BCIG BRAINSTORMING SESSION: "Synthetic Gene Design: good practice, poor theory”

Clinical Center (Building 10) Medical Board Room (Room 2C116)

DESCRIPTION: The past decade has witnessed rapid growth in the practice of synthesizing protein-coding gene sequences that were designed at a purely conceptual level (rather than built from a physical DNA template). But as the biotechnology that enables this procedure continues to improve, a clear strategy for the rational design of genes remains elusive. Here we review the fusion of applied molecular biology, bioinformatics and molecular evolution responsible for this emerging field. We discuss the growing awareness that "optimizing" gene expression is a complex, multilayered concept. We highlight the interdependence of coding sequence features that has hindered the development of clear design principles and the need for standards that would facilitate direct comparison of different experiments. We advocate a model by which differently motivated research communities could synergise their efforts, achieving their own research goals while contributing to the progress of the others.

NIH CONTACT: Jim DeLeo, 301-496-3848 jdeleo@nih.gov

BCIG WEB SITE: www.nih-bcig.org

NIH VISITOR INFORMATION: http://www.nih.gov/about/visitor/

3:00 pm to 4:30 pm September 7, 2006

FACILITATORS:

Stephen J. Freeland
University of Maryland Baltimore County

FACULTY POSITION
Aug 2001-present
Assistant Professor, Dept Biological Sciences, University of Maryland Baltimore County (UMBC).
At UMBC, I lead a research lab of Ph.D., Masters’ and undergraduate students in developing an interactive web of bioinformatics tools for genome exploration and analysis. The toolkit uses (and extends) evolutionary theory surrounding the origin and evolution of the genetic code to explore and understand the genomic ‘subtext’ of coding sequences.

POST-DOCTORAL RESEARCH EXPERIENCE June 2001-Aug 2001 John Templeton Foundation summer support, Dept. EEB, Princeton University. (co-PI with Prof. Laura Landweber)
Summer support to pursue investigations of chance and chemical determinism in the evolution of the genetic code. This grant has funded supervision of an undergraduate research project to investigate the plausibility of reconstructing the ancestral form of biosynthetic enzymes that are purported to have ‘invented’ new amino acids during the early evolution of life.

June 1999-June 2001 HFSP (Human Frontiers Science Program) Fellow, Dept. EEB, Princeton University. (supervisor: Prof. Laura Landweber)
A two year collaborative research program investigating the evolution of the genetic code, and the subsequent implications for molecular evolution. This fellowship has involved a diverse combination of research initiatives, from the development and use of special analysis software, through statistical analysis to laboratory synthesis of predicted gene sequences for functional experiments within E coli.

Nov. 1998-June 1999 DIMACS Fellowship, Dept. EEB, Princeton University. (supervisor: Prof. Laura Landweber)
A six month post-doctoral fellowship laying the groundwork for a collaborative research program into the origin and evolution of the genetic code. Lead to a major review paper on theories of code evolution, and the launch of novel software development, sequence analysis and literature reviews to synthesise current information about code evolution.