Biomedical Engineering and Bioengineering Commons^™

Extent And Effects Of Selection To Reduce Synthetic Cost Of Highly Expressed Proteins, Esley Marvin Heizer Jr

Browse all Theses and Dissertations

Organisms that preferentially utilize less biosynthetically expensive amino acids in highly expressed genes exhibit metabolic efficiency. Exploration of this phenomenon has been limited to six prokaryotes.

I present a large scale analysis of metabolic efficiency in prokaryotic organisms and analysis of two eukaryotes (Saccharomyces cerevisiae and humans). Examination of 73 bacteria reveals the presence of metabolic efficiency in 66 organisms. The average correlation between amino acid biosynthetic cost and CAI scores in these organisms is -0.21. The seven organisms that did not exhibit metabolic efficiency are all Lactobacilli and highly auxotrophic. Saccharomyces cerevisiae exhibits significant trends between average amino acid …

Population Fit Threshold: Fully Automated Signal Map Generation For Baseline Correction In Nmr-Based Metabolomics, Daniel C. Homer

Browse all Theses and Dissertations

Baseline correction of NMR-based metabolomic spectra is a key step in data processing to elucidate biomarkers of diseased and toxic states. Automated baseline correction methods often use human-selected parameters. Presented is a method for automated baseline correction using parameters selected from and without manipulation of the spectrum. The focus is on generating an accurate signal map based on the differentiating characteristics of baseline noise and signal. The presented method of signal map generation and baseline correction was developed and tested on 13C and 1H NMR spectra. The spectra were as simple as chemical standards containing less than 25 signal peaks …

Induction Of P53 Dependent Cellular Senescence Through Hdmx Inhibition Or Ypel3 Expression, Kelly Lynn Robbins Miller

Browse all Theses and Dissertations

Mutations in p53 that compromise its function have been reported in approximately half of all human cancers (Vousden et al., 2002). The other half of human tumors that retain wild-type p53 have a dysfunctional p53 pathway through other mechanisms (Wade et al., 2009). Activation of p53 leads to cell cycle arrest, DNA repair, apoptosis and senescence, however, the pathway leading to cellular senescence is the focus of this study. Cellular senescence is a process leading to irreversible arrest of cell division. Under normal physiologic conditions, the activity of p53 is kept in check by its negative regulators, Mdm2 and MdmX. …

Cytochrome C Oxidase From Rhodobacter Sphaeroides: Oligomeric Structure In The Phospholipid Bilayer And The Structural And Functional Effects Of A C-Terminal Truncation In Subunit Iii, Teresa L. Cvetkov

Browse all Theses and Dissertations

Cytochrome c oxidase (COX) of the mitochondrial electron transport chain catalyzes the reduction of oxygen to water while concomitantly translocating protons across the inner mitochondrial membrane. This two part dissertation is a structural and functional investigation of COX using the bacterial model system from Rhodobacter sphaeroides (R.sph.).

First, the oligomeric structure of R.sph. COX within the lipid bilayer was investigated using discontinuous sucrose gradient ultracentrifugation. Utilizing this technique, liposomes containing R.sph. COX (pCOV) were separated from liposomes lacking enzyme (COV). The net buffering capacity and degree of light scattering per COX molecule were reduced in pCOVs, making them well suited …

Finding Cadaveric Human Head Masses And Center Of Gravity: A Comparison Of Direct Measurement To 3d Ing, Grant Corwin Roush

Browse all Theses and Dissertations

Mass properties of the human head are critical elements in developing neck injury threshold criteria in acceleration and impact environments. In order to accurately simulate the dynamics of the head in impact and acceleration environments, valid mass properties data for the human head must exist.

The purpose of this study was two-fold: First, to directly measure and generate a useful data set of human head mass properties and anthropometry, and second, compare the results from the direct measurement to measurements obtained using computed tomographic (CT) analyses of the human head. Four cadaveric human heads, all male, were measured.

