Digital Commons Network^™

Genotyping On Custom Arrays Using A Parallel Data Pipeline, Brian Albere

Master's Theses and Capstones

In the past, genotyping (determining a set of alleles in an organism) has been an extremely challenging process. The time, monetary, and technology demands of the task have limited genotype data to a small variety of scientific model organisms with the capacity to conduct genetic crosses. New sequencing technology from companies such as NimbleGen, however, can generate custom organism-specific microarrays at relatively low cost. The combination of these arrays and the knowledge of species' genome-wide SNPs allow genotype experiments, such as generation maps, QTL studies, and natural population variation studies, to be conducted on virtually any organism. Although the NimbleGen …

New Methods For The Construction And Characterization Of Molecules On An Addressable Array, Bo Bi

All Theses and Dissertations (ETDs)

Microelectrode array has great potential as a platform for building "addressable" molecular libraries and being utilized to probe the ligand-receptor binding events in "real-time". To achieve this objective, a complete study would generally include three phases: 1) to enable and expand site-selective chemistry on the array; 2) to understand structural information of the molecules loaded; and 3) to develop research protocols of electrochemical analysis on the device to monitor those molecular interactions. While 2), quality-control analysis, is a core task of this thesis, the studies in other phases that drove this work or derived from it, are also discussed in …

Synthesis, Characterization And Biological Studies Of Some Piperazines And Their Metal Complexes / Muhammad Saleh Salga, Muhammad Saleh Salga

Student Works (2010-2019)

Piperazine derived Schiff bases were synthesized by an ethanolic condensation of 2- (piperazin-1-yl)ethanamine with either salicylaldehyde (LSP), 5-chlorosalicylaldehyde (LCS), 5-bromosalicylaldehyde (LBS), 5-nitrosalicylaldehyde (LNS), 5-hydroxy salicylaldehyde (LDH), 4-hydroxysalicylaldehyde (DHS), 5-methoxysalicylaldehyde (LHM) or 4-methoxysalicylaldehyde (HMS). Other Schiff bases were obtained from 1-(2- hydroxyphenyl)ethanone (2HP) and 1-(2,4-dihydroxyphenyl)ethanone (DHP). Schiff basemetal complexes of Cu(II), Zn(II) and Cd(II) were prepared by direct synthesis which yielded 1:1 metal-ligand ratio. The solid product formed was collected, washed with ethanol, recrystallized from suitable solvent and dried in a vacuum desiccator. The Schiff bases and their metal complexes were fully characterized by spectroscopic methods such as IR, 1H NMR, …

Studies On Antidiabetic And Other Biological Activities Of Centratherum Anthelminticum / Aditya Arya, Aditya Arya

Student Works (2010-2019)

In search of phytomedicine for diabetes, this preliminary screening was conducted on twelve (12) different plants for hypoglycemic activity and antioxidant potential in the in vitro and in vivo study models. Amongst all, Centratherum anthelminticum seeds demonstrated maximum hypoglycemic and antioxidant potential. Therefore, the defatted crude methanolic fraction of the Centratherum anthelminticum seeds (CAMFs) was selected for detailed antidiabetic activity on the in vitro cell-based biological studies on mouse pancreatic cells, β-TC6 and on type 1 and type 2 diabetic rats for 4-weeks. The results of this study indicate that CAMFs showed potential antidiabetic effect on β-TC6 cells and confirmed …

Utilization Of Protein Tertiary Contacts To Improve Protein Structure Prediction Using Sequence Homology, Trung Thanh Nguyen

Master's Theses

The structure of a protein ultimately determines its function; therefore, knowledge of three-dimensional structure is essential for understanding its function and mechanism of action. The two most common methods for determining protein structure are x-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy. These methods are quite successful but can be very time-intensive and costly. An alternative method is protein structure prediction, where structure is computationally predicted from amino acid sequence. As opposed to x-ray crystallography and NMR spectroscopy, protein structure prediction is not encumbered by potential experimental problems. In this research, we attempted to determine if certain protein structure features, …

