Investigations into selective metabolic aspects of bifidobacteria: carbohydrate metabolism, fatty acid biosynthesis and plasmid biology

The gastrointestinal tract (GIT) is a diverse ecosystem, and is colonised by a diverse array of bacteria, of which bifidobacteria are a significant component. Bifidobacteria are Gram-positive, saccharolytic, non-motile, non-sporulating, anaerobic, Y-shaped bacteria, which possess a high GC genome content. Certain bifidobacteria possess the ability to produce conjugated linoleic acid (CLA) from linoleic acid (LA) by a biochemical pathway that is hypothesised to be achieved via a linoleic isomerase. In Chapter two of this thesis it was found that the MCRA-specifying gene is not involved in CLA production in B. breve NCFB 2258, and that this gene specifies an oleate hydratase involved in the conversion of oleic acid into 10-hydroxystearic acid. Prebiotics are defined as non-digestible food ingredients that beneficially affect the host by selectively stimulating growth and/or activity of one or a limited number of bacteria in the colon. Key to the development of such novel prebiotics is to understand which carbohydrates support growth of bifidobacteria and how such carbohydrates are metabolised. In Chapter 3 of this thesis we describe the identification and characterisation of two neighbouring gene clusters involved in the metabolism of raffinose-containing carbohydrates (plus related carbohydrate melibiose) and melezitose by Bifidobacterium breve UCC2003. The fourth chapter of this thesis describes the analysis of transcriptional regulation of the raf and mel clusters. In the final experimental chapter two putative rep genes, designated repA7017 and repB7017, are identified on the megaplasmid pBb7017 of B. breve JCM 7017, the first bifidobacterial megaplasmid to be reported. One of these, repA7017, was subjected to an in-depth characterisation. The work described in this thesis has resulted in an improved understanding of bifidobacterial fatty acid and carbohydrate metabolism, Furthermore, attempts were made to develop novel genetic tools.

Aspects of the biology of Mya arenaria and Ensis spp. (Mollusca; Bivalvia) in the Irish Sea and adjacent areas

This study was undertaken to investigate the general biology, including the reproductive cycle and health status, of two clam taxa in Irish waters, with particular reference to the Irish Sea area. Monthly samples of the soft shell clam, Mya arenaria, were collected from Bannow Bay, Co. Wexford, Ireland, for sixteen months, and of the razor clam, Ensis spp. from the Skerries region (Irish Sea) between June 2010 and September 2011. In 2010, M. arenaria in Bannow Bay matured over the summer months, with both sexes either ripe or spawning by August. The gonads of both sexes of E. siliqua developed over autumn and winter 2010, with the first spawning individuals being recorded in January 2011. Two unusually cold winters, followed by a warmer than average spring, appear to have affected M. arenaria and E. siliqua gametogenesis at these sites. It was noted that wet weight of E. siliqua dropped significantly in the summer of both 2010 and 2011, after spawning, which may impact on the economic viability of fishing during this period. Additional samples of M. arenaria were collected at Flaxfort (Ireland), and Ensis spp. at Oxwich (Wales), and the pathology of all clams was examined using both histological and molecular methods. No pathogenic conditions were observed in M. arenaria while Prokaryote inclusions, trematode parasites, Nematopsis spp. and inflammatory pathologies were observed at low incidences in razor clams from Ireland but not from Wales; the first time these conditions have been reported in Ensis spp. in northern European waters. Mya arenaria from sites in Europe and eastern and western North America were investigated for genetic variation using both mitochondrial (cytochrome oxidase I (COI) and 16S ribosomal RNA genes) and nuclear markers (10 microsatellite loci). Both mitochondrial CO1 and all nuclear markers showed reduced levels of variation in certain European samples, with significant differences in haplotype and allelic composition between most samples, particularly those from the two different continents, but with the same common haplotypes or alleles throughout the range. The appearance of certain unique rare haplotypes and microsatellite alleles in the European samples suggest a complicated origin involving North American colonization but also possible southern European Pleistocene refugia. Specimens of Ensis spp. were obtained from five coastal areas around Ireland and Wales and species-specific PCR primers were used to amplify the internal transcribed spacer region 1 (ITS1) and the mitochondrial DNA CO1 gene and all but 15 razor clams were identified as Ensis siliqua. Future investigations should focus on continued monitoring of reproductive biology and pathology of the two clam taxa (in particular, to assess the influence of environmental change), and on genetics of southern European M. arenaria and sequencing the CO1 gene in Ensis individuals to clarify species identity

