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<title>PhD theses</title>
<copyright>Copyright (c) 2013 Royal College of Surgeons in Ireland All rights reserved.</copyright>
<link>http://epubs.rcsi.ie/phdtheses</link>
<description>Recent documents in PhD theses</description>
<language>en-us</language>
<lastBuildDate>Wed, 08 May 2013 07:55:38 PDT</lastBuildDate>
<ttl>3600</ttl>








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<title>A protease resistant insulin like growth factor binding protein 4 as a treatment for prostate cancer</title>
<link>http://epubs.rcsi.ie/phdtheses/58</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/58</guid>
<pubDate>Wed, 10 Apr 2013 03:45:39 PDT</pubDate>
<description>
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	<p><strong>The insulin-like growth factor (IGF) pathway consists of two ligands, IGF I and IGF II, their </strong><strong>two receptors, the IGF I receptor (IGF IR) and IGF MR along with several soluble insulin-like </strong><strong>growth factor binding proteins (IGFBPs). The IGFBPs bind to and modify IGF activity. </strong><strong>However, proteases such as pregnancy associated plasma protein A (PAPP-A) can cleave </strong><strong>IGFBPs, releasing active IGF I to stimulate the IGF IR. Stimulation of the IGF IR leads to </strong><strong>activation of the Akt or mitogen-activated protein kinase (MAPK) pathway that can lead to </strong><strong>transformation, differentiation, proliferation and angiogenesis. Increased IGF IR expression </strong><strong>has been reported in prostate cancer tissue relative to normal or benign tissue. Therefore, </strong><strong>targeting the IGF pathway may prove useful in treating prostate cancer.</strong></p>
<p><strong>Tissue microarrays of prostate tumours were stained with an antibody to the IGF IR. </strong><strong>IGF IR expression was significantly associated with Gleason grade with IGF IR expression </strong><strong>higher in Gleason grade 3 relative to normal/benign prostatic hyperplasia (BPH) tissue and </strong><strong>lower in Gleason grade 5 relative to Gleason grade 3 tissue. There was no significant </strong><strong>difference in plasma IGF I levels between BPH and prostate cancer patients (Gleason score </strong><strong>5 or Gleason score 7). However, there were significantly higher plasma levels of the IGFBP </strong><strong>4 protease, PAPP-A, in Gleason score 5 patients relative to BPH patients.</strong></p>
<p><strong>PC-3M-luc2 cells are a human androgen independent cell line lacking the androgen </strong><strong>receptor. The PC-3M-luc2 cells stably express luciferase allowing them to be imaged </strong><em>in v iv o </em><strong>using bioluminescent imaging. Expression of the IGF pathway components was assessed in </strong><strong>these cells to ensure the IGF pathway was active. Western blot analysis showed that the </strong><strong>PC-3M-luc2 cells expressed the IGF IR which was activated by IGF I. IGFBP 3, IGFBP 4 </strong><strong>and PAPP-A were also expressed. PC-3M-luc2 cells were shown to proliferate in response </strong><strong>to IGF (E3R) (an analogue of IGF I that cannot be bound by IGFBPs) by bromodeoxyuridine </strong><strong>(BrdU) assay. However, the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-</strong><strong>sulfophenyl)-2H-tetrazolium (MTS) assay showed PC-3M-luc2 cells proliferated in response </strong><strong>to IGF I. IGF (E3R) also significantly increased vascular endothelial growth factor (VEGFies) </strong><strong>expression in PC-3M-luc2 cells.</strong></p>
<p><strong>We assessed a PAPP-A resistant mouse IGFBP 4 (dBP4) as a strategy to neutralise </strong><strong>the IGF I ligand. dBP4 was developed by mutation of the PAPP-A cleavage site from 119-</strong><strong>KHMAKVRDIRSKMK-133 to 119-AAMAAVADASAMA-133 and cloned into pTriEx4 Neo</strong><strong>plasmid with C-terminal His-tag for expression in human embryonic kidney cells. Purified </strong><strong>dBP4 was resistant to PAPP-A cleavage and retained IGF I binding capacity. </strong><em>In v itro </em><strong>, dBP4 </strong><strong>significantly inhibited tubule formation by endothelial cells relative to controls or IGF I treated </strong><strong>cells suggesting that dBP4 possesses anti-angiogenic properties.</strong></p>
<p><strong>A Tet inducible expression system was used </strong><em>in v iv o </em><strong>to test the effect of dBP4 on </strong><strong>tumour growth and metastasis in subcutaneous, orthotopic and experimental metastasis </strong><strong>models of prostate cancer. The inducible Tet-On system allowed dBP4 expression to be </strong><strong>induced by doxycycline. Following implantation of PC-3M-luc2 dBP4 cells into non-obese </strong><strong>diabetic, severe combined immunodeficiency, gamma </strong><strong>2 </strong><strong>receptor null (NSG) mice, tumours </strong><strong>and metastasis were monitored by bioluminescent imaging and/or caliper measurements. In </strong><strong>the subcutaneous tumour model, dBP4-expressing subcutaneous tumours were significantly </strong><strong>smaller than controls and in the orthotopic model, bioluminescence was reduced relative to </strong><strong>controls. Mice bearing dBP4-expressing subcutaneous tumours survived significantly longer </strong><strong>than controls. There was no survival difference between mice bearing dBP4-expressing </strong><strong>prostate tumours and controls. IGF I expression within the dBP4-expressing subcutaneous </strong><strong>and prostate tumours was decreased relative to controls. Western blot analysis of tumour </strong><strong>lysates showed that dBP4 inhibited IGF IR activation in both the subcutaneous and prostate </strong><strong>tumours, which may be a consequence of reduced IGF I within the dBP4-expressing </strong><strong>tumours. However, activated Akt was only decreased in the subcutaneous tumours relative </strong><strong>to controls. As tumours require vasculature in order to supply oxygen and nutrients essential </strong><strong>for tumour growth, expression of VEGF was assessed in the subcutaneous tumours. Control </strong><strong>tumours expressed VEGF</strong><strong>164</strong><strong>/</strong><strong>165</strong><strong>, which was not expressed in the dBP4-expressing </strong><strong>subcutaneous tumours.</strong></p>
<p><strong>dBP4 expression inhibited tumour growth in both subcutaneous and orthotopic-</strong><strong>prostate cancer models. As dBP4 expression inhibited endothelial cell tubule formation and </strong><strong>abolished VEGF</strong><strong><sub>164/165 </sub></strong><strong>expression within PC-3M-luc2 tumours growing subcutaneously, this</strong></p>
<p><strong>suggests that dBP4 has either anti-angiogenic or anti-proliferative properties and may</strong></p>
<p><strong>therefore have value as a therapeutic for prostate cancer.</strong></p>

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</description>

<author>Gemma Kirwan</author>


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<title>The application of voxel-based methods to magnetic resonance imaging in the study of psychiatric disorder.</title>
<link>http://epubs.rcsi.ie/phdtheses/57</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/57</guid>
<pubDate>Tue, 09 Apr 2013 07:01:53 PDT</pubDate>
<description>
	<![CDATA[
	<p>While there are a number of psychiatric disorders as classified by the major international coding systems, however, the application of modem neuroimaging methods has only been utilised on a limited basis with some disorders receiving more research attention than others. Consequently, psychiatric phenotypes that have been relatively understudied are investigated further in this thesis. These disorders correspond to psychiatric disorder in: 22ql 1 deletion syndrome, temporal lobe epilepsy, antisocial personality disorder and Asperger syndrome. Subjects with each of these diagnoses were recruited and then compared to healthy matched controls using the application of novel whole-brain voxel-based analyses to their magnetic resonance imaging data whereby white matter integrity and/or brain tissue volume was assessed in each experimental study of this thesis.</p>
<p>In Study 1, young people with 22ql 1 deletion syndrome were found to have significant differences in both white matter microstructure and volume. Additionally, there was preliminary evidence that within 22ql 1 deletion syndrome, some regional differences in fractional anisotropy were associated with allelic variation in COMT and with schizotypy. In Study 2, while significant grey and white matter volume deficits were found in temporal lobe epilepsy with comorbid psychosis, these abnormalities encompassed not only the medial temporal lobe structures but also extended to lateral temporal and extratemporal regions whereby some of the deficits also overlapped with those found in schizophrenia.</p>
<p>In Study 3, reduced fractional anisotropy was found in antisocial personality disorder and psychopathy in tracts of interhemispheric, posterior brain and frontal lobe networks. Additionally, fractional anisotropy deficits in the frontal lobe demonstrated a significant negative correlation with psychopathy measures. Finally, in Study 4, adults with Asperger syndrome were specifically recruited and found to not only demonstrate impairments in white matter microstructural integrity in regions relevant to social skills and behaviour but also in more widespread white matter networks.</p>