Biomass And Mass Balance Isotope Content Of Mussel Seep Populations, Philip Martin Riekenberg

LSU Master's Theses

Cold seep mussels, Bathymodiolus childressi, are common cold seep constituents that form large populations at upper continental slope (500-1000 m) cold seep sites in the Northern Gulf of Mexico. These mussels utilize methane present through symbiotic relationships with methanotrophic bacteria. This study uses a coupled isotope technique to determine the relative incorporation of respiratory carbon in the shell as a measure of the availability of methane between different seep sites. This method indicates a higher abundance of methane at the Brine Pool site than at the Bush Hill site which appears significantly more resource limited and that changes in methane …

Behavioral And Immunological Phenotypes Of Transgenic Mice Overexpressing Human Secreted Amyloid Precursor Protein Alpha: Implications For Autism, Antoinette R. Bailey

USF Tampa Graduate Theses and Dissertations

Autism is a heterogeneous neurodevelopmental disorder that is characterized by impaired social interaction and communication as well as restricted and repetitive behaviors and focused interests. In addition to the cardinal behavioral characteristics observed for diagnosis, autistic individuals exhibit a number of comorbid conditions as well as a variety of aberrant immunological features. Recent studies report that plasma from autistic children contained elevated levels of secreted amyloid precursor protein alpha (sAPP-á), the á-secretase cleavage product of the amyloid precursor protein (APP) which is ubiquitously expressed in the brain, spleen, thymus and other organs. Interestingly, the sAPP-á fragment functions as a neurotrophic …

The Effects Of Food Insecurity On Mental Wellbeing In Monteverde Costa Rica, Robert Eugene Cowherd

USF Tampa Graduate Theses and Dissertations

The rapid expansion of ecotourism in the Monteverde zone of Costa Rica has increased the incidence in food insecurity in the area. Changes in food preferences and availability have led to a more homogenized diet that is increasingly delocalized and reliant on processed foods. Additionally, there has been a rapid economic shift away from agricultural and dairy farming to an economy more reliant on tourism. This NSF supported study builds upon data from a longitudinal investigation (#BNS 0753017) examining the nutritional effects of this rapid economic transition. Using a mixed methods approach, a culturally appropriate scale of stress was developed …

Assessment Of Pulmonary Fibrogenic Potential Of Multi Walled Carbon Nanotubes In Vitro., Anurag Mishra

Graduate Theses, Dissertations, and Problem Reports (ETD)

Multi-walled carbon nanotubes (MWCNT) have many applications due to their unique mechanical and electrical properties. However, these fiber shaped materials have been shown to possess unusual fibrogenic activity in vivo and are currently the focus of intense toxicological investigations. To date very few detailed mechanistic studies on the fibrogenic activity of CNT have been reported. The aim of this series of studies is to determine fibrogenic potential of well dispersed MWCNT in human lung cell culture models and develop a novel platform for understanding the cellular mechanisms of MWCNT-induced lung fibrosis. Dispersion of large agglomerates of MWCNT in suspension to …

A Role For Reactive Oxygen Species In Photodynamic Therapy, Michael Price

Wayne State University Dissertations

Photodynamic therapy (PDT) is based on the ability of certain photosensitizing agents to selectively localize in neoplastic cells and their vasculature. Subsequent irradiation at a wavelength corresponding to a photosensitizer absorbance band excites the photosensitizer molecules, leading to energy transfer reactions and fluorescence. It was initially concluded that the phototoxic effect occurred when energy from the excited state of the photosensitizer was transferred to dissolved oxygen to form singlet oxygen. This product has a very brief half-life and will cause cellular damage only in the immediate vicinity of its formation. But an excited-state photosensitizer can also interact with oxygen to …