Molecular and cellular aspects of the SREBP pathway

The SREBP (sterol response element binding proteins) transcription factors are central to regulating de novo biosynthesis of cholesterol and fatty acids. The SREBPs are regulated by retention or escape from the ER to the Golgi where they are proteolytically cleaved into active forms. The SREBP cleavage activating protein (SCAP) and the INSIG proteins are essential in this regulatory process. The aim of this thesis is to further characterise the molecular and cellular aspects surrounding regulation of SREBP processing. SREBP and SCAP are known to interact via their carboxy-terminal regulatory domains (CTDs) but this interaction is poorly characterised. Significant steps were achieved in this thesis towards specific mapping of the interaction site. These included cloning and over expression and partial purification of tagged SREBP1 and SREBP2 CTDs and probing of a SCAP peptide array with the CTDs. Results from the SREBP2 probing were difficult to interpret due to insolubility issues with the protein, however, probing with SREBP1 revealed five potential binding sites which were detected reproducibly. Further research is necessary to overcome SREBP2 insolubility issues and to confirm the identified SREBP1 interaction site(s) on SCAP. INSIG1 has a central role in regulating SREBP processing and in regulating stability of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), a rate limiting enzyme in cholesterol biosynthesis. There are two protein isoforms of human INSIG1 produced through the use of two in-frame alternative start sites. Bioinformatic analysis indicated that the presence of two in-frame start sites within the 5-prime region of INSIG1 mRNA is highly conserved and that production of two isoforms of INSIG1is likely a conserved event. Functional differences between these two isoforms were explored. No difference in either the regulation of SREBP processing or HMGCR degradation between the INSIG1 isoforms was observed and the functional significance of the two isoforms is as yet unclear. The final part of this thesis focused on enhancing the cytotoxicity of statins by targeted inhibition of SREBP processing by oxysterols. Statins have significant potential as anti-cancer agents as they inhibit the activity of HMGCR leading to a deficiency in mevalonate which is essential for cell survival. The levels of HMGCR fluctuate widely due to cholesterol feedback of SREBP processing. The relationship between sterol feedback and statin mediated cell death was investigated in depth in HeLa cells. Down regulation of SREBP processing by sterols significantly enhanced the efficacy of statin mediated cell death. Investigation of sterol feedback in additional cancer cell lines showed that sterol feedback was absent in cell lines A- 498, DU-145, MCF-7 and MeWo but was present in cell lines HT-29, HepG2 and KYSE-70. In the latter inhibition of SREBP processing using oxysterols significantly enhanced statin cytotoxicity. The results indicate that this approach is valid to enhance statin cytotoxicity in cancer cells, but may be limited by deregulation of SREBP processing and off target effects of statins, which were observed for some of the cancer cell lines screened.

Aspects of the biology of the parasite Bonamia ostreae with a view to gaining a greater understanding of how to alleviate its impact on the European flat oyster, Ostrea edulis.

The parasite Bonamia ostreae has decimated Ostrea edulis stocks throughout Europe. The complete life cycle and means of transmission of the parasite remains unknown. The methods used to diagnose B. ostreae were examined to determine sensitivity and reproducibility. Two methods, with fixed protocols, should be used for the accurate detection of infection within a sample. A 13-month study of two stocks of O. edulis with varying periods of exposure to B. ostreae, was undertaken to determine if varying lengths of exposure would translate into observations of differing susceptibility. Oyster stocks can maintain themselves over extended periods of time in B. ostreae endemic areas. To identify a well performing spat stock, which could be used to repopulate beds within the region, hatchery bred spat from three stocks found in the North sea were placed on a B. ostreae infected bed and screened for growth, mortality and prevalence of infection. Local environmental factors may influence oyster performance, with local stocks better adapted to these conditions. Sediment and macroinvertebrate species were screened to investigate mechanisms by which B. ostreae may be maintaining itself on oyster beds. Mytilus edulis was positive, indicating that B. ostreae may use incidental carriers as a method of maintaining itself. The ability of oyster larvae to pick up infection from the surrounding environment was investigated by collecting larvae from brooding oysters from different areas. Larvae may acquire the pathogen from the water column during the process of filter feeding by the brooding adult, even when the parents themselves are uninfected. A study was undertaken to elucidate the activity of the parasite during the initial stage of infection, when it cannot be detected within the host. A naïve stock screened negative for infection throughout the trial, using heart imprints and PCR yet B. ostreae was detected by in-situ hybridisation.

