Progress 07/01/08 to 06/30/10
Outputs
OUTPUTS: Great Salt Lake Microbes Report: Our initial assessment of the microbial diversity in the Great Salt Lake has proven very fruitful. We have been able to apply some ecological models to look at real-time geographic patterns associated with horizontal gene transfer in the environment. This type of modeling becomes crucial to determine the rate and extent of transfer of genes in a real world setting and has applications in genetically modified crops as well as in antibiotic resistance in human and animal medicine. Since much of the world's arable land is in arid regions with high salt concentrations, we have designed two studies to model the response and adaptation of organisms to salt stress. The first in collaboration with Pacific Northwest National Laboratory studies the proteins expressed under osmotic shock and correlates these proteins with function and ecology within the environment. The second study focuses on adaptation of a bacterium over evolutionary time-scales. We have sequenced a bacterium isolated from the Great Salt Lake that is very closely related to a marine strain found off the shores of Hawai'i. We have found that many of the functional groups that have diverged evolutionarily are those involved in stress response. Results from these experiments were presented at the American Cell Biology Association meetings in December, 2009. Experimental results were also presented at the 2010 annual meetings of the International Embryo Transfer Society. Results were also presented in Beijing China in the Join US-China Animal and Dairy Science meetings and in workshops in Hohhot and Tian China in November 2009. Results from the Great Salt Lake work were presented at the Join Genome Institute workshops in fall 2009 and spring 2010. PARTICIPANTS: Ken White - Utah State University, ADVS, CIB; Chris Davies - Utah State University, ADVS, CIB; Lee Rickords - Utah State University, ADVS, CIB; Kamal Rashid- Utah State University, ADVS, CIB; Jacob Parnell - Utah State University, Biology, CIB; Giovanni Rompato - Utah State University, CIB; Patti Champine - Utah State University, CIB; Roger Kjelgren - Utah State University, PSC, CIB; Yeomao Shen - Xiamen University; Shengchai Lin - Xiamen University; Y. Hu - Northwest Agricultural University (China) TARGET AUDIENCES: Biotechnology - 500; animal genomics - 250; microbial genomics - 275; natural products chemistry - 100; Food processors - 75; production agrictulture - 450 PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Many of the biogeochemical processes in the Great Salt Lake have wider ramifications than the lake itself. Over the past decade, scientists have become aware of extremely high concentrations of methylmercury in the Great Salt Lake; this has environmental and ecological problems as the GSL is a major migratory route for fowl. The conversion of relatively harmless forms of mercury to the deadly methylmercury is currently unknown. We have initiated a study to determine if this conversion is due to sulfate reducing bacteria. Once the process of conversion is known, we anticipate that we will be able to significantly narrow treatment options. Finally, we have discovered an organism in the salt-saturated brine of the Great Salt Lake with some biotechnological implications. One of the key features of this organism is that it can precipitate carbon dioxide as carbonate. Our preliminary findings suggest that precipitation is a biological function and is controlled by genes within the organism. We have sequenced the organism and have applied for resources to investigate the genes involved in this previously unknown biogeochemistry. We have also found that some of the organisms in extremely high salt environments appear to produce bioactive compounds. Although preliminary, we hypothesize that these compounds may be novel and could be developed for use in human medicine. Animal Genomics: We successfully evaluated the differential gene expression of somatic cell nuclear transfer (SCNT) bovine embryos as compared to control embryos. Interestingly there is a large amount of fidelity in the expression patterns between control and SCNT embryos, however there are some interesting differences in developmentally important genes. We will continue to study the effects of aberrant gene expression on developmental failure in SCNT pregnancies.