Prevalence And Genotypes Of Enterocytozoon Bieneusi In Weaned Beef Calves On Cow-Calf Operations In The Usa, Mónica Santín, David Dargatz, Ronald Fayer

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

To determine the prevalence and genotype distribution of Enterocytozoon bieneusi in weaned beef calves in the USA, fecal samples were collected from 819 calves (6– 18 months of age) from 49 operations. Feces were sieved and subjected to density gradient centrifugation to remove fecal debris and to concentrate spores. DNA extracted from each sample was subjected to the polymerase chain reaction (PCR) to amplify the complete internal transcriber spacer (ITS). All PCR-positive specimens were sequenced to determine the genotype(s) present. Overall, E. bieneusi was detected in 34.8% of the 819 fecal samples. The highest prevalence was found in the Midwest …

Evidence From Micromorphology And Gross Morphology Of The Genus Loranthus (Loranthaceae) In Iran, Robabeh Shahi Shavvon, Shahryar Saeidi Mehrvarz, Narges Golmohammadi

Turkish Journal of Botany

The genus Loranthus L. (Loranthaceae) is represented in Iran by 2 species: Loranthus europaeus Jacq. and L. grewingkii Boiss. & Buhse; the latter species is endemic to the area of Flora Iranica. The plants of Loranthus are hemiparasites growing on various host trees such as Quercus infectoria Oliv., Acer monspessulanum L., and Armeniaca vulgaris Lam. In order to investigate the range of morphological variation in different populations of these species, an inclusive gross morphological and micromorphological study was conducted. For this purpose, the anatomical characteristics of the stem, leaf, petiole, and fruit were also investigated. The most prominent features were …

Radiation Hybrid Fine Mapping Of Two Fertility-Related Genes: Marking The Path To Wheat Hybrids, Filippo Maria Bassi

Plant Sciences

Over one billion people, more than 1/9th of the global population, are undernourished. Feeding the ever increasing population has to be the most important goal of plant sciences. Since cultivated areas are not likely to increase, I will need to produce more with what is available. This can be summarized in one word: yield. Unfortunately, wheat’s yield is expected to increase only 1.13% by 2019, a prediction that if converted into reality will likely indicate that I failed to cope with the world demographic increase. A new strategy to revolutionize wheat production is required, and some believe that this change …

Morphological Characterization And Molecular Mediated Genetic Variation Of Thief Ants (Hymenoptera: Formicidae), Ralph B. Narain, Shripat T. Kamble, Thomas O. Powers

Department of Entomology: Faculty Publications

The morphological characterization and molecular genetic variation were determined in populations of thief ants, Solenopsis molesta (Say). The genetic variations were elucidated using mitochondrial deoxyribonucleic acid (mDNA) sequences of cytochrome oxidase I. DNA from thief ants was extracted with Qiagen’s Gentra PUREGENE DNA Isolation Kit using their solid tissue protocol. Polymerase chain reactions (PCR) were run on the extracted DNA using primers Lep-F1 (forward) and Lep-R1 (reverse). The DNA products were concentrated and purified by Microcon Centrifugal Filter Unit YM-100. Purified DNA samples were sequenced at the University of Arkansas Medical Sciences (UAMS) DNA Sequencing Core Facility. The sequences were …

Modelling Female Mating Success During Mass Trapping And Natural Competitive Attraction Of Searching Males Or Females, John A. Byers

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Simulation models of insects encountering sex pheromone with or without mass trapping in which the searching sex is either male (moths and many insect species) or female (some true bugs, beetles, and flies) were developed. The searching sex moved as a correlated random walk, while the opposite sex remained stationary (calling) and released an attractive sex pheromone. The searching sex was caught when encountering a pheromone-baited trap, and females mated when encountering a male. An encounter with pheromone was defined by the searcher’s interception of a circle termed the effective attraction radius (EAR_c). Parameters of movement (speed and …