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<author>Frederick Sundram</author>


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<title>Chasing electrons : exploring the redox balance of platelet functions</title>
<link>http://epubs.rcsi.ie/phdtheses/56</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/56</guid>
<pubDate>Mon, 08 Apr 2013 06:13:34 PDT</pubDate>
<description>
	<![CDATA[
	<p>The platelet redox environment consists of the blood plasma and within it the lowmolecular weight thiols glutathione and cysteine. Both glutathione and cysteine exist as independent redox couples comprising carefully controlled ratios of the reduced (GSH, Cys) and oxidised (GSSG, CySS) form of each thiol. These ratios yield a GSH/GSSG redox potential and a Cys/CySS redox potential in the plasma. Changes in the redox status of the plasma are manifested by alterations in either the glutathione or cysteine redox potential and are associated with the progression of a large number of disease states including cancer, atherosclerosis and schizophrenia. In addition, oxidative changes in either of the plasma redox potentials have been directly linked with risk factors for cardiovascular disease. The post-translational modification of critical cysteine thiol groups on proteins is linked to such alterations in both the GSH/GSSG and Cys/CySS redox potentials and occurs extracellularly and intracellularly. Platelet integrins in particular are prime targets for redox modification due to their high cysteine content. Although the role of thiol/ disulphide bond exchange in platelet activation is established the effects of a changing redox environment on platelet reactivity are unclear. The aims of this thesis therefore, are to explore the impact and consequences of such changes on platelet function.</p>
<p>Platelet activation was significantly diminished in the presence of either reducing GSH/GSSG or Cys/CySS redox potentials. Moreover, this response was most notable when platelets were activated with collagen only. The redox modulated effects were shown to be specific to the integrin ɑ<sub>2</sub>β<sub>1</sub>, through a mechanism involving disulphide bond reduction. An analysis of the platelet integrin β<em> </em>subunits revealed the presence of the greatest number of potentially reactive cysteine residues within the Pi subunit when compared to the other platelet integrin beta subunit β<sub>3</sub>.</p>
<p>Furthermore, platelet proteins were S-glutathionylated in a reducing extracellular redox environment. The findings of this thesis reveal for the first time how exquisitely sensitive collagen-induced platelet activation is to alterations in the external redox environment. This, in fact, is potentially a novel demonstration of reductive stress regulating platelet reactivity and provides a novel avenue for therapeutic intervention using physiological redox reagents or their precursors.</p>

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<author>Desmond D. Murphy</author>


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<title>Investigating the Role of Life Events on Youth Mental Health Outcomes: A Population-Based Follow-Up Study.</title>
<link>http://epubs.rcsi.ie/phdtheses/55</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/55</guid>
<pubDate>Mon, 08 Apr 2013 04:50:59 PDT</pubDate>
<description>
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	<p><strong>Background: </strong><strong>To address a lack of systematic epidemiological research on youth mental health in Ireland,</strong><strong> </strong><strong>the first large-scale cross-sectional school-based study (The Challenging Times Study) was </strong><strong>carried out eight years ago to determine the prevalence rates of psychiatric disorders in a </strong><strong>population of 212 urban Irish adolescents aged 12-15 years. Baseline results showed that </strong><strong>15.6% of the study population met criteria for a current psychiatric disorder. Eight years later </strong><strong>the present study identified 169 of the 212 (80%) young people now aged 19-23 years.</strong></p>
<p><strong>The aims of the study were to examine: 1) the mental health outcomes and social and </strong><strong>occupational functioning of a cohort of young people (now aged 19-23 years), 2) the </strong><strong>association between life stresses such as poor family functioning, parental separation / </strong><strong>divorce and peer relations, substance use and anti-social behaviour and mental health </strong><strong>outcomes in young adulthood.</strong></p>
<p><strong>Method: </strong><strong>Two hundred and twelve young people, who participated in the original Challenging Times </strong><strong>Study, were invited to participate in an assessment interview. Mental health outcomes and </strong><strong>social and occupational functioning were assessed using the Structured Clinical Interview for </strong><strong>DSM-IV psychiatric diagnoses (SCID I), the Achenbach Adult Self Report and Achenbach </strong><strong>Adult Behaviour Checklist (parental questionnaire).The Me Master Family Assessment </strong><strong>Device was used as a measure of family functioning whilst the Global Assessment of </strong><strong>Functioning (GAF) scale measured quality of life and general functioning. The Stressful Life </strong><strong>Events Schedule for Children and Adolescents a semi-structured interview was used to </strong><strong>identify factors associated with mental ill-health.</strong></p>
<p><strong>Results: </strong><strong>Using a weighted population prevalence analysis, 24.3% (22.4 - 28.9) of the young people </strong><strong>met the criteria for a psychiatric disorder at follow-up, including 5.4% (4.1 - 7.6) with a mood </strong><strong>disorder, 11.2% (9.5 -14.3) with an anxiety disorder, 8.2% (6.7 -11.0) with a substance use </strong><strong>disorder and 7.7% (6.2 -10.4) with alcohol disorders. Logistic regression revealed that an </strong><strong>adolescent diagnosis of being “at risk” of a psychiatric disorder at the Challenging Times </strong><strong>original study was not predictive of poor mental health outcomes at follow-up. Specific </strong><strong>stressful life events were identified as factors associated with poor mental health outcomes.</strong></p>
<p><strong>Conclusion: </strong><strong>This study offers an understanding of the prevalence rates and psychosocial factors </strong><strong>associated with psychiatric disorders in young adulthood in an Irish context. It emphasises </strong><strong>the need for youth mental health Intervention and prevention programmes that equip young </strong><strong>people with the necessary coping skills to deal with life’s many challenges.</strong></p>

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<author>Dearbhla Connor</author>


