Life Sciences Commons^™

Quantifying Mutational Impacts On Intrinsic Dna Flexibility In Prokaryotic Genomes, Mohammed Alawad

Theses

The existence of synonymous codon biases across all taxonomic groups is a long standing problem in biology. While codon bias seems to be adequately explained by the maintenance of translation efficiency and accuracy in some organisms, there is still no adequate explanation of why codon biases universally track the intergenic gc content, as these regions of the genome would not be under selection pressures affecting translation. One part of the story may come from the triplet nature of codon in which each third position defines the minor groove width and thus affects the basic structure of the DNA by altering …

Performance Comparison Of Five Rna-Seq Alignment Tools, Yuanpeng Lu

Theses

Aligning millions of short reads to a reference genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data is discrete in nature, therefore with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. To provide guidance in the choice of alignment algorithms, five different alignment tools for RNA-Seq data are evaluated. In order to compare the …

Polyaseeker: A Computational Framework For Identifying Polyadenylation Cleavage Site From Rna-Seq, Xiao Ling

Theses

Alternative polyadenylation (APA) of mRNA plays a crucial role for post-transcriptional gene regulation. Recently, advances in next generation sequencing technology have made it possible to efficiently characterize the transcriptome and identify the 3’end of polyadenylated RNAs. However, no comprehensive bioi nformatic pipelines have fulfilled this goal. The PolyASeeker, a computational framework for identifying polyadenylation cleavage sites from RNA-Seq data is proposed in this thesis. By using the simulated RNA-seq dataset, a novel method is developed to evaluate the performance of the proposed framework versus the traditional A-stretch approach, and compute accurate Precisions and Recalls that previous estimation could not get. …

A Gpu Program To Compute Snp-Snp Interactions In Genome-Wide Association Studies, Srividya Ramakrishnan

Theses

With the recent advances in the next generation sequencing technologies, short read sequences of human genome are made more accessible. Paired end sequencing of short reads is currently the most sensitive method for detecting somatic mutations that arise during tumor development. In this study, a novel approach to optimize the detection of structural variants using a new short read alignment program is presented.

Pairwise interaction effects of the Single Nucleotide Polymorphisms (SNPs) have proven to uncover the underlying complex disease traits. Computing the disease risk based on the interaction effects of SNPs on a case - control study is a …

Genome Wide Search For Pseudo Knotted Non-Coding Rnas, Meghana S. Vasavada

Theses

Non-coding RNAs (ncRNAs) are the functional RNA molecules that are involved in many biological processes including gene regulation, chromosome replication and RNA modification. Searching genomes using computational methods has become an important asset for prediction and annotation of ncRNAs. To annotate an individual genome for a specific family of ncRNAs, a computational tool is interpreted to scan through the genome and align its sequence segments to some structure model for the ncRNA family. With the recent advances in detecting an ncRNA in the genome, heuristic techniques are designed to perform an accurate search and sequence-structure alignment. This study uses a …

Deer Impact And Plant Resistance Traits, Xueyang Fan

Theses

White-tail deer (Odocoileus virginianus), a generalist herbivore, are widely considered to influence ecological communities, ecosystems and human wellbeing by foraging preferentially on certain plant species. Previous research has shown that high deer density can change the relative abundance of tree species in forest communities. Furthermore, some evidence shows that resistance traits of plants can influence plant photosynthetic ability which is an important factor in an ecosystem. The purpose of this experiment is to test whether plant resistance traits can change within species when they are exposed to high levels of deer herbivores. The experiment, established in 1979, enclosed …

Rna-Sequence Analysis Of Human Melanoma Cells, Jharna Miya

Theses

RNA-sequencing refers to the use of high throughput sequencing technologies that are used to sequence cDNA in order to get the complete information of a sample’s RNA content. The objective of this study is to analyze this data in different aspects and to characterize gene expression. Besides this characterization, the data was also used to investigate the effect of sequencing depth on gene expression measurements.

This research focuses on quantitative measurement of expression levels of genes and their transcripts. In this study, complementary DNA fragments of cultured human melanoma cells are sequenced and a total of 139,501,106 million 200-bp reads …

Development Of A Recombinant Lactobacillus Salivarius For Prophylactic Applications Against Mycobacterium Avium Subspecies Paratuberculosis And Johne’S Disease, Christopher Johnston

Theses

Current whole-cell vaccines against Mycobacterium avium subsp. paratuberculosis, the etiological agent of Johne’s disease, are unable to provide complete protection against infection. Moreover, such whole-cell formulations interfere with diagnostic tests for bovine tuberculosis (Mycobacterium bovis). The development of subunit vaccines, those which are preferentially based on one, or a select few, immunodominant protective antigens is considered as the realistic next step in overcoming these issues. The (MAP) K-10 genome is a single circular chromosome of 4,829,781 base pairs and encodes 4,350 predicted ORFs. In order to identify MAP specific proteins for subsequent incorporation within a mucosal based vaccine development, a …

Evaluation, Adaptation And Validation Of A Model To Predict Grass Growth In Ireland, Christina Hurtado Uria

