Renal ischaemia-reperfusion injury (IRI) is a major cause of acute kidney injury (AKI) which is in turn the leading cause of morbidity and mortality in hospitalized patients. The principle aim of this thesis was to evaluate potential new therapies that might afford protection against IRI in both in vitro and in vivo settings. Recent evidence suggests that nitrite (NO2-) may play an important role in protecting the myocardium from IRI. Our initial work into the role of NO2- in an in vitro model of renal IRI in proximal tubular epithelial cells provided evidence that NO2- can prevent apoptosis and preserve cell viability. This lead to an in vivo study where high NO2- concentrations (50 mg/L) were given orally to rats for 7 days prior to inducing renal IRI but no beneficial effects of this treatment were observed. Another potential treatment identified was thiamine (vitamin B1) and this, like NO2-was investigated to see if it had the potential to protect rats from AKI injury. It has been previously recognized that in renal IRI the high energy phosphate ATP is found to be severely depleted whilst is is known that thiamine can play a pivotal role in generating ATP. Furthermore, thiamine has previously been demonstrated to protect against myocardial ischaemic injury and has the ability to reduce myocardial infarct size. In vitro, thiamine was found to reduce the degree of apoptosis in cultured HK-2 cells caused by ischaemia whilst in vivo it afforded protection against AKI caused by renal IRI by anti-apoptotic, anti-inflammatory and anti-oxidant mechanisms. Finally, a study into the possible therapeutic role of gene therapy with bone morphogenic protein 7 (BMP-7) in renal IRI was undertaken. Previous work has established that i.v. BMP-7 is able to protect against renal IRI but it has also been associated with ectopic bone formation at the site of injection. Therefore another method to increase circulating BMP-7 was sought. We initially found that BMP-7 gene therapy could attenuate apoptosis and preserves cell viability in an in vitro model of renal IRI. However, whilst in vivo gene therapy with electroporation of BMP-7 plasmid DNA increased BMP-7 expression in mice serum 2 days post electroporation, it was unable to protect the animals against IRI induced AKI. In rats the direct injection of naked DNA BMP-7 plasmid systematic 2 days prior to renal IRI was able to upregulate BMP-7 expression 4 days later in kidney tissue. Despite this it was unable to afford protection against renal IRI. Apoptosis and necrosis play a crucial role in the pathogenesis of renal IRI induced AKI. In this thesis we investigated the role of three putative therapeutic agents and their role in apoptosis and necrosis in vitro in PTECs and in vivo against renal IRI induced AKI. All three therapeutic drugs were able to attenuate apoptosis in PTECs but were unable to protect against necrosis, whilst against renal IRI induced AKI only thiamine was found to be protective. Thiamine appears to hold the most promise and more work needs to be undertaken so that its potential benefit in AKI can be realised.

Ischaemic heart disease is the most common cause of mortality in the western hemisphere and it is rapidly becoming the leading cause of death globally. Moreover, therapeutic interventions by cardiologists and cardiac surgeons frequently subject the heart to acute I/R injury, which in itself can cause mortality. Recent investigations of adult stem cells have primarily focused on their regenerative potential for chronic ischaemic heart disease. In this thesis, I have investigated the hypothesis that adult bone marrow derived stem cells are cardioprotective in acute regional myocardial I/R injury. In a rat model of left anterior descending coronary artery (LAD) reversible occlusion and reperfusion, I demonstrate that an intravenous bolus of adult bone marrow derived (1) bone marrow mononuclear (BMNNC) and (2) mesenchymal stem cells (MSC) upon reperfusion can attenuate infarct size. This effect is comparable to ischaemic preconditioning (IPC), which is the gold standard for cardioprotection. Next, I demonstrated the mechanisms for adult stem cell cardioprotection are principally anti-apoptotic and depend upon stem cell secreted factors to (1) activate phosphatidylinositide 3-kinase (PI3)/Akt cell survival kinase-signaling pathway (2) inhibit glycogen synthase kinase-3β (3) inhibit p38MAPK (4) inhibit nuclear translocation of p65NF-κB. 7 Proteomic analysis of myocardium subjected to I/R and treated with either BMMNC or BMMNC derived supernatant (BMS) upon reperfusion demonstrated higher expression of a whole host of pro-survival proteins. These were notably (1) 14-3-3-ε protein (2) anti-oxidant peroxiredoxin-6 (3) heat shock protein (HSP) αB-crystallin, HSP72, HSP tumour necrosis factor receptor-1 associated protein, and HSP ischaemia responsive protein-94 (4) glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (5) mitochondrial aconitase and mitochondrial voltage-dependent anionselective channel protein-1. Thereafter, I investigated the mobilization of endogenous bone marrow stem cells and trafficking to the ischaemic myocardium by stromal cell derived factor-1 (SDF-1) /chemokine, receptor type 4 (CXCR4) signaling. I demonstrate high up-regulated expression of CXCR4 and CD26 in BMMNC following IPC, which might have a role in IPC-mediated cardioprotection. Finally, and in concordance with this finding I demonstrate that both IPC and an exogenous MSC bolus upon reperfusion can synergize to abolish acute myocardial I/R injury.

