer."

CARC hosts and supports short and full-semester classes throughout the academic year and the summer. For information about using CARC resources for instruction, please contact info@carc.unm.edu.