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<title>Gait impairment in cervical spondylotic myelopathy: Analysis, impact on function, and effect of surgical intervention</title>
<link>http://epubs.rcsi.ie/phdtheses/54</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/54</guid>
<pubDate>Fri, 05 Apr 2013 08:46:01 PDT</pubDate>
<description>
	<![CDATA[
	<p>Chest pain is one of the most frequent complaints in medical settings, yet more than half of cases have no detectable cause. Once a cardiac cause has been excluded, patients are typically discharged with a label of non-cardiac chest pain (NCCP). Patients with NCCP have been shown to have poor outcomes in terms of continued symptoms, distress, and continuing concern about heart disease. In addition, NCCP represents a significant burden to health services. The aetiology and management of NCCP is under-researched and poorly understood. This study sought to examine the predictors of persistent pain and health service use for patients in whom a cardiac diagnosis had been excluded. It also sought to explore how patients interpreted their symptoms in the context of normal test results, and the impact of their experiences with health services on these interpretations.</p>
<p>A mixed-methods design was adopted. A prospective cohort study was initially conducted with 145 participants with chest pain who attended exercise stress testing and had normal test results. At one-year follow-up, 69% reported continued pain. In addition, nearly half of participants had returned to their general practitioner and one in ten had attended the emergency department for the investigation of chest pain. In logistic regression analyses, the variables heartburn, pain precipitated by movement, cardiac anxiety, illness perceptions, and lack of communication about test results were predictive of persistent chest pain. When participants with continued chest pain were categorised into persistent healthcare users and non-persistent healthcare users, these variables were predominantly associated with participants with persistent health service use for chest pain. In addition, a number of psychological variables including anxiety and depression distinguished the persistent service users. Employment appeared to be a protective factor against persistent pain and related service use.</p>
<p>A small sample of participants from this cohort was interviewed in a qualitative study informed by the principles of Interpretative Phenomenological Analysis (IPA). Analysis revealed three predominant themes: 1) the disempowerment of normal test results; 2) limbo - the inner struggle of negating and relating to potential causes; and 3) the inadequacy of healthcare to validate and care for symptoms. The dynamic, complex process of interpreting symptoms and deciding whether to seek healthcare was illuminated.</p>
<p>The results indicate that interventions targeting the assessment of a potential gastro-oesophageal or musculoskeletal cause and the reduction of cardiac anxiety are likely to improve outcomes in these patients. Improved communication with patients is also indicated. Psychological factors appear to drive persistent service use and interventions targeting these are likely to reduce medical costs. Patients with NCCP are not a homogenous patient group and an individualised, stepped-care approach to management appears to be warranted.</p>

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<author>Ailish Marie Malone</author>


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<title>Non-Cardiac Chest Pain: the Role of Physical, Psychosocial, and Service-Related Factors in the Persistence of Pain and Health Service Use</title>
<link>http://epubs.rcsi.ie/phdtheses/53</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/53</guid>
<pubDate>Fri, 05 Apr 2013 06:58:37 PDT</pubDate>
<description>
	<![CDATA[
	<p>Chest pain is one of the most frequent complaints in medical settings, yet more than half of cases have no detectable cause. Once a cardiac cause has been excluded, patients are typically discharged with a label of non-cardiac chest pain (NCCP). Patients with NCCP have been shown to have poor outcomes in terms of continued symptoms, distress, and continuing concern about heart disease. In addition, NCCP represents a significant burden to health services. The aetiology and management of NCCP is under-researched and poorly understood. This study sought to examine the predictors of persistent pain and health service use for patients in whom a cardiac diagnosis had been excluded. It also sought to explore how patients interpreted their symptoms in the context of normal test results, and the impact of their experiences with health services on these interpretations.</p>
<p>A mixed-methods design was adopted. A prospective cohort study was initially conducted with 145 participants with chest pain who attended exercise stress testing and had normal test results. At one-year follow-up, 69% reported continued pain. In addition, nearly half of participants had returned to their general practitioner and one in ten had attended the emergency department for the investigation of chest pain. In logistic regression analyses, the variables heartburn, pain precipitated by movement, cardiac anxiety, illness perceptions, and lack of communication about test results were predictive of persistent chest pain. When participants with continued chest pain were categorised into persistent healthcare users and non-persistent healthcare users, these variables were predominantly associated with participants with persistent health service use for chest pain. In addition, a number of psychological variables including anxiety and depression distinguished the persistent service users. Employment appeared to be a protective factor against persistent pain and related service use.</p>
<p>A small sample of participants from this cohort was interviewed in a qualitative study informed by the principles of Interpretative Phenomenological Analysis (IPA). Analysis revealed three predominant themes: 1) the disempowerment of normal test results; 2) limbo - the inner struggle of negating and relating to potential causes; and 3) the inadequacy of healthcare to validate and care for symptoms. The dynamic, complex process of interpreting symptoms and deciding whether to seek healthcare was illuminated.</p>
<p>The results indicate that interventions targeting the assessment of a potential gastro-oesophageal or musculoskeletal cause and the reduction of cardiac anxiety are likely to improve outcomes in these patients. Improved communication with patients is also indicated. Psychological factors appear to drive persistent service use and interventions targeting these are likely to reduce medical costs. Patients with NCCP are not a homogenous patient group and an individualised, stepped-care approach to management appears to be warranted.</p>

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<author>Aisling Sheehan</author>


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<title>The localization of Foxo3a in the mitrochondria</title>
<link>http://epubs.rcsi.ie/phdtheses/52</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/52</guid>
<pubDate>Fri, 05 Apr 2013 04:02:14 PDT</pubDate>
<description>
	<![CDATA[
	<p>The members of the subclass 0 of the Forkhead family of transcription factor are ubiquitous signaling proteins which are involved in various cellular mechanisms such as cell cycle arrest, detoxication, DNA repair, atrophy, metabolism, cell death and control of lifespan, and aging. One of the members of the Foxo family of transcription factor, namely Foxo3a, has been described to be expressed throughout the brain, in particular in the hippocampus, and to have a role in neurological disorders, being activated by insults such as stroke and epilepsy. A prevailing view is that harmful seizures in epilepsy activate Foxo3a in order to eliminate damaged neurons by apoptosis.</p>
<p>Experiments in this thesis were aimed at providing insight into a new localization of Foxo3a within mitochondria. Presently, it has been shown that Foxo3a was localized to mitochondria in several organs in mice, and that Foxo3a binds to the regulatory region of the mitochondrial DNA. The localization of Foxo3a within hippocampal mitochondria of mice was altered during experimentally induced <em>status epilepticus </em>(SE). The mitochondrial level of Foxo3a dropped dramatically after SE. Notably, a drop in mtDNA transcription was observed concomitant with the drop of Foxo3a levels in mouse hippocampal mitochondria. Experiments in this thesis also demonstrate that transcription of mitochondrial DNA is enhanced by the overexpression of Foxo3a in a hippocampal cell line HT-22. Finally, the overexpression of a mitochondrially targeted Foxo3a fusion protein led to a significant protection of the HT-22 cells against cell death induceexposure to glutamate or epoxomicin, but not staurosporine. These data suggest a novel physiological role for Foxo3a in mitochondria, protecting the cell from harmful insults caused by stressors such as oxidative stress and possibly by regulation of the mtDNA.</p>

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<author>Aurelien Caballero-Caballero</author>


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<title>Characterisation of calpain activation in response to excitotoxic events in primary neurons</title>
<link>http://epubs.rcsi.ie/phdtheses/51</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/51</guid>
<pubDate>Fri, 05 Apr 2013 02:35:45 PDT</pubDate>
<description>
	<![CDATA[
	<p>Excitotoxicity resulting from excessive Ca²+ influx through glutamate receptors contributes to neuronal injury after stroke, trauma, and seizures. Increased cytosolic Ca²+ levels activate a family of calcium-dependent proteases with papain-like activity, the calpains. Here we investigated the role of calpain activation during NMDA-induced excitotoxic injury in embryonic (E16-E18) murine cortical neurons that underwent either: (i) excitotoxic necrosis, characterized by immediate deregulation of Ca²+ homeostasis, a persistent depolarization of mitochondrial membrane potential <em>(Ay/m), </em>and insensitivity to <em>bax</em>-gene deletion; (ii) excitotoxic apoptosis, characterized by recovery of NMDA-induced cytosolic Ca²+ increases, sensitivity to <em>bax </em>gene deletion, and delayed Ai//m depolarization and Ca²+ deregulation; or (iii) that were tolerant to excitotoxic injury. Interestingly, treatment with the calpain inhibitor calpeptin, overexpression of the endogenous calpain inhibitor <em>calpastatin, </em>or gene silencing of <em>calpain </em>protected neurons against excitotoxic apoptosis, but did not influence excitotoxic nccrosis. Calpeptin failed to exert a protective effect in oax-deficient neurons, but protected <em>bid- </em>and e/'m-deficient neurons similarly to wild-type cells. To identify when calpains became activated during excitotoxic apoptosis, we monitored calpain activation dynamics by time-lapse fluorescence microscopy, using a calpain-sensitive Forster resonance energy transfer probe.</p>
<p>We observed a delayed calpain activation that occurred downstream of mitochondrial engagement and directly preceded neuronal death. In contrast, we could not detect significant calpain activity during excitotoxic necrosis or in neurons that were tolerant to excitotoxic injuiy. Oxygen/glucose deprivationinduced injury in organotypic hippocampal slice cultures confirmed that calpains were specifically activated during .ax-dependent apoptosis and in this setting function as downstream cell death executioners. Lastly, <em>box </em>gene deletion prevented NMDA-induced alterations to <em>Ay/m, </em>hyperpolarisation and depolarisation were notably diminished, and affected neuronal calcium handling, resulting in increased neuronal survival.</p>

