2007 Projects

Research has shown that the regular use of games and puzzles can aid in reducing or even reversing age related cognitive decline. This has triggered the development and marketing of a number of electronic based game systems. Often times, however, the games are not played consistently enough to be effective due to rapid decline in users' interest, the dependence on the user's initiation, and the impersonality of the games. In this project, we propose to make game systems more effective through two features: Personalization and Integration. The games' quality and effectiveness is enhanced by tailoring them to user's interests, life experience, and memories, all of which can be mined in a non-intrusive way from the user's personal computer. Integrating games with the user's daily computer activity takes the burden off of the user and increases the likelihood of the user's participation. In this paper we discuss the technical issues and algorithms used related to the mining of a person's computer to create a useful profile, and the issues and implementation of a ubiquitous system that adds value rather than interferes or competes with the user's other activities.

Superoxide Dismutase (SOD) is an enzymatically significant protein that is abundant in the cytoplasm and mitochondria of most cells. It eliminates potentially toxic superoxide radicals by converting them to water and hydrogen peroxide which can then be eradicated by the cell. The protein, itself, is a dimer consisting of two homologous domains, each containing a Tyrosine (Tyr) residue. Misfolding of SOD creates aggregates that are correlated to Amyotrophic Lateral Sclerosis (Lou Gehrig's disease). The purpose of this study is to elucidate the folding pattern of SOD using parallel biochemical experimentation and computational methods to determine the intermediate steps in its folding and unfolding. In the biochemical experimentation portion, SOD is prepared for Fluorescence Resonance Energy Transfer (FRET) analysis. FRET is used to determine the distances between the Tyr residues on each dimer, illustrating the intermediate folding steps. Simultaneously, a molecular dynamics computational method is being used to model the folding of SOD. Additionally, a deterministic computational model is being developed.

Nanomaterials are being developed for use in an increasingly wide range of applications and have already entered the marketplace in many commonplace products. This has prompted concerns regarding the potential for harmful health effects as a result of exposure to nanomaterials. Nanoparticles, specifically, often display very different properties compared to larger particles of the same material creating the potential that they may impact the body and/or the environment in unforeseen ways. This research was aimed at investigating the effects of gold nanoparticles on mouse embryonic stem cells (mESCs) to elucidate any potential toxicity or teratogenic effects which may prove harmful to a developing human embryo. Gold nanoparticles were selected in particular because of the recent interest in using them for drug delivery purposes. Previous studies with a heterogeneous mixture of gold nanoparticles revealed that they promote ESC growth and inhibit differentiation. In this study, homogeneous gold nanoparticles varying in size from 2 nm to 100 nm were investigated. Preliminary results have suggested that 50 nm and 100 nm particles may promote growth of ESCs. However, 2 nm and 5 nm particles have not shown much of an effect to this point on ESC growth, colony number, and size. Confirmation of these tentative preliminary results is currently being sought in set of follow up experiments.

The project focuses on long range patterns which can be Helitrons or Matrix attachment Regions (Mars). Helitrons are a novel family of transposable sequences that can jump and integrate into different regions of the eukaryotic genome. Despite their high abundance in many eukaryotic genomes, it is not known whether these elements are still active. We described a null mutation caused by a recent insertion of a helitron into the maize Shrunken2 (Sh2) gene encoding for ADP-glucosepyrophosphorylase, which provided evidence that helitrons may be functional. PCR based screening, is being implemented to monitor helitron activity in various maize lines for somatic and germinal reversion events of a maize mutant harboring a helitron. In order to investigate the possible impact of human domestication on Sh2 gene expression, we have cloned and are characterizing Sh2 gene from maize ancestor, Teosinte. In addition, one of the applications of the completion of Human Genome project will be generating small libraries of DNA fragments with common functionalities. This will be beneficial in functional mapping. Matrix attachment region (Mars) is an example of such functional group. The three students participating in this project are integrating bioinformatics, genetic and molecular tools to discover and catalog helitrons and Mars. In the Matrix attachment region part, sequences corresponding to 59 unique eukaryote MARs were retrieved from GeneBank. These were searched for occurrences of consensus patterns using 39 regular expressions reported in literature. After normalizing the result, a statistical correlation of the actual occurrences of the patterns was compared to their expected occurrences to establish the level of association of a given regular expression based pattern to its presence in MARs.. A database containing MARs and Helitrons as well as the related information about the features has been implemented. A web-based information retrieval system will be utilized to display sequences and features stored in the database. This information resource will be available for public access.

Alzheimer's disease is one of the top ten leading causes of death in the United States. A recent study by The Johns Hopkins University estimated that by 2050, one in 85 people worldwide will be living with Alzheimer's disease. According to the study, if intervention could delay the progression of the disease by a modest one year, there would be about 3.7 million fewer patients with the disease who require high level of care such as a nursing home in 2050. Research suggests that the combination of physical and mental exercise reduces the progression of cognitive degeneration. The project focuses on creating an assistive technology system to promote both physical exercise and cognitive stimulation for patients suffering from Alzheimer's disease and other dementias. The system incorporates a portable mini stationary bike and an interactive visual multiple choice question game. Physical exercise is provided by the bike while cognitive stimulation is provided by the game that targets areas such as memory, judgment, problem solving, recollection, and matching, to impede dementia. Research has shown that certain multi-sensory stimulants such as fiber optic lights and selective colors can be used to relax and control agitation of patients with dementia. By incorporating these stimulants into the design, we have created a safe and fun way for patients with dementia to complete physical and mental exercise.