Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