Biochemical Studies Of Abce1, Lynn Sims

Electronic Theses and Dissertations

The growth and survival of all cells require functional ribosomes that are capable of protein synthesis. The disruption of the steps required for the function of ribosomes represents a potential future target for pharmacological anti-cancer therapy. ABCE1 is an essential Fe-S protein involved in ribosomal function and is vital for protein synthesis and cell survival. Thus, ABCE1 is potentially a great therapeutic target for cancer treatment. Previously, cell biological, genetic, and structural studies uncovered the general importance of ABCE1, although the exact function of the Fe-S clusters was previously unclear, only a simple structural role was suggested. Additionally, due to …

Morphological And Neuroanatomical Changes Associated With The Induction Of Neurodegeneration And Life Span Reduction In Drosophila Melanogaster By Glia Targeted Expression Of Cdh1/Rap/Fzr, An Activator Of The Anaphase Promoting Complex, Israel Nnah

Dissertations and Theses

"The retina aberrant in pattern (rap) gene encodes the Fizzy-related protein (Fzr), an activator of the E3 ubiquitin ligase complex: the Anaphase Promoting Complex/Cyclosome (APC/C). APC/C facilitates the cell cycle stage-specific degradation of cyclins and other mitotic regulators, resulting in the inactivation of Cdk (Cyclin Dependent Kinase) complexes, thus promoting completion of mitosis. Previous studies from our laboratory have shown that Rap/Fzr (the Drosophila homolog of the mammalian Cdh1) regulates glia differentiation and promotes neuron formation. Recent studies have shown that the glia specific over expression of Rap/Fzr causes progressive neurodegeneration and life span reduction preceded by temperature sensitive paralysis, …

An Entrepreneurial Perspective On The Business Of Being In Our Profession Conference: The Law: Business Or Profession: The Continuing Relevance Of Julius Henry Cohen For The Practice Of Law In The Twenty-First Century, Steven H. Hobbs

Articles

No abstract provided.

Cervical Human Papillomavirus Infection Among Young Women Engaged In Sex Work In Phnom Penh, Cambodia: Prevalence, Genotypes, Risk Factors And Association With Hiv Infection, Marie-Claude Couture, Kimberly Page, Ellen S. Stein, Neth Sansothy, Keo Sichan, John Kaldor, Jennifer L. Evans, Lisa Maher, Joel Palefsky

Nursing and Health Professions Faculty Research and Publications

Background

Although cervical cancer is the leading cancer in Cambodia, most women receive no routine screening for cervical cancer and few treatment options exist. Moreover, nothing is known regarding the prevalence of cervical HPV or the genotypes present among women in the country. Young sexually active women, especially those with multiple sex partners are at highest risk of HPV infection. We examine the prevalence and genotypes of cervical HPV, as well as the associated risk factors among young women engaged in sex work in Phnom Penh, Cambodia.

Methods

We conducted a cross-sectional study among 220 young women (15–29 years) engaged …

Distribution Of Mysis Diluviana In Nearshore Lake Ontario, Sean J. Maxwell

Master's Theses and Capstones

Opossum shrimp Mysis diluviana are an important trophic link in Lake Ontario, and in all of the lakes where they occur. Their temporal and spatial distributions are not well documented in the nearshore area (<30 m bottom depth), where alewives and other fish increasingly depend on them as a food source. This study describes their distributions over three years (2009 to 2011) from April through November using data collected from Tucker trawls and multi-frequency hydroacoustics; both deployed over incremental depths. Mysis was found to occur in the nearshore area in 69.6% of the trawl surveys. Maximum densities occurred in April and early May and were located in the deepest (30-m) contour. The density and frequency of occurrence of Mysis increased exponentially from shore. Hydroacoustic methods were effective in quantifying of Mysis density in 42% of the echograms when they were present in simultaneously obtained samples.

