Research Interests
Our research interests include broadly the fields of molecular biology, genomics, functional genomics and biotechnology of halophilic Archaea (haloarchaea). Haloarchaea are excellent models for fundamental processes, such as DNA replication, transcription and gene regulation, and translation and for mechanisms of survival in extreme environments. They are superb experimental organisms, being both easy to culture and genetically tractable. Over the last 20 years, our research interests developed along three lines: (1) Analysis of high-frequency gas vesicle mutants, quite surprisingly, led to the identification of a large gvp gene cluster with over a dozen genes required for biogenesis of the buoyant organelles. Genetic and immunological analysis implicated nearly all the gvp genes in wild-type gas vesicle formation. (2) Analysis of the large replicon coding for gas vesicles, pNRC100, propelled us into mapping and sequencing the entire Halobacterium sp. NRC-1 genome. High-throughput sequencing and whole-genome annotation was done with collaborators at 12 institutions. We hosted the genome jamboree in Amherst in January 2000 and published the complete genome sequence in October 2000 in PNAS. (3) A combination of research on global gene regulation and bioinformatic analysis of the genome led to post-genomic analysis of the physiological capability of the organism, including aerobic and anaerobic respiration, purple membrane synthesis, UV and ionizing radiation resistance, etc.

Recent efforts have been directed at advancing Halobacterium sp. NRC-1 into the forefront of biology as a model system and developing its biotechnological potential. Our accomplishments include the following: (1) We tested our genetic knockout system for analysis of gene function and gene regulation in multiple studies. One study focused on arsenic resistance genes, which led to the discovery of a novel methylase gene involved in detoxification. (2) We mapped functional replication origins for the large chromosome and extrachromosomal pNRC replicons. A complex relationship between members of the large orc-cdc6 family and rep genes and cis-acting genomic regions were revealed. (3) We developed a custom in situ whole genome oligonucleotide microarray for transcriptome analysis. The microarray was tested after exposure to a variety of environmental perturbations. This platform provided excellent design flexibility and requires minimum labor. (4) We generated a 2-D map of the proteome of our model. (5) We developed bioinformatics tools and databases for genome annotation, comparative genomics, and global gene regulation studies (see our HaloGenome website).

In addition to our major research interests, an important professional goal is to contribute to science education and communication. To advance these goals, we have edited a laboratory manual on Halophiles, published by Cold Spring Harbor Laboratory Press and developed a set of set of interactive computer modules for teaching concepts in molecular genetics, called MOLGENT. We have also initiated a new set of laboratory kits (New Model Microbe) for teaching fundamental biological concepts using halophiles to high school and college students, marketed through Carolina Biological Supply Company. These kits are being used at many institutions (for some examples, see our Outreach projects). Finally, we have launched a new open access, peer-reviewed, online journal named Saline Systems, published by BioMed Central. Papers published in Saline Systems are full-text archived in PubMed Central. The goal of the journal is to foster integration, cooperation, and communication among a diversity of scientists studying the biology of coastal and inland saline environments and halophilic organisms.