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BIOENGINEERING
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 Control
and Analysis of DNA and RNA Using Nanoscale Pores
Mark Akeson, Dept. of Biomolecular Engineering
Mark Akeson's research is focused on
the use of nanopore detectors - instruments built around a tiny pore in a membrane
or thin, solid-state wafer. These pores are just big enough to allow a single
strand of DNA to pass through. Akeson and his collegues use the detectors to
understand the dynamics and structure of DNA duplex ends, including those of
retrotransposons and HIV. Akeson also investigates the coupling of processive
DNA-modifying enzymes to nanopores, both protein and solid-state. Together with
UCSC Professors William Dunbar and David Deamer, he has demonstrated enzymatic
control of single DNA in nanopores with sequence specificity and real-time feedback
control. [More]
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 Nanopore
Methods of DNA Analysis
David Deamer, Biomolecular Engineering
Professor David Deamer and his collaborators
investigate physical properties of single DNA molecules. Together, they developed
a biomolecular nanopore detector that rapidly discriminates between nearly identical
strands of DNA. [More]
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 Bioinformatic
Tools for Sequence Analysis and Prediction
Richard Hughey, Dept of Biomolecular Engineering and
Dept. of Computer Engineering
Richard Hughey's research group focuses on two areas:
the Kestrel programmable sequence analysis accelerator and the SAM Hidden Markov
Modeling system. Kestrel is a single-board parallel processor designed to speed
biological sequence analysis. The Kestrel research group, which includes Professor
Kevin Karplus, designed and built the system, and has applied the machine to
Smith & Waterman searching, SAM HMMs, conformational chemistry, graph coloring,
and other areas. Hughey and Dr. Anders Krogh originally developed SAM -- a collection
of algorithms and software used to create statistical models of RNA, DNA, and
protein families with profile hidden Markov models. Since then, the Hughey and
Karplus groups have collaborated to extend and improve SAM. [More]
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 Nano-
and Microfabrication Technology for Biomedical and Diagnostic devices
Mike Isaacson, Dept. of Electrical Engineering
Michael Isaacson's research group uses
technology developed by the semiconductor industry to study biological systems
and develop biomedical devices. The work involves fabrication techniques and
imaging tools for making and visualizing devices and structures on the nanoscale.
For example, the group has developed microelectronic devices that can be implanted
into insect brains to record signals from the brain's neural circuits. Interestingly,
information about how the neural circuits work can then be used to further improve
microelectronic devices. [More]
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 Protein
Structure Prediction and Design
Kevin Karplus, Dept. of Biomolecular Engineering
Kevin Karplus' research group develops tools
and techniques for protein structure prediction and protein design.
He collaborates with Richard Hughey's group on the development of
the SAM tool suite for profile hidden Markov models, particularly
on developing protocols for using the tools for high-accuracy detection
of remote relationships between proteins. Karplus' group has used
these tools themselves to earn an international reputation for accurate
prediction of protein structure: secondary structure, tertiary structure,
and contact prediction. In the biannual Critical Assessment of Structure
Prediction "contests", his group has presented papers (the "prize" for
the contest) in CASP2 through CASP7. The group also collaborates
extensively with UCSC wet-lab biologists in predicting structure
and function for proteins of interest to them, and is starting work
on designing novel proteins. [More]
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 Applications
of Adaptive Optics for Biological Microscopy
Joel Kubby, Dept. of Electrical Engineering
Professor Joel Kubby is collaborating
with engineers, physicists and biologists to utilize Adaptive Optics for the
improvement of deep tissue imaging of living cells. Current biological microscopy
is incapable of obtaining high quality live imaging in samples greater than
30 microns beneath the plasma membrane, where many critical cellular processes
occur. Much of the degradation in image quality is the result of local differences
in the refractive index, both within the sample and between the sample and the
immersion lens. Adaptive optics was first used to correct for image aberrations
in astronomical imaging. Kubby and his colleagues believe that the same principles
that improved resolution in telescopes can be adapted to improve confocal, two-photon,
and spinning disk microscopy systems that are crucial for biological research.[ More] |
 Microelectronics
for the Development of Retinal Prothesess
Wentai Liu, Dept. of Electrical Engineering
Prof. Wentai Liu directs UCSC's Integrated BioElectronics
Research (IBR) Group, which develops miniaturized electronics for interfacing
with biological systems and replacement of lost biological functionality. For
example, the group has pioneered development of retinal prostheses to restore
vision in blind patients with Retinitis Pigmentosa (RP) and Age-related Macular
Degeneration (AMD) through development of next generation retinal implants.
