Core--Environmental Molecular Analysis

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Molecular technologies have become key to a more in-depth understanding of the complex processes and interactions of microbial communities, and are especially important to a mechanistic understanding of bioremediation processes. New tools are constantly being developed to aid this objective but their application and optimization to microbial research under environmentally relevant conditions is not easy. Our overall goal is to use and enhance these technologies for understanding how microbes react to environmental changes in situ rather than simply as laboratory pure cultures. This can best be done by a support core with interacting components. We will develop new tools and discover new genes involved in degradation of polyaromatic compounds. This process will require the support of a variety of enabling technologies, the most central of which are provided and optimized in this support core. The specific aims of this core proposal are to provide needed support in three related areas: (1) microarray development and enhancement, (2) automated bioinformatic analyses of PCR product sequences and biodegradative gene clusters, and (3) high throughput screening and sequencing of environmental clones. The project brings together the strengths of a multidisciplinary team of researchers, each one acting in their own areas of expertise. The Center for Microbial Ecology (CME) and the Department of Civil and Environmental Engineering at Michigan State University has developed a microarray platform that will support our proposed genomic analyses. CME's Microbial Informatics Group manages the Ribosomal Database Project and has developed a bioinformatic platform for sequence analyses and other data analysis tools. The Biotechnology Center for Agriculture and the Environment at Rutgers University has developed a high throughput screening facility with an emphasis on screening cultures and clones. These three components will form an interacting triad supporting the environmental research projects, and will exchange at a general level strategies and concepts with the Biomedical Informatics core and toxicology projects that use genetic and microarray array technologies.