NASA Chooses Sequencing Software from CLC bio for Exobiological Research

The Exobiology Branch of the NASA Ames Research Center in Moffett Field, California, has chosen bioinformatics software from CLC bio for analyzing sequencing data which revolves around hypersaline microbial mat systems that are found worldwide in exotic locations such as Baja, Mexico, and Solar Lake, Egypt, to name a few.

Exobiology - also known as astrobiology - is an interdisciplinary field, combining aspects of astronomy, biology and geology, which is focused primarily on the study of the origin, distribution and evolution of life.

Microbial mat communities represent, in gross morphology, some of the earliest known microbial communities on Earth. As a common form of microbial community existing on Earth during the Precambrian, and dominant in the Proterozoic era, these systems are hypothesized to have played a significant role in the development of modern oceanic and atmospheric conditions.

Dr. Stefan J. Green, scientist from the Exobiology Branch of the NASA Ames Research Center, states: “We are currently employing various molecular tools to characterize shifts in community structure of the total microbial population as a result of alterations in sulfate and salinity levels.

Our initial molecular analyses are performed using a fairly standard DNA extraction-PCR amplification-denaturing gradient gel electrophoresis (DGGE) methodology. We are employing a wide variety of primers for PCR-DGGE analyses and while many of these primer sets amplify regions of the 16 or 18S rRNA gene, we are also exploring a variety of primer sets to target functional genes. Such functional gene analyses can provide information regarding microbial function and phylogeny.

CLC Combined Workbench is very useful in our manipulations of sequence data recovered from our exobiological analyses. In particular, the software has been useful in assembling complete and long gene sequences from multiple sequence reactions - with the sequencing trace visible for all overlapping reactions. For example, the dsrAB genes are approximately 1900 bp in length, and require a minimum of 3 sequencing reactions.

The gene annotation feature is also highly beneficial, by helping establish, for example, where the dsrA gene ends and the dsrB gene begins, based on other sequences in Genbank. The wide variety of other tools in CLC's software are extremely useful – BLAST searches from within the program, in silico restriction digests, alignments, rudimentary phylogenetic trees, among a lot of other features.

One of the worst facets of sequence analysis is the constant reformatting that must be performed to analyze the data with different programs - and with CLC's software the need for many of these manipulations are eliminated. Thank you for creating such nice software!”