Functional Genomics Seed Grant
Abstracts from Awarded Programs
2006 - 07
Bioinformatic Profiling of Responses to Utah Urban Air – A Multi-Disciplinary Study
Name |
Department |
|---|---|
| PI – Roger Columbe, PhD | ADVS |
| Co-PI – Randy Martin, PhD | Engineering |
| Co-PI – Philip Silva, PhD | Chemistry & Biochemistry |
It is no longer news that the air in many of Utah’s urban centers is frequently the dirtiest in the nation. Stagnant air during frequent winter atmospheric inversions concentrate emissions from transportation, industry, agriculture and other sources resulting in increases in fine particulate air pollution called PM2.5 (particulate matter < 2.5 µm mean diameter). During several episodes in January-February 2004, the air in Logan and Cache Valley was some of the worst ever recorded in the United States. The general consensus is that PM2.5 is unhealthy, but there is less agreement over the actual health risk posed by breathing these microscopic particles. Epidemiologic studies suggest an association between atmospheric PM2.5 and asthma, chronic obstructive pulmonary disease, emphysema, lung cancer, and sudden death. These particles are chemically complex, and their precise organic and inorganic composition is unique to each location. Uncertainty over the actual risk posed to human health is a major obstacle to instituting steps to reduce this pollutant from urban air. Modern human health risk assessment involves identification of molecular markers of disease as an alternative to traditional toxicology studies involving hundreds of laboratory animals. We propose to evaluate the genomic and proteomic responses in human lung cells exposed to PM2.5 collected from Cache Valley. An analysis of the chemical composition of fine particles will be correlated with gene-level responses. Profiling global effects of toxic chemicals on gene expression has been recognized as a powerful tool in determining the risk posed to human health.
Investigating Genes Involved in Embryonic Skin Development by Characterizing the AP-2γ Mutant Skin Phenotype
Name |
Department |
|---|---|
| PI – Quinton Winger, PhD | ADVS |
| Co-PI – Brian Gowen, PhD | ADVS |
| Co-PI – Ramona Skirpstunas, PhD | Veterinary Diagnostic Laboratory |
The formation of skin, during the development of an embryo, is dependent on the correct orchestration of gene expression timing necessary to guide differentiation. We have determined that AP-2γ is one such example of a gene necessary for normal skin formation. Mice mutant for AP-2γ are not capable of producing functional skin and mutants die before birth or are born dead. AP-2γ is a transcription factor that binds to a specific DNA consensus sequence in other genes and stimulates their gene expression. During embryonic development of the skin AP-2γ is expressed in the basal cell layer, a layer known to contain the proliferating keratinocytes and skin stem cells. It is our hypothesis that AP-2γ acts on these cells to stimulate expression of skin differentiation factors that guide the cells through differentiation. This proposal will compare the skin of the mutant mice to control mice to identify genes that are reduced in expression due to the mutation. These genes will be studied to determine if their reduced expression is the result of the AP-2γ mutation. Understanding the molecular pathways regulated by AP-2γ during skin differentiation will provide key information regarding the signals involved in triggering skin differentiation. This knowledge will then be applied to improving medical methods including the regeneration of skin from skin stem cells and the prenatal genetic diagnosis of skin disease.
2005 – 06
Development of Hyaluronic Acid Gels as Resorbable Implant Materials Having Intrinsic Antibacterial Properties--Direct Applications in Middle Ear Ventilation Tubes
Name |
Department |
|---|---|
| PI - David Britt, PhD | Biological & Irrigation Engineering |
| Co-PI – Thomas Hauser, PhD | Mechanical & Aerospace Engineering |
| Co-PI – Albert Park, PhD | University of Utah, Otolaryngology |
The long-term goal of this research seeks to develop the ideal middle ear ventilation tube. The ideal ventilation tube would be: (1) resorbable, providing a specific, predefined duration of middle ear ventilation; (2) biocompatible, enhancing tympanic membrane healing following resorption; (3) anti-microbial, resisting bacterial attachment through both passive and active mechanisms, thus avoiding becoming a source of chronic infection. To combine these desired features in a single device, we propose to fabricate and characterize ventilation tubes (VT) from hyaluronic acid (HA) hydrogels containing antimicrobial silver oxide. Our motivation of developing HA-VTs stems from prior studies demonstrating the biocompatibility and woundhealing character of resorbable HA gels in the middle ear [1-3] as well as other anatomical locations [4-6]. Preliminary studies of these materials as candidates for VTs by Dr. Albert Park (Co-PI) have demonstrated biodegradable properties that obviate the need for surgical removal, a predictable duration of ventilation, and excellent biocompatibility characteristics. The suitability of HA as a resorbable VT is further supported by studies demonstrating reduced bacterial interaction with HA gels, attributed to electrostatic repulsion between the negatively charged bacterial outer membrane and the highly sulfonated HA [7]. For this one-year research proposal, we will narrow our focus to microbe interactions with a commercial HA gel (Carbylan™). Our specific aims are: (1) to apply advanced scanning probe and confocal microscopy techniques to characterize the intrinsic anti-microbial characteristics of HA gels, and (2) to investigate loading the porous gel network with antimicrobial silver oxide salts as a further prophylactic measure. Pseudomonas aeruginosa, which is frequently cultured from middle ear effluent of patients with otitis media, will be used for these studies. Paralleling these two aims, we will develop a mass transport model to describe the interplay among HA gel dissolution, silver oxide release, and bacteria viability.