Acute kidney injury (AKI) is a major risk factor for chronic kidney disease (CKD). For patients who recover from AKI, there is a 25% increase in the risk of CKD, and a mortality rate of up to 50% after 10 years. Nuclear factor kappa-B (NF-κB) is a family of transcription factors that regulates the transcription of many proteins that play a key role in inflammation. Inhibitor of IκB kinase (IKK) is directly upstream of NF-κB. My aim was to investigate a) the role of IKK in the progression of AKI to CKD, and b) whether its inhibition attenuates renal fibrosis. In this thesis I used a model of unilateral renal ischaemia-reperfusion injury with contralateral nephrectomy, to firstly map the acute time course of AKI. From the data generated from the time course, I decided to treat the animals at 24 h post reperfusion with the IKK inhibitor, IKK16, as i) this was at the peak of renal dysfunction (24 h post reperfusion), and ii) prior to the activation of NF-κB (48 h post reperfusion). The inhibition of IKK at 24 hours post reperfusion, as a delayed treatment, successfully attenuated renal dysfunction, NF-κB activation and renal structural damage. I subsequently increased the recovery time after ischaemia-reperfusion in my rat model to 28 days to study the development of fibrosis post AKI. The inhibition of IKK at 24 hours post reperfusion successfully attenuated the development of fibrosis, formation of myofibroblasts, macrophage infiltration, the expression of pro-fibrotic markers and the deposition of extracellular matrix components at 28 days post reperfusion. In addition, the delayed inhibition of IKK at days 7-13 post unilateral ureteral obstruction in a rat model, successfully attenuated the development of fibrosis, formation of myofibroblasts, macrophage infiltration, the expression of pro-fibrotic markers and the deposition of extracellular matrix components. These data indicate that the activation of the IKK complex drives tubulointerstitial fibrosis, and suggests that the inhibition of IKK could be a useful pharmacological tool for the creation of therapies to combat AKI and the subsequent development of fibrosis, via the reduction of both inflammation and the prevention of the expression of pro-fibrotic markers.