The group's goal is to create implants that will enable facial recognition and
independent mobility. [More]
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 High
Energy Physics Comes to the Aid of Neurobiology
Alan Litke, Santa Cruz Institute for Particle
Physics
Alan Litke is physicist who
is also interested in neurobiology. Several years ago, Litke began
to utilize principles from his research on detection of particles in
high-energy-physics collisions in order to develop electrode arrays
that can be used to detect signals from the individual output neurons
of live retinal tissue. Litke and neurobiologist E. J. Chichilnisky
from the Salk Institute used this technology to discover a type of
retinal cell that may help monkeys, apes, and humans see motion. [More]
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 A
Virtual White Cane for the Visually Impaired
Roberto Manduchi, Dept. of Computer Engineering
Professor Roberto Manduchi's
research group in UCSC's Department of Computer Engineering develops
algorithms for computer analysis of images and other sensor information.
One project involves design of a hand-held laser sensor and processor,
which together enable the visually impaired to efficiently and conveniently
sense their external evironment. [More]
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 Tools
for Studying Genes and Proteins
Nader Pourmand, Dept. of Biomolucular Engineering
The Pourmand lab develops new tools and technologies
that integrate biology, electronics, and nanofabrication for the detection
and study of genes and proteins. These tools are specifically designed
to increase the speed and lower the cost of sample analysis. The lab
directs particular attention to the development of medically relevant
technology, such as instruments for pathogen detection. Pourmand is
also spearheading UCSC's effort to establish a new high-throughput,
high-quality sequencing facility. [More]
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 Neural
Circuits: Function, Development, and Treatment
Alexander "Sasha" Sher, Santa Cruz Institute
for Particle Physics
Our brain is a highly sophisticated
system that receives information about the outside world, processes
it, and determines our reaction to it. These functions are realized
through billions of individual neurons that are connected in vast and
complicated circuits and use electrical signals to communicate with
each other. The Sher lab is using unique large scale multielectrode
recording systems developed by a collaboration of physicists, biologists,
and engineers to study function, development and treatment of neural
circuits. Sher's research is focused particularly on the retina and
visual system. In addition, in collaboration with prof. Alan Litke,
Sher lab participates in the development of new techniques for recording
and stimulation of neural activity. [More]
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 Integrated
Optofluidics: Detecting and Analyzing Single Molecules on a Chip
Holger Schmidt, Dept. of MCD Biology
Optofluidics describes the combination
of optics and microfluidics and holds great promise for novel devices for biomedical
instrumentation, analytical chemistry and other fields that deal with liquid
analytes. A highly desirable extension of optofluidics is to use integrated
optics to replace the bulky microscopy analysis that is still commonly in use.
This would allow development of a fully planar, fully integrated lab on a chip.
[More]
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 The
Application of Molecular and Nanomaterial Systems to the Detection
and Treatment of Cancer
Jin Zhang , Dept. of Chemistry
and Biochemistry
The Zhang research group is interested in the application
of molecular and nanomaterial systems in conjunction with optical spectroscopy
and related techniques for biomedical detection and treatment, with
emphasis on cancer therapies and cancer biomarker detection. Specific
projects include: 1) investigation of mechanisms of photodynamic therapy
and catalytic therapy based on porphyrins, phthalocyanines, and related
compounds; 2) detection of small molecule, protein, and DNA cancer
biomarkers using fluorescence based on quantum dots (QDs) and surface-enhanced
Raman scattering (SERS) based on metal nanostrutcures; and 3) photothermal
imaging and therapy of cancer using unique metal nanostructures. This
research involves systematic study of the structural, optical, and
photophysical as well as photochemical properties of the materials
using a combination of microscopy, x-ray, spectroscopy, and electrochemistry
techniques. [ More] |
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