Nanoparticle targeting to enteroendocrine cells: An approach to reduce dietary-induced obesity
Name |
Department |
|---|---|
| PI: Tim Gilbertson, PhD | College of Science |
| CPI: Kytai Nguyen, PhD | Univ. of Texas-Arlington |
| CPI: Anhong Zhou, PhD | College of Engineering |
This interdisciplinary proposal seeks to bring together three different disciplines, biology, biomedical engineering, and biosensing to develop the technology to counteract a growing epidemic in the Western world, obesity. Specifically, Drs. Timothy Gilbertson (Biology), Kytai Nguyen (BIE), and Anhong Zhou (BIE) have been working together to develop the use of nanoparticles to deliver pharmaceuticals and genes to specific cell types that play a central role in the control of food intake, the enteroendocrine cell (EEC1). EECs respond to nutrient intake with the release of cholecystokinin (CCK), a peptide hormone that plays a central role in satiety. We will test the hypothesis that the use of biodegradable nanoparticles can deliver pharmaceuticals and genes specifically to enteroendocrine cells to enhance cholecystokinin release. Our basic approach will be to use an established cell line of cholecystokinin (CCK)-secreting EEC cells to work out the details of targeting nanoparticles correctly and specifically to EECs. To do this we will manufacture in the Nguyen lab, 100 nm biodegradable PLGA nanoparticles that contain blockers of the DRK channels (or genes encoding CCK) identified in the Gilbertson lab. These nanoparticles will be tagged with antibodies against the specific taste receptors that are expressed in EECs to target them specifically to these cells of interest. Since the strength of the antibody-receptor interaction dramatically affects cellular uptake and particle distribution, the Zhou lab will use atomic force microscopy to measure the antibody-receptor interaction directly to select the optimal antibody for tagging the nanoparticles. Upon their uptake by endocytosis into the EEC cells, the degradation of the PLGA will result in release of the drugs or genes of interest that ultimately cause enhanced CCK release following nutrient stimulation. Successful outcomes will be assessed directly by release of CCK from the EECs in culture by ELISA assay. These initial experiments will set the stage for the expansion of this in vitro approach to an in vivo approach using animal models to determine their efficacy in the control of food intake and, ultimately, as an obesity treatment.
Functional genomics of a novel membrane-associated receptor for the steroid 1,25(OH)2D3 (12,5 D3-MARRS protein)
Name |
Department |
|---|---|
| PI: Ilka Nemere, PhD | College of Agriculture |
| CPI: Quinton Winger, PhD | College of Agriculture |
| CPI: Ken White, PhD | College of Agriculture |
We have recently reported on the mandatory role played by the 1,25D3-MARRS protein in the rapid, hormone-stimulated uptake of the phosphate in intestine. This novel receptor for an active metabolite of vitamin D also shows correlations with age-related changes in both phosphate and calcium absorption. In order to more directly test the role of the 1,25D3-MARRS protein in vivo, we propose to produce a conditional gene knockout in the mouse. Using Cre/loxP technology, this mouse will normally express the protein during development (eliminating the risk of producing an embryonic lethality), but upon tissue specific expression of Cre recombinase the gene will be mutated. This will allow us to analyze the phenotype in young and adult animals in particular with regard to bone morphology, and steroid-stimulated phosphate and calcium uptake. We anticipate that the 1,25D3-MARRS protein will be critical for maintenance of normal phosphate and calcium homeostasis. This experiment will allow us to better understand the physiological role of the 1,25D3-MARRS protein in live animals.