Digital Commons Network^™

Exploiting Bacteriophages And Associated Peptidoglycan Hydrolases With Potential For Biocontrol In Food Related Applications, Lorraine Endersen

Theses

The work presented in this thesis describes the isolation and characterisation of novel bacteriophages, and the subsequent exploitation of their bactericidal properties against two opportunistic food related pathogens, Mycobacterium avium subsp. paratuberculosis (MAP) and Cronobacter sakazakii.

MAP is a proven animal pathogen known to cause Johne’s disease in cattle but has been implicated as a causative agent of Crohn’s disease in humans. Despite the fact that this association has yet to be proven, significant focus has been directed towards evaluating the consequences of consuming milk contaminated with MAP. Accordingly, six mycobacteriophages were isolated and characterised in terms of temperature and …

Characterisation And Applications Of Natural Lactic Acid Bacteria With Emphasis On Weissella Cibaria And Associated Exopolysaccharide, Kieran M. Lynch

Theses

The work presented in this thesis characterises natural cereal-derived lactic acid bacteria and examines their potential application in the dairy fermentation area, with special emphasis on the sourdough isolate, Weissella cibaria MGl and its associated glucan homoexopolysaccharide. This strain is notable for its high-level production of dextran, being termed a “hyper-producef’. Genome sequencing and analysis of a number of IV. cibaria strains was performed in the context of available genomic data for other Weissella species, with special focus on the metabolic traits of W. cibaria MGl, and the results represent the first study to explore members of the Weissella genus …

The Expression Pattern Of Death Associated Protein Kinase1 In Normal Dorsal Root Ganglion Neurons And Following Peripheral Nerve Injury, Maryam Sulaiman Mohammed Al Saadi

Theses

Death-associated protein kinase 1 (DAPK1) is a calcium/calmodulin (Ca^2+/CaM) regulated serine/threonine kinase. An increasing body of evidence supports the significance of DAPK 1 protein in cancer and CNS diseases. The role of DAPK in peripheral nerve regeneration and neuropathic pain remains completely unexplored. The aim of this study is to investigate the expression pattern of DAPK1 along with key pro-and anti-apoptotic cell signaling molecules (p53, Bax, Akt, ERK5, p38) and to verify the possibilities of DAPKI1-NMDA NR2B relationship in dorsal root ganglion neurons (DRG) after 2 hours, 7 days and 14 days following a sciatic nerve injury. Gene …

Reproductive Schedule And Traits Of Hybopsis Amblops (Bigeye Chub) In The Flint River System, Huntsville, Alabama, Crissy L. Tarver

Theses

The goal of this study was to ascertain a reproductive schedule and describe reproductive traits of Hybopsis amblops in the Flint River system in Huntsville, AL. Members of this species were collected from the Flint River from May, 2013 to July, 2014. The standard length (SL) of each fish was measured using digital slide calipers. Gross body mass (GBM) and gonadal mass (GM) were obtained using a digital balance. In adult fish, gonadosomatic indices (GSI) were calculated to aid in determining reproductive timing. Ovaries and oocytes were categorized into developmental stages. Total fecundity (TF) of each female was calculated from …

Identification Of The Molecular Target Of The Doc Toxin Of The P1 Bacteriophage Plasmid Addiction System, Darren Ferree

Theses

Doc toxin from the bacteriophage P1 plasmid addiction operon kills daughter cells that are cured of plasmid. At the beginning of this project it was known that Doc is a kinase that transfers the phosphoryl group from the gamma position of ATP to some unidentified target protein of approximately 45 kDa molecular weight. To better characterize this target, assays were conducted to determine optimal conditions for Doc-dependent phosphorylation of target, and these conditions were then used to generate samples for analysis by two-dimensional polyacrylamide gel electrophoresis, liquid chromatography-coupled tandem mass spectrometry, and immunoprecipitation. The results of these experiments indicate that …

