•

•

•

•

•

•

•

Dietlind Gerloff leads a bioinformatics research group that examines the structural/evolutionary principles of interactions between proteins. Her research team combines such principles with computer science to make sense of the recent, vast accumulation of functional genomics data. The group has produced several protein structure models for biomedically important target proteins, including the malaria transmission-blocking vaccine candidate, Pfs230. They have also developed visualization tools for yeast and malaria functional genomic data. [More]

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]

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]

The Camps laboratory uses molecular genetic and computational approaches to study the biological consequences of random changes in genetic information (mutations) that occur spontaneously or as a result of environmental insults. Camps' group couples the generation of random mutant libraries with specific selections or screens to study the functional impact of point mutations and to establish how genes evolve to create new biological activities under selective pressure. This work is relevant for the identification of risk factors of disease, understanding the origins of drug resistance, and engineering enzymatic activities. The Camps laboratory also use induction of random genetic alterations (mutagenesis) as an indicator of DNA damage for high-throughput screening of chemical libraries to identify DNA damaging agents. Through this approach, the Camps aims at exploiting the particular susceptibility of rapidly replicating cells to DNA damage for therapeutic purposes in and effort to find lead compounds that complement or enhance existing anti-tumor therapies. [More]

Karen Ottemann's laboratory investigates how bacteria translate chemical and physical cues in their environment into adaptive responses. Mistakes in sensation and subsequent gene expression by bacteria may result in their elimination by the 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 that chemotaxis aids multiple aspects of infection, and also can promote a host inflammatory response. [More]

Fitnat Yildiz's laboratory investigates signaling and regulatory networks of Vibrio cholerae, the causative agent of the Asiatic cholera. She and her colleagues are particularly interested in those mechanisms that allow the pathogen to adapt to changes in its habitat. The bacteria's ability to survive in different growth modes in aquatic environments is closely linked to seasonal epidemics of cholera. Yildiz's laboratory is attempting to identify and characterize genes and processes associated with phase variations of the pathogen. Their results will be useful for prediction and control of epidemics of this devastating disease. [More]

Cells show extraordinary diversity in size and shape.  The mechanisms by which cells control their growth and size are poorly understood and represent a fundamental unsolved problem in cell biology.  The goal of the Kellogg laboratory's work is to elucidate these mechanisms. Their approach is to use biochemistry, genetics, and mathematical modeling to understand signaling networks that are required for control of cell size and cell growth. [More]

The nuclear pore complex (NPC) is a large protein structure embedded in the double-membrane of a cell's nucleus. This porin structure regulates all transport between the nucleoplasm and the cytoplasm of the cell. Research in the Rexach lab focuses on fundamental aspects of nucleocytoplasmic transport and on the architecture of the nuclear pore complex. [More]