Digital Commons Network^™

Comparison Of Commercial Dna Extraction Kits With That Of Organic Extraction Procedures Using Simulated Forensic Evidence Samples, Denise Nicole Dent

Master's Theses

DNA analysis has become essential to the world of forensics in recent years. The success of such analysis requires effective methods for the extraction of DNA Two straight extraction methods: the organic phenolchloroform extraction method and the ReliaPrep^TM Blood gDNA Miniprep System (Promega Corporation, Madison WI), and two differential extractions: the differential organic phenol-chloroform extraction method and a Differex extraction method (Promega Corp.), were compared and assessed to determine their effectiveness in extracting DNA from blood and semen in simulated forensic samples. Real-time PCR quantitation was used to quantify the concentration of DNA recovered from each extraction. Once the …

Critical Node Analysis For Water Distribution System Using Flow Distribution, Michael Hopkins

Master's Theses

The expansive nature of water distribution system makes them susceptible to threats such as natural disasters and man-made destructions. Vulnerability assessment research efforts have increased since the passing of “Bioterrorism Preparedness and Response Act” in 2002 to harden WDS. This study aimed to develop a method that locates critical nodes without hydraulic analysis of every failure scenario, applicable for any size WDS, incorporates critical infrastructure, and capable of verifying method accuracy. The Flow Distribution method is the application of the gravity model, typically used to predict traffic flows in transportation engineering, to a distribution system. Flow distribution predicts the amount …

Cross-Cultural Contact On Ship Island, Mississippi: An Analysis Of The French Warehouse Site Ceramic Assemblage From An Aboriginal And Engendered Perspective, Barbara Thedy Hester

Master's Theses

This thesis is a study of the Aboriginal ceramics recovered from the French Warehouse site (22HR638 or GUIS 98) located on Ship Island, a barrier island in the Mississippi Sound. The goals of the thesis are to determine both the regional source(s) of the pottery and date(s) of site occupation by identifying temper agents and ceramic types and varieties. It also seeks to determine the nature of site use by analysis of vessel form and function. Two scenarios are explored. If the ceramic vessels are of homogeneous forms, then they are likely products of trade alone. However, if they are …

Efficiency Of Using Commercial Dna Extraction Kits And The Organic Extraction Method In Removal Of Polymerase Chain Reaction Inhibitors, Brandi Jo Payne

Master's Theses

The first step in the determination of a perpetrator of a crime using DNA profiling is obtaining good quality DNA. The substrate on which the body fluid is located may contain substances that can co-extract with DNA and may inhibit subsequent PCR analysis. In this study, the efficiency of the removal of such contaminants were tested using three different methods, namely the PrepFiler DNA extraction kit, DNA IQ DNA extraction system, and the organic DNA extraction protocol. One, two, five, and ten μl of whole blood were deposited on soil, wood chips, and cotton swatches treated with bleach. DNA was …

East Of The Tracks: Grassroots Environmentalism In South Mississippi, Heather Kay Sanchez

Master's Theses

Environmental justice literature challenges the disparity and oppression regarding the quality of life associated with residential environments among communities of color. Recent disasters, such as hurricane Katrina, the Tennessee coal sludge disaster (December 2008), and the BP Oil Spill (2010) have garnered visibility for environmental issues, particularly in the south. Nevertheless, the topic has largely been ignored in Mississippi among academia, many advocacy groups, and at the state level despite the emergence of several community based grassroots environmental groups throughout Mississippi in recent years. From Columbia, to Crystal Springs, to Hattiesburg, a coalition of environmental groups is forming with Hattiesburg …

Mass Spectrometry Based Free Radical Induced Fragmentation Study Of Chemically Modified Cysteine Containing Peptides, Veronika Vitalyevna Dubniakova

Master's Theses

Modification of cysteine containing peptides by the thiol group of cysteine with radical precursors allows a simple and localized generation of radical species in the collision cell of mass spectrometer. The proof of principle and the analysis of the radical derived fragments of a set of different model peptides are described further in the manuscript as well as the importance and potential applications of the method.

