The plasma protein complement factor H (fH, 155 kDa) regulates the activity of the alternative pathway of complement activation. Factor H is monomeric, and its 20 CCP modules are arranged in a predominantly elongated conformation, joined by linking sequences that vary in length, with the longest linkers occurring in the central portion of the molecule. CCP modules 1 through 4 of fH host its capacity to act as a cofactor for fI-mediated proteolytic degradation of C3b and its ability to accelerate the decay of the C3 convertase, C3bBb, thereby regulating the so-called tick-over activation of the alternative pathway. Mutations in this part of fH might compromise its function and lead to underregulation of the alternative pathway. It is hypothesized that this can cause predisposition to diseases such as atypical haemolytic uraemic syndrome (aHUS) and age-related macular degeneration (AMD). In the current work, the known disease-associated mutations R53H and R78G were compared to wild-type in terms of fluid-phase cofactor assays, C3b-binding affinity and the ability to accelerate the decay of the convertase. In addition, the protective variant, I62, was also inspected because its protective role might be explained by an increased regulatory activity. The second, linked, aim of this project was to employ Forster resonance energy transfer (FRET) to study the link between conformation and function in fH. FRET is valuable for obtaining long-distance restraints up to a maximum of 100 °A and is therefore particularly useful for inferring domain orientations within multidomain proteins. This approach to measure long-range inter- and intramolecular distances is a convenient way to complement NMR-based structural investigations, which rely on short-range restraints. It is also a valuable complement to X-ray crystallography since it is a solution technique that can be conducted under physiological conditions. By using site-directed mutagenesis in the current work, free cysteines were introduced into CCP modules 1-4 at strategic points, which were then used for attachment of fluorescent tags. C3 possesses an internal thioester which can be labelled with a fluorophore upon activation to C3b. Intermolecular FRET measurements were thus undertaken to gain information about the interaction between the two proteins that is crucial for understanding functional activity. The CCP modules in the centre of fH may be responsible for introducing a bend into fH that brings the N-teminus close to the C-terminus (the latter is important for host versus non-host discrimination) joined by the longest linkers occurring in the whole molecule. This coincidence of two relatively small CCP modules, 12 and 13, with the highest number of eight amino acids between them, is hypothesised to reflect some unique architectural features. To explore the structural details of this portion of fH by FRET, single-labelled cysteine mutants were further modifed to provide a recognition site for transglutaminase (TGase), which can be enzymatically labeled with a second fluorophore. This stoichiometrically-labelled protein was used for intramolecular FRET studies.

The aims of this study were to analyse known and potential biomarkers of common and genetically complex human disorders and to identify genetic and environmental variation associated with plasma biomarker concentrations. Two groups of protein biomarkers were analysed. First, plasma complement factor H (CFH) was selected as a potential biomarker for age-related macular degeneration (AMD), since common variants in the CFH gene show strong association with this disorder. Secondly, two isoforms of amyloid-β (Aβ40 and Aβ42) were selected as biomarkers for Alzheimer disease (AD) since Aβ deposits are major constituents of the amyloid plaques characteristic of this disorder. Physiological and anthropometric measurements and samples of human and genomic DNA were collected from a population sample of 1,021 individuals from the Croatian island of Vis. Quantitative determination of plasma Aβ40 and Aβ42 concentrations was performed using enzyme-linked immunosorbent assays. Heritabilities and significant covariate effects were estimated for each trait in the Croatian data set. Genome-wide linkage and association analyses were conducted for the biomarker traits. A novel finding was the genome-wide significant association between a CFH and several polymorphisms close to and within the CFH gene. The strongest association was with an intronic SNP within CFH, which explained 28% of the total trait variance (P < 10-50). The association was also replicated in a Dutch sample set. A SNP haplotype was identified which accounted for a higher proportion of the phenotypic variance. Conditional haplotype analysis showed that the effect of this haplotype on plasma CFH concentration was independent of the CFH Y402H variant, and significantly stronger than a deletion of the adjacent CFHR3/CFHR1 which was already known to affect AMD susceptibility. Genetic analysis of 382 AMD cases and 201 controls was consistent with the CFH Y402H variant being the strongest AMD susceptibility locus. Variation in plasma CFH concentration was found to explain up to 1.8% of the variation in susceptibility to AMD with an odds 2.1 (95% C.I. 1.3-3.4, P = 0.003). SNPs that were strongly associated with a CFH concentration also influenced AMD susceptibility (P < 0.05) independently of the CFH Y402H polymorphism. Functional analysis of genomic regions associated with plasma CFH is needed to identify the causal variants. Associations were observed between plasma Aβ40 concentration and several novel candidate loci, spanning regions of approximately 0.2 Mb, on chromosomes 9 and X. Similarly, novel associations with plasma Aβ42 were found in several regions, each spanning 0.2-0.4 Mb, on chromosomes 2, 5, 9, 15 and 20. The proportion of the phenotypic variance in plasma Aβ42 explained by these putative associations ranged between 1.8 and 2.8%. However, none of the associated SNPs was significant after correction for multiple testing, therefore replication is required. Finally, attempts were made to identify and quantitate new protein biomarkers of disease in human plasma using mass spectrometry. Development and optimisation of techniques was initially undertaken to deplete high-abundance plasma proteins and improve signal:noise ratio. This allowed the assessment of downstream proteomic approaches including MALDI-TOF mass spectrometry (MS), capillary electrophoresis (CE) and ion exchange chromatography (IEC), each with the potential for large-scale quantitation of plasma proteins. Although the analysis of single protein analytes, using CE and IEC proved promising, the results highlighted the difficulty associated with MALDI-TOF and protein ionisation techniques in analysing complex mixtures such as plasma.