For the …

Computer-Based Skeletal Age Assessment Using Hand/Wrist Radiographs In Children 8-18 Years Old, Zhihong Ni

Browse all Theses and Dissertations

Children's skeletons mature at different rates, and they can be affected by a variety of factors including disease, hormone imbalance or genetics. The assessment of skeletal maturity is a frequently performed procedure that allows the detection of hormonal, growth or genetic disorders. Several methods have been developed to estimate skeletal maturity. Most methods evaluate hand/wrist radiographs using indicators such as the ratios of various bone widths, the onset of the ossification of epiphysis and epiphyseal-diaphyseal fusion. Among those methods, the FELS method differs from others in the application of different grades to each indicator and the provision of a confidence …

Charaterization Of Chlorpyrifos Toxicity On The Pancreatic Beta Cell Line Rinm5f, Zhongyu Yan

Browse all Theses and Dissertations

Chlorpyrifos (CPF) is a well-known organophosphate (OP) insecticide that inhibits acetylcholinesterase (AChE). Organophosphates have been shown to induce hyperglycemia in both humans and animals that cannot be explained by AChE inhibition alone. Pancreatic β-cells are responsible for secreting insulin and playing a fundamental role in glucose homeostasis. The aim of this research was to investigate CPF toxicity on the insulin secreting β-cell line RINm5f (RIN). In the first part of this dissertation, we determined that cytotoxic concentrations of CPF between 50 µM and 200 µM induced a dose-dependent increase in RIN cell apoptotic and necrotic death (p<0.05). Lower doses, i.e., 5-25 µM did not induce apoptosis or necrosis. In further mechanistic studies, inhibitors of c-Jun N-terminal kinase (JNK) and P38 pathways, i.e., SP600125 and SB202190, successfully attenuated CPF-induced apoptosis (p<0.05), suggesting cell death is mediated by JNK and/or p38. In addition, N-Acetyl-L-cysteine (NAC), an antioxidant, inhibited apoptosis suggesting that oxidative stress is also involved in RIN cell death. In the second part of this dissertation, low dose CPF's effects on insulin synthesis and secretion was studied. Our results showed that RIN cells treated with CPF for 4 hr exhibited a dose-dependent decrease in insulin secretion in response to stimulation by 50 mM potassium (p<0.05). Insulin secretion stimulated by 25 mM glucose also showed significant decreases upon incubation with various doses of CPF (p<0.05). Insulin synthesis involves proteolytic cleavage of proinsulin at two specific sites. The enzymes responsible for promoting proinsulin cleavage, i.e, prohormone convertase (PC) 1/3 and 2 (PC2), contain a serine hydrolase catalytic triad, His-Asp-Ser, similar to AChE. CPF modification of PC enzymes similar to AChE, could potentially interrupt the conversion of proinsulin to insulin and disrupt insulin secretion. PC2 enzyme activity was significantly inhibited by CPF at concentrations as low as 10 µM (p<0.01). RIN cells, for the first time, were found to secrete proinsulin was through a constitutive instead of a regulated pathway. In summary, our results show that CPF not only exerts a direct cytotoxic effect at concentrations above 50 µM, but also significantly impairs insulin secretion at lower doses. Low dose CPF could potentially affect endocrine function in vivo by inhibiting the proinsulin processing enzyme PC2.

Radio Frequency Controlled Stimulation Of Intracellular Gold Or Silver Nanoparticle Conjugates For Use As Potential Sensors Or Modulators Of Biological Function, Richard Craig Murdock

Browse all Theses and Dissertations

The objective of this investigation was to further explore the ability of a radio frequency (RF) signal to interact with metal nanoparticles (NPs) for the purposes of remote stimulation or control of cellular processes. Gold and silver NPs have shown the ability to be heated by electromagnetic frequencies, especially for the purpose of deactivating abnormal cells. However, the heating of the NPs in these previous studies was constant and uncontrolled. For this study, our hypothesis was by investigating the RF heating characteristics of NPs and its impact on surface functionalizations, a remotely stimulated control mechanism can be developed at the …

Characterization And Improvement Of A Cone-Beam Ct Scanner For Quantitative Imaging, Jimish Dilip Joshi

Browse all Theses and Dissertations

Computed tomography (CT) has various applications in different fields. In our case, the cone-beam CT scanner is used in the industrial field for qualitative and quantitative assessment of Procter and Gamble products. The Flash CT scanner, on which we do our research, has a microfocus x-ray tube, a detector size of 30 cm x 40 cm and a rotating stage for the object to be imaged. The x-ray tube can be operated up to 225 kV. Non-linearities in the response of the detector, scatter and beam hardening may cause false interpretations of the image values. To allow appropriate assessment of …

Cellular Effects Of Replicating A Polypurine-Polypyrimidine Sequence And The Interactions Of Due-B With Replication Proteins, Shere Lynne Myers

Browse all Theses and Dissertations

This work investigates two questions regarding DNA replication. The first aim examines the interactions of DUE-B with replication proteins and the second explores the cellular effects of replicating a polypurine polypyrimidine sequence in human cells.