A river of memory: landscape, narrative and identity in the Lee Valley, Co. Cork, Ireland

In moments of rapid social changes, as has been witnessed in Ireland in the last decade, the conditions through which people engage with their localities though memory, individually and collectively, remains an important cultural issue with key implications for questions of heritage, preservation and civic identity. In recent decades, cultural geographers have argued that landscape is more than just a view or a static text of something symbolic. The emphasis seems to be on landscape as a dynamic cultural process – an ever-evolving process being constructed and re-constructed. Hence, landscape seems to be a highly complex term that carries many different meanings. Material, form, relationships or actions have different meanings in different settings. Drawing upon recent and continuing scholarly debates in cultural landscapes and collective memory, this thesis sets out to examine the generation of collective memory and how it is employed as a cultural tool in the production of memory in the landscape. More specifically, the research considers the relationships between landscape and memory, investigating the ways in which places are produced, appropriated, experienced, sensed, acknowledged, imagined, yearned for, appropriated, re-appropriated, contested and identified with. A polyvocal-bricoleur approach aims to get below the surface of a cultural landscape, inject historical research and temporal depth into cultural landscape studies and instil a genuine sense of inclusivity of a wide variety of voices (role of monuments and rituals and voices of people) from the past and present. The polyvocal-bricoleur approach inspires a mixed method methodology approach to fieldsites through archival research, fieldwork and filmed interviews. Using a mixture of mini-vignettes of place narratives in the River Lee valley in the south of Ireland, the thesis explores a number of questions on the fluid nature of narrative in representing the story and role of the landscape in memory-making. The case studies in the Lee Valley are harnessed to investigate the role of the above questions/ themes/ debates in the act of memory making at sites ranging from an Irish War of Independence memorial to the River Lee’s hydroelectric scheme to the valley’s key religious pilgrimage site. The thesis investigates the idea that that the process of landscape extends not only across space but also across time – that the concept of historical continuity and the individual and collective human engagement and experience of this continuity are central to the processes of remembering on the landscape. In addition the thesis debates the idea that the production of landscape is conditioned by several social frames of memory – that individuals remember according to several social frames that give emphasis to different aspects of the reality of human experience. The thesis also reflects on how the process of landscape is represented by those who re-produce its narratives in various media.

The ‘Celtic’ dimension of pre-first World War religious discourse in Britain: Wellesley Tudor Pole and the Glastonbury phenomenon

This article will explore the contribution made to the construction of discourse around religion outside of mainstream Christianity, at the turn of the twentieth century in Britain, by a Celticist movement as represented by Wellesley Tudor Pole (d.1968) and his connection to the Glastonbury phenomenon. I will detail the interconnectedness of individuals and movements occupying this discursive space and their interest in efforts to verify the authenticity of an artefact which Tudor Pole claimed was once in the possession of Jesus. Engagement with Tudor Pole’s quest to prove the provenance of the artefact, and his contention that a pre-Christian culture had existed in Ireland which had extended itself to Glastonbury and Iona creating the foundation for an authentic Western mystical tradition, is presented as one facet of a broader, contemporary discourse on alternative ideas and philosophies. In conclusion, I will juxtapose Tudor Pole’s fascination with Celtic origins and the approach of leading figures in the ‘Celtic Revival’ in Ireland, suggesting intersections and alterity in the construction of their worldview. The paper forms part of a chapter in a thesis under-preparation which examines the construction of discourse on religion outside of mainstream Christianity at the turn of the twentieth century, and in particular the role played by visiting religious reformers from Asia. The aim is to recover the (mostly forgotten) history of these engagements.

Creating religious place in Ireland: Hindu public places of worship and the Indian sculpture park

This paper examines the creation of religious place. It argues that the designation of a place as “religious” is a subjective and creative act which is dependent upon the perception and past, or memory, of the viewer. The paper focuses specifically on the creation of public places of worship by Hindu groups in the Dublin city area of Ireland and on the varied perceptions of the Indian Sculpture Park in County Wicklow. The creation of public places of worship results in places classified as “religious” due to the intention of the creator, the terminology used and the types of activities that take place in the space. This is in contrast to places such as the Indian Sculpture Park in County Wicklow which was created as a secular space but which is viewed by some Hindus as an outdoor temple due to the presence of sculptures of the Hindu deity Ganesh. Other Hindus do not view the space as having any religious significance and so its religiosity is contested. This points to the fact that the creation of religious place is a creative act of interpretation which is dependent upon the perception and past of the viewer and which changes over time.