In patients with age-related macular degeneration, a monolayer of cells in the eyes called retinal pigment epithelium differ from healthy ones in morphology. It is therefore important to quantify the morphological changes, which will help us better understand the physiology, disease progression and classification. Classification of the RPE morphometry has been accomplished with whole tissue data. In this work, we focused on the spatial aspect of RPE morphometric analysis. We used the second-order spatial analysis to reveal the distinct patterns of cell clustering between normal and diseased eyes for both simulated and experimental human RPE data. We classified the mouse genotype and age by the k-Nearest Neighbors algorithm. Radially aligned regions showed different classification power for several cell shape variables. Our proposed methods provide a useful addition to classification and prognosis of eye disease noninvasively.

A Thesis submitted to The University of Arizona College of Medicine - Phoenix in partial fulfillment of the requirements for the Degree of Doctor of Medicine. / Genetic association studies simplify genotype‐phenotype relationship investigation by considering only the presence of a given polymorphism and the presence or absence of a given downstream phenotype. Although such associations do not indicate causation, collections of phenotypes sharing association with a single genetic polymorphism may provide valuable mechanistic insights. In this thesis we explore such genetic pleiotropy with Deep Phenotype Association Studies (DeePAS) using data from the Age‐Related Eye Study 2 (AREDS2). We also employ a novel text mining approach to extract pleiotropic associations from the published literature as a hypothesis generation mechanism. Is it possible to identify pleiotropic genetic associations across multiple published abstracts and validate these in data from AREDS2? Data from the AREDS2 trial includes 123 phenotypes including AMD features, other ocular conditions, cognitive function and cardiovascular, neurological, gastrointestinal and endocrine disease. A previously validated relationship extraction algorithm was used to isolate descriptions of genetic associations with these phenotypes in MEDLINE abstracts. Results were filtered to exclude negated findings and normalize variant mentions. Genotype data was available for 1826 AREDS2 participants. A DeePAS was performed by evaluating the association between selected SNPs and all available phenotypes. Associations that remained significant after Bonferroni‐correction were replicated in AREDS. LitWAS analysis identified 9372 SNPs with literature support for at least two distinct phenotypes, with an average of 3.1 phenotypes/SNP. PheWAS analyses revealed that two variants of the ARMS2‐HTRA1 locus at 10q26, rs10490924 and rs3750846, were significantly associated with sub‐retinal hemorrhage in AMD (rs3750846 OR 1.79 (1.41‐2.27), p=1.17*10‐7). This associated remained significant even in populations of participants with neovascular AMD. Furthermore, odds ratios for the development of sub‐retinal hemorrhage in the presence of the rs3750846 SNP were similar between incident and prevalent AREDS2 sub‐populations (OR: 1.94 vs 1.75). This association was also replicated in data from the AREDS trial. No literature‐defined pleiotropic associations tested remained significant after multiple‐testing correction. The rs3750846 variant of the ARMS2‐HTRA1 locus is associated with sub‐retinal hemorrhage. Automatic literature mining, when paired with clinical data, is a promising method for exploring genotype‐phenotype relationships.