Development Of A Novel Wet Algal Lipid Extraction Technique, Chen Zhang

Theses

A novel procedure, ASAPALLE, for lipid extraction from wet algae, Nannochloropsis Salina, was developed and reported. This method does not require pre-dehydration of algal biomass and the total extraction time needed is under one minute. The ASAPALLE extraction was compared with hexane Soxhlet extraction to evaluate the lipid extraction efficiency and the lipid profile. Algal lipid yield of the ASAPALLE extraction was 14.3% of the total dry algal biomass weight, while the hexane Soxhlet extraction after 18 hours yielded 7.9% of algal lipid. The total lipid content was approximately 14.6%, determined by a modified Bligh-Dyer method. The quality of the …

Phytochemical Analysis Of Antileishmanial Plants : A Drug Discovery Approach, Samon Shrestha

Theses

Phytochemical analysis of three antileishmanial plants from Monteverde, Costa Rica and Abaco Island, Bahamas, has been carried out by use of column chromatography for phytoseparation, and NMR and IR spectroscopy for structural elucidation. Ruyschia phylladenia contained betulinic acid as major component, with significant amount of lupeol. Eugenia monteverdensis contained beta-Sitosterol, betulinic acid and barbinervic acid. Tabebuia bahamensis contained large amount of ursolic acid. Betulinic acid inhibited promastigotes of L. amazonensis significantly but was also toxic to mouse macrophages. Lupeol and betulinic acid did not show antimicrobial activity while beta-Sitosterol inhibited Aspergillus niger strongly. Barbinervic acid expressed good inhibition of Bacillus …

Gold Nanodisk Array Surface Plasmon Resonance Sensor, Xueli Tian

Theses

Surface plasmon resonances in periodic metal nanostructures have been investigated for sensing applications over the last decade. The resonance wavelengths of the nanostructures are usually measured in the transmission or reflection spectrum for chemical and biological sensing. In this thesis, I introduce a nanoscale gap mediated surface plasmon resonance nanodisk array for displacement sensing and a super-period gold nanodisk grating enabled surface plasmon resonance spectrometer sensor. The super-period gold nanodisk grating has a small subwavelength period and a large diffraction grating period. Surface plasmon resonance spectra are measured in the first order diffraction spatial profiles captured by a charge-coupled device …

The Isolation, Purification And Characterization Of The Dna Ligase From Thermococcus Thioreducens Strain Ogl-20pt, James Wolfsberger

Theses

DNA ligases are highly conserved in their primary sequence across the three domains of life and are important in DNA replication, recombination, and repair. The enzyme functions in an AMP-dependent reaction to close nicks in the DNA phosphodiester backbone. In this study, the hyperthermophilic DNA ligase Tthlig from the archaeon Thermococcus thioreducens is characterized. Tthlig is a recombinant protein cloned from genomic DNA with a sequence of 559 amino acid residues. Phylogenetic analysis placed Tthlig in a tight cluster with organisms of the order Thermococcales. Amino acid residue sequence analysis showed significant sequence conservation with other DNA ligases. The structure …

Cognitive Studies On A Mouse Model Of Tyrosinemia Type I, Sarah Bradham Coker

Theses

Hereditary Tyrosinemia Type 1 (TTI) is an autosomal recessive disorder that is characterized by the deficiency of the fumarylacetoacetase (FAH) enzyme in the tyrosine catabolic pathway, resulting in the elevation of tyrosine and its byproducts in the blood, cerebrospinal fluid (CSF), and tissues. The accumulation of the toxic metabolites succinylacetone and fumarylacetoacetate in the liver and kidneys leads to catastrophic effects and death if not treated. The current treatments available for TTI patients are pharmacotherapy with nitisinone (NTBC) with diet modification and/or a liver transplant, each with its own associated risks. Recently, data has been published showing that TTI patients …

Aerodynamic Performance Of Flexible Flapping Wings In Hover At Fruit Fly And Bumblebee Scales, Madhu K. Sridhar

Theses

Aeroelastic response at fruit fly and bumblebee scales is explored using a well-validated Navier-Stokes equation solver, fully-coupled with a linear Euler-Bernoulli beam solver. Hover flight is considered with passive pitch at low Reynolds numbers. A systematic study with varying motion amplitudes and wing stiffness showed that the optimal efficiency at both scales was observed at lower reduced frequencies and frequency ratios, whereas lift was the highest at the higher reduced frequency and frequency ratio. The aeroelastic response at bumblebee scale was non-periodic and more unsteady when compared to fruit fly scale, consistent with the higher Reynolds number for the bumblebee. …

