Keck Conference Joins Biology, Computation

Keck Conference Joins Biology, Computation

BY LIA UNRAU
Rice News Staff
Dec. 3, 1998

The structure of viruses and using genetic statistics to study population size were among the wide range of research topics presented Nov. 20 at the W.M. Keck Center’s Annual Research Conference on Computational Biology.

About 50 research posters were presented and four speakers gave presentations at the daylong meeting held in Galveston.

Thad Harroun, a graduate student in the physics department at Rice, won the Dunn Foundation Prize for best poster titled “Computer Simulation of Hydrophobic Matching and Membrane Protein Interactions.” Harroun is a Houston Area Molecular Biophysics Program (HAMBP) fellow. Co-authors on the poster include Rice graduate students William Heller, Thomas Weiss and Lin Yang and Rice Professor of Physics Huey Huang.

Honorable mentions include Elaine C. Liong, Keck Center predoctoral fellow, biochemistry and cell biology department at Rice, for her poster, “Structural and Functional analysis of Proximal Pocket Mutants of Sperm Whale Myoglobin”; and Usman Qazi, graduate student, pathology and laboratory medicine, University of Texas Medical School, for his poster, “3-D Reconstructions of Fab-labeled Human Alpha-2 Macroglobulin Provide Details of its Structural Change for Proteinase Entrapment.”

The Best Undergraduate Poster Prize went to Willy Hwang, a Keck Center undergraduate fellow in the Department of Medicine, Baylor College of Medicine, for his poster, “In-vitro Mechanics of the Costal Mouse Diaphragm.”

“The purpose of this conference is to get the two cultures [computation and biology] together to have meaningful dialogues about scientific projects,” says George Phillips, Rice professor of biochemistry and cell biology and scientific and training director of the Keck Center. “The only way to do that is to get people face to face.”

At the conference, Phillips spoke about “Emerging styles of computing: network as computer”; Robert Fox, University of Texas-Medical Branch, discussed “Design of miniproteins”; Bill Cook, the Noah Harding Professor of Computational and Applied Mathematics at Rice, gave a presentation titled, “Did you hear the one about the traveling salesman?” and Olivier Lichtarge, Baylor College of Medicine, presented “A primer: Genes, genomes and their computational analysis.”

As discussed in Phillip’s talk, members of the Keck Center are helping to develop software for the National Center for Supercomputing Application’s (NCSA) Biologist’s Workbench, a browser-based computing system with supercomputers in the background that is emerging as a possible way for biologists to be most productive by taking advantage of networked, high-powered systems.

“The bottom line is that the network is becoming the computer,” he said.

Among the poster presentations was work from Baylor College of Medicine researchers, who presented their work on the structure of rotavirus antibody complexes. Rotavirus is responsible for most cases of infant gastroenteritis. They used three-dimensional electron cryomicroscopy to map the antibody-virus complexes and to study one of the little understood rotavirus proteins involved in entering the host cell and other functions. Their work located a specific region where protein binding takes place. The research was presented by Joseph Pesavento, Keck Center predoctoral fellow, and Sharmila Mukherjee, Sue Crawford, Mary Estes and B.V.V. Prasad, all of Baylor.

Demographic change in populations may involve periods of growth, decline or no change in population size. It is known that these changes leave signatures on the genetic make-up of the population. Rice statisticians Patrick King, a Keck Center predoctoral fellow; Marek Kimmel, professor of statistics; and Ranajit Chakraborty of the Human Genetics Center at the University of Texas Health Science Center have developed a statistical method called the Imbalance Index to identify growth patterns using genetic data, effective population size and genetic mutation rate. Its properties were used to demonstrate likely bottlenecks and expansions in the populations of modern humans on different continents.

In other research presented, Baylor researchers are studying the structure of viruses that are enveloped in a membrane, and use the membrane to fuse with a host cell. Because fusion is such an important event in the life cycle of these kinds of viruses, studying the structure of the virus in the state of fusion should allow researchers to observe which parts of the virus structure change to interact with the host membrane. It will also give them insight into how the virus initiates fusion. Angel Paredes, a Keck Center postdoctoral fellow, Steve Ludtke, Ali Saad and Wah Chiu of Baylor, and Dennis Brown of North Carolina State University are conducting these structural studies.

The W.M. Keck Center for Computational Biology is a joint program of Baylor College of Medicine, Rice University and the University of Houston, founded by the W. M. Keck Foundation and currently supported by the Dunn Foundation, the National Library of Medicine and the National Science Foundation. For more information about the center see .