Our research in the Nanopore Technology group focuses on developing methods for more efficient, detailed transcriptome and genome sequencing. The next-generation sequencing (NGS) instruments that have revolutionized modern genomics cannot read RNA directly, nor can they resolve the long, repetitive sequence gaps and structural variants in the human genome. We are working to bridge these technical gaps with nanopore strand sequencing, a process we co-invented in 1989 that reads an individual DNA or RNA strand as an applied electric field drives the strand through a biological nanopore. The rate at which each strand moves through the nanopore is controlled by a processive enzyme at the pore orifice. Changes in ionic current, each associated with a unique ‘word’ 3-6 bases long, are detected with single-nucleotide precision and algorithms read the changing current to call the strand’s bases and infer their sequence.
Recently, we have worked with Oxford Nanopore Technologies (ONT) in their efforts to develop a commercial nanopore DNA sequencer, drawing on fundamental methods we established at UC Santa Cruz. This device, the MinION, weighs 100 grams and is being tested in 1000 laboratories worldwide to identify bacterial strains in clinics, pinpoint Ebola infections at the point of care in West Africa, and detect splice variants in human samples.
Over the next five years, we will use the MinION along with ONT’s high-throughput PromethION to investigate cellular differentiation, neurological disorders, and cancer. Specifically, we have four goals: 1) to read genomic DNA strand exceeding 300,000 bases, 2) to improve the platform’s sequencing accuracy by resolving the homopolymeric tracts in MinION DNA reads so that it approaches the 99.99% (Phred score 40) required for analyzing human DNA samples, 3) to read mRNA splice variants directly, and 4) to resolve age-related sequence and structural changes by achieving direct, complete reads of human mitochondrial DNA.
I joined UC Santa Cruz in 1996 from a position at the National Institutes of Health in molecular biology, and hold a Ph.D. in soil microbiology from UC Davis, as well as a B.A. in twentieth century European history with a minor in biology from UC San Diego. See my publications, or hear me describe my research.
My work is in the field of molecular ecology and evolution, two closely related disciplines that use genomics to study how populations adapt to their environments. In the Bernardi lab, we ask and answer questions about the speciation of marine fish, an area of inquiry that has changed rapidly as high-throughput sequencing makes genomic testing increasingly practical. Such genomic information makes it easier than ever before to demonstrate where populations of fishes diverged into separate species, or to show that morphologically indistinguishable fish are actually genetically distinct species. We work in four main areas—identifying the genetic bases of adaptation to local environments, surveying the changing populations in the Mediterranean resulting both from climate change and from fish entering the Mediterranean from the Red Sea via the Suez Canal, studying the sustainability of subsistence coral reef fishing in Yap State, Micronesia, and performing long-term monitoring of the Moorea Coral Reef and its ecology. All this work allows us to gain a deeper understanding of the molecular underpinnings of how fish species adapt to their local environments.
I came to UC Santa Cruz in 1994, following positions at the Pasteur Institute in Tunis, Tunesia, and at Stanford’s Hopkins Marine Station in Pacific Grove. I hold an M.S. and Ph.D. in molecular biology working on the genome organization of fishes from the University of Paris, where I also earned my B.A. You can learn more about my research, or find a listing of my publications.