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<author>Beatrice D&apos;Orsi</author>


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<title>Therapeutic Aerosol Bioengineering to treat Mycobacterium tuberculosis infection</title>
<link>http://epubs.rcsi.ie/phdtheses/50</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/50</guid>
<pubDate>Wed, 27 Mar 2013 08:08:44 PDT</pubDate>
<description>
	<![CDATA[
	<p>Tuberculosis is primarily a pulmonary pathogen, which employs alveolar macrophages as its niche environment. Approximately one third of the world’s population is affected with either an active or latent form of Tuberculosis infection. Despite its high prevalence and emerging resistance strains there has been little growth in the therapeutic armamentarium against the mycobacterium. Although current therapy against infection is effective, it has several draw-backs including: lengthy treatment regimen, high prevalence of adverse drug reactions and poor patient adherence. Hepatotoxicity is a particular issue with traditional anti-tubercular formulations; these are oral based and consequently are subject to first pass metabolism, the metabolites produced at this point can cause inflammation of the liver. The high dosing requirements via the oral route to treat this pulmonary pathogen could be circumvented by localising therapy to the lungs in an inhalable anti-tubercular formulation.</p>
<p>Targeting anti-tubercular therapeutics to alveolar macrophages using microparticle technology aims to reduce systemic toxicity, increase local concentrations of therapeutics and potentially reducing the frequency of dosing requirements. Localising therapy increases local concentration levels of anti-tubercular therapeutics, however, if these therapeutics are encapsulated into a particulate delivery system they can have longer retention time in the lungs also. There has been extensive research into inhaled TB therapies to target anti-MTb drugs directly to the lungs. The work presented herein sought to improve alveolar macrophage targeting by preparing microparticles with optimal targeting properties containing anti-tubercular molecules. The use of novel excipients and microparticles in respiratory drug delivery is limited by the understanding of how these molecules interact with biological systems. The use of high content imaging platforms both in vitro and in vivo<em></em>employed within this thesis will serve as a framework for development and testing of other respiratory delivery systems. The microparticles used in this study are based on poly (lactide-co-glycolic) acid(PLGA), a biodegradable polymer broken down through non-enzymatic hydrolysis into lactic and glycolic acid monomers.</p>
<p>This polymer is currently FDA approved for non-pulmonary use and by developing a robust understanding of particle - cell interaction, it might bolster the argument for approval of its use in the lungs for specific clinical indications such as TB.</p>
<p>This project has developed bioengineered microparticle carrier systems to efficiently target the alveolar macrophage, the niche environment of the pathogen. These microparticle delivery systems are composed of a biodegradable polymer (PLGA), which encapsulates a drug with the goal of achieving optimal cellular concentrations of the therapeutic within the cell. The work has demonstrated that 2.1pm sized microparticles are optimal for targeting alveolar macrophages <em><em>in vitro </em></em>without affecting cellular viability. The use of coatings such as gelatin (Type A) significantly enhanced microparticle uptake by THP-1 cells and alveolar macrohpages obtained from bronchoalveolar lavage of human volunteers.</p>
<p>The compatibility of these microparticles with a range of anti-tubercular drugs (PAS, rifampicin and capreomycin) has also been demonstrated. Drug loaded microparticles exhibited a controlled release profile over 21 days and were shown to be effective at impairing <em><em>Mycobacterium tuberculosis </em></em>(MTb)growth in an <em><em>in vitro </em></em>cell model.</p>
<p>Several obstacles must be overcome before a successful inhalable therapy can be developed. In order for an inhalable anti-tubercular formulation to be successful it must be capable of depositing in the alveolar region of the lungs. These obstacles include patient physiology, device selection, powder flowability and aerosol properties. All these parameters are inter-linked. The device employed (Spinhaler) is a single dose drypowder inhaler device that is simple to use, cheap and a high respirable fraction was achieved with this device. Optimisation of the lyophilisation process enhanced aerosol performance while the addition of mannitol (5% w/w) to coated microparticles was required for optimal aerosol performance. However, a caveat to this is that it was achieved at a high flow-rate, which may not be representative of patients with severely impaired lung function. Newer dry-powder inhaler devices are capable of achieving high respirable doses at low flow-rates and may be used to further develop the technology described in this thesis.</p>
<p>Simulating the phagocyte is an exciting concept in the design of novel anti-tubercular therapies and in addition to drug targeting to alveolar macrophages, the microparticle delivery systems showed potential to modulate innate immune responses to MTb infection. Microparticles coated with gelatin (Type A) produced the highest level of NFkB induction and autophagasome formation. This resulted in a significant reduction of MTb viability when infected cells were treated with drug-free coated microparticles. Uncoated microparticles gave a non-significant decrease in MTb viability.</p>
<p>Combining the immune activating properties of these microparticles with the chemotherapeutic effect of anti-tubercular drugs provides a new formulation for old drugs that could improve sputum conversion times and* by localising this therapy to the lung, non-specific systemic side-effects could be avoided.</p>
<p>Finally, a novel coating of Interferon-gamma (IFN-y) on these drug loaded microparticles was designed to achieve maximal immune, stimulation with the combinatorial effect of the chemotherapeutic (rifampicin). This formulation showed promise <em><em>in vitro </em></em>but the small pilot study suggested potential immunopathology caused by the IFN-y coated microparticles. Optimisation of the dosing regimen may be required for further <em><em>in vivo </em></em>development. The <em><em>in vitro </em></em>work establishes this combinatorial potential of an immune modulating agent on the microparticle surface combined with a chemotherapeutic inside the particle, particularly with reference to resistance strains of MTb infection. The establishment of an <em><em>in vivo </em></em>imaging system to measure mycobacterial growth / killing in real-time herein will also expedite development of further novel inhalable anti-tubercular formulations.</p>

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<author>Ciaran Lawlor</author>


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<title>Modulation of apoptosis signalling by proteasome inhibition : a single cell analysis</title>
<link>http://epubs.rcsi.ie/phdtheses/49</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/49</guid>
<pubDate>Tue, 26 Mar 2013 09:40:41 PDT</pubDate>
<description>
	<![CDATA[
	<p>The proteasome inhibitor bortezomib has been successfully used in cancer therapy. Proteasome inhibition modulates various signalling pathways and causes cell death in cancer cells while sparing normal cells. In this thesis we characterise the apoptotic signalling kinetics and sequential events in response to proteasome inhibition in single cells. We identified a novel non-canonical pathway to apoptosis induction in cells with an inhibited intrinsic apoptotic pathway. Proteasome inhibition promoted the apical activation of caspase-8 in these cells. For the first time we demonstrated that autophagy induction in response to proteasome inhibition is critical for caspase-8 activation. Caspase-8 activation resulted in limited apoptosis, which can be further increased by antagonism of the endogenous caspase inhibitor XIAP. Therefore our findings provide an alternative treatment strategy to restore apoptosis susceptibility in highly resistant cancer cells.</p>
<p>Proteasome inhibitors have also been used to re-sensitise resistant cancer cells to TRAIL treatment. Since no kinetic data from single cells are available yet, it is not known whether, when and where the intracellular signalling kinetics of TRAIL-induced apoptosis are affected by proteasome inhibition. We therefore quantified the signalling kinetics of TRAIL-induced apoptosis in response to proteasome inhibition in single cells. Depending on the TRAIL concentration we found two modulation sites, which interfered with TRAIL signalling kinetics upon proteasome inhibition: caspase-8 activation at low doses and the threshold for mitochondria1 permeabilisation at high doses. Our results suggest that upregulation of cFLIP and Mcl-1 by impaired protein degradation were responsible for delayed caspase-8 activation and prolonged caspase-8 activation before MOMP, respectively. Our findings therefore indicate that the synergy between TRAIL and proteasome inhibition is probably based on the stabilisation of active caspases rather than enhanced DISC formation, as is often proposed in the literature.</p>

