Life Sciences Commons^™

Fast Program For Sequence Alignment Using Partition Function Posterior Probabilities, Meera Prasad

Theses

The key requirements of a good sequence alignment tool are high accuracy and fast execution. The existing Probalign program is a highly accurate tool for sequence alignment of both proteins and nucleotides. However, the time for execution is fairly high. The focus is therefore, to reduce the running time of the existing version of Probalign, maintaining its current accuracy level.

The thesis conducts a detail analysis of the performance of Probalign to bring down the running time of the existing code. A modified version of Probalign, Version 1.4 is released. A new program for sequence alignment with faster computation is …

The Cell Biology Of Multi-Nucleated Giant Cell Formation, Johnathan L. Bartee

Theses

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Aminormotiffinder - A Graph Grammar Based Tool To Effectively Search A Minor Motifs In 3d Rna Molecules, Ankur Malhotra

Theses

RNA Motifs are three dimensional folds that play important role in RNA folding and its interaction with other molecules. They basically have modular structure and are composed of conserved building blocks dependent upon the sequence. Their automated in silico identification remains a challenging task. Existing motif identification tools does not correctly identify motifs with large structure variations. Here a “graph rewriting” based method is proposed to identify motifs in real three dimensional structures. The unique encoding of A Minor Searcher takes into consideration the non canonical base pairs and also multipairing of RNA structural motifs. The accuracy is demonstrated by …

Extra Food Intake And Depressive Symptoms In Adolescents: Is There A Relationship?, Elizabeth Bradshaw

Theses

This pilot study explored the potential role of food on young people’s mental health. Specifically, the aim was to determine if a relationship exists between extra food intake and depressive symptoms in adolescents’ age 12-17 years. It has been documented that mental health problems in young people result from a complex interaction of risk and protective factors. Eating behaviours and food intake has been investigated in early adolescence (age 10-14), however the specific contribution of extra food on depressive symptoms in mid adolescence has not been determined.

Extra food intake and depressive symptoms were collected from girls and boys in …

Characterisation Of Bacterial Extracellular Polysaccharides (Eps) And Other Complex Carbohydrates With Prebiotic Potential, Padraigin Murphy

Theses

Prebiotics are selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon host well-being and health’ It is not the prebiotic by itself but rather the changes induced in microflora composition that is responsible for its effects. Several sources of prebiotic were used in this study, namely extracellular polysaccharides (EPS) originating from Lactic Acid Bacteria (LAB), barley, oat. Laminaria digitata. Laminaria hyperborea and Saccharomyces cerevisiae. EPS-producing LAB were isolated from a wide variety of environmental and gastrointestinal niches. The strains were typed and classified according to their EPS-producing ability …

Enhanced Surveillance And Characterisation Of Three Significant Gram-Positive Pathogens, Annmarie Mollaghan

Theses

Clinical microbiology has been revolutionised in recent years by the introduction of molecular biology. Traditionally, the gold standard for diagnosis in the clinical microbiology laboratory has been culture, which in some cases, is gradually being replaced by molecular detection methods, particularly where the pathogen is difficult to grow or to identify, or when the significance of an organism is dependent on the detection of specific markers of pathogenicity, such as toxins. Many fastidious bacteria which are difficult to culture and present public health implications, i.e. Mycobacterium tuberculosis. Chlamydia trachomatis and Neisseria gonorrhoea, can now be detected using commercial molecular assays …

Purification, Characterisation And Applications Of A Cloned Staphylococcal Bacteriophage Lysin For The Control Of Multi-Drug Resistant Staphylococcus Aureus Including Mrsa, Mark Fenton

Theses

The work presented in this thesis focuses on the purification, characterisation and practical applications of an anti-staphylococcal lysin (LysK) and its single-domain truncated derivative (CHAP_k) against pathogenic staphylococci including meticillin resistant Staphylococcus aureus (MRSA). Both proteins were purified to greater than 90% homogeneity. Affinity chromatography was applied as the optimum method for LysK purification and ion-exchange chromatography was successfully applied to CHAP_k. The lytic spectrum of LysK was investigated by zymogram analysis where the enzyme exhibited strong activity against a range of staphylococci regardless of their origin, sequence type (ST) or antibiotic resistant profile. This analysis …

Identification And Characterization Of Equine Rotaviruses In Southern Ireland, Crystal Cronin

Theses

Group A Rotaviruses(GARVs) are enteric pathogens which induce acute gastroenteritis in infants, neonates and the young of many animal species. During a 4 year study (2005-2009), 64 fecal samples from symptomatic foals, from several counties, in the south of Ireland, were molecularly characterized to determine the VP& (G type), VP4 (P type), and NSP4 antigenic specificities. Globally, G3 [P12] and G14[P12] are recognized as the predominant equine GARV strains. Twenty-two samples (34.38%) were found to contain G3 viruses, while 21 samples (32.81%) contained G14 viruses. In this study, there was a distinct increase in the incidence of mixed infections circulating …

The Evolution Of Bacteriophages E11/2 And E4/Lc For Control Of Verocytotxigenic E.Coli At Key Stages In The Beef Chain, Bríd Coffey

Theses

The objective of this thesis was lo evaluate the potential of bactcriophages e4/1 c and cl 1/2 ns biocontrol agents for E. coli O157:H7. Initially, e4/lc and el 1/2 were subjected to high-throughput 454 sequencing. The data generated revealed that e4/I c (47,112 bp) is very similar to the lytic E. coli phages RTP and JK06. Interestingly, differences within the tail module led to the identification of a putative site of attachment to E. coli O157:H?. Comparative genomic analysis indicated that el 1/2 (168,470 bp) is a novel member of the T-even group, with high degrees of similarity to T4 …

High Resolution Hybrid Mass Spectrometry For The Determination Of Marine Biotoxins, Azaspiracids, And Their Biotransformation Products., Zuzana Skrabakova

Theses

Azaspiracids (AZAs), polyether marine toxins, are produced by marine microalgae and accumulate in filter-feeding bivalve molluscs, such as mussels, clams, oysters and scallops, while grazing on phytoplankton, from which they derive nutrition. Although being discovered quite recently, AZAs have caused several human intoxication events and thus became a problem for health authorities and shellfish industries. The rapid development of highly sensitive liquid chromatography multiple tandem mass spectrometry (LC-MS/MS, LC-MS") methods enabled the identification of numerous AZA analogues and added to the control of shellfish contamination. Tandem mass spectrometry techniques, while being highly selective and sensitive for determination of AZAs in …

Composition - Structure - Property Relationships In Strontium / Zinc Doped Glass-Ceramics., Mark Looney

Theses

Calcium silicate ceramics are amongst a group of ceramic materials currently utilised as bone graft materials. However, current calcium silicate grafts offer little therapeutic potential and poor mechanical properties. The objective of this project was to examine the composition-structure-property relationships arising from the incorporation of therapeutic ions of strontium (Sr) and zinc (Zn) into calcium silicate glass-ceramics (GC) in order to allow for healthy bone regeneration and antibacterial efficacy. Five compositions were studied with varying mole fractions of Sr and Zn. The GC’s were characterised using differential scanning calorimetry (DSC), x-ray diffraction (XRD) at room and ascending temperatures, x-ray tomography …