Religious memory as a conveyor of authoritative tradition: The necessary and essential component in a definition of religion

In a landmark book published in 2000, the sociologist Danièle Hervieu-Léger defined religion as a chain of memory, by which she meant that within religious communities remembered traditions are transmitted with an overpowering authority from generation to generation. After analysing Hervieu-Léger’s sociological approach as overcoming the dichotomy between substantive and functional definitions, this article compares a ritual honouring the ancestors in which a medium becomes possessed by the senior elder’s ancestor spirit among the Shona of Zimbabwe with a cleansing ritual performed by a Celtic shaman in New Hampshire, USA. In both instances, despite different social and historical contexts, appeals are made to an authoritative tradition to legitimize the rituals performed. This lends support to the claim that the authoritative transmission of a remembered tradition, by exercising an overwhelming power over communities, even if the memory of such a tradition is merely postulated, identifies the necessary and essential component for any activity to be labelled “religious”.

Aspects particuliers de l'immunologie des voies génitales.

SCOPUS: ar.j

The protective role of religious coping in adolescents' responses to poverty and sexual decision-making in rural Kenya.

In this study, we explored how adolescents in rural Kenya apply religious coping in sexual decision-making in the context of high rates of poverty and Human Immunodeficiency Virus (HIV). Semi-structured interviews were conducted with 34 adolescents. One-third (13) reported religious coping related to economic stress, HIV, or sexual decision-making; the majority (29) reported religious coping with these or other stressors. Adolescents reported praying for God to partner with them to engage in positive behaviors, praying for strength to resist unwanted behaviors, and passive strategies characterized by waiting for God to provide resources or protection from HIV. Adolescents in Sub-Saharan Africa may benefit from HIV prevention interventions that integrate and build upon their use of religious coping.

CONSERVATIVE AND PROGFESSIVE ASPECTS OF THE SONATA FROM LATE BEETHOVEN TO PROKOFIEV

The term 'sonata' arose in the early seventeenth-century Baroque period and was originally used to distinguish instrumental (sonata) music from vocal music. Later. the sonata style, as a reliable yet flexible compositional framework, was extensively shaped and utilized throughout the Classical period. Subsequently, in the Romantic period, freer creative, individualistic. and expressive musical elements began to be preferred by composers in their use of harmonj., tone color, form, and rhythm. However, even during the revolutionary Romantic period in music. the compositions which did not have a pre-defined format (character pieces, etc) were often comfortably framed and limited within the recognizable boundaries provided by the Classical sonata style. The sonata format, when used as a tool in musical composition, provides logical boundaries that may serve to organize any unexpected emotional expressions on the part of the composer. Yet the sonata framework is also flexible enough to allow freedom of expression. In the Romantic period and beyond, composers had relied, some more than others, upon the sonata's adaptable blend of stability and flexibility. In my opinion, it is more persuasive to express oneself musically within the framework of an established musical style. Thus, I have chosen my dissertation topic as the performance of six pieces incorporating elements of the reliable and flexible sonata style. The sonata of each composer that I have selected clearly demonstrates a tension between logic and emotion expressed within the sonata framework. However, the compositions can be divided interestingly into two groups, such as 'conservative' and 'progressive' group. The 'conservative' group consists of composers who seemed to strive for greater freedom of self-expression within the constraints of the traditional sonata form. On the other hand, the 'progressive' group consists of composers who seemed more to rely upon the sonata form to rein in and add stability to their highly individual and emotional musical ideas. It is my hope that this project will provide a stimulating viewpoint from which to consider the evolution and utilization of the sonata style especially as it is applied to the composition and performance of these six diverse and interesting pieces.

Rain dances in the dry season: overcoming the religious congruence fallacy

Religious congruence refers to consistency among an individual’s religious beliefs and attitudes, consistency between religious ideas and behavior, and religious ideas, identities, or schemas that are chronically salient and accessible to individuals across contexts and situations. Decades of anthropological, sociological, and psychological research establish that religious congruence is rare, but much thinking about religion presumes that it is common. The religious congruence fallacy occurs when interpretations or explanations unjustifiably presume religious congruence. I illustrate the ubiquity of religious incongruence, show how the religious congruence fallacy distorts thinking about religion, and outline an approach to help overcome the fallacy.