A Gas Chromatographic/Mass Spectral Analysis Of Aromatic Medicinal Plants From Yemen, Bhuwan Khatri Chhetri

Theses

Yemen is a small country located in the southwestern part of the Arabian Peninsula. Yemen’s coastal lowlands, eastern plateau and deserts give it a diverse topography, which along with climatic factors make it opulent in flora. Despite the introduction of western medicinal system during the middle of the twentieth century, herbal medicine still plays an important role in Yemen. However, little has been done on the study of the aromatic medicinal plants that have been used through ages to cure and heal diseases. To this end, in collaboration with Deparment of Pharmacognosy, Faculty of Pharmacy, Sana’a University, Yemen the essential …

Conversion Of Neural Network Models To State-Space Models For Model-Based Control Design, Sai Susheel Praneeth Kode

Theses

The objective of this research is to implement an artificial neural network into a closed-loop model based control law that requires a state space model. Model based control laws are strongly preferred due to the existence of mathematical proofs for their performance. With mathematical proof of performance, the controller is guaranteed to work correctly within a designed domain of operation. However, deriving physics based mathematical models and accurately identifying the parameters of such models are cumbersome, or sometimes impossible, for complex nonlinear systems. This limits the application domain of model based controllers. Neural networks are a great tool for modeling …

Evolution, Systematics & Geographic Parthenogenesis Of Ilyodromus (Crustacea, Ostracoda), Rylan James Shearn

Theses

Most multicellular organisms reproduce sexually at some point in their life cycle. This is paradoxical because being asexual is theoretically far more advantageous. Asexual organisms do not need to find and court new mates, they reproduce at a faster rate, and with no males, all members of the population contribute toward population growth rate. With over 20, often mutually exclusive hypotheses, this paradox resists a synthesised explanation, and continues to represent one of the largest gaps in our understanding of fundamental evolutionary theory. Clearly, more real world studies are required that document the selective mechanisms underlying differences in evolutionary fitness …

An Intrinsic Case Study Into The Appropriateness Of A Bespoke Training Model As An Approach To Supporting The Postgraduate Demonstrator In Developing Pedagogical Skills Suitable For Undergraduate Scientific Laboratories., Barry Ryan

Theses

Postgraduate demonstrators (PGDs) are crucial to the smooth running of undergraduate teaching laboratories; however, they are oftentimes exiled to superficial duties such as enforcing health and safety and procedural instruction. The aim of this intrinsic case study was to characterise the support required by postgraduate demonstrators (PGDs) to develop the key pedagogical skills that would assist them in effectively demonstrating undergraduate science teaching labs. Through supporting PGD development, it is hoped to centralise the PGD in the undergraduate teaching lab and set in place the foundations for a move towards undergraduate teaching labs that encompass aspects of tailored research in …

“The Relationship Between Approaches To Learning And Assessment Outcomes In Undergraduate Optometry Students”, Linda Moore

Theses

A cross-sectional quantitative study was implemented to identify and analyse student approaches to learning (SALs) in the four stages of an undergraduate optometry honours degree programme. Study results will be used to inform optometric educators of the SAL trends of this student cohort. Seventy-three undergraduate optometry students participated in the study. Individual participant SAL scores were calculated using the shortened Study Process Questionnaire (R-SPQ-2F) for a semester-long academic module identified for each programme stage. Only R-SPQ-2F main scale SAL scores measuring the deep approach (DA) and surface approach (SA) were included in the final analyses, due to poor internal consistency …

An Exploration Of The Perspectives Of The Stakeholders On The Early Childhood Care And Education (Ecce) Scheme In Ireland, In Relation To Children’S Transition Into Primary School, Ciara Allen

Theses

The purpose of this study is to explore the Early Childhood Care and Education (ECCE) scheme in Ireland and a child’s transition from a pre-school setting to the formal primary school environment, from the perspective of parents, pre-school practitioners, primary school teachers and childcare organisations. The ECCE initiative was introduced in January 2010 for all children between the ages of 3 years and 3 months and 4 years and 6 months, offering them one year of free pre-school (50/38 weeks) prior to commencing primary school. This research identifies the need to study a child’s transition into formal schooling, as research …

