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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] |
 Nanopore Methods of DNA Analysis
David Deamer, Biomolecular Engineering; Chemistry
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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 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 the past 6 CASPs. 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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 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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 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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 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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 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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 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] |
 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. |
 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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 Integrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip
Holger Schmidt, Dept. of Electrical Engineering
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] |
 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. Litke also collaborates with UCSC Professor David Feldheim and has recently begun using these detectors to investigate emergent properties in networks of hundreds of synaptically connected cortical neurons. [More] |
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