Sequencing and annotating genomes.
Comparative genomic analysis of pathogenic and attenuated strains of Mycoplasma gallisepticum
Steven Geary’s research interests are microbe-host interactions and evolution of microbial virulence, specifically involving bacterial pathogens of the genus Mycoplasma and primarily Mycoplasma gallisepticum; both in its natural poultry host and in the novel host, the American house finch. The lab uses comparative and functional genomics, transcriptomics, and in vivo models to investigate mechanisms of mycoplasmal pathogenesis, vaccine design, and virulence evolution. Website: http://patho.uconn.edu/people/faculty/indeste.html
Evolution of beneficial and pathogenic microbes.
Joerg Graf’s research interests are microbe-microbe and microbe-host interactions, especially involving beneficial microbes and the innate immune system, as well as the evolution of pathogenic and beneficial associations between bacteria and animals. The techniques include genetic approaches to make mutants in bacteria, microscopic techniques to locate bacteria inside host animals, and next-generation sequencing to sequence 16S/18S rRNA genes, sequence genomes, metagenomes and transcriptomes.
Genomics, proteomics and transcriptomics of bacteria (actinomycetes) that infect higher plants and fix atmospheric nitrogen; diversity of fungi associated with surface ripened cheese
Benson's research interests include microbial biogeography, including the molecular and genomic interactions of bacteria with their environment, and the genomic evolution controlling distribution of microbes in several environments. The specific areas of interest include plant-microbe and insect-microbe microbiomes, and the distribution and diversity of microorganisms associated with cheese.
Phylogenomics of Microbial Symbionts
Jonathan Klassen studies microbial community ecology, especially using the fungus-growing ant symbiosis as a model system to understand how microbial interaction networks evolve. He uses genomic sequencing of both cultured isolates and environmental samples to understand the evolutionary history and distribution of these symbionts with high phylogenetic resolution, and focuses particularly on using genomics to identify novel microbial natural product gene clusters to both determine their evolution and for application in drug discovery. He is also interested in developing methods for high-throughput microbial genome analysis, especially to minimize quality issues resulting from draft-quality genome sequencing.
Reconstruction of ancestral proteins to examine the evolution of proteins inherited as a result of horizontal gene transfer
Dr. Noll’s laboratory studies the physiology and molecular genetics of hyperthermophilic bacteria and archaea to shed light on their mechanisms of evolution, cellular structure, and potentials for biofuel generation. Strictly anaerobic, extremely thermophilic bacteria belonging to the group Thermotogales are the primary organisms under study. Our evolutionary studies focus on how the evolution of sugar transporters including their horizontal transfer among bacteria and archaea affects the binding properties of their proteins. Another research focus involves the unique cell envelope found in the Thermotogales, a structure with features perhaps reminiscent of cell barriers found in ancestors of bacteria and archaea. Finally a new effort to engineer thermophiles for use in biofuels generation is underway, an effort that seeks to address some of the major impediments to biomass utilization. Full genome sequences for several members of the Thermotogales have become available due to the efforts of our lab and this information is being used to guide these studies. Genomic and proteomic approaches are being used for these projects.
Sequencing and annotating genomes of dinoflagellates using whole genome shotgun and BAC library sequencing techniques.
Senjie Lin's lab studies molecular ecology, evolution, and functional genomics of marine algae. Current research focuses on genome and transcriptome sequencing and analyses on dinoflagellates and other algae using high-throughput techniques.
Understanding how beneficial symbioses are established and maintained
The Nyholm laboratory explores beneficial host/microbe interactions, ultimately trying to understand the mechanisms by which bacterial symbionts and their animal hosts communicate and how the host’s innate immune system might influence these interactions. We are currently studying how these complex associations are established, regulated and maintained. We use the model association between the Hawaiian bobtail squid, Euprymna scolopes, and the bioluminescent bacterium Vibrio fischeri, to to understand mechanisms of host/symbiont specificity. We are also exploring a bacterial consortium that is found in a reproductive gland of female squid and is hypothesized to provide antimicrobial and/or antifouling compounds in order to protect the developing, externally laid embryos.