Evaluation Of Magnesium-Based Alloys As Degradable Biomaterials, Nan Zhao

Theses

Biomaterials including ceramic material, polymer material, metallic material and composite material have been used in biomedical scaffolds, artificial tissues, and drug delivery systems for a long time. Magnesium (Mg) and Mg-based alloys are a new generation of degradable metallic materials that have attracted great attention in the last ten years. The advantages of Mg alloys as biomaterials are their good biocompatibility and biodegradability. Mg as an essential element in human body is an enzyme cofactor for over 300 biochemical reactions. However, the degradation process of Mg material may hinder the potential application. The purpose of this study is to evaluate …

Processing Pre-Existing Connect-The-Dots Puzzles For Educational Repurposing Applications, Elizabeth Kilgore Shelby

Theses

Connect-the-Dots puzzles are puzzles which contain labeled dots in a sequence. These puzzles are mostly designed as a way for children to hone in on their counting skills, while having fun. These same puzzles, which are available in abundance online and with modification, can be used to aid students in other areas of education such as spelling. Research shows that the addition of visual imagery provides a significant impact in spelling performance. The objective of this research is to develop an algorithm for processing Connect-the-Dots puzzles to assist in the replacement of the original numbers in the puzzle with characters …

Spatial Incidence Of Adult Obesity In The State Of Alabama, Mary G. Odhiambo

Theses

No abstract provided.

Workplace Well-Being: Examining The Mental And Psychological Health And Safety Of Non-Unionised And Unionised Employees, Peter O'Mahony

Theses

A quantitative case study was conducted to gain a deeper understanding of the mental and psychological health and safety of non-unionised and unionised employees within the researcher's organisation, a multi-national pharmaceutical company based in Ireland. One hundred and sixty-seven employees and seven senior managers were surveyed to explore their perspectives of psychological health and safety risks in the workplace across thirteen different psychosocial factors which are known to either have positive or negative effects on the psychological health and well-being of an employee.

The Guarding Minds at Work (GM@W) online survey resources were considered appropriate methods to collect the necessary …

Hyperglycemia And Inhibition Of The Monocarboxylate Transporter 1 (Mct1) Enhances Growth Arrest In Cancer Cells, Aleksandra I. Pivovarova

Theses

Many cancer cells rely predominately on glycolysis for their energy production, even in the presence of oxygen. They proceed further and reduce the glycolysis product pyruvate to lactate, by means of fermentation, for continued ATP production. This phenomenon is called the Warburg effect, and is associated with an upregulation of glycolysis and increased lactate production. A persistent increase in glycolysis and ATP turnover leads to an intracellular proton accumulation, which could eventually lead to cell damage and death by cytosolic acidification. However, cancer cells avoid acidification and maintain an appropriate intracellular pH by employing monocarboxylate transporters for the coupled export …

Analysis Of Host-Parasite Interactions Between Darters (Etheostoma) And Monogenoidean Gill Parasites (Aethycteron) In Flat Creek And Mill Creek, Kara Million

Theses

This study sought to investigate the parasite-host relationships between two darter assemblages and their gill parasite populations, and to compare the biodiversity present in both systems. Eight darter species were collected over the course of one year from two sites in Tennessee, Flat Creek and Mill Creek, and parasite counts were performed on all sample populations. Parasite loads were compared across darter species in each site to determine whether infection levels differed significantly between host species. Phylogenetic trees containing mitochondrial and nuclear markers were constructed for each set of organisms using Bayesian analysis, and the trees were examined for congruence …

A Nucleotide Sequence Level Approach To Detection Of Lateral Gene Transfer In Eukaryotic Genomes, David E. Gray

