Genes: New High Fashion on Campus?

The year 2001 marks the beginning of a new era in which we know the entire genome sequence for several organisms, including our own species, Homo sapiens.  We are now faced with making sense and use out of the vast assemblage of information about our genome.  Molecular biology once pursued the understanding of gene structure and expression. Now, the field of bioinformatics has the task of organizing and understanding the design and evolution of the large databases we know as genomes.  The sheer vastness of the data will require new approaches to handling databases and accessing the data therein.  This opportunity to develop new technology and methodology might be likened to the challenge of landing a human on the moon.  One approach will be to compare our genome architecture to that of closely and distantly related species - not comparing gene structure but rather the clusters and orderings of genes on the chromosomes on which they lie.  The evolution of gene patterns may teach us about the function of the large amount of "junk" DNA that lies between the transcribed DNA that codes for proteins and structural RNAs.  The Biology Department has joined the cadres of scientists who will be exploring genome organization in a variety of species.
 
In 1998 The University of Massachusetts Automated DNA Sequencing Facility was established with Biology faculty member Ron Adkins as Director.  Since its opening, the facility has applied its machinery to the sequencing of DNA of over 200 different species.  The facility services the sequencing needs of 60 laboratories in the 5-College community.  Each year sees its usage increasing with a 6,400 sequence throughput in the past year, representing 3.2 million nucleotide pairs identified.  Facility director Ron Adkins is interested in the deep structure of mammalian phylogenetic divergence as exemplified by this tree of mammalian evolutionary branching, excerpted from one of his earlier publications, which includes primates, tree shrews (Tupaia), flying lemurs (Cynocephalus), bats (Chiroptera), mice (Mus), cows (Bos) and armadillos (Dasypus).  Ron's current research is exploring the evolution of the deep structure of the speciose group of mammals which includes mice and rats.  Another Biology faculty member Yin-Long Qiu uses the facility to study plant genomics.  Microbiology Professor Derek Lovley used the facility extensively to contribute to the Geobacter genome project.  Biology courses use the facility to provide training in the application of the tools of molecular biology.
 
In addition to genomics research per se, the facility is being used by university geneticists in a variety of ways.  Geneticist Randy Phillis explains typical scenarios: "Once we have induced a mutation in our organism of choice, we can identify the locus of the mutation and sequence the gene.  Then we can compare that gene to the worldwide database of gene sequences and perhaps find homologous genes whose properties have been identified previously.  This gives us clues to how our gene works.  Second, we can engineer a mutation in a known gene in order to explore the effects of such a mutation.  The sequencing facility can quickly allow us to check that our engineering created the mutation we desired."
 
The Sequencing Facility is an indicator of the serious commitment the University and its biology faculty have made to support modern genomics research and teaching.