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 The ATP Synthase Modeling Project
Hongyun Wang, Dept. of Applied Mathematics and Statistics
Hongyun Wang uses both biophysics and molecular modeling techniques to examine mechanisms that convert chemical energy of ATP into mechanical work in biological systems.. [More]
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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 is the founder of the UCSC Nanopore Project, which has pioneered the use of ion channels ("nanopores") for the analysis of single RNA and DNA molecules. The proect is now co-directed by Deamer and Professor Mark Akeson and involves faculty collaborators from UCSC and other institutions, as well as numerous postdoctoral fellows, graduate and undergraduate students. [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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 Marine Natural Products as Anti-Cancer Compounds
Phil Crews, Dept. of Chemistry and Biochemistry
The Crews laboratory investigates the chemical structure and biological activity of chemical compounds that are derived from marine organisms. Among its many research projects, the laboratory collaborates with scientists at other research institutions and pharmaceutical industries to explore the identification and development of naturally occuring compunds in the fight against cancer. [More]
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 Linking Energy Metabolism and Oxygen Utilization
Ólöf Einarsdóttir, Chemistry and Biochemistry
Ólöf Einarsdóttir's Laboratory is interested in fundamental properties of energy transfer in living organisms. Their work focuses on the respiratory chain that provides energy for the cell. Einarsdóttir's principle focus is an enzyme called cytochrome oxidase. Chemical, structural, and functional analyses of this enzyme promise to provide important insight into its role in certain diseases. [More]
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 Lipooxygenase Inhibitors as Potential Anti-Cancer Drugs
Ted Holman, Dept. of Chemistry & Biochemistry
Lipoxygenases are enzymes implicated in a broad range of human cancers, as well as cardiac and inflammatory diseases. Ted Holman's laboratory examines the enzymatic mechanism and biological function of lipoxygenase in the hopes of developing novel inhibitors. In collaboration with UCSC Professor Phil Crews, his laboratory has identified potent lipoxygenase inhibitors and are currently characterizing their structure/function reactivity. The results of this work will shed light on their potential as anti-cancer agents. [More]
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Dynamics of Biomedical Molecules in Vision, Allostery, and Folding
David Kliger, Chemistry & Biochemistry
The Kliger lab uses time-resolved spectroscopy to study protein reactions. Proteins are central to health, making study of their structure and function critical. While traditional biochemical methods provide insight about the later steps in function, modern optical methods (particularly pulsed lasers and polarized light) reveal previously unknown steps occurring on a short time scale, which are important in biomedical processes. Such information can lead to the development of new and more effective drug therapies. [More]
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Chemical Genetics
Scott Lokey, Dept. of Chemistry and Biochemistry
The laboratory of Scott Lokey uses a small molecule approach, called chemical genetics, to study signaling pathways related to cell cycle checkpoints and the actin cytoskeleton. In one study, Lokey and his co-workers are developing screens of natural compounds that can be used to examine how cells detect their own DNA damage. Studies such as these might lead to development of a new class of chemotherapeutic agents. [More]
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 Remarkable Protein Structures ..... and Where They Go Wrong
Glenn Millhauser, Department of Chemistry
In modern biochemistry, structural determination is essential for understanding the function of biomolecules. Scientists in Glenn Millhauser's laboratory use peptide synthesis, nuclear magnetic resonance spectroscopy (NMR), and electron paramagnetic spin resonance spectroscopy (EPR) to examine the structure and analyze the function of proteins that have been implicated in several debilitating diseases. This includes the prion protein, which is responsible for mad cow disease and the related human affliction, Creutzfeldt-Jakob disease. They have also examined a novel signaling molecule, called AGRP, which is involved in energy balance and metabolic pathologies, such as diabetes and obesity. [More]
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 Molecular Mechanisms of Cell Cycle Regulation and Cancer
Seth Rubin, Chemistry and Biochemistry
The Rubin laboratory uses a variety of structural and biochemical techniques to investigate the molecular mechanisms that control the eukaryotic cell cycle. The aim is to elucidate detailed molecular pictures of protein-protein interactions and how these interactions are regulated by structural and chemical modifications. Improper regulation of these protein interaction networks is commonly associated with aberrant cell proliferation and cancer. [More]