The cereal seed plays a crucial role in society – both in the “food as medicine” paradigm, but also in food security. It is the starch and proteins present in the seed that lend it importance in these dissimilar anthropomorphic activities. This thesis investigation first characterized the post-translational processing of the potential diabetogen, wheat globulin-3. Globulin-3-like peptides were observed primarily in the embryo. These peptides varied significantly in their molecular masses and isoelectric points, as determined by two dimensional electrophoresis and immunoblotting. Five major polypeptide spots were sequenced by mass spectrometry, allowing for the development of a model of the post-translational events contributing to the globulin-3 processing profile. Three separate investigations of starch granules from different cereal species were performed. In the first series of experiments, pathogen-susceptible maize kernels were injected with either conidia of the fungal pathogen Fusarium graminearum or sterile water controls. Proteins in the desiccated fungal remnants on the surface of the kernels as well as in the endosperm and embryo tissues of the control and infected kernels were isolated and these proteomes were sequenced using tandem mass spectrometry. Approximately 250 maize proteins were identified. These proteins were classified into functional categories. There was an increased representation of defense proteins in the both the embryo and endosperm tissues of infected maize samples. The proteome of the fungal remnants was composed of 18 proteins. Several of these proteins were categorized as being involved in the metabolism of plant-sourced molecules, or in stress response. The second series of experiments detail the investigation of commercially prepared rice and maize starches using tandem mass spectrometry. The majority of identified proteins, in both rice and maize samples, were involved in either carbohydrate metabolism or storage. Markers for seed maturity and for starch mobilization were also documented. Finally, the third series of experiments investigated the non-host proteomes present in commercially-prepared starches. Non-host proteins from a variety of species, including Homarus americanus were found in the starch samples. This documentation of H. americanus proteins in these starch samples may have food safety implications with regards to shellfish allergies.

The cereal seed plays a crucial role in society – both in the “food as medicine” paradigm, but also in food security. It is the starch and proteins present in the seed that lend it importance in these dissimilar anthropomorphic activities. This thesis investigation first characterized the post-translational processing of the potential diabetogen, wheat globulin-3. Globulin-3-like peptides were observed primarily in the embryo. These peptides varied significantly in their molecular masses and isoelectric points, as determined by two dimensional electrophoresis and immunoblotting. Five major polypeptide spots were sequenced by mass spectrometry, allowing for the development of a model of the post-translational events contributing to the globulin-3 processing profile. Three separate investigations of starch granules from different cereal species were performed. In the first series of experiments, pathogen-susceptible maize kernels were injected with either conidia of the fungal pathogen Fusarium graminearum or sterile water controls. Proteins in the desiccated fungal remnants on the surface of the kernels as well as in the endosperm and embryo tissues of the control and infected kernels were isolated and these proteomes were sequenced using tandem mass spectrometry. Approximately 250 maize proteins were identified. These proteins were classified into functional categories. There was an increased representation of defense proteins in the both the embryo and endosperm tissues of infected maize samples. The proteome of the fungal remnants was composed of 18 proteins. Several of these proteins were categorized as being involved in the metabolism of plant-sourced molecules, or in stress response. The second series of experiments detail the investigation of commercially prepared rice and maize starches using tandem mass spectrometry. The majority of identified proteins, in both rice and maize samples, were involved in either carbohydrate metabolism or storage. Markers for seed maturity and for starch mobilization were also documented. Finally, the third series of experiments investigated the non-host proteomes present in commercially-prepared starches. Non-host proteins from a variety of species, including Homarus americanus were found in the starch samples. This documentation of H. americanus proteins in these starch samples may have food safety implications with regards to shellfish allergies.

The cereal seed plays a crucial role in society – both in the “food as medicine” paradigm, but also in food security. It is the starch and proteins present in the seed that lend it importance in these dissimilar anthropomorphic activities. This thesis investigation first characterized the post-translational processing of the potential diabetogen, wheat globulin-3. Globulin-3-like peptides were observed primarily in the embryo. These peptides varied significantly in their molecular masses and isoelectric points, as determined by two dimensional electrophoresis and immunoblotting. Five major polypeptide spots were sequenced by mass spectrometry, allowing for the development of a model of the post-translational events contributing to the globulin-3 processing profile. Three separate investigations of starch granules from different cereal species were performed. In the first series of experiments, pathogen-susceptible maize kernels were injected with either conidia of the fungal pathogen Fusarium graminearum or sterile water controls. Proteins in the desiccated fungal remnants on the surface of the kernels as well as in the endosperm and embryo tissues of the control and infected kernels were isolated and these proteomes were sequenced using tandem mass spectrometry. Approximately 250 maize proteins were identified. These proteins were classified into functional categories. There was an increased representation of defense proteins in the both the embryo and endosperm tissues of infected maize samples. The proteome of the fungal remnants was composed of 18 proteins. Several of these proteins were categorized as being involved in the metabolism of plant-sourced molecules, or in stress response. The second series of experiments detail the investigation of commercially prepared rice and maize starches using tandem mass spectrometry. The majority of identified proteins, in both rice and maize samples, were involved in either carbohydrate metabolism or storage. Markers for seed maturity and for starch mobilization were also documented. Finally, the third series of experiments investigated the non-host proteomes present in commercially-prepared starches. Non-host proteins from a variety of species, including Homarus americanus were found in the starch samples. This documentation of H. americanus proteins in these starch samples may have food safety implications with regards to shellfish allergies.