Ph-Responsive Polymers For Biosurfaces: An Investigation Of Solution Properties And Surface Modifying Performance, Yuhong Wei

Master's Theses

Gantrez® copolymers are used widely in the personal care industry, but their mechanisms of interaction with dental surfaces are poorly understood. In this study, we determined a number of the solution and polymer properties that control deposition, adsorption and adhesion in Gantrez® polymer aqueous solutions to model dental surfaces. QCM studies specifically showed that polymer adsorption to model hydroxyapatite surfaces occurred only in solutions with polymer concentration above c*. Adsorption and adhesion was greater in solutions of higher pH, where greater charge density along the polymer backbone was expected. For films prepared via spin-coating onto mica surfaces, addition of surfactants …

Multi-Circle Detections For An Automatic Medical Diagnosis System, Dingran Lu

Master's Theses

Real-time multi-circle detection has been a challenging problem in the field of biomedical image processing, due to the variable sizes and non-ideal shapes of cells in microscopic images. In this study, two new multi-circle detection algorithms are developed to facilitate an automatic bladder cancer diagnosis system: one is a modified circular Hough Transform algorithm integrated with edge gradient information; and the other one is a stochastic search approach based on real valued artificial immune systems. Computer simulation results show both algorithms outperform traditional methods such as the Hough Transform and the geometric feature based method, in terms of both precision …

Investigation Of A Commercial Product (Biowish™) For Nitrogen Management, Eva Lee

Master's Theses

Abstract

Investigation of a Commercial Product (BiOWiSH­­^TM) for Nitrogen Management

Eva Lee

BiOWiSH–Aqua, which has the capability of treating nitrogen from wastewater through bioaugmentation, is a commercial product consisting of a blend of microorganisms developed by BiOWiSH Technologies. A study of the treatment of nitrogen compounds (i.e. , , and ) using Biowish–Aqua was conducted using small scale experiments (flask experiments) and large scale experiments (column reactor experiments). In this work, column reactors were created to test Biowish–Aqua’s nitrogen treating capabilities by providing enough depth to simulate the dissolved oxygen gradient that can be observed in a pond. …

American Pika (Ochotona Princeps): Persistence And Activity Patterns In A Changing Climate, Cody P. Massing

Master's Theses

An increasing amount of evidence suggests that as temperatures increase, montane animals are moving upward in elevation (IPCC 2007, Parmesan and Yohe 2003). As suitable habitats rise in elevation and then disappear altogether, these animals could be pushed to extinction. The American pika, Ochotona princeps, is a montane mammal that lives in western North America, usually at elevations above 1500 m (Smith and Weston 1990). Recent evidence suggests that pika population numbers are dropping in response to rising temperatures (Beever et al. 2010). The pika is a small herbivorous lagomorph, a relative of hares and rabbits. Its habitat is …

Autonomous Tracking And Following Of Sharks With An Autonomous Underwater Vehicle, Esfandiar Manii

Master's Theses

This thesis presents the integration of an acoustic tracking system within an autonomous underwater AUV (AUV) to enable real-time tracking of sharks tagged with artificial acoustic sources. The tracking system consists of two hydrophones and a receiver unit that outputs a measurement of the relative angle to the tagged shark. Since only two hydrophones are used, the sign of the relative angle measurement is unknown. To overcome this ambiguity, a particle filter algorithm was developed to estimate the position of the acoustic source. When combined with an active control system that drives vehicle to obtain different orientations with respect to …

Mechanical Properties Of Bone Due To Sost Expression: A 3-Point Bending Assessment Of Murine Femurs, Kainoa John Peterson