Theses

Budgeting grass supply allows producers to minimise the quantity of purchased feed required in the diet of grazing livestock. One tool for managing grass supply could be a mathematical model that can simulate grass growth. The development of such a model would allow better management around the variability of feed supply and help identify feed surpluses and deficits, and therefore increase the accuracy of management decisions. This would be a key feature of profitable milk and meat production systems in the future which will be hugely important as global food demand increases due to population growth. It is forecasted that …

Identification And Characterisation Of Campylobacter Ureolyticus: A New And Emerging Gastrointestinal Pathogen, Susan Bullman

Theses

Campylobacter jejuni is universally recognized as the leading bacterial cause of human gastroenteritis. However, within recent years a growing number of non- jejuni/coli Campylobacter species have been acknowledged as emerging human and animal pathogens. Advances in molecular diagnostics and development of pioneering culture methodologies have led to the detection of a range of under-appreciated and nutritionally fastidious Campylobacter species, including C. ureolyticus. Herein, we provide the first report of C ureolyticus in the faeces of patients presenting with gastroenteritis and suggest a role for this organism as an emerging enteric pathogen.

Employing a two-tiered molecular study, we report C. ureolyticus …

How The Use Of Social Media As A Public Relations Tactic Has Aided Animal Rescue Organisations In Raising Awareness Of Their Cause, Carole Hennessy

Theses

This study aims to contribute to the understanding of the non-profit sector, in particular animal welfare organisations and how social media can be used as a Public Relations tactic which in turn enables them to raise awareness of their cause.

A qualitative research design was deemed the most suitable by the researcher. Semi-structured interviews and a content analysis in the form of a netnographic analysis of the chosen non-profit organisations Facebook pages were used to collect the primary data. Interviewees were chosen on the basis they had knowledge, experience and exposure in their area.

Research findings indicate that social media …

Novel Liquid Chromatography - Fourier Transform Mass Spectrometry (Ms) And Triple Quadrupole Ms Methods For The Determination Of Diarrhetic Shellfish Poisoning (Dsp) Toxins., Bébhine Carey

Theses

Harmful algal blooms (HABs) appear to be on the rise globally, which not only has a negative impact on the shellfish industry but can also cause human and animal intoxications. In order to advance our knowledge of HABs, specific and sensitive analytical methods are required to aid in monitoring shellfish and algal samples for biotoxins, harmful to consumers.

The Isolation And Characterisation Of Acientobacter Baumannii Bacteriophage, Mohamed Farag M. Elbreki

Theses

Acinetobacter baumannii is a pathogen, which has an increasing prevalence of multidrug resistance. It exists widely in natural environments, and frequently in health-care settings where it has proven difficult to eradicate using antibiotic therapy. A possible alternative to conventional antibiotics is the use of bacteriophages (phages) as antibacterials. In this project, extensive screening of environmental samples such as soils, sewage and waters was undertaken to identify suitable phages. Three phages were successfully isolated from municipal waste in the Cork area. These were subsequently characterized in detail and examined by electron microscopy, which showed that they were all of the Myoviridae …

Exploitation Of The Bacteriophage-Derived Peptidase Chapk, Pierre-Mehdi Hadbi

Theses

This project investigated an anti-staphylococcal bacteriophage-derived peptidoglycan hydrolase enzyme, namely a cysteine-histidine amydohydrolase/peptidase (CHAP_k). The study focused firstly on optimizing the production of recombinant CHAP_k, which was previously cloned in an E. coli expression system, and sets out the resulting optimal Standard Operating Procedures (SOPs) for production, purification and determination of concentration and activity of the resulting protein stock. A typical yield resulting from the investigation was 300pg of CHAP_k from one litre of E.coli culture. The activity of the purified enzyme was typically in the region of 190U nmol ’. Secondly, the project investigated …

The Interaction Between Hedgehog And Tgf-Β Signalling Pathways In Malignant Mesothelioma, Keyuri Koriya

Theses

Malignant mesothelioma (MM) is an aggressive cancer, the consequence of which is neoplastic transformation of mesothelial cells and is strongly associated with previous asbestos exposure. The disease is associated with poor patient survival due to difficulties in diagnosis and treatment options currently available. Therefore, it is essential to identify novel molecular targets that can be used to develop new treatment opportunities. Hedgehog (Hh) and transforming growth factor-beta (TGF-β) signalling pathways are involved in numerous overlapping developmental processes as well as tissue repair and tumorigenesis. Recently, TGF-β has been shown to induce the expression of Hh signalling effector molecules, the Gli …

Determining A New Alignment Scoring Matrix For Disordered Proteins, Adam Handen

Theses

Intrinsically disordered proteins (IDPs) are polypeptide sequences that do not form a rigid three dimensional structure when isolated in the cytosol of the cell. These sequences are very common in most genomes, and usually are involved in many protein-protein interactions. IDPs also play a key role in many diseases, including cancer and Huntington's disease. However, IDPs are difficult to study because of their amorphous shape, high mutation rate, and unique amino acid composition. These obstacles make homology studies especially difficult.

This study focused on generating a new substitution matrix designed to aid in homology studies of IDPs. The matrix was …