Senior Investigators

Mark Akeson, Chair of Biomolecular Engineering and Professor of Biomolecular engineering.My research focuses 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. We use the detectors to understand the dynamics and structure of DNA duplex ends, including those of retrotransposons and HIV. I also investigate the coupling of processive DNA-modifying enzymes to nanopores, both protein and solid-state. Together with UCSC Professors William Dunbar and David Deamer, we have demonstrated enzymatic control of single DNA in nanopores with sequence specificity and real-time feedback control.

David Deamer, Research Professor of Biomolecular Engineering at the University of California (Santa Cruz) is Director of a newly-established Astrobiology Center, a collaboration of NASA Ames and University of California researchers. He has recently published two new books. First Life: Discovering the Connections between Stars, Cells, and How Life Began (University of California Press, 2011). Deamer also co-edited Origins of Life with Jack Szostak, published by Cold Spring Harbor Press in 2010. Deamer's research focuses on how linear macromolecules traverse nanoscopic channels. Single-stranded nucleic acid molecules can be driven electrophoretically through a nanoscopic channel embedded in a lipid-bilayer membrane. The presence of the polynucleotide in the channel affects the ionic conductance in a manner related to chain length, concentration and base sequence. This observation has considerable potential for characterizing DNA and RNA in microscopic volumes of nucleic acid solutions. Recent reviews by Deamer (2011) and Branton, Deamer et al.(2008) describe the promise and challenges of nanopore sequencing.

Hugh Olsen. My research interests have historically focused on gene expression at the RNA and protein level with genes involved in cancer, in cellular homeostasis , and with the general gene class of G-protein coupled receptors.  Currently, my interests have shifted to more practical applications of gene expression and protein engineering. These include engineering of mesophilic proteins to extreme conditions, as well as, discovery and expression of genes from extremophiles. These studies are aimed to provide new enzymes/proteins for research and industry.

Kate Lieberman. We study the molecular mechanics of individual DNA polymerase complexes at the single molecule level, with sub-milllisecond and single nucleotide precision. We work in close collaboration with Dr. Hongyun Wang, Applied Mathematics and Statistics, UCSC.

David Bernick. We study organisms from extreme environments, the viruses that prey on those organisms, and the unique enymes that they possess. I have recently found novel small RNA from archaeal organisms that live at temperatures over 80°C (the hyperthermophilic archaea), and have been researching viruses that cohabit cells of hyperthermophiles. We are currently investigating salt-loving (halophilic) archaea and their viruses (the haloviruses). Recent studies have been carried out in the San Francisco Bay area, and the pink lakes of southern California. This effort focuses on both the unique DNA-processing enzymes of viruses and the dynamic relationship of host-viral communities.

Research Staff

Robin Abu-Shumays

Graduate Students

Joseph Dahl

Andrew Smith

Miten Jain

Arthur Rand

Logan Mulroney

Undergraduate Researchers

Stanislav Fridland

Jordan Hughey

Maxmilian Genetti