Publications
- No publications reported this period
- Stevens, J.R., Bell, J.L, Aston, White, K.L. 2010. A Comparison of Probe-Level and Probeset Models for Small-Sample Gene Expression Data. BMC Bioinformatics, , USA 11:281:
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Progress 07/01/08 to 06/30/09
Outputs
OUTPUTS: The goal of this work was to understand the dynamics of food borne disease and animal reproduction based on the genome networks, develop robust and predictive technologies for gene expression assessment, and to exploit functional genomics for agriculturally important animals and microbes at the Center for Integrated BioSystems (Utah State University). Where appropriate, the efforts included individuals with specific content expertise that were relevant to the goals. The overarching goal was to define strategies that lead to improved safety of agricultural products using genomics. Patents: Pate, B. J., K. L. White, and B. C. Weimer. 2007. Bovine Sperm Membrane Proteins for fertilization. U.S. Patent pending. B. Weimer and P. Desai. 2007. Compositions and methods for use syringopeptin 25A and rhamnolipids. U.S. Patent pending. PARTICIPANTS: Bart Weimer - Utah State University, Nutrition & Food Sciences, CIB Ken White - Utah State University, ADVS, CIB Dong Chen - Utah State University, Nutrition & Food Sciences, CIB Bala Ganesan Utah State University, Nutrition & Food Sciences, CIB Kum Park - Utah State University, CIB Patti Champine - Utah State University, CIB Yajun Wu - Utah State University, PSC, CIB Roger Kjelgren - Utah State University, PSC, CIB Yeomao Shen - Xiamen University Shengchai Lin - Xiamen University Y. Hu - Northwest Agricultural University (China) TARGET AUDIENCES: Biotechnology - 500 animal genomics - 250 microbial genomics - 275 natural products chemistry - 100 Food processors - 75 production agrictulture - 450 PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Bioactive compound discovery. Microbes play an important role in the rhizosphere and oceans. In stressful environments unusual microbes are found that produce unexpected compounds. Using classical isolation, phylogenetic analysis, and metagenomics we found the bioactive content of hypersaline environments to search for new antimicrobial compounds to be high. Further work is needed to identify and isolate the compounds. In collaborations with Xiamen University we found a compound with varying cellular activities depending on the concentration. It is non-toxic, stable, and available for production at high concentrations. It has anti-cancer activity and reduces metastasis. The mechanism of action is under study. Additional studies are underway to determine the potential for commercialization. Pathogen adherence to host cells. Salmonella is a common inhabitant of meat, especially poultry, on the grocery store shelf and at the farm. The worldwide survival, sero-diversity, and impact from foodborne disease are increasing. This study is examining the proteins needed to survive temperature treatments during poultry processing that enable survival. Over 300 protein changes occurred that enabled survival and growth in meat. Further work is progressing to define the exact set of proteins that enable survival with the goal of using this protein as an inhibition target to limit the survival and growth of Salmonella in the food chain. Studies are underway to define the impact of cold shock on the infectivity of Salmonella. This program also examined persistence of human and animal pathogens in the environment that is mixed use - agriculture, industrial, recreation, and wild life. Molecular Events of Fertilization. Animal fertility is an important aspect of production agriculture. Over 40 new proteins involved in egg/sperm interactions were defined. New membrane proteins that have specific binding sequences, which are known to be involved in these interactions, have been found. We are using 2D-DIGE, gene expression, and MS/MS are being used to define the proteins. To date, we have identified 5 new proteins in the egg/sperm interaction that are critical to this interaction. These proteins are being characterized to improve reproduction strategies in cattle. Molecular Diagnostics. Diagnosis of disease is very challenging in food and animals. This effort focused on using qPCR and phylogenomics to detect pathogens in food, animals, and the environment. This effort successfully designed qPCR assays for food organisms, pathogens, probiotic bacteria. Additionally we used commercial re-sequencing arrays to detection viruses from environmental samples that are used by agriculture and recreational activities. Gene expression chips and phylogenomic chips were used to determine the microbial diversity of the locations and samples to find many unexpected organisms to be present. However, occurrence of pathogens did not correlate with the amount of diseases. GMO testing, identification, and training. In collaboration with the Dominican Republic we designed a workforce training course that serviced their biotechnology industry and was offered twice.
Publications
- No publications reported this period
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