UCSC forms new Department of Biomolecular Engineering

The University of California, Santa Cruz, has established a new Department of Biomolecular Engineering within the Baskin School of Engineering. The department is the new home for UCSC's renowned programs in bioinformatics, and includes faculty and researchers with interests in nanotechnology, protein engineering, and DNA microarrays (also known as "gene chips").

The department's unique interdisciplinary blend of engineering, computer science, biology, and chemistry represents a powerful new approach to biomedical discovery, said David Deamer, a professor of chemistry and biochemistry and acting chair of the new department.

"We are the only department like this in the country. Our faculty are interested in biomolecules, genomics, nanotechnology, and biomedical applications, with a strong emphasis on computational approaches in their research," Deamer said.

The department's senior faculty include David Haussler, a Howard Hughes Medical Institute investigator and director of UCSC's Center for Biomolecular Science and Engineering, and Kevin Karplus, director of the engineering school's undergraduate and graduate programs in bioinformatics. Haussler and Karplus are both leaders in the field of bioinformatics, which applies computational techniques to complex problems in molecular biology. They transferred to the new department from computer science and computer engineering, respectively. Another bioinformatics expert, professor of computer engineering Richard Hughey, will also be affiliated with the new Department of Biomolecular Engineering as a consulting faculty member.

In addition to the bioinformatics programs, plans for the department include the establishment of new undergraduate and graduate degree programs in biomolecular engineering. Karplus emphasized that the department is not concerned with conventional "biomedical engineering," such as the development of prosthetic devices. Rather, biomolecular engineering refers to engineering "of, with, or for biological molecules," he said.

Examples include protein engineering (the computational design of proteins to enhance or modify their functions), the development of sensors that integrate biomolecules with electronic components, and new laboratory devices and analytical tools for studying gene regulation, protein expression, and other complex biological systems.

One project that illustrates several aspects of biomolecular engineering is the nanopore analytical instrument being developed by research scientist Mark Akeson with Deamer, Haussler, and their students. The nanopore instrument is built around a membrane containing a tiny hole just a few nanometers in diameter (a nanometer is one-billionth of a meter). An electrical field drives single molecules such as DNA through the nanopore. As a molecule enters the pore, it produces an electrical signal that provides information about its concentration, identity, and composition. The pore itself is a naturally occurring bacterial toxin made of self-assembling protein molecules. Potential applications of the nanopore device include ultrarapid DNA sequencing.

"Mark Akeson's research on nanopore analysis is a good example of the kind of research we are calling biomolecular engineering. It involves biomolecules and has clear biomedical applications; we are using computer algorithms to analyze the information we get from it; it has nanoscale elements; and, of course, it is engineering because we are developing a new technology," Deamer said.

Several new faculty members have been recruited in recent years to join the fledgling department. They include Assistant Professors Todd Lowe, Carol Rohl, and Joshua Stuart. Lowe, who won a prestigious Sloan Research Fellowship last year, uses DNA microarrays and combines computational and experimental approaches in his research on gene expression and comparative genomics. Rohl's research interests include protein structure prediction and protein engineering. Stuart's interests include DNA microarray analysis, genome-wide analysis of gene regulation, and comparative functional genomics.

Recruitment is currently under way for a permanent chair of the new department. The new department chair will also become the first holder of an endowed chair in biomolecular engineering funded by a major gift last year from Jack Baskin, a retired engineer and a leading philanthropist in the Santa Cruz community.

Long-range plans for the Department of Biomolecular Engineering include the hiring of additional faculty over the next several years for an eventual total of 14 faculty members.

The interdisciplinary focus of the department will foster collaboration with other departments in the School of Engineering and in the Division of the Physical and Biological Sciences, Deamer said.

"I like to think of this department as another example of UCSC leading the exploration of a new area, just as 20 years ago Chancellor Robert Sinsheimer first proposed the idea of sequencing the human genome," he said.


Note to reporters: You may contact Deamer at (831) 459-5158 or deamer@chemistry.ucsc.edu, and Karplus at (831) 459-4250 or karplus@soe.ucsc.edu.