Master's Theses

Sclerostin, a protein coded for by the SOST gene, is an osteocyte-expressed negative regulator of bone formation. The absence of SOST in the genome may have an effect on bone formation both during skeletal maturation and full maturity. This study attempts to determine significant differences in the mechanical properties of bone that expresses SOST compared to bone that does not. One hundred femur samples from 6, 8, and 12 month old mice were obtained from Lawrence Livermore National Labs and loaded until failure using three-point bending. Results showed significant differences in treatment group effects for cross sectional area, yield force, …

The Synthesis Of A Homologous Series Of Alkyl Lumazines And Their Application To The Dispersion Of Carbon Nanotubes, William P. Kopcha

Master's Theses

In this thesis, the synthesis of a series of alkyl lumazine surfactants (LC_n) is reported. Their application to the dispersion of both CoMoCAT and HiPco single-walled carbon nanotubes (SWNTs) is examined in detail and the thermal stability and chirality selection properties of dispersions made with these surfactants were compared both between themselves and with an alkyl flavin surfactant (FC₁₂). Lumazine alkyl chain length exhibited some control over the quality and the quantity of SWNTs dispersed. LC₁₀ was deemed most appropriate for comparison with FC₁₂ based on considerations of solubility and nanotube individualization. …

Supportive Housing For Families In Child Welfare: Client Characteristics And Risk Factors At Intake, Kellie G. Randall

Master's Theses

Many families involved in the child welfare system also face housing difficulties. Housing problems can disrupt family preservation efforts and delay reunifications from foster care. Supportive housing programs work with families who have dual vulnerabilities in housing and child welfare to integrate services and improve outcomes. Families in these programs might face barriers in addition to their housing and child welfare needs, but little is known about other risk factors in this population. This study uses a sample of 80 clients referred to a supportive housing for families program in order to examine the rate and prevalence of other risk …

Detection Of Sk2 Channels On Hippocampal Neurons, Jamie L. Maciaszek

Master's Theses

Calcium-activated small conductance potassium channels (SK) are crucial for synaptic plasticity, sleep, and learning and memory (Hammond, Bond et al. 2006; Cueni, Canepari et al. 2008; Lin, Lujan et al. 2008). Despite the recent progress on SK channel physiology, the precise spatial organization of SK channels in neurons has remained unknown. Such knowledge is critical as the subcellular distribution of SK channels is an important determinant of neuronal excitability. Currently, there are no techniques to image ion channel distribution quantitatively at the nanometer scale in living cells. Here, it is demonstrated that integration of natural toxins with single molecule atomic …

Improved Synthesis Of The Longtailed Mealybug Pheromone, Johanna M. Bakonyi

Master's Theses

No abstract provided.

Strawberry Growth, Yield, Fruit Nutrition, And Control Of Verticillium Wilt With Pre-Plant Soil Fumigants, Ozone, And Biological Control, Justin J. Scurich

Master's Theses

Verticillium wilt is a widespread soilborne disease of strawberry historically controlled by soil fumigation with methyl bromide (MB). MB was banned by the United Nations in 1995 and will be completely phased out by 2015. Research has concentrated on alternative methods of disease control without finding a single alternative able to replace MB in widespread disease control and yield increase. For the current study, strawberries were greenhouse grown in container pots filled with soil from both infested and non-infested areas of a commercial strawberry field in Watsonville, CA. Treatments included pre-plant soil fumigation with commercially available formulations of methyl bromide, …

Combustion Simulations Using Graphic Processing Units, Mingjie Wang

Master's Theses

Graphic processing units (GPUs) are powerful graphics engines featuring high levels of parallelism and extreme memory bandwidth, which constitute a powerful computing platform to solve complex problems involving chemically reacting flows. In the present study, computer programs for combustion simulations with detailed chemical kinetic mechanisms were compiled in the Compute Unified Device Architecture (CUDA) language for NVIDIA GPU architecture. Ignition processes were simulated under constant pressure and constant volume conditions using an explicit 4^th order Runge-Kutta algorithm for time integration. Sufficiently small time steps were identified with time scale analysis to ensure the integration stability. The program was validated …

The Creation Of An Anodic Bonding Device Setup And Characterization Of The Bond Interface Through The Use Of The Plaza Test, Tim M. Mccrone

Master's Theses

Recently there has been an increased focus on the use of microfluidics for the synthesis of different products. One of the products proposed for synthesis is quantum dots. Microfluidics often uses Polydimethylsiloxane for structure in microfluidic chips, but quantum dots use octadecene in several synthesis steps. The purpose of this work was to create a lab setup capable of anodically bonding 4” diameter wafers, and to characterize the bond formed using the Plaza test chip so that microfluidic devices using glass and silicon as substrates could be created.

