APPLICATIONS

Since the 2001 launch of the Human Genome Project, which released a first draft of the entire sequence of human DNA, many researchers have dedicated themselves to creating a library of comprehensive, species-specific genetic sequence "maps" available for study. Scientists at LSU recently took part in the International Rhesus Macaque Sequence and Analysis Consortium, which successfully detailed the full DNA sequence of the rhesus macaque, the third primate - including humans - to undergo sequencing. The results will be published in the journal Science on Friday, April 13. The rhesus macaque, a primate species that had a common ancestor with humans and chimps but diverged from the human-chimp lineage approximately 25 million years ago, still shares about 93 percent of its genome sequence with humans. This makes the macaque an integral part of primate evolutionary studies and could allow researchers to gain a better understanding of HIV/AIDS in humans. "Mapping the macaque genome is a significant achievement for many reasons," said Mark Batzer, Andrew C. Pereboom Alumni Departmental Professor of Biological Sciences at LSU and leader of two of the sequence analysis units of the consortium. "It provides additional insight into the pathways involved in the infection and spread of pathogens in primates, which could potentially lead to the development of new and improved treatment options, vaccines and other preventative measures in humans." Mobile elements, an integral part of this study and one of Batzer�s specialties, are "selfish" DNA sequences that duplicate themselves many times and integrate throughout the genomes in which they reside. These elements exist at copy numbers of 100,000 elements or more, make up about 50 percent of primate genomes and were generally thought to have no function. However, these elements have an impact on genome structure and are even involved in shaping genomes. Mobile elements have also been shown to cause many diseases in humans such as breast cancer, familial hypercholesterolemia and Tay-Sachs and can also be involved in the creation of new genes and gene families. As a consequence, the impact of mobile elements on genomes in general, and on primate genomes in particular, is multifaceted. Genetic and physiological similarities with humans make rhesus macaques the most commonly used nonhuman primate in biomedical research. Their response to infectious diseases such as SIV, or simian immunodeficiency virus, is similar enough to the human reaction to HIV, or human immunodeficiency virus, that these primates serve as a dominant model for disease studies and vaccine development. Because of this, access to the complete macaque sequence offers scientists even more in-depth research avenues into current and pressing health issues affecting society today. Mobile elements are commonly utilized for evolutionary and population genetic studies. Batzer and his colleagues investigated the overall mobile element composition and evolution of mobile elements within the rhesus genome in a companion paper also published in the April 13th issue of Science. This detailed and complex analysis was a collaboration with Brygg Ullmer, assistant professor of computer science at LSU�s Center for Computation & Technology, or CCT, along with Web Miller from the Pennsylvania State University, University Park, Pa., and Arian Smit from the Institute for Systems Biology in Seattle, Wash. Ullmer used CCT�s state-of-the-art supercomputing facilities, including SuperMike, for the computational analysis of the rhesus macaque genome. "To get a sense for the importance of high-performance computing to this project, a single run of our analysis would have taken 20 to 30 years - nonstop - on a common desktop computer," Ullmer said. The data generated by Batzer, Ullmer and the rest of the International Consortium will bolster research in neuroscience, behavioral biology, endocrinology and many other important fields of study. It will also allow scientists to further study the history of genetic diversity and ancestral population structure of macaques, particularly Chinese and Indian rhesus macaques. While these two groups look the same, they are known to be genetically different. A result of this disparity is that the two populations show a different susceptibility to SIV. One of the many possible benefits that may arise because of the results of this study is the potential for researchers to gain a better understanding of HIV/AIDS in humans.