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</description>

<author>Maike A. Laussmann</author>


</item>






<item>
<title>Identifying new transcriptional targets for SRC-1 in breast cancer</title>
<link>http://epubs.rcsi.ie/phdtheses/48</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/48</guid>
<pubDate>Tue, 26 Mar 2013 08:16:47 PDT</pubDate>
<description>
	<![CDATA[
	<p>SRC-1 is a p160 nuclear receptor co-activator protein that has been implicated as an important mediator of breast cancer metastasis. A small number of direct SRC-1 target genes have been identified to date. The aim of this work was to verify the recently discovered SRC-1 target SlOOB and to adopt a genome wide approach using modern, high throughput technologies to identify new SRC-1 transcriptional targets.</p>
<p>To identify novel SRC-1 target genes luminal B LY2 breast cancer cells were used to perform the first ChlP-sequencing experiment of SRC-1. Affymetrix whole genome expression arrays were used to analyse gene expression in LY2 cells treated with SRC-1 siRNA in comparison with those treated scrambled siRNA to complement the ChlP-seq experiment. SRC-1 peaks within the genome were focused near transcription starts sites and often in close proximity to an estrogen response element. Three new putative SRC-1 target genes were selected for further validation.</p>
<p>ADAM22 is a transmembrane disintegrin protein that has been shown to mediate cell migration but has yet to be implicated in tumourigenesis. Knockout, overexpression and ChlP studies confirm ADAM22 as an SRC-1 target gene. Expression of ADAM22 was identified in 49% of patients with breast cancer and its expression was associated with an almost two fold increase in rate of disease relapse. Two other genes, namely BCAS3 and CUXl were identified and validated as SRC-1 target genes and both of these have a known role in breast tumour progression. Elevated levels of SlOOB were detectable in the blood of 10% of patients with breast cancer. Elevated serum SlOOB at time of diagnosis is an independent predictor of disease progression in breast cancer.</p>
<p>An unbiased, genome wide approach has identified a variety of novel, direct SRC-1 target genes. A series of molecular and translational studies have validated SlOOB as a clinically important and detectable target of SRC-1 while ADAM22, as transmembrane protein may offer the first therapeutic target to disrupt the central role of SRC-1 in mediating breast cancer metastasis.</p>

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</description>

<author>Damian McCartan</author>


</item>






<item>
<title>Characterisation of angiogenin uptake and signalling in astrocytes</title>
<link>http://epubs.rcsi.ie/phdtheses/47</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/47</guid>
<pubDate>Tue, 26 Mar 2013 07:54:59 PDT</pubDate>
<description>
	<![CDATA[
	<p>Amyotrophic Lateral Sclerosis (ALS) is a progressive, fatal neurodegenerative disease of the motor system affecting both upper and lower motoneurons. The majority of ALS cases occur sporadically, however roughly 10 % show a hereditary component. Mutations in the hypoxiainducible factor angiogenin segregate with ALS pedigrees and the protein is expressed in motoneurons. Angiogenin shows potent neuroprotective properties <em>in vitro </em>and <em>in vivo </em>and application of recombinant human angiogenin to mixed spinal cord cultures revealed non-neuronal uptake of the protein. As the disease affects both motoneurons and non-neuronal neighbouring cells like astrocytes and microglia, a paracrine mechanism of neuroprotection has been suggested.</p>
<p>This study was performed to gain insights into the mechanism of angiogenininduced neuroprotection via surrounding glial cells focusing on astrocytes. The vesicular internalisation of recombinant human angiogenin by primary astrocytes was investigated in culture using pharmacological inhibitors, cell transfection and immunocytochernistry. This revealed that angiogenin endocytosis by astrocytes is clathrin-dependent and involves dynamin for vesicle scission. Vesicle budding and trafficking do not require a functional microtubule network. A fraction of the internalised angiogenin is targeted for lysosomal degradation, while the majority remains in uncharacterised sorting endosomes. The receptor for angiogenin on astrocytes was identified to be the heparansulfate proteoglycan syndecan 4 by colocalisation studies and protein knock down.</p>
<p>To further elucidate the role of angiogenin in paracrine neuroprotection, modification of the astrocyte secretome was investigated in response to angiogenin treatment by quantitative mass spectrometry. Metabolic protein labelling by Stable Isotope Labelling with Amino acids in Culture (SILAC) was optimised for primary astrocytes and proteins were identified by Fourier transform tandem mass spectrometry (nano-LC-FT-MSIMS). This screen identified over 1,500 proteins in the supernatant of primary astrocytes, many of which are known to exhibit extracellular location like components of the Extracellular Matrix (ECM), cytokines, growth factors and growth factor binding proteins. However, proteins with established intracellular function like splicing factors and ribosomal proteins were detected, too. Quantification using the MaxQuant software showed significant regulation of over 100 proteins in response to angiogenin treatment. The most strongly regulated proteins are involved in modifying the ECM or contribute to immune responses and might be responsible for the neuroprotective effects of angiogenin. These data also suggest the involvement of surrounding immune and endothelial cells in the biological activity of angiogenin. Additionally, local transfer of factors involved in protein translation from astrocytes to surrounding cells may be affected by angiogenin.</p>
<p>In conclusion, this study has shed new light on the role of angiogenin in the complex cellular interplay in the Central Nervous System (CNS) focusing on astrocytes and how they interact with neighbouring cells. Further studies will be necessary to elucidate the functional signalling outcome of angiogenin focusing on its neuroprotective activities, in particular regarding ALS pathology with the aim of finding new therapies for this fatal disease.</p>

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</description>

<author>Alexandra Skorupa</author>


</item>






<item>
<title>Research in pharmacy education - lessons from programme design and development at a new School of Pharmacy</title>
<link>http://epubs.rcsi.ie/phdtheses/46</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/46</guid>
<pubDate>Wed, 16 Jan 2013 06:59:38 PST</pubDate>
<description>
	<![CDATA[
	<p>Pharmacy education is an evolving field, influenced by a complex relationship between National, European and International policies, regulation and practice. The opening of a new School of Pharmacy, at a time of great change, provided the context for the research question:</p>
<p><em>How is pharmacy education, delivered by a new School of Pharmacy, with new undergraduate and postgraduate curricula, novel teaching and assessment strategies, reflected in student perception, performance and preparedness for professional practice, and what are the lessons for educators?</em></p>
<p>The thesis addresses three major areas; interprofessional education, competency assessment and evaluation. Quantitative methods, including the use of validated tools (Readiness for Interprofessional Learning Scale, Attitudes to Health Professionals Questionnaire, Course Experience Questionnaire), and relevant research ("MPharm: Where are we now" and the "Pharmacy Education and Accreditation Reviews" reports) were employed. Analysis of examination results and tracking of student progress was also undertaken.</p>
<p>An unexpected finding was that early interprofessional education was less successful than anticipated. Views on professional identity and stereotypes influenced a desire for uniprofessional education. However, online interprofessional education can facilitate learning of large groups of geographically dispersed professionals and may offer potential for postgraduate interprofessional education.</p>
<p>The research highlights the value of the Objective Structured Clinical Examination (OSCE) for assessing competency in pharmacy, but emphasises the importance of embedding quality assurance into the design and delivery with due regard for validity and reliability. The research indicates that it is helpful to reflect on the outcomes to determine if assessment policies are robust and credible.</p>
<p>Evaluation strategies are important in the development of new programmes. The introduction of the National Pharmacy Internship Programme provided a unique and previously unexplored opportunity to move beyond student perception, evaluate outcomes at entry-to-practice and benchmark the quality of education.</p>
<p>Some additional significant findings emerge from tracking student progress. There is no evidence that a lack of advanced second-level science education has a deleterious effect on performance. Graduate students perform better than school leavers, despite having significantly lower points on entry. their merit in considering a graudate entry programme, although it is not the currently proprosed strategy for pharmacy education in Ireland.</p>
<p>Pharmacy education, delivered by a new School of Pharmacy using novel and outcomes focused teaching and assessment strategies was reflected well in student perception, performance and preparedness for practice. The research is timely and important as Ireland moves towards the development of a new five-year integrated programme where the students are prepared to directly enter professional practice.</p>

