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US-Egypt Cooperative Research: Development of Microarrays for Evaluating Phylogenetic and Functional Diversity of the Microbial World

0211267<br/>Hashsham<br/><br/>Description:<br/>This award is for support of a joint research project by Dr. Syed Hashsham, Assistant Professor, Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan and Dr. Essam Zaki, Genetic Engineering & Biotechnology Research Institute (GEBRI), Mubarak City of Scientific Research, Alexandria, Egypt. They plan to develop a microbial diversity microarray that will encompass the key elements of microbial biodiversity in both functional and phylogenetic sense. There is a need for such a comprehensive microarray in areas such as diagnostics, air, water, food, animal, and plant safety, soil and root ecology, and waste treatment. Approximately 1,000 oligonucleotide probes will be designed using available sequences in existing phylogenetic and structural gene databases. For selected organisms and functions, probes will also be designed to detect single nucleotide polymorphisms and to differentiate among strains relevant to human health. Additional probes targeting large phylogenetic and functional groups in a nested manner will also be included. This latter set of probes will be helpful in exploring the extant of the uncultured microbial world. Specificity and sensitivity of gene probes, and quantification of molecular data will be the three key aspects of this work. The potential of the array will be evaluated in describing and differentiating biodiversity of water bodies of different level of perturbation such as the Nile River, Lake Michigan and remote springs at Yellowstone National Park. Hypotheses related to stability of microbial communities in response to perturbations will be tested, and links between stability and biodiversity will be evaluated.<br/><br/>Scope:<br/>Studies of the genetic composition and ecology of native bacterial populations have been constrained by their dependence on culture-based methods. Several mixed microbial communities have been analyzed by various molecular methods. These methods are generally non- quantitative, may differentiate only 20-30 populations, may only give a coarse pattern of fingerprint (instead of diversity), and may not give any functional information. The proposed development may lead to the broader application of the microarray technology in the future. It is expected that a transfer of microarray technology to Egypt will be accomplished, leading to potential use in local applications. Dr. Hashsham's work in sites in Egypt will expand the environments for testing of the microbial diversity array. The project will give graduate students of Dr. Hashsham, who are supported from other sources, an opportunity to engage in international research collaboration. This collaborative project will help the career of Dr. Hashsham, who is a recent Ph.D. graduate, and will help enhance Egypt's research in the area of biodiversity.

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