February 16, 2004
UCSC forms new Department of Biomolecular
By Tim Stephens
UCSC 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").
Research in biomolecular engineering includes the development of
the nanopore instrument for DNA analysis. This molecular model shows
a DNA molecule passing through the nanopore channel.
Image: M. Akeson
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.
Nanopore analytical instrument
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
Endowed chair in biomolecular engineering
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,"
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