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</description>

<author>Judith Strawbridge</author>


</item>






<item>
<title>Cellular and molecular basis of mammary microcalcifications</title>
<link>http://epubs.rcsi.ie/phdtheses/45</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/45</guid>
<pubDate>Thu, 07 Jun 2012 09:00:08 PDT</pubDate>
<description>
	<![CDATA[
	<p>Mammary microcalcifications represent one of the most reliable mammographic features of non-palpable breast cancer and are often the sole indicator of the disease. However, it is unknown whether these microcalcifications are a sign of degeneration or an active cellular process. The aims of this project were to establish and characterise an <em>in vitro </em>model of mammary mineralisation in monolayer, 3D scaffolds and <em>in vivo </em>and to investigate the molecular mechanisms involved in this process, focusing on the potential roles bone matrix proteins and microRNAs. Several mammary cell lines were capable of depositing hydroxyapatite <em>in vitro </em>when treated with an osteogenic cocktail (10mM p-glycerophosphate and 50pglml ascorbic acid). Mineralisation potential was found to be associated with more aggressive mammary cell phenotypes. Increasing concentrations of p-glycerophosphate, calcium and exogenous hydroxyapatite enhanced 4T1 cell migration. In contrast, exogenous calcium oxalate had no effect. Real-time RTPCR detected changes in the expression of alkaline phosphatase (ALP), bone sialoprotein, osteopontin (OPN) and collagen type I in mineralising 4T1 cells. These are all known markers of osteoblast mineralisation. 4T1 cells were also capable of mineralising within 3D collagen scaffolds when treated with the osteogenic cocktail. In contrast, no mineralisation was detected following BMP217 treatment of the 4T1 cells in the scaffolds. Further studies found that BMP2 enhances the mineralisation of 4T1 cells <em>in vitro, </em>however an exogenous source of phosphate is essential to this process. The <em>in vivo </em>mineralisation potential of 4T1 and 4T1.2 cells was also examined. These cells were implanted in the mammary fat pad of BALBIc mice and mineralisation was confirmed in 6 out of 11 primary tumours. Inhibition of ALP and sodium-phosphate cotransporter pumps by treatment with levamisole and phosphonoformic acid respectively, inhibited rnineralisation of 4T1 cells. Exogenous ALP was found to enhanced mineralisation. Exogenous OPN and pyrophosphate had no effect on mineralisation of 4T1 cells, however this may be due to high endogenous levels of ALP which would counteract the potential inhibitory effects of OPN and pyrophosphate. The 4T1 cells were found to have greater ALP activity in comparison to the non-mineralising MCFlOa cell line. The potential role of microRNAs in mammary mineralisation was examined using microRNA microarrays. 25 differentially regulated microRNAs were identified in mineralising of 4T1 cell. Many of the predicted targets of these microRNAs are regulators of osteoblast mineralisation. Of particular interest are miR-20-5p, which was upregulated and mmu-miR- 133a, which was downregulated as the same pattern of expression has been reported in the literature for physiological osteogenesis. This is the first time that mammary cell lines have been shown to be capable of mineralising <em>in vitro. </em>The results presented here indicate that the formation mammary microcalcifications may be an active regulated process and several markers of osteoblast mineralisation have been identified that may play a key role in this process.</p>

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</description>

<author>Rachel Cox</author>


</item>






<item>
<title>Genome-wide mapping of MYCN transcription factor binding sites and identification of clinically relevant targets in neuroblastoma.</title>
<link>http://epubs.rcsi.ie/phdtheses/44</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/44</guid>
<pubDate>Thu, 07 Jun 2012 07:59:05 PDT</pubDate>
<description>
	<![CDATA[
	<p>Neuroblastoma is a highly genetically heterogeneous form of paediatric cancer with clinical behaviour which can range fiom localised tumours with good prognosis, to widespread metastatic disease with rapid clinical progression and death. High level genornic amplification of the MYCN gene occurs in approximately 20 to 25% of cases and this aberration is the most important genetic indicator of poor clinical outcome. Despite the use of intensive multimodal therapy, patients with MYCN amplified neuroblastoma tumours have less than a 30% chance of 5- year survival. Thus the characterisation of MYCN binding in the NB genome and identification of downstream MYCN targets is critically important for the development of alternative treatment regimens and improving patient survival. The aim of this study was to elucidate MYCN genome-wide binding patterns and to determine its functional effects on downstream target genes, and thereby to identify MYCN function in neuroblastoma disease pathogenesis. To achieve this we performed chIP-chip analysis of MYCN binding sites in neuroblastoma cell lines expressing both high and low levels of the MYCN protein in order to characterise the binding behaviour of MYCN in these states. Our analysis has revealed that MYCN preferentially binds to the non-canonical E-box sequence of CATGTG and to additional motifs when it is overexpressed; potentially indicating that MYCN binding becomes less specific when it is highly abundant. Through gene expression profiling, we also describe a set of novel MYCN target genes which are enriched for genes related to cell cycle regulated upregulated in response to increased levels of MYCN in both tumours and cell lines. Surprisingly, we also observed a striking correlation between MYCN binding and DNA hypermethylation status at interlintragenic sites and within the promoter regions of genes, indicating a novel role for MYCN in the regulation of chromatin structure. We surmised that this association was likely due to the interaction of a methyl-binding protein. ChIP-chip analysis of MECP2 binding sites within the neuroblastoma genome revealed that -70% of hypermethylated MYCN binding sites were also occupied by MECP2. The association was not limited to regions of hypermethylation however, as MeCP2 was also found to co-occupy sites with MYCN which were free of detectable levels of hypermethylation. In conclusion, this study characterises the genome-wide association of MYCN to genomic loci in cell lines expressing both high and low levels of MYCN and characterizes the E-Box motifs to which this oncogenic protein binds. We also describe a set of novel MYCN target genes which are upregulated in response to <strong><em>u </em></strong>increased levels of MYCN which may also play a role in neuroblastoma tumourigenesis. Additionally, we have observed MYCN binding to regions of DNA hypermethylation at a higher than expected frequency and identify the methyl binding protein MECP2 as an interaction partner of MYCN at these loci. Future transcription factor method development may allow a similar such analysis to be performed in primary tumours, thus elucidating finther the mechanism of action of h4YCN in NB pathogenesis.</p>

