2009 Projects

The long-term goal of this project is to develop ultra-wideband imaging technique for early detection of tissue damage. Tissue damage can be difficult to detect, especially when it begins underneath the surface of the skin. Slight changes in compartment pressure or blood flow below the epidermis have the potential to develop into a serious condition, such as pressure ulcers, peripheral vascular disease, Raynaud's disease, or Buerger's disease. Advancements in imaging technology have assisted in detecting these types of tissue damage; however, there is still a need for a more practical device that can be easily used in a clinical setting. UWB is a very promising technique because it has the capability to detect small adjustments in dielectric properties, which can change with minor alterations in perfusion and internal pressure. SIBHI students are expected to use the software XFDTD to build the model of damaged tissues, simulate the UWB propagation in normal and damaged tissue, and develop image reconstruction algorithms.

Transposable elements, or jumping genes, are the most abundant entity of many eukaryotic genomes, including that of humans, and have played a major role in their evolution and expression. Helitrons are a recently discovered novel superfamily of eukaryotic transposable elements. Despite high divergence in both sequence and length, Helitrons share conserved sequences of fifteen to twenty base pairs at the 5b and importance in several eukaryotic genomes, including those of maize, rice, and the brown bat, an active Helitron has not been reported to date from any organism. They have been proposed to transpose via rolling circle mechanism. They frequently capture gene sequences and multiply them in different regions of the genome. The mechanism and biological relevance of gene capture remains undetermined. Sometimes captured genes are transcribed, giving rise to chimeric transcripts containing coding regions of several different genes. This transcription may form a driving mechanism for the evolution of new genes within a genome.und of about thirty-five base pairs at the 3bTransposable elements, or jumping genes, are the most abundant entity of many eukaryotic genomes, including that of humans, and have played a major role in their evolution and expression. Helitrons are a recently discovered novel superfamily of eukaryotic transposable elements. Despite high divergence in both sequence and length, Helitrons share conserved sequences of fifteen to twenty base pairs at the 5b and importance in several eukaryotic genomes, including those of maize, rice, and the brown bat, an active Helitron has not been reported to date from any organism. They have been proposed to transpose via rolling circle mechanism. They frequently capture gene sequences and multiply them in different regions of the genome. The mechanism and biological relevance of gene capture remains undetermined. Sometimes captured genes are transcribed, giving rise to chimeric transcripts containing coding regions of several different genes. This transcription may form a driving mechanism for the evolution of new genes within a genome.u and importance in several eukaryotic genomes, including those of maize, rice, and the brown bat, an active Helitron has not been reported to date from any organism. They have been proposed to transpose via rolling circle mechanism. They frequently capture gene sequences and multiply them in different regions of the genome. The mechanism and biological relevance of gene capture remains undetermined. Sometimes captured genes are transcribed, giving rise to chimeric transcripts containing coding regions of several different genes. This transcription may form a driving mechanism for the evolution of new genes within a genome.

The objective of this project is to implement computational approaches to discover Helitrons in the maize genome and determine the structure of genes captured by these elements. These methods will provide clues to the mechanism of gene capture. This project will also attempt to identify captured genes that are potentially transcribed, which may shed light on their possible biological functions. In addition, we propose to provide experimental evidence to validate the efficacy of computational searches by Reverse transcription polymerase chain reaction (RT-PCR), a laboratory technique which entails reverse transcribing RNA into complementary DNA (cDNA) and amplifying this cDNA via polymerase chain reaction (PCR).

Currently in the United States there are eight million Americans suffering from mild cognitive impairment (MCI) which impedes upon short term memory. One of the common consequences of short term memory loss is the inability to remember where everyday items are located. Previous research has suggested that the action of searching for misplaced items creates frustration and anxiety in persons with MCI which ultimately precipitates the problem further. The vision of this research group is to reduce frustration and enhance daily living as well as to contribute to the longevity of independent living within the household. To achieve this task, a locating device that tracks lost items for persons with MCI will be developed. Certain items such as glasses, wallets, cell phones, etc. will be tagged with sensors. Once any of these items are lost the person with MCI will be able to locate the item using the locating device. Incorporated with the device will be a laser beam to outline a circle around where the object is located. Another feature on the locating device will be the capability to access day and time as well as music. These two features have been proven to reduce frustration in persons with MCI. Ultimately, the objective of the device is to reduce frustration and stress in persons with MCI as well as in their families and healthcare providers.i

This reserach project is intended to engage the undergraduate investigators in the study of longer poly-Q pepticide misfolding structures implicated in Huntington family of desease that curtail in motor coordination and emotional wellness. The tools adopted for study are chemistry FRET experiments under various ambient conditions this will be aided by amber molecular dynamics simulations of pepticides at hand. Novel applicatations of improved computer reinforcement learning known as Q-learning will be addressed by using both FRET data set and molecular dynamics output in order to discover pepticide structures.

Deformation and strain are important measures for characterizing behaviors of biomaterials, particularly in musculoskeletal tissues and prostheses. An existing approach for strain measurement is strain gauge which provides only localized information. It is also a contact method. Thus, a full-field, no-contacting optical method for 3D-strain/stress measurements is highly expected. As a whole-field, non-contacting technique, digital stereo images correlation (DSIC) has its unique high-resolution in determining 3D deformations and strains. While it has achieved great success for strain measurement in engineering materials, its applications for biomaterials is limited due to relatively soft samples with wet surface. Therefore, the current DSPI systems are difficult to measure strain of fresh biomaterial materials under biological conditions.

The specific goal of the proposed SIBHI project is to make the current DSIC system robust for biomaterials with wet surface. The proposed project will contribute to unravel the role of mechanical deformations and strains in biological systems. In cellular biomechanics, the proposed device can potentially unravel the role of local strain distributions, particularly deformation of the membrane raft. In mechanotransduction of bone, the mechanism underlying load-driven bone formation is not well understood. The proposed DSPI system will be a powerful tool to investigate the role of strains in induction of fluid flow and/or pressure gradient in a nanometric scale.

Obstructive sleep apnea (OSA) is an increasingly prevalent systemic disorder that manifests itself in breathing pauses during deeper stages of sleep. Besides excessive daytime fatigue and sleepiness, chronic OSA induces progressive, profound pathological changes in cardiovascular and neurological function, and is also suspected to play a role in the Metabolic Syndrome that exacerbates the disorder. The lack of a chronically instrumented animal model hampers progress in understanding of this disorder. We propose the development of an instrumentation system that allows exposure of a canine to controlled obstructive apneic episodes. The system uses a set of fully implantable sensors to monitor the animal's vital signs. Data is radiotelemetered to a computer where it is used to determine sleep-wake phases in real-time and is also stored for post-experimental data analysis. Based upon the real-time analysis of sleep state, the system creates an airway obstruction by telemetric control of a shutter valve that is mounted to a chronic tracheotomy tube. The degree and time course of the obstruction can be arbitrarily set by the investigator to mimic obstructive sleep apnea episodes as they occur in humans. This proposed project will initiate collaboration between Beaumont and Oakland University researchers and will allow in-depth investigations of sleep apnea causes and effects.