Syntheses And Characterization Of Water-Soluble Phythalocyanines For Diagnosis And Treatment Of Cancer, Benson Getenga Ongarora

LSU Doctoral Dissertations

Ongarora, Benson Getenga, B.S., Moi University, 2005 Doctor of Philosophy, Fall Commencement, 2012 Major: Chemistry Syntheses and Characterization of Water-Soluble Phthalocyanines for Diagnosis and Treatment of Cancer Dissertation directed by Professor M.Graҫa H. Vicente Pages in dissertation, xi. Words in abstract, 251. ABSTRACT Chapter 1 describes the general properties of phthalocyanines, synthesis of metallo-phthalocyanines, their photophysical features and their uses. The concepts of PDT and targeted therapeutics are also introduced. Chapter 2 describes the syntheses, characterization, photophysical studies and biological evaluation of cationic phthalocyanines. The trimethylaminophenoxy substituted phthalocyanines were synthesized through statistical condensation method, which gave a statistical mixture of …

Synthesis, Cellular Studies, And Computational Analysis Of Porphyrin And Bodipy Conjugates With Affinity For Epidermal Growth Factor Receptor, Alecia Michelle Mccall

LSU Doctoral Dissertations

Chapter 1 is a description of the basic fundamental concepts of porphyrins and BODIPYs, (including synthetic methodologies), a general mechanism of the processes of EGFR, and computational concepts that are elaborated upon in future chapters. Chapter 2 is a discussion solely on the porphyrins that were synthesized to be used as fluorophores for EGFR-targeted conjugates, both peptidic and non-peptidic. The porphyrins were primarily synthesized via the Lindsey method as well as by O-alkylation of tetrahydroxy porphyrins. Synthesis of PEG linkages are discussed as well through three methodologies. Chapter 3 is a presentation of the synthesis, characterization, cellular studies, and computational …

Total Synthesis Of A Virotoxin And Analogs For Conformational Studies, Benson Jumba Edagwa

LSU Doctoral Dissertations

This dissertation describes the first total synthesis of alloviroidin in trace amounts, along with that of three analogs containing L-proline (Pro), trans-3-hydroxyproline (3-Hyp) or cis-4-hydroxyproline (4-hyp) residue substituting for 2,3-trans-3,4-trans-dihydroxyproline in the natural product. We report herein an efficient strategy that provides a dipeptide containing a (2S,4S)-4,5-dihydroxyleucine (dihyLeu) residue, including a diastereoselective dihydroxylation. Nα-Carbobenzyloxy-(2S)-4,5-dehydroleucine was coupled with valine ethyl ester to give a dipeptide that was subjected to a Sharpless asymmetric dihydroxylation to introduce the diol. The relative configuration at C4 was assigned as S by X-ray crystallography after derivatization as an α-amino-γ-lactone hydrochloride salt. The preparation of the 2-(methylsulfonyl)tryptophan …

Single-Molecule Detection Of Molecular Beacons Generated From Ldr On Thermoplastic Microfluidic Device For Bioanalysis, Zhiyong Peng

LSU Doctoral Dissertations

Current clinical techniques for nucleic acid detection and analysis often involve PCR, lacking adequate specificity or sensitivity to meet the stringent requirements in certain applications. This research aims to develop an innovative molecular assay and the associated hardware to rapidly signal the presence of certain targets using reporter sequence found in their genome without requiring PCR. This assay coupled the sensitivity of single-pair fluorescence resonance energy transfer (spFRET) with the specificity of ligase detection reaction (LDR) to provide near real-time readout of target biomarkers. Heightened concerns on potential bioterrorism threats, such as rapid dissemination of pathogenic bacteria or viruses into …