La neuroplasticité (NP), définie comme la capacité du système nerveux à s’adapter aux changements environnementaux, est un phénomène intrinsèque au fonctionnement cérébral et essentiel à son homéostasie. La NP est par définition impliquée dans toutes les maladies du cerveau dont les troubles psychiatriques. Différents troubles psychiatriques peuvent être utilisés comme autant de modèles pour étudier les différentes facettes de la NP de façon translationnelle : du moléculaire au comportemental permettant alors d'améliorer la compréhension de la régulation de la NP et de son implication dans l'étiopathogénie des troubles psychiatriques et de leurs traitements.La neuroplasticité individu-dépendante−La NP individu-dépendante permet de concevoir les gènes impliqués dans les troubles psychiatriques comme des gènes de sensibilité à l’environnement plutôt que comme des gènes de vulnérabilité aux maladies. Ainsi, tous les sujets n’ont pas la même sensibilité à l’environnement. Si l'on considère les gènes de vulnérabilité aux maladies comme des gènes de sensibilité à l’environnement, également appelés gènes de plasticité, les individus qui les portent présentent logiquement une susceptibilité plus grande à l'environnement qu'il soit "négatif" (ex.: maltraitance infantile) ou "positif" (ex.: environnement enrichissant). Ce concept a été proposé dans un modèle intégratif d'un trouble psychiatrique très fréquent: le trouble de personnalité borderline.La neuroplasticité âge-dépendante−La NP opère tout au long de la vie mais est régulée différemment selon les périodes de développement. Ces modifications liées à l’âge sont non seulement quantitatives (nombre de neurones impliqués) mais également qualitatives (type de modification). La régulation neuroplastique est donc dépendante de l'âge et entraine des conséquences comportementales différentes selon l'âge de survenue d'un évènement ou d'une expérience. La dimension âge-dépendante de la NP permet d'apporter un nouveau regard sur l'étiopathogénie des troubles psychiatriques, notamment sur les liens entre le trouble de personnalité borderline (TPB) et l’état de stress post-traumatique. Nous avons réalisé une étude génétique d'association, avec réplication interne, sur des gènes impliqués dans la régulation de l'axe du stress dans le TPB d'après l'hypothèse que le TPB et le PTSD constitueraient une seule et même entité dont la principale différence étiologique serait l'âge de survenue du traumatisme.La neuroplasticité symptôme dépendante−Les modifications neuroplastiques chez des sujets adultes sains ont été mises en évidence dans plusieurs types de situations. L'aspect adaptatif de la NP peut également être impliqué dans la pathogenèse d'un trouble, on parle d'adaptation plastique à la pathologie. Cet aspect a été étudié dans un symptôme psychiatrique fréquent : l'hallucination, définie comme une perception sans objet et nous avons proposé la première étude de neuroimagerie multimodale chez des patients souffrant de schizophrénie présentant des hallucinations visuelles. L'objectif de cette étude était d'étudier la connectivité du complexe hippocampique (HC) selon la modalité hallucinatoire, i.e. auditive ou visuelle dans deux groupes de patients souffrant de schizophrénie: un groupe avec uniquement des hallucinations auditives (AH) et un groupe avec des hallucinations audio-visuelles. Des différences de connectivité ont été mises en évidence sur la voie mésolimbique et entre aires visuelles et complexe hippocampique. La présence d’hallucinations visuelles est également associée à des modifications plastiques du volume et de la forme de l’hippocampe et nos résultats sont compatibles avec des modifications