Two stainless steel electrodes placed on top of a hot plate were …

A Business Plan For The Implementation Of A Green Gardener Certification Program In San Luis Obispo County, Laura Anne Ramage Hebert

Master's Theses

The intention of this thesis is to create a business plan for the implementation of a Green Gardener Certification Program in San Luis Obispo County. There is a need locally to conserve resources and to reduce pollution. Landscape maintenance professionals need the opportunity to receive further training in their field for licensing purposes as well as to get an edge in a competitive industry. The public of San Luis Obispo County deserves the opportunity to select a landscape maintenance professional that has been certified “green”.

In 2000, Santa Barbara City and County Water Agencies implemented a Green Gardener certification program …

The Proteomic Response Of Sea Squirts (Genus Ciona Congeners) To Hyposalinity Stress, James S. Koman

Master's Theses

The ascidian species Ciona savignyi and C. intestinalis are invasive species but show interspecific differences in their population response to hypo-saline stress associated with heavy winter-run off events that are predicted to become more frequent due to climate change. Despite an almost world-wide distribution, C. intestinalis seems to be more susceptible to hypo-saline stress than the geographically more limited C. savignyi. Given that the genomes of both species are fully sequenced, we were able to compare their proteomic response to both acute and chronic salinity to characterize the mechanisms that are responsible for setting tolerance limits to hyposaline conditions …

Development Of A Standardized Method For Comparing Biomechanical Properties Of Various Sternal Closure Techniques, Ramzi P. Hawit

Master's Theses

Background:

33.6% of all deaths in America are caused by cardiovascular disease. An estimated 82.6 million adults (>1 in 3) in America have some form of cardiovascular disease. There were over 400,000 bypass surgeries requiring open-heart surgery. Sternal dehiscence is associated with a morbidity rate of over 47% if mediastinitis supervenes. A rigid closure is required to avoid healing complications, and wire, plates, and bands are all used in an attempt to make a better closure. The purpose of this study it to compare multiple closures and validate a new testing method.

Methods:

Polyurethane foam blocks will be used, …

Dc Dielectrophoretic Assisted Anti-Fouling Filtration System, Nathan M. Cohen

Master's Theses

Filtration processes, whether on the microfluidic, clinical treatment systems, or industrial scale (e.g., point-of-care diagnostics, dialysis, and biopharmaceutical manufacturing, respectively), are often inseparable from membrane clogging (fouling). As a consequence, most, if not all, filtration systems require frequent maintenance to maintain functionality and efficiency. The thesis of this project hypothesizes that Dielectrophoresis can be combined with standard filtration to reduce filter fouling, extending membrane life, and enabling continuous operation. This project investigates a method to reduce fouling, add specificity and efficiency, and decrease the cost and challenge of filtration based biofluid separations.

To substantiate this thesis, we designed, fabricated, and …

Vitamin D Sub-Set Analysis From The Flash Study, Megan Bishop, Laura Hall, Ann Mcdermott, Aydin Nazmi

Master's Theses

Vitamin D is important to the health of college students. The objective of our study was to measure sun exposure, skin pigmentation, vitamin D intake, and serum 25-hydroxyvitamin D (25[OH]D) in a subset of participants from The Following the Longitudinal Aspects of Student Health (FLASH) Study to determine the best predictors of 25(OH)D status. Participants were college-aged freshman who had their blood drawn in spring (Visit 1) and fall 2010 (Visit 2) at California Polytechnic State University (Cal Poly), San Luis Obispo, CA. (35.3°N). Vitamin D intake was measured using a 28-day food frequency recall questionnaire (specific to vitamin D …

Landbird Response To Fine-Scale Habitat Characteristics Within Riparian Forests Of The Central California Coast, Ronald E. Melcer Jr.