Toxicity And Availability Of Copper And Zinc To Queen Conch, Amber L. Garr

Electronic Theses and Dissertations 2010 - 2019

The presence of heavy metals and other pollutants is detrimental to marine ecosystems. The queen conch, once an important fisheries species in the Florida Keys, has not sufficiently recovered after a 25-year fishery closure. Research has shown high levels of copper and zinc in the gonads and digestive glands of adult conch found in the nearshore waters. Four sites relevant to queen conch larval recruitment were tested in 2010 for the presence of copper and zinc in the water, phytoplankton, sediment, and seagrass epiphytes over seven months. Both metals were detected in all sample types and no seasonal or geographical …

Proposed Expanded Green Space Plan Using Gis For Natural Areas In Palm Beach County, Corrie. Rainyn

Electronic Theses and Dissertations 2010 - 2019

In the past 25 years, Palm Beach County has acquired more than 31 million acres of public preserves consisting of numerous native habitats that are home to threatened and endangered flora and fauna. Both endemic habitats and plant species benefit from expansion and connectivity through the adoption of native plants in surrounding areas. The next step in conserving these protected, larger areas is to identify ways to connect them in order to reduce their isolation and improve their likelihood of continued ecosystem health. This study aims to perform an analysis using a GIS database of Palm Beach County's Eastern urban …

Environmental Change And Place-Based Identities: Sponge Fishing In Tarpon Springs, Florida, Michael Suver

USF Tampa Graduate Theses and Dissertations

Abstract

As the environmental consequences of urbanization and climate change become apparent in coastal communities, it has become important to understand how residents of these communities experience and approach their changing environments. This becomes especially significant in places where nature-based livelihoods constitute a major part of the economy. This thesis focuses on the city of Tarpon Springs, located along the Gulf of Mexico in Florida, where sea sponge fishing is an important contributor to the local economy while also being central to place-based tourist and ethnic identities. It seeks to understand how environmental changes in the sea sponge economy will …

Wholeistic EducationTm, Cerissa Leigh Desrosiers

Antioch University Dissertations & Theses

This dissertation introduces Wholeistic Education^TM (WED^TM), an innovative, values-based, interdisciplinary pro-social theory that is the culmination of centuries of scientific and philosophical learning and exploration about optimal mental health and human development. WED is based on basic human nature and universal human rights, and so it applies to all variations of human society- racial, ethnic, religious, or otherwise. WED is a foundation theory to which any targeted implementation strategy can be applied. It is both a proactive strategy for seeking and maintaining health before a crisis arises in families, schools, and organizations as well as a treatment …

Statins In Unconventional Secretion Of Insulin-Degrading Enzyme And Degradation Of The Amyloid-Β Peptide, K Glebov, J Walter

Peninsula Medical School

Population-based studies demonstrated that statins might decrease the risk of developing Alzheimer’s disease (AD). Statins inhibit the 3-hydroxy-3-methyl-glutaryl-coenzyme-A reductase and thereby de novo synthesis of cholesterol. Cell culture and animal studies indicated that cholesterol affects the proteolytic processing of the amyloid precursor protein and the generation of amyloid-β (Aβ). Recently, we have demonstrated that statins can also stimulate the degradation of Aβ. The statin-induced clearance of Aβ could be attributed to increased release of the insulin-degrading enzyme (IDE) via an exosome-related unconventional secretory pathway. Interestingly, this statin-induced secretion of exosome-associated IDE was independent of cellular cholesterol concentrations, but rather caused …

Development Of An In-Cell Förster Resonance Energy Transfer Technique To Study Protein Structure Inside Living Cells, Victoria Lynn Murray

Wayne State University Dissertations

The goal of my thesis is to develop an in-cell fluorescence technique that allows for measurement of the distances between fluorescence acceptors and donors within a protein or between two proteins inside the correct intracellular compartment of living cells. The successful achievement of this goal will allow us to obtain high-resolution structural information from a protein, one key step towards high-resolution structural biology of proteins inside the living cell.

To achieve this goal, we will apply the fluorescence resonance energy transfer (FRET) technique to the specifically labeled proteins inside the cells. Our rationale is to specifically label the protein(s) of …