symptômes-dépendantes de cette structure. [...] / The study of the neuroplasticity (NP) has been emphasized to improve the comprehension of pathophysiology of psychiatric disorders, including biomarkers for predicting and monitoring treatment response. NP can be defined as the ability of the nervous system to respond to intrinsic or extrinsic stimuli by reorganizing its structure, function and connections and can be described from a translational perspective at many levels, from molecular to cellular to systems to behaviour. Psychiatric disorders are characterized by a high degree of heterogeneity (pathophysiological, etiologic and clinical levels) which can be conceived as an advantage when examined from the perspective of the NP. In fact, psychiatric disorders can be used as models to study the different aspects of the NP.Individual-dependent plasticity−The lack of susceptibility genes related to several psychiatric disorders may be due to tendency to look for genetic effects on disease rather than genetic effects on vulnerability to environmental causes of disease. In fact, \\\"vulnerability genes\\\" may function more like \\\"plasticity genes\\\", resulting in greater susceptibility of individuals to both positive (e.g., environmental support and enrichment) and negative (e.g., childhood maltreatment) facets of environmental experiences. This concept has been proposed in an integrative model of a frequent psychiatric disorder : the borderline personality disorder (BPD). Age-dependent plasticity−There are qualitatively and quantitatively different changes in the brain in re¬sponse to what appears to be the same experience at dif¬ferent ages. This aspect of NP has been studied by using the \\\"Borderline Personality or Complex Posttraumatic Stress Disorder controversy\\\" with a genetic association study, with independent replication, on genes associated with the physiological response to stress in the hypothalamic–pituitary–adrenal (HPA) axis. Symptom-dependent plasticity−Adaptative neuroplastic modifications in the structure and function of the human brain in response to environmental demands have been showed in numerous situations in healthy controls. Interestingly, NP have also been associated to adaptation to pathology in several psychiatric disorders. A recent example has been provided by the study of visual hallucinations in schizophrenia patients. Hallucinations can be defined as perceptions in the absence of external stimuli. In schizophrenia, hallucinations constitute the most typical and disabling symptoms of the disorder and may manifest in all sensory modalities. Several MRI findings support the hypothesis that distinct patterns of connectivity, particularly within networks involving the hippocampal complex (HC), could be associated with different hallucinatory modalities. The aim of our study was to investigate HC connectivity as a function of the hallucinatory modality, i.e., auditory or visual in two carefully selected subgroups of schizophrenia patients with only auditory hallucinations (AH) or with audio-visual hallucinations (A+VH). Hippocampal volume and shape analysis showed localized hippocampal hypertrophy in the A+VH group. These structural findings indicate that plastic changes are associated with hallucinations. Indeed, the hippocampus is capable of plastic deformation, and the present findings are consistent with experience-dependent shape modifications of the hippocampus that involve mechanical tension along the axon.This PhD thesis highlights several arguments that the NP perspective provide new insights to the pathophysiology, to improve and emphasize therapeutic innovation of psychiatric disorders.