Theses

Detection of lateral gene transfer (LGT) in eukaryotes has previously relied almost exclusively on phylogenetic analysis of amino acid sequences. This study developed a method for detection of eukaryotic LGT at the nucleotide sequence level. A pipeline was constructed consisting of Perl scripts that automate BLAST searches, phylogeny construction, and selection of phylogenetic trees indicating LGT. This pipeline was tested on the genomes of a bdelloid rotifer, Adineta vaga, and the pea aphid, Acyrthosiphon pisum, using known LGT events as positive controls, as well as on a soil fungus, Laccaria bicolor, and a the black cottonwood tree, Populus trichocarpa. Analysis …

Identification Of A Putative Nuclease From Thermococcus Thioreducens, Jayson Isaza Pagan

Theses

A putative nuclease from Thermococcus thioreducens was expressed in E. coli BL21 (DE3)-Rosetta cells (6.2 g/l). The recombinant protein (TthNuc) was purified using heat precipitation, anion exchange chromatography, and size exclusion chromatography to a purity of 99%. A BLASTp search of the NR database found TthNuc to be 85% identical to an uncharacterized, RecJ endonuclease from the same genus. TthNuc exhibits in vitro divalent metal ion dependent catabolism of single and double stranded DNA. TthNuc was qualitatively shown to have in vitro nuclease activity between 37°-95°C and above pH 8.4 at 75°C. A three dimensional similarity search of the PDB …

Knowledge, Attitude, And Practice Of Electronic Nicotine Delivery Devices Among College Students, Kelly B. Vazquez

Theses

Electronic nicotine delivery devices (e-cigarettes) have increased in popularity over the past decade and new research will benefit the community, especially healthcare providers, as they will be providing education. To conduct this study, a Knowledge, Attitude, and Practices survey was administered to students on one college campus using Qualtrics software. Results revealed that 99.4% of students were aware of e-cigarettes, 55.2% had friends who used them, 54% viewed them as safer than cigarettes, 26.3% were unaware of chemicals used, 62.7% were bothered by their use, 58.3% supported ban placements (especially females), and 55.5% thought they could be effective for smoking …

Novel Experimental Method For Studying Trajectories And Wing Kinematics Of Freely Flying Butterflies, Jacob Taylor Cranford

Theses

A novel experimental technique is presented for gathering data on the kinematics and trajectories of flapping insects. An optical tracking facility was used to record the free flight of the Monarch Butterfly (Danaus plexippus). The 5.7mx9.1mx3.0m capture volume allowed enough space to capture large numbers of sequential wing flaps. The system automatically tracked small reflective markers, which were modified to reduce the effects of additional mass on butterfly flight characteristics. This technique was used to record 2,000 flights of 86 different butterflies. A data analysis method is also presented that efficiently extracts information on flapping and body motion. A sample …

A Strategy To Improve Nutrition And Increase Physical Activity In Primary School Children., Lisa Delaney

Theses

Introduction: Paediatric obesity has become a global epidemic with many countries developing strategies to help tackle its prevalence. School based physical activity (PA) and nutrition interventions have proven to play a promising role in tackling childhood obesity.

Background: Project Spraoi is an Irish primary school based intervention. The intervention was delivered to an intervention school to help enhance PA and nutritional behaviour amongst pupils. The intervention school was assigned an 'Energizer'; a trained PA and nutrition change agent who worked with the school to achieve the objectives. For evaluation purposes a control school was recruited.

Methodology: Pupils from the intervention …

A Structured Reality, Jeremy Berke

Theses

Science has become an arbiter of truth in today's society. For example, think of how people say "It's a scientific fact" to imply that their position is infallible. As such, we should understand what science can tell about the universe. In this thesis I argue that science is telling us about the structure of reality, and that science only illuminates the relations among things, and not the things themselves.

Sustainable Packaging Design Visually Explained Guidebook Prototype, Sara Almudhaf

Theses

As the fields of graphic and packaging design continue to evolve, it is important to keep their applications sustainable and green. Unaware graphic and packaging designers need to have an easy-to-comprehend source of information about sustainability. Developing an educational information graphics guidebook prototype has potential to serve as a unique tool for understanding the need for sustainable packaging design. The purpose of it is to eases the understanding of a complex system and enables users to discover relationships and connections among design, economy, environment, and society.

This prototype project involved designing a comprehensive sustainability symbol set where no satisfactory symbol …