Aging is an intrinsic process that is independent of obvious disease. In contrast to normal aging, age-related diseases are conditions that typically manifest at advanced ages, are associated with explicit pathology and cause disability and premature death. We used Drosophila as a model to investigate the molecular-genetic mechanisms associated with aging and age-related disease. Age-related locomotor impairment (ARLI) is a serious condition for the elderly and greatly impacts their quality of life. Toward identifying genes and mechanisms that influence ARLI, we performed a forward genetic screen using Drosophila mutants. This screen identified a loss of function mutant in PDK1, a component of the insulin signaling pathway. Additional loss of function mutants in the insulin signaling pathway genes PI3K Dp110, and AKT also delayed ARLI. These results suggest a role for insulin signaling in ARLI. Wolfram Syndrome (WFS) is a progressive neurodegenerative disease that is caused by mutations in the genes WFS1 and CISD2. The function of CISD2, the most recently identified gene has not been fully resolved. We used RNAi to knockdown wfs2, the fly ortholog of CISD2 to identify genes and pathways associated with wfs2 that will provide insight into the normal function of this gene. Through a targeted genetic screen in the Drosophila eye we identified that wfs2 interacts with two lysosomal storage disease genes PPT1 and CLN3. These results suggest that WFS and lysosomal storage diseases may be influenced by common molecular-genetic mechanisms. Furthermore, wfs2 may play a role in the neurodegenerative pathways associated with lysosomal storage disease. Oxidative stress is associated with aging and age-related disease. To identify genes that can protect against endogenous oxidative stress we performed a candidate suppressor screen. This screen revealed that expression of wild-type Ataxin-3 suppressed the short lifespan of Sod2 knockdown flies. The ubiquitin associated function of Ataxin-3 was determined to be important for this suppression. Interestingly, Ataxin-3 expression also extended the short lifespan due to knockdown of thioredoxin reductase in muscle. These results suggest that Ataxin-3 expression may play a protective role against enhanced endogenous oxidative stress due to reduced function of a number of antioxidant enzymes.

La dégénérescence maculaire liée à l’âge (DMLA) représente actuellement la principale cause de cécité dans les pays industrialisés. Les traitements disponibles ne concernent qu’une partie des cas (DMLA néovasculaire) et n’évitent pas toujours le développement de déficiences visuelles sévères. L’identification de facteurs modifiables, tels que la nutrition, pourrait représenter des moyens de prévention permettant de diminuer la fréquence de cette maladie handicapante dans nos populations. L’objectif de la thèse était d’étudier d’un point de vue épidémiologique, la relation entre nutrition et DMLA chez les 963 sujets de l’étude Aliénor (Antioxydants Lipides Essentiels Nutrition et maladies OculaiRes), âgés de 73 ans et plus, avec un intérêt particulier pour les lipides. La relation entre les lipides et la DMLA repose principalement sur la potentielle implication du métabolisme lipidique dans la physiopathologie de la DMLA, ainsi que sur le triple rôle structurel, fonctionnel et protecteur des acides gras polyinsaturés (AGPI) n-3 au sein de la rétine. Dans un premier temps, nous avons mis en évidence une diminution du risque de DMLA chez les sujets ayant des apports alimentaires élevés en AGPI n-3. L’estimation des apports alimentaires étant sujette à de nombreuses imperfections (déclaration des sujets, biais de mémorisation, imprécisions des tables de composition alimentaire…), nous avons ensuite utilisé un biomarqueur du statut en AGPI n-3 afin de s’affranchir de ces limites. Ce travail nous a permis de mettre en évidence une diminution du risque de DMLA prévalente et incidente chez les sujets ayant des niveaux plasmatiques élevés d’AGPI n-3. Enfin, nous avons étudié les relations de certains gènes impliqués dans le métabolisme lipidique avec DMLA, les niveaux de lipides sanguins et de xanthophylles. Il ressort que les sujets TT pour le polymorphisme du gène LIPC (rs493258) présentaient un risque diminué de DMLA ainsi que des niveaux plasmatiques de zéaxanthine plus élevés. Ces travaux viennent compléter et enrichir la littérature à ce sujet et apportent des arguments nouveaux quant au rôle des AGPI n-3 dans la rétine ; ils pourront également servir de support en matière de recommandations nutritionnelles et de prévention de la DMLA. Nos travaux sur l’implication des gènes du métabolisme des lipides soulèvent de nouvelles questions quant aux mécanismes impliqués dans cette pathologie et pourraient suggérer de nouvelles pistes de recherche thérapeutiques et préventives. / Age-related macular degeneration (AMD) is the leading cause of blindness in industrialized countries. Current treatments are limited to the neovascular form of the disease only and do not always prevent the development of severe visual impairment. The identification of modifiable risk factors, such as nutrition, may lead to preventive strategies, which may have the potential to reduce the impact and burden of AMD on the global aging population. The objective of the thesis was to study the association between nutrition and AMD in the 963 subjects, aged 73 years or older, from the Alienor Study, with a particular emphasis on lipids. The relationship between lipids and AMD is primarily based on the potential involvement of lipid metabolism in the pathogenesis of AMD and on the structural, functional and protective roles of omega-3 polyunsaturated fatty acids (PUFAs) in the retina. First, we showed that high intakes of omega 3 PUFAs were associated with a decreased risk for AMD. Estimation of dietary intakes being affected by many imperfections (bias in reporting, memory bias, inaccuracies from food composition tables...); we used an omega 3 PUFAs biomarker in order to overcome these limitations. This second work showed that high plasma levels of omega 3 PUFAs were associated with a decreased risk for prevalent and incident AMD. Finally, we studied the associations of genes involved in lipid metabolism with AMD, plasma lipids and xanthophylls. It appears that subjects bearing TT genotype for LIPC gene had a decreased risk of AMD and higher plasma levels of zeaxanthin. These results provide new arguments about the role of omega-3 PUFAs in the retina. They can also provide support and recommendations for prevention of AMD. This work on genes involved in lipid metabolism suggest new questions about mechanisms involved in AMD and may suggest new way of research in treatment and prevention.