Changing American Congregations: Findings from the Third Wave of the National Congregations Study

The third wave of the National Congregations Study (NCS-III) was conducted in 2012. The 2012 General Social Survey asked respondents who attend religious services to name their religious congregation, producing a nationally representative cross-section of congregations from across the religious spectrum. Data about these congregations was collected via a 50-minute interview with one key informant from 1,331 congregations. Information was gathered about multiple aspects of congregations’ social composition, structure, activities, and programming. Approximately two-thirds of the NCS-III questionnaire replicates items from 1998 or 2006-07 NCS waves. Each congregation was geocoded, and selected data from the 2010 United States census or American Community Survey have been appended. We describe NCS-III methodology and use the cumulative NCS dataset (containing 4,071 cases) to describe five trends: more ethnic diversity, greater acceptance of gays and lesbians, increasingly informal worship styles, declining size (but not from the perspective of the average attendee), and declining denominational affiliation.

Using Behavioral Insights For a Better Understanding of Economic Decisions (Regarding Savings, Inequality and Dishonesty)

This dissertation consists of three essays on behavioral economics, with a general aim of enriching our understanding of economic decisions using behavioral insights and experimental methodology. Each essay takes on one particular topic with this general aim.

The first chapter studies savings behavior of the poor. In this project, partnering with a savings product provider in Kenya, we tested the extent to which behavioral interventions and financial incentives can increase the saving rate of individuals with low and irregular income. Our experiment lasted for six months and included a total of twelve conditions. The control condition received weekly reminders and balance reporting via text messages. The treatment conditions received in addition one of the following interventions: (1) reminder text messages framed as if they came from the participant’s kid (2) a golden colored coin with numbers for each week of the trial, on which participants were asked to keep track of their weekly deposits (3) a match of weekly savings: The match was either 10% or 20% up to a certain amount per week. The match was either deposited at the end of each week or the highest possible match was deposited at the start of each week and was adjusted at the end. Among these interventions, by far the most effective was the coin: Those in the coin condition saved on average the highest amount and more than twice as those in the control condition. We hypothesize that being a tangible track-keeping object; the coin made subjects remember to save more often. Our results support the line of literature suggesting that saving decisions involve psychological aspects and that policy makers and product designers should take these influences into account.

The second chapter is related to views towards inequality. In this project, we investigate how the perceived fairness of income distributions depends on the beliefs about the process that generated the inequality. Specifically, we examine how two crucial features of this process affect fairness views: (1) Procedural justice - equal treatment of all, (2) Agency - one's ability to determine his/her income. We do this in a lab experiment by varying the equality of opportunity (procedural justice), and one's ability to make choices, which consequently influence subjects’ ability to influence their income (agency). We then elicit ex-post redistribution decisions of the earnings as a function of these two elements. Our results suggest both agency and procedural justice matter for fairness. Our main findings can be summarized as follows: (1) Highlighting the importance of agency, we find that inequality resulting from risk is considered to be fair only when risk is chosen freely; (2) Highlighting the importance of procedural justice, we find that introducing inequality of opportunity significantly increases redistribution, however the share of subjects redistributing none remain close to the share of subjects redistributing fully revealing an underlying heterogeneity in the population about how fairness views should account for inequality of opportunity.

The third chapter is on morality. In this project, we study whether religious rituals act as an internal reminder for basic moral principles and thus affect moral judgments. To this end, we conducted two survey experiments in Turkey and Israel to specifically test the effect of Ramadan and Yom Kippur. The results from the Turkish sample how that Ramadan has a significant effect on moral judgments to some extent for those who report to believe in God. Those who believe in God judged the moral acceptability of ten out of sixty one actions significantly differently in Ramadan, whereas those who reported not to believe in God significantly changed their judgments only for one action in Ramadan. Our results extends the hypothesis established by lab experiments that religious reminders have a significant effect on morality, by testing it in the field in the natural environment of religious rituals.

This thesis is part of a broader collaborative research agenda with both colleagues and advisors. The programming, analyses, and writing, as well as any errors in this work, are my own.

Classical and quantum aspects of the extended antifield formalism

Agrégation de l'enseignement supérieur, Orientation sciences