CIB Projects and Collaborations
Our Center focuses on several areas of important research, the newest efforts being metabolomics and bioinformatics. Additionally, our researchers have been involved in exciting advancements such as equine cloning, creation of genomics databases and successful milestones within the following projects.
Alfalfa Stress Acclimation
Alfalfa is the top cash crop in the state of Utah and other arid western states. This plant thrives in diverse habitats that range from irrigation to dry land production. The methods that the plant uses to deal with the water stress is of particular importance. Alfalfa (Medicago sativa) and related species (Medicago truncatula) acclimate to stress by changing gene expression and metabolism. It is critical to delineate the modulation of gene expression in response to drought and salinity stress, in order to genetically engineer crop plants to be more resistant to stress with the potential increase yield. We are determining the specific set of genes whose expression is up- or down-regulated in response to drought and salinity stress using gene expression technologies in collaboration with scientists at the Noble Foundation. This study will enable selection of more stress tolerant crop plants, and provide a better understanding of the molecular mechanisms underlying plant stress acclimation.
Metagenomics of Cropland Soils
Non-nitrogen fixation and crop productivity can often be improved by yearly planting cycles where intermittently, nitrogen-fixing plants like alfalfa are grown. This keeps the soil from being depleted of nitrogen that is necessary for plant growth year after year. We are using metagenomics to characterize the diversity of microbial communities between soils that have growth of alfalfa and fallow fields. This approach provides insight about then organisms that are beneficial to the crop health, but are uncultured. Discoveries from this project will lead to new knowledge about microbe/plant association that will lead improved crop health and strategies to reduce fertilization needs.
Metagenomics Hot Springs and the Great Salt Lake
Metagenomics is being use to study the large number of uncultured populations in the environment that borders agricultural lands in Utah. This approach is providing an insight into the large microbial diversity that impacts the production of crops and animals in regions that are largely affected by drought and salt stress. The industrial sites located around the lake (salt harvesting, oil refineries, etc.) and hot springs that flow into waterways will change the ecology and the water quality for agricultural needs. This project is determining the ecology of the Great Salt Lake and the extensive hot springs in the context of metabolic abilities for unique organisms and metabolism for their impact on agriculture in Utah.
Pathogen Ecology in Ready-to-eat Foods
During the shelf life of ready-to-eat products, such as lunch meats the microbial flora changes. Despite extensive studies using predictive microbiology, very little is known about how the ecology and succession of spoilage and pathogenic organisms. In addition, these approaches have not yielded sufficient information about pathogen growth to control their persistence during the product shelf life. This study is determining the ecology of the turkey with and without Salmonella addition using metagenomics and gene expression studies to determine the genetic events that lead to persistence of this pathogen directly in the food product.
Molecular Diagnostics
Diagnosis of disease causing organisms is playing an ever-increasing role in agriculture and health. Existing technology uses immunological and genetic analysis to determine the organism or toxin identity. There is a need for high through put technologies that can provide specific identity information about the contaminant with little sample processing. The aim of this work is to provide new detection methods that are based on cellular interactions and genetic content that rapidly provides information about the total contaminants. The studies rely on genomic tools to probe the possible genomes present from animal food sources. This project will provide molecular tools to capture, concentrate, and identify pathogens. In addition, sample-processing strategies are developing to allow prediction of infectivity based on the biological molecules required for cellular association.
Proteolipidomics / Lipidomics
Eukaryotic organisms respond to their environments by activating signal transduction pathways that involve proteins and lipids. These pathways require production and relocation of signaling molecules to create a cascade of associations that result a complex web of communication via molecular interactions. Very little is known about the potentially thousands of protein:lipid interactions that occur within cells during normal growth and development. We are designing lipid microarray chips that enable us to detect and identify the contingent of proteins/lipid associations in a cell needed for communication in different environmental conditions. This effort is applicable to agricultural, environmental, and biomedical sciences.
Molecular Events of Fertilization
Cellular communication and interaction are critical parameters for biological regulation. These phenomena are underlying principles in disease, immunological reaction, fertilization, and growth among others. Fertilization is of specific interest in this project. At fertilization, the sperm bind to the egg via receptors that trigger a series of intracellular events that lead to cellular development. A hallmark of these interactions is calcium oscillation, which is pivotal to oocyte activation and development. This project focuses on defining the binding events and molecules used by the sperm and egg in agriculturally important animals. Gene expression and proteomic tools are being used to reveal the genetic events in both the sperm and egg during binding and subsequent activation.
Natural Product
Bioactive compounds are importance for treating cancer and other human maladies. Natural products have had a major impact as templates or direct treatments for cancers and infective diseases. During 1981–2002, about 60% of the small-molecule new chemicals introduced as drugs worldwide are related natural products. Studying natural products will help to find new drugs in the future. CIB set up a Natural Product Group in year 2006. Our approach is to collaborate with others around the world and to isolate compounds from our own unique microbial isolates. We are actively pursuing collaborations in China, India, and the Dominican Republic. Our group has two collaborations in China (one at a university and one with a hospital clinic) to isolate and prove the efficacy of natural Chinese remedies. We have built up anticancer and antimicrobial careening labs with 12 cancer cell lines and 15 microbial. From the Cytotoxic study, gene expression study and protein expression study of three bioactive compounds, two patent applications for bioactive compounds have been filed and two manuscripts have been submitted.
Metabolomics of Alcohol Utilization in Yeast
The first eukaryotic genome sequenced was that of Saccharomyces cerevisiae. Coupled with the fact that it is a genetically and biochemically tractable organism, S. cerevisiae has emerged as a model for many studies of eukaryotic gene expression. In addition, it is widely used commercially for the production of flavors and fragrances. An example of this is the bioconversion of alcohols to organic acids. The genetic details of alcohol metabolism and how it alters the expression of genes in S. cerevisiae is being studied. The metabolomics studies of this biotransformation include gene expression, proteomics, and metabolite analysis. Data will be assembled from these different sources to identify genes and pathways related to activities determining the metabolic mechanisms for optimization of product formation. This information will enable the genetic modification of yeast for maximal bioconversions of agricultural products.