A fundamental question in language research is the extent to which linguistic and cognitive systems interact. The aim of this thesis is to explore that relationship across new contexts and over the entire adult lifespan. This work centers on two branches of empirical research: the first is an investigation into the impact of later-life language learning on cognitive ageing (chapters 2-4), and the second examines the cognitive mechanisms underlying communicative perspective-taking from young adulthood into old age (chapter 5). The results of these chapters demonstrate that changes to one's linguistic environment can affect cognitive functions at any age, and similarly age-related changes to cognition can affect linguistic abilities, shedding light on the extent to which language and the brain are intricately connected over the lifespan. In the discussion (chapter 6), I consider how this work contributes new insights to the field, opening the door for future research to explore methods of improving cognitive abilities and linguistic behavior in old age.

The immune system is a complex network of tissues, cells and proteins which protects us against infections and invading pathogens we encounter every day. Immunosenescence refers to age-related impairments in immune function which may contribute to increased prevalence and severity of infectious disease in the elderly. How and why ageing affects the immune system is not fully understood. Using a naturally aged mouse model, work in this thesis shows that the abundance of a rare type of lymphocyte, known as NKT cells, increased across multiple immune organs. Additionally, macrophage abundance was also altered in the lymph nodes of aged mice. Invariant NKT (iNKT) cells express an invariant T cell receptor (TCR) which recognises lipids presented on the CD1d molecule. iNKT cells can be activated and respond to invading pathogens either by recognition of antigens through TCR-CD1d interactions or cytokine-dependent means. Less is known about NKT-like cells, which also express NK cell-associated surface markers, such as CD49b, but lack an invariant TCR. Data within this thesis show that both iNKT and NKT-like cell populations are abundant in the spleen and liver of aged mice. iNKT and NKT-like cells can be divided into subpopulations based on their expression of surface markers or transcription factors, and data suggests that not all subpopulations of these cells are affected by age equally. For instance, flow cytometry showed that while spleen-derived iNKT cells are significantly increased in aged mice, within the iNKT cell population the percentage representation of CD4+ cells are significantly reduced with age. Additionally, data indicates that both iNKT and NKT-like cells from aged mice show compromised responses to in vitro stimulation compared to young controls. Using bone marrow chimeras, where either young cells are reconstituted within an aged mouse or old cells are reconstituted within a young mouse, provided the opportunity to determine whether the aged environment contributes to this diminished response. Data demonstrates that the aged environment plays at least a partial role in these age-related changes to response to stimulation, however the young environment seems unable to reverse these changes. Macrophages are phagocytes which are found within all organs of the body. Studies in this thesis show that CD169+ macrophages have diminished numbers in the lymph nodes of aged mice, but this did not seem to affect the capture of the model antigen, dextran. Further studies revealed ageing affects macrophage populations differently in the different tissues within the body. For example, macrophage numbers remain constant in the spleen with ageing, but appear to increase in density in the lungs. To conclude, ageing can cause dramatic changes to the numbers and function of different cells of the immune system across multiple organs. Furthering our understanding of the ageing immune system and the underlying mechanisms which cause age-related decline in immune function is important to design strategies to improve the quality of the lives of the elderly.