<p>Mitochondrial dysfunction has been linked to a number of age-associated disorders and recent evidence has shown that mitochondrial function is necessary for osteoblast differentiation and osteoclast survival. Although bone tissue was once thought to be an ‘inert’ tissue, research from the past decade in bone metabolism has demonstrated pathways linking bone and whole body energy metabolism. However, with mitochondria being the central energy provider in cells there is a paucity of research exploring the impact of mitochondrial function on bone tissue, with the bulk of work focused in cell culture. This thesis aimed to explore mitochondrial content and function after endurance training and an exhaustive bout of running in two different animal models. The first study explored the effect of progressive mitochondrial dysfunction on mitochondrial gene expression and bone strength in the polymerase gamma mouse model of mitochondrial dysfunction. The therapeutic efficacy of endurance training on mitochondrial parameters and bone strength were evaluated as well. The second study utilized the Koch-Britton rat model of low capacity and high capacity runners. This model has demonstrated that selection for low and high running capacity has led to a significant divergence in mitochondrial content and function between these two groups. Mechanical strain in the form of exercise has been established as playing a key role in regulating bone health however the underlying mechanisms are still being described. The untrained status and inherent differences in aerobic capacity allow for the elucidations of bone adaptations that may be a result of aerobic capacity. The effect of an exhaustive bout of exercise on mitochondrial gene expression and enzyme activity in LCR and HCR rats was studied. Taken together these studies demonstrate that exercise is beneficial for promoting bone health and may do so by altering mitochondrial content and stress resistance through the FoxO family of transcription factors.</p> / Doctor of Philosophy (Medical Science)

<p>The focus of this thesis was the role of fibrocytes in chronic lung disease. These bone marrow derived cells have been identified in the lung and the circulation in patient samples and animal models of lung injury. However, the precise mechanistic role of the fibrocyte is still to be elucidated.</p> <p>Live assessment of lung changes in animal models of chronic lung disease allows for real time observation of changes, and gives a readout which can be translated to humans who undergo similar tests. In this thesis, we adapted an existing model of lung injury, and delivered a discrete treatment to a single lung lobe while monitoring its successful delivery.</p> <p>I also developed a robust system to examine the relationship between fibrocyte response, and cytokine expression previously identified in chronic lung disease. We found a connection between cytokine expression and fibrocyte mobilisation. Our model showed that fibrocyte mobilisation in the presence of existing lung injury does not improve and rather can worsen existing lung injury. This was a significant finding as it confirms the role of the fibrocyte as a participator or conductor in fibrogenesis and it suggests that this cell may play a role in the development of chronic lung diseases.</p> <p>Finally, we contributed to the ongoing characterisation of the fibrocyte as a prospective biomarker. We confirmed the cell’s identity by characterising it by its known markers and biological characteristics. We also identified the presence of this cell in chronic lung disease and linked its presence to disease progression.</p> / Doctor of Philosophy (Medical Science)

This thesis presents the findings from an ethnography of stem cell science based on fieldwork with researchers in two connected laboratories in Scotland and the United States. It explores stem cell scientists' complicated interactions with live stem cell cultures within national projects of translational regenerative medicine. This analysis both draws upon and contributes to the social studies of biomedicine, reproductive studies and science and technology studies. I examine how stem cell scientists, involved in an international research initiative, navigate the challenging landscapes of translational regenerative medicine and attempt to transform fragile live cell cultures into successful biotechnical, medical and economic products. By considering translational regenerative medicine as an effort to reformulate the relationship between biology and technology in terms of applicability and utility, I illuminate tensions between the specific practices of care that enable stem cell growth in vitro and the elusive goals of national projects of biotechnological innovation. A major focus of this study is the means by which scientists in the two laboratories manage the inherent uncertainties of both cell culture and translational science. By exploring how researchers react to unstable and unpredictable cellular behaviour in the laboratory, while also managing the expectations of government and external funding bodies, I provide a portrait of the complex sociality of contemporary bioscience. In addition to the international collaboration between the two laboratories, I explore scientists' interdisciplinary work with medical specialists and public engagement with stakeholders in regenerative medicine. In doing so, I pay attention to the ways in which scientists themselves deal with and reflect on the relational and interdependent nature of their endeavours. Drawing on twenty-two months of ethnographic fieldwork and fifty qualitative interviews, I show how stem cell scientists' new engagement practices also inform scientific work and the care of stem cells in the laboratory. In short, I argue that translation of science across different sites at once creates and depends on new social relations between stem cells, people and communities. After providing an overview of the literature, central questions and methodology that frame this thesis, I introduce the opportunities and challenges that translational regenerative medicine goals create for the care of stem cells in vitro. From there, I zoom out beyond the tissue culture flask to demonstrate how the necessity for science applicability creates new responsibilities for scientists to connect with stakeholders in regenerative medicine outside of the laboratory. I conclude that a consideration of scientists' ties and societal links is significant for an understanding of the connection between the biological and the technological.