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</description>

<author>Derek Murphy</author>


</item>






<item>
<title>Estrogen receptor-coactivator interactions in resistance to aromatase inhibitor treatment for breast cancer.</title>
<link>http://epubs.rcsi.ie/phdtheses/43</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/43</guid>
<pubDate>Thu, 31 May 2012 08:39:50 PDT</pubDate>
<description>
	<![CDATA[
	<p>Aromatase inhibitors (Al) are the newest form of endocrine therapy for estrogen receptor (ER)-positive postmenopausal breast cancer and have demonstrated excellent efficacy in clinical trials; however, a proportion of patients treated with Als will relapse with resistant disease. Resistance to endocrine therapy is characterised by cross-talk between ERa and membrane growth factor receptors, such as the epidermal growth factor receptor (EGFR) family, resulting in increased signalling. In Al-resistant molecular models this results in proliferation in the absence of estrogen. The steroid receptor coactivator AIBI increases transcriptional activity of ERa. The aim of this study was to elucidate the role of AlBl as an ERa coactivator in development of resistance to Al treatment, and the consequent effects on estrogenregulated genes. An aromatase-overexpressing breast cancer cell line was established by transfecting the aromatase gene into ER-positive breast cancer cells. This cell line was treated with the Al, letrozole, over an extended period until cells became resistant to the drug. Proliferation assays demonstrated that growth of the Alresistant cell line was independent of estrogen and therefore was not inhibited by letrozole. Co-immunoprecipitation showed that interaction of ERa with AlBl was intensified in Al-resistant cells compared with Al-sensitive cells, in a ligandindependent manner. Treatment with epidermal growth factor (EG F) increased the association of ERa with AlBl in Al-resistant cells. EGF also stimulated proliferation of these cells, indicating an increased dependence of these cells on growth factormediated signalling. In these Al-resistant cells, recruitment of ERa and AlBl to the promoters of estrogen-responsive genes, pS2 and c-myc was demonstrated in the presence of letrozole, but recruitment to the cyclinDl promoter remained sensitive to estrogen treatment. These patterns of recruitment were matched by mRNA and protein expression levels of the three target genes. Inhibition of c-Jun N-terminal kinase (JNK) reduced the protein expression of cyclinD1. It was proposed that this differential gene regulation was due to indirect binding of ER to the cyclinDl promoter, in contrast to pS2 and c-myc, where ER binds directly to estrogen response elements (ERE). Fluorescent coassociation of ERa with AlBl demonstrated increased colocalisation of these proteins in Al-resistant cells compared with Al-sensitive cells. In primary breast cancer cultures from ER-positive patients who had not received endocrine therapy, coassociations of ER with AlBl were increased by androstenedione and disrupted by letrozole. In a tissue microarray of 447 breast cancer patients, expression of AlBl was demonstrated to predict disease recurrence in patients who were treated with an Al. This research has demonstrated that epidermal growth factor signalling is involved in activating increased interactions between ERa and AlBl in the development of resistance to Al treatment, resulting in ligand-independent proliferation of Al-resistant cells. AlBl is emerging as an important marker of response to Al therapy in breast cancer.</p>

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</description>

<author>Jane O&apos;Hara</author>


</item>






<item>
<title>A multi-centre randomised controlled trial evaluating exercise and manual therapy for osteoarthritis of the hip.</title>
<link>http://epubs.rcsi.ie/phdtheses/42</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/42</guid>
<pubDate>Thu, 31 May 2012 08:24:18 PDT</pubDate>
<description>
	<![CDATA[
	<p>Exercise therapy (ET) is recommended in the management of hip OA, although the limited research to date shows small effects for reduction in pain and improvement of physical function. Manual therapy (MT), which comprises joint mobilisations and other hands-on techniques is commonly used by physiotherapists in Ireland as an adjunct to ET for hip OA but lacks evidence of efficacy. Therefore, this RCT (EMPART- Exercise and Manual Physiotherapy Arthritis Research Trial) was undertaken to primarily determine the clinical effectiveness of physiotherapy-based ET with and without MT for hip OA. A secondary aim was to ascertain the impact of an 8-week waiting period for physiotherapy on outcomes. A total of 131 people with hip OA recruited from four hospitals were initially randomised to one of three groups: ET (n=45), ETIMT (n=43) and wait-list control (n=43). Both intervention groups received treatment for 8 weeks, control group participants remained on the waiting list (8 weeks) and were subsequently randomised into the ET or ETIMT group. Their data were pooled with original treatment group data: ET (n=66) and ETIMT (n=65). All participants were assessed post-treatment (9 weeks) and at 18 weeks. The primary outcome was the WOMAC physical function (PF) subscale and secondary outcomes included physical performance tests, pain severity, hip range of motion (HROM), anxietyldepression, quality of life, pain medication usage, patient-perceived change and patient satisfaction. Ethical approval was obtained at all sites. Data were analysed according to intention-to-treat principles to determine between-group differences for the three groups at baseline and 9 weeks, and the two treatment groups at baseline, 9 and 18 weeks. Results for the primary study aim showed no significant difference in WOMAC PF between ET and ETIMT groups at 9 weeks (mean diff -0.91; 95%CI; -6.28, 4.44) and 18 weeks (mean diff -1.41; 95%CI; -7.12, 4.29) or other outcomes except 'patient satisfaction with outcome', which was greater for ETIMT group (p=0.02). Results for the three groups (secondary aim) showed significant improvement in WOMAC, HROM, pain severity and patient perceived improvement in the ET and ETIMT groups compared to the control group, with no significant difference between the three groups in the remaining outcomes. Qualitative interviews of a small sample of EMPART participants found that despite low patient expectations, results were positive for most patients in terms of predominantly physical outcomes. Questionnaire surveys of the EMPART physiotherapists established they generally viewed participation in EMPART as positive and they would continue to use the ET and MT protocols in clinical practice, with some modifications regarding frequency and duration of the interventions. Results indicate that MT has no further benefit as an adjunct to ET for hip OA, but patients can deteriorate in pain and function measures while waiting for physiotherapy. These findings have implications for clinicians who can use treatment time more efficiently and enhance selfmanagement principles for those with hip OA. It also has implications for those managing waiting lists to develop initiatives to minimise waiting times for those receiving physiotherapy.</p>

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</description>

<author>Helen P. French</author>


</item>






<item>
<title>Investigation of signalling pathways in high grade glioma in order to predict responsiveness to tyrosine kinase inhibitors.</title>
<link>http://epubs.rcsi.ie/phdtheses/41</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/41</guid>
<pubDate>Wed, 30 May 2012 08:52:11 PDT</pubDate>
<description>
	<![CDATA[
	<p>High grade gliomas are the most common primary brain tumour in adults and are virtually uniformly fatal. Therapies that target specific pathway proteins, such as tyrosine kinases, are transforming the treatment of many cancer types. Initial studies using tyrosine kinase inhibitors (TKls) in the treatment of high grade glioma demonstrated reduced tumour volumes in certain patient populations (Butowski and Chang, 2005, Mellinghoff et al., 2005). However, subsequent survival studies have been disappointing (De Witt Hamer, 2010). To help clarify the potential role of such agents, it has been suggested that clinical trials should seek to identify subgroups of patients most likely to respond to molecular targeting with TKls.</p>
<p>In this study it is hypothesised that the pathway expression profiles of high grade gliomas may predict response to EGFR I PDGFR pathway blockade with TKls. Specifically, it was determined if EGFR, EGFRvIII, PDGFR c-KIT and c-ABL expression together with PTEN expression and downstream activation of AKT and P70s6K predicted response to EGFR or PDGFR blockade with erlotinib, gefitinib or imatinib. The immunohistochemical (IHC) expression profiles of the EGFR I PDGFR pathway in formalin fixed paraffin embedded sections of high grade gliomas and in primary cultures derived from the same tumours were established. This facilitated the characterisation of changes introduced as a result of in <em>vitro </em>culturing. Next, response to treatment with TKls was determined for each treated primary culture using anti-proliferation toxicity assays. Response was correlated with the above expression profiles and with patient survival data.</p>
<p>Tumour expression profiles showed that no one protein of the EGFR 1 PDGFR pathway significantly influenced overall survival and that diagnostic grade remained the best prognostic indicator of outcome. The EGFR I PDGFR pathway profiles remained stable over time in patients with repeat biopsies. Comparison of pathway profiles between tumour tissue and their derived primary cultures demonstrated the introduction of significant genomic and protein differences as a result of culturing. Increased surface receptor tyrosine kinases were observed with an opposing decrease in activation of the downstream pathway proteins when the cells were grown <em>in vitro. </em>Despite these differences, the overall EGFR I</p>
<p>PDGFR pathway profile of primary cultures retained key signature characteristics reflective of the coordinated pathway disruption observed in high grade gliomas. This verified their use as a biologically representative model of high grade glioma in determining if biomarkers predicting response to tyrosine kinase inhibitors (TKls) could be identified in the EGFR I PDGFR pathway. It became apparent that although some cultured tumours responded to therapy with TKls, this response was not statistically related to the pathway proteins that were evaluated in this study.</p>
<p>EGFR <em>1 </em>PDGFR <em>in vitro </em>pathway status was a poor predictor of <em>in vitro </em>responsiveness to molecular blockade using the TKls: erlotinib, gefitinib and imatinib. In conclusion the complexity and evasiveness of signalling pathways in high grade gliomas coupled with the possible emergence of alternate, deviant signalling pathways combine to minimise the likelihood that single agent pathway inhibitors will have a significant clinical benefit for glioma patients at this time.</p>