Localisé entre l'Epithélium Pigmentaire Rétinien (EPR) et les segments externes des photorécepteurs, l'espace sous-rétinien est une zone immunosuppressive ; régulée par des signaux comme la thrombospondine-1 (TSP-1) ou Fas Ligand (FasL), qui empêchent l'accumulation des phagocytes mononucléés (PMs), en particulier des monocytes inflammatoires. La Dégénérescence Maculaire Liée à l'Age (DMLA) est associée à une rupture de l'immunosuppression de cet espace, et s'accompagne d'une accumulation de PMs ; causant la mort des photorécepteurs, la dédifférenciation de l'EPR et une néovascularisation pathologique. Des études d'associations génétiques ont établi un lien entre la DMLA et un haplotype qui affecte le locus 10q26, qui contient trois gènes : PLEKHA1, ARMS2 et HTRA1. L'haplotype est associé à une augmentation de la transcription de HTRA1 dans les lymphocytes ou les cellules de l'EPR. HTRA1 code pour une sérine protéase qui a une multitude de substrats ; mais le mécanisme par lequel elle pourrait être impliquée dans la pathogenèse de la DMLA reste inconnu. TSP-1 est une glycoprotéine exprimée par l'EPR, les macrophages résidents et inflammatoires. Le domaine C-terminal de TSP-1 contient deux séquences VVM qui peuvent chacune interagir avec un récepteur CD47. Dans cette étude, nous montrons que HTRA1 clive TSP-1 et inhibe l'élimination des PMs régulée par l'interaction entre TSP-1 et CD47 à l'état physiologique, in vitro et in vivo. L'activation pharmacologique de CD47 nous a permis d'annuler les effets pro-inflammatoires de HTRA1 et pourrait représenter un espoir thérapeutique pour le contrôle de la progression de la DMLA chez les patients porteurs de l'haplotype à risque. / Localized between the Retinal Pigment Epithelium (RPE) and the photoreceptors outer segments, the subretinal space is an immunosuppressive zone, mediated by signals such as Thrombospondin-1 (TSP-1), Fas Ligand (FasL) that prevent the accumulation of Mononuclear Phagocytes (MPs) and in particular pathogenic inflammatory monocytes. Age related Macular Degeneration (AMD) is associated with a breakdown of this immunosuppressivity and an accumulation of MPs, which causes photoreceptor degeneration, RPE dedifferentiation and pathological neovascularization. Genome association studies showed a strong link between AMD and a relatively common haplotype of 10q26 locus that contains the PLEKHA1, ARMS2 and HTRA1 genes. The disease haplotype is associated with increased HTRA1 transcription in cell types such as lymphocytes and RPE cells. HTRA1 is a serine protease with a number of substrates, but the mechanism by which it might be involved in AMD pathogenesis is unknown. TSP-1 is a glycoprotein expressed by RPE, resident macrophages and inflammatory macrophages. The C-terminal domain of TSP-1 contains two VVM sequences that can each interact with a CD47 receptor. We show that HTRA1 induced subretinal MP accumulation is dependent on TSP-1 deactivation in an RPE/Mo co-culture model and in a laser induced inflammation model in vivo. This pathogenic effect of HTRA1 was reversible by synthetic CD47 agonists. Our study reveals a comprehensive mechanism how the risk-allele 10q26 participates in the pathogenesis of AMD and opens new therapeutic avenues to restore subretinal immunosuppressivity and inhibit the inflammation-dependent neurodegeneration.

A hearing impairment is primarily diagnosed by measuring the hearing thresholds at a range of auditory frequencies (air-conduction audiometry). Although this clinical procedure is simple, affordable, reliable and fast, it does not offer differential information about origins of the hearing impairment. The main goal of this thesis is to quantitatively link specific cochlear pathologies to certain changes in the spectral and temporal characteristics of the auditory system. This can help better understand the underlying mechanisms associated with sensorineural hearing impairments, beyond what is shown in the audiogram. Here, an electromechanical signal-transmission model is devised in MATLAB where the parameters of the model convey biological interpretations of mammalian cochlear structures. The model is exploited to simulate the cell-level cochlear pathologies associated with two common types of sensorineural hearing impairments, 1: presbyacusis (age-related hearing impairment) and, 2: noise-induced hearing impairment. Furthermore, a clinical study, consisting of different psychoacoustic and physiological tests, was performed to trace and validate the model predictions in human. The results of the clinical tests were collated and compared with the model predictions, showing a reasonable agreement. In summary, the present model provides a biophysical foundation for simulating the effect of specific cellular lesions, due to different inner-ear diseases and external insults, on the entire cochlear mechanism and thereby on the whole auditory system. This is a multidisciplinary work in the sense that it connects the ‘biological processes’ with ‘acoustic modelling’ and ‘clinical audiology’ in a translational context.