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RNA Catalysis
William Scott, Dept. of Chemistry and Biochemistry
Ribozmes are RNA-based enzymes whose comparatively recent discovery came as major surprize to the scientific community, as it has always been assumed that only proteins could be enzymes. Researchers in the Scott laboratory are trying to understand how ribozymes work, using X-ray crystallography and other biochemical and biophysical techniques. The potential use of ribozymes as therapeutic agents that target RNA viruses (such as HIV) and pathological mRNAs (such as oncogene transcripts) is well-documented. Although the primary motive for our research is to answer questions of a fundamental scientific nature, it is hoped that the results of these studies will provide practical information to the scientific and medical communities to enable more potent and effective ribozyme-based pharmaceuticals to be developed by others. [More]
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 Magnetic Resonance Techniques for the Detection and Management of Human Disease
Tom Schleich, Chemistry and Biochemistry
Tom Schleich's research focuses on the development, validation, and implementation of magnetic resonance based techniques for the detection and management of human acute and chronic disease states. His strategy follows a theme of theory, computer simulation, experimental validation, and application. [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] |
 How Bacterial Pathogens Sense and Respond to Host Environments
Karen Ottemann, Dept. of Microbiology and Environmental Toxicology
Professor Karen Ottemann's laboratory investigates how bacteria translate chemical and physical cues in their host environment into adaptive responses. Mistakes in sensation and subsequent gene expression by bacteria may result in their elimination by the host immune response or peristaltic flow. Elucidation of such processes will hopefully lead to identification of anti-bacterial drug targets. Ottemann is particularly interested in the role of chemoreceptors and chemotaxis associated with the bacterium Helicobacter pylori. This pathogen infects some 3 billion humans and can lead to serious disease, including ulcers and cancer. Ottemann and her colleagues have discovered two of the first chemoreceptors known to aid in the process of bacterial colonization. [More]
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 The Dynamics and Function of Chromatin Structure
Hinrich Boeger, Dept. of MCD Biology
Eukaryotic organisms must package an enormous amount of genetic information in their chromosomes. DNA and proteins form a complex called chromatin, which enables this information to be compacted into a very small space within the nucleus. However, these chromatin structures must also be periodically unfolded in order to make genes accessible to regulatory factors and the molecular machinery that transcribes their information to make functional proteins for the cell. Hinrich Boeger's lab studies the unfolding of chromatin structures in the context of gene regulatory events. [More]
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 Membrane Function and Calcium Regulation
Barry Bowman, Dept. of MCD Biology
One third of the genes in all organisms encode membrane proteins, most of which transport molecules from one compartment to another. We use Neurospora crassa as our model organism. The complete genome has been sequenced for this filamentous fungus. It has 10,000 genes, twice the number in yeast, and a complete collection of knockout mutants is being generated. [More]
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 Organelle Transport and Neurodegeneration
Bill Saxton, Dept. MCD Biology
The Saxton lab studies mechanisms that drive intracellular transport and cytoplasmic organization, using Drosophila as a model organism. To generate and maintain proper cytoplasmic order and thus their complex functions, cells use microtubules and force-generating motor proteins to transport RNAs, proteins, mitochondria and other organelles to appropriate locations. Neurons are especially dependent on such microtubule-based cytoplasmic transport, because their signaling functions rely on extraordinarily long cytoplasmic extensions (axons and dendrites) that require import of many components from their cell bodies. ..... [More]
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 Regulation of Pre-mRNA Splicing and Post-Transcriptional Regulation by Micro RNAs
Alan Zahler, MCD Biology
The human genome carries the blueprint for the creation of proteins, the molecular machines that carry out most of the work in the body. However, the diversity of the pool of available proteins is greatly enhanced by alterative splicing of our genes. The Zahler laboratory examines the nematode Caenorhabditis elegans in order to understand the regulatory mechanisms of this alternative splicing. [More]
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