DUE-B siRNA decreases the chromatin binding of essential replication proteins Cdc45, PCNA and RPA. DUE-B also co-immunoprecipitates with Cdc45 and TopBP1. In vitro kinase assays suggest that the checkpoint protein ATR may phosphorylate DUE-B. These experiments lend further evidence that DUE-B plays an important role in the initiation of eukaryotic DNA replication.

To investigate the effects of replicating a polypurine-polypyrimidine sequence prone to secondary structure …

Multiwall Carbon Nanotubes Alter The Thermal Profile And Antibiotic Elution Of Orthopaedic Bone Cement, Alison Carroll Tickle

University of Kentucky Master's Theses

Multiwall carbon nanotubes (MWNTs) have extraordinary mechanical and thermal transport properties. They significantly improve the static and dynamic mechanical properties of acrylic orthopaedic bone cement when added to the dry cement polymer powder. Understanding the role MWNTs play on bone cement polymerization temperatures will lead to improved mechanical integrity of the cement-bone interface in joint arthroplasties. It was determined through thermal testing that MWNTs increased the polymerization time of the methylmethacrylate by 45-460% and decreased the peak exothermic temperature of bone cement with and without antibiotics. The flow of heat produced during polymerizing cement was reduced 25-85% with the addition …

Effect Of Magnetron Frequency On Heating Pattern In Domestic Oven, Sohan Birla, Krishnamoorthy Pitchai, Jeyamkondan Subbiah, David D. Jones

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

In this study a computer model was developed to simulate microwave heating of a model food with a range of magnetron frequencies. The range was decided upon performing the frequency spectrum analysis of microwave leakage from the microwave oven. Simulation results showed that the magnetron input as sinusoidal frequency from 2.44 GHz to 2.48 GHz generates different heating profiles. The simulated heating profiles were compared with experimental heating profiles obtained by using an IR camera. None of simulations with individual frequency exactly matches with experimental temperature profile. The closet match between simulated and observed temperature profiles was found with 2.46 …

Heating Performance Assessment Of Domestic Microwave Ovens, Krishnamoorthy Pitchai, Sohan Birla, Jeyamkondan Subbiah, David D. Jones

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Due to inherent nature of standing wave patterns of microwaves inside a cavity and dielectric properties of different components in a food, microwave heating leaves non-uniform distribution of energy inside the food volumetrically. Achieving heating uniformity plays critical role in improving the safety of microwave heated products. In this paper, we present a method for assessing heating uniformity within domestic microwave ovens. A custom designed container
was used to assess heating uniformity of a range of microwave ovens using IR camera. The study suggested that the best place to place food in a microwave oven is not at center but …

Testing Fuel Efficiency Of A Tractor With A Continuously Variable Transmission, Bart A. Coffman, Michael F. Kocher, Viacheslav I. Adamchuk, Roger M. Hoy, Erin E. Blankenship

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A John Deere 8530 IVT tractor (Waterloo, Iowa) with a continuously variable transmission (CVT) that could be operated in automatic (CVT) or manual (fixed gear ratio) mode was tested for fuel consumption at a setpoint travel speed of 9 km·h^‐1 with 17 different drawbar loads. Linear regression analysis results showed that with the throttle set to maximum in both transmission modes, operating the tractor with the transmission in the automatic mode was more fuel efficient than operating with the transmission in the manual mode when the drawbar power was approximately 78%, or less, of maximum power. When load transition …

Testing Of Rtk-Level Satellite-Based Tractor Auto-Guidance Using A Visual Sensor System, Dwight Easterly, Viacheslav I. Adamchuk, Roger M. Hoy, Michael F. Kocher

