<OL> <LI>Study gene expression in laboratory & natural populations. <BR>1.1. Study how animal pathogens survive & infect. Outcome: Select stress tolerant crop plants & understand molecular mechanisms underlying stress responses. <BR>1.2. Define binding events between sperm & egg to increase success in cloning & pregnancy of animals. Outcome: Genetic events in sperm & egg during binding, activation & determinants that allow pregnancies to progress to term revealed. <LI> Functional genomics to define growth and survival of organisms.<BR> 2.1. Find new molecules used by microbes to bind host intestinal cells. Outcome: Understand microbial methods that cause disease & enhance our ability to manipulate microbial communities to reduce infection. <BR>2.2. Determine microbial ecology of turkey with/out Salmonella. Define genetic events that lead to persistence during storage. Outcome: Understand molecular events leading to pathogen survival during shelf life. Design rational intervention strategies to limit pathogenic bacteria. <BR>2.3. Isolate & characterize a pool of genetically un/defined acid resistant Lb. casei ATCC 334 mutants for transcriptional profiling. Outcome: Understand mechanisms for acid tolerance & resistance in lactic acid bacteria. Promote US competitiveness biomaterials & biochemicals.<BR> 2.4. Provide new detection methods based on cellular interactions & genetic content. Discover tools to provide information about contamination of a sample. Outcome: Molecular tools to capture, concentrate, & identify pathogens from food & animals. Detection tools for animal agriculture, food processors & environmental scientists. <LI> Discovery of bioactive natural products. <BR>3.1. Study anti-cancer & anti-microbial compounds. Find new compounds from extreme environments that produce bioactive compounds. Outcome: Provide new compounds to inhibit pathogenic bacteria. Provide new natural compounds with characteristics for therapeutic use. <BR>3.2. Define the required components of communication that constitute cellular networks during inhibition with natural products. <BR>Outcome: New theories & understanding of how cells communicate during assault with compounds that inhibit their growth. Ability to control gene expression & cellular communication with new uses via natural products. <BR>3.3. Evaluate & facilitate gene expression in agricultural animal species. Outcome: Identify conserved & variable sequences within regulatory regions of functional genes. Better assignment of function to specific genes within animal genome & mapping of genes in one species to those of another animal model. <LI>Workforce training programs in agricultural genomics. <BR>4.1. Instruct scientists about design and completion of microarray experiments and data analysis. Outcome: Arm agricultural scientists with needed analytical tools to utilize gene expression arrays for plants, animals, & microbes. The partnership with key industrial partners is important so others can begin to acquire the needed hardware. <BR>4.2. Results & applications of biotechnology & these projects disseminated. Outcome: Materials developed to speak to scientists & public. Further development & refinement of existing materials.
Non-Technical Summary: The goal of this work is to understand dynamic genome networks, develop robust and predictive technologies for gene expression assessment, and to exploit functional genomics for agriculturally important animals and microbes. Scientists in the Center for Integrated BioSystems at Utah State University will lead the studies in this project. Where appropriate, the efforts will include individuals with specific content expertise that is relevant to the goals. Targeted areas are found in the objectives that follow. The Center for Integrated BioSystems (the Center) is a biotechnology-focused research center that provides workforce training; core service laboratories for advanced technologies in genomics, proteomics, and metabolomics; and research programs in animal and microbial genomics. A primary focus of the Center is to provide a core service laboratory to USU investigators in the life sciences, specifically in agriculture. The agricultural users have needs that are expanding beyond the current capabilities in the Center. Therefore, a significant portion of the effort in this work will be to refine the technology and equipment offerings in the CIB to meet the needs of agricultural biotechnology research and advanced techniques for genome discovery. An important aim of this work is to bring genomic technologies to the forefront of study at the interface between the environment and agriculture. <P> Approach: 1.1. Persistence of Pathogens in the environment. We will use gene expression and metabolomics to identify genes regulating stress responses. 1.2. Molecular Events of Fertilization. Gene expression arrays and proteomic tools will be used to determine the genetic events in both the sperm and egg during binding and subsequent activation. 2.1. Pathogen adherence to host cells. Assays will be done to bind microbes and host intestinal cell lines that use specific cross-linking molecules to form directly tethered partner molecules between the host and the microbe. Subsequent signal transduction and gene expression changes in the host and the microbe will be determined to clearly define new targets to inhibit. 2.2. Ecology of Microbes During the Shelf Life of Ready-To-Eat Foods. This study will use metagenomics and gene expression arrays to determine the genetic events that lead to persistence of this Salmonella during storage. 2.3. Acid Stress in Lactobacillus casei. (conducted by Dr. J. Broadbent) This study will utilize whole genome microarrays derived from the finished genome sequence for Lb. casei ATCC 334 to identify genes whose expression in acid environments is up regulated in acid-tolerant mutants of this bacterium. 2.4. Molecular Diagnostics. The studies will rely on arrays of probes for gene expression and DNA content. Sample-processing strategies will be developed that allow prediction of infectivity using array formats with various biological molecules. 3.1. Anti-bacterial and Anti-cancer compound Discovery. These studies will use gene expression, proteomics, and metabolomics to to characterize the methods of production for these compounds, find new compounds,and possible uses. 3.2. Mechanism of Action for Bioactive Compounds Regulatory Networks. Metabolites will be determined during cell growth stages and combined with data describing the gene expression, proteome content, and conditions. Metabolic products and communication theory will be used to construct interaction networks that define the cellular communication structure for growth, survival, and disease. 3.3. Comparative Animal Gene Expression. Using target sequences, we will sequence similar regions in different breeds to better understand potential genetic variation within regulatory regions. This will provide information critical for continued development of resources for recombinant events and other targeting strategies that will allow genetic modification of the genome and the study of biological outcomes for selected genomic regions within the animal model. 4.1. GMO testing and identification. The Center will instruct scientists about design and completion of microarray experiments and data analysis training. 4.2. Stakeholder Education and Information Dissemination. The CIB will create stakeholder accessible information in print and on the web. Student experiments will be posted on the CIB web site to exemplify the principles in this work, yet have application in agriculture. Computational models and work sheets will be hosted as well.