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</description>

<author>Rachel K. Howley</author>


</item>






<item>
<title>Progresses on the development of stereoselective [2+2], [2+3] and [4+3] cycloadditions.</title>
<link>http://epubs.rcsi.ie/phdtheses/40</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/40</guid>
<pubDate>Wed, 23 May 2012 07:06:47 PDT</pubDate>
<description>
	<![CDATA[
	<p>The present work dealt with the preparation of some key intermediates and their use for the generation of chemical diversity. In Chapter 2 we described a Catalytic Asymmetric Conjugate Addition of isocyanoacetates to 4-nitro-5-styrylisoxmles. In Chapter 3 we described a new strategy for the preparation of medium sized oxepanes  oxocanes and oxonanes. In Chapter 4 we described a novel route to alkene-hctionalised monobactams and their potential in diversity oriented synthesis is still in progress.</p>

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</description>

<author>Paolo Disetti</author>


</item>






<item>
<title>Histological evaluation of putative biomarkers in prostate cancer</title>
<link>http://epubs.rcsi.ie/phdtheses/39</link>
<guid isPermaLink="true">http://epubs.rcsi.ie/phdtheses/39</guid>
<pubDate>Tue, 22 May 2012 03:36:42 PDT</pubDate>
<description>
	<![CDATA[
	<p>Prostate cancer is a significant cause of illness and death in males. Marked disease heterogeneity is associated with prostate cancer. Current detection strategies do not detect the disease at an early stage and cannot distinguish aggressive versus non aggressive prostate cancer leading to over-treatment of the disease and associated morbidity. Thus, prostate cancer is a disease that would benefit from the discovery of novel biomarkers for both early detection and treatment selection. In October 2003, the Prostate Cancer Research Consortium (PCRC), a multidisciplinary, trans-institutional collaboration composed of researchers from University College Dublin's Conway Institute, Trinity College Dublin's Institute for Molecular Medicine, the Royal College of Surgeons in Ireland and Dublin City University, was established. Using a comprehensive approach which involves utilizing genomic, transcriptomic and proteomic platforms and using a highthroughput biomarker validation approach, the consortium's overall aim is to identify novel biomarkers of prostate cancer. This PhD project aims to evaluate the potential prostate cancer biomarkers in tissue which are identified in the discovery projects within the PCRC. Following previous proteomic analysis within the PCRC group, Zinc-a-2- glycoprotein (ZAG), Proteasome subunit P type 6 (PSMB-6), Vitamin D binding protein (VDBP) and Kininogen-1 (KNG-I) were found to be upregulated in the serum of prostate cancer patients. The tissue expression profile of these proteins was investigated to determine if ZAG, PSMB-6, VDBP and KNG-1 were also upregulated in prostatic tumour epithelial cells in the tissue of prostate cancer patients. ZAG expression in epithelial cells of the prostate was inversely associated with Gleason grade (BPH>G3>G4/G5). PSMB-6 was not expressed in either tumour or benign epithelium. However, strong PSMB-6 expression was noted in stromal and inflammatory cells. KNG-I and VDBP were not found to be expressed in prostate tissue blood. These results indicate ZAG as a possible predictive marker of Gleason grade. The inverse association between grade and tissue expression with a rising serum protein level is similar to that seen with <strong></strong>PSA. In addition the results for all proteins (ZAG, PSMB-6, KNG-1 and VDBP) highlight the challenges in trying to associate the protein levels in serum with tissue expression. Following methylation analysis of Wingless signalling (Wnt) molecules and their antagonists using Quantitative Methylation-Specific PCR (QMSP), secreted frizzled related protein 2 (SFRP-2) was found to be highly methylated in prostate cancer. The prostatic tissue expression profile of SFRP-2 was investigated to determine whether there was a correlation between SFRP-2 methylation and SFRP-2 expression in prostate cancer. Strong to moderate SFRP-2 expression was observed in benign prostatic hyperplasia (BPH) epithelial cells and negative to weak SFRP-2 expression observed in tumour epithelium particularly Gleason grade 3 and 4. However, in Gleason grade 5 carcinoma there was a 40:60 split in the immunoexpression of SFRP-2, where 40% displayed strong to moderate SFRP-2 expression and 60% displayed negative SFRP-2 expression in epithelial cells. A morphological difference was noted in the Gleason grade 5 tumours that had strong to moderate expression of SFRP-2 (Type A) and the Gleason grade 5 tumours that had no SFRP-2 expression (Type B). It was also noted that biochemical recurrence occurred after 5 years in patients that had strong to moderate SFRP-2 expression in Gleason grade 5 tumours and had "Type A morphology. These preliminary results propose SFRP-2 as a possible marker of histologically benign glands and a possible subgroup of Gleason grade 5 tumours that may predict prognosis and biochemical recurrence. The use of well-characterised antibodies is vital for clinical diagnostics and protein studies. One of the major challenges facing researchers and clinicians in the area of cancer research is the lack of high quality, well characterised antibodies to novel proteins. Successful antibody generation depends on the use and availability of high quality antigen. However, like antibodies to novel proteins in cancer research, there is also a lack of high quality, well characterised, commercially available antigens to these proteins. Thus, generating antibodies to these targets is not straightforward and often requires heterologous production of recombinant proteins. SFRP-2 is a novel marker in prostate cancer and paucity of quality antigen and antibody is an impediment to research on this marker. An antigen grade recombinant protein was designed, produced and used as an immunogen in an avian immune model to determine whether a recombinant antibody against SFRP-2 can be generated based on the polyclonal serum response of the chicken. The first strategy taken to produce the SFRP-2 antigen involved using a prokaryotic <em>(E. coli) </em>expression system. Both a pGS21 -a vector containing a glutathione-s-transferase (GST) tag and a PET-28b(+) vector modified to contain a heart fatty acid binding protein (hFABP) tag were transformed into E. <em>coli </em>cells for soluble SFRP-2 recombinant fusion protein expression which could be subsequently used as an immunogen in an avian immune model. However, both fusion proteins were insoluble in the form of bacterial fusion proteins trapped within the bacterial cell periplasm. The second strategy taken to produce a soluble SFRP-2 antigen involved using a "cell-free" translation expression system. "Cell-free" translation is an <em>in vitro </em>expression system that does not require the use of a host cell to express the target protein. Soluble expression of SFRP-2 was achieved. However, the yield of the soluble protein was too low for its use as either an immunogen or in molecular applications. The challenges and difficulties faced in this study may reflect the lack of high quality, well characterised, commercially available antibodies to novel cancer targets such as SFRP-2.</p>

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<author>Gillian O&apos;Hurley</author>


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