Master's Theses

Riparian corridors in California are known to be an important but reduced and degraded resource for landbirds. In spite of previous research, the habitat characteristics that correlate with high landbird abundance remain poorly understood. In particular, the scale at which predictive models are useful (fine scale, watershed, sub-region or region) is ill defined. Herein, point count-based abundance indices for 8 riparian associated/obligate species with uniform and high detection probabilities are correlated with biotic and abiotic habitat variables: a sums of squares procedure is used to select the top 5 predictive variables for each species, best fit linear models are selected …

Responsive Materials Via Diels-Alder Chemistry, Gregory Alan Strange

Master's Theses

The corrosion of infrastructure imposes a significant monetary cost, and at times human cost, upon society. Methods to improve corrosion resistance of materials are described herein which utilize the reversibility of the Diels-Alder reaction to impart thermal responsiveness upon materials. Such stimuli responsiveness can potentially play a role in self healing properties which lead to reduced cracking and thus increased corrosion protection.

Reversible Diels-Alder chemistry was utilized to manipulate the surface energy of glass substrates. Hydrophobic dieneophiles were prepared and attached to glass slides and capillaries to yield a nonwetting surface. Thermal treatment of the surfaces cleaved the Diels-Alder linkage, …

Comparing The Demographics Of Two Steelhead Populations And Their Habitat Characteristics, Eileen Ann Baglivio

Master's Theses

Currently, little is known about the demographics of the Oncorhynchus mykiss irideus, or steelhead trout, populations in San Luis Obispo County. Specifically, demographic information including length, age, and condition when first leaving a watershed for the open ocean is lacking. This thesis takes a closer look at a biological and environmental data collected by the California Department of Fish and Game Central Coast Steelhead and Coho Salmon project under the direction of Associate Biologist Jennifer Nelson. The main goal of this thesis is to analyze demographic and habitat data from the steelhead populations of two northern San Luis Obispo …

The Design And Fabrication Of A Microfluidic Reactor For Synthesis Of Cadmium Selenide Quantum Dots Using Silicon And Glass Substrates, Peter Robert Gonsalves

Master's Theses

A microfluidic reactor for synthesizing cadmium selenide (CdSe) quantum dots (QDs) was synthesized out of a silicon wafer and Pyrex glass. Microfabrication techniques were used to etch channels into the silicon wafer. Holes were wet-drilled into the Pyrex glass using a diamond-tip drill bit. The Pyrex wafer was anodically bonded to the etched silicon wafer to enclose the microfluidic reactor. Conditions for anodic bonding were created by exposing the stacked substrates to 300V at ~350oC under 5.46N of force. A syringe containing a room temperature CdSe solution was interfaced to the microfluidic reactor by using Poly (dimethylsiloxane) (PDMS) as an …

The Multi-Scale Dynamics Of Executive Function, Jason Anastas

Master's Theses

Cognitive control is a central issue in developmental psychology. Traditional theories of psychology solve this problem by positing a top-down central executive, which coordinates cognitive resources in pursuit of goals. We propose an alternative explanation: cognitive control arises from physical interactions across many different timescales within the system. College and preschool aged participants were asked to complete a simple executive function task, card sorting. We found that multi-scale physical interactions differed depending on experimental constraints, and that executive function in these cases was driven primarily by flexibility in multi-scale interactions, rather than the dominance of one scale. This suggests that, …

Injury Risk At Work, Safety Motivation, And The Role Of Masculinity: A Moderated Mediation, Timothy J. Bauerle

Master's Theses

No abstract provided.