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The use of satellite-based positioning has advanced considerably in the world of agriculture, providing a range of technical solutions that include the automated steering of tractors and self-propelled machinery. With the development of auto-guidance systems comes the need to evaluate their performance. Given that current precision and accuracy claims are relatively small in magnitude, it is imperative there be a testing system capable of detecting errors with ten times greater accuracy-- possibly as little as a few millimeters. A visual sensor was adopted to achieve this level of measurement resolution. The sensor was used to determine the cross-track error estimates …

Using A Vision Sensor System For Performance Testing Of Satellite-Based Tractor Auto-Guidance, Dwight Easterly, Viacheslav I. Adamchuk, Michael F. Kocher, Roger M. Hoy

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A vision sensing system for the measurement of auto-guidance pass-to-pass and long-term errors was implemented to test the steering performance of tractors equipped with auto-guidance systems. The developed test system consisted of an optical machine vision sensor rigidly mounted on the rear of the tested tractor. The center of the drawbar hitch pin point was used as the reference from which to measure the deviation of the tractor’s actual travel path from its desired path. The system was built and calibrated to a measurement accuracy of better than 2 mm. To evaluate the sensor, two auto-guidance systems equipped with RTK-level …

Modeling Changes In Biomass Composition During Microwave-Based Alkali Pretreatment Of Switchgrass, Deepak R. Keshwani, Jay J. Cheng

Department of Agricultural and Biological Systems Engineering: Faculty Publications

This study used two different approaches to model changes in biomass composition during microwave-based pretreatment of switchgrass: kinetic modeling using a time-dependent rate coefficient, and a Mamdani-type fuzzy inference system. In both modeling approaches, the dielectric loss tangent of the alkali reagent and pretreatment time were used as predictors for changes in amounts of lignin, cellulose, and xylan during the pretreatment. Training and testing data sets for development and validation of the models were obtained from pretreatment experiments conducted using 1–3% w/v NaOH (sodium hydroxide) and pretreatment times ranging from 5 to 20 minutes. The kinetic modeling approach for lignin …

Ultrasound-Assisted Osmotic Dehydration Of Strawberries: Effect Of Pretreatment Time And Ultrasonic Frequency, Juan Garcia-Noguera, Francisca I. P. Oliveira, Maria Izabel Gallão, Curtis L. Weller, Sueli Rodrigues, Fabiano A. N. Fernandes

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Pretreatment of fruits prior to drying has shown success in reducing drying time and costs. In this work, ultrasound-assisted osmotic dehydration has been implemented as a method to increase water diffusivity and reduce drying time in strawberries. Strawberry halves were immersed in distilled water and in two different concentrations of sucrose solutions while pretreatment time and ultrasonic frequency levels were varied to determine their effect on drying time, water loss, and soluble solids gain. A microscopic analysis was carried out to evaluate the formation of microchannels and other changes to the fruit tissue structure. Greater sucrose concentration used in ultrasound- …

Retrofit Of Distillation Columns In Biodiesel Production Plants, Nghi Nguyen, Yaşar Demirel

Yaşar Demirel Publications

Column grand composite curves and the exergy loss profiles produced by the Column-Targeting Tool of the Aspen Plus simulator are used to assess the performance of the existing distillation columns, and reduce the costs of operation by appropriate retrofits in a biodiesel production plant. Effectiveness of the retrofits is assessed by means of thermodynamics and economic improvements. We have considered a biodiesel plant utilizing three distillation columns to purify biodiesel (fatty acid methyl ester) and byproduct glycerol as well as reduce the waste. The assessments of the base case simulation have indicated the need for modifications for the distillation columns. …

Nonequilibrium Thermodynamics Modeling Of Coupled Biochemical Cycles In Living Cells, Yaşar Demirel

Yaşar Demirel Publications

Living cells represent open, nonequilibrium, self organizing, and dissipative systems maintained with the continuous supply of outside and inside material, energy, and information flows. The energy in the form of adenosine triphosphate is utilized in biochemical cycles, transport processes, protein synthesis, reproduction, and performing other biological work. The processes in molecular and cellular biological systems are stochastic in nature with varying spatial and time scales, and bounded with conservation laws, kinetic laws, and thermodynamic constraints, which should be taken into account by any approach for modeling biological systems. In component biology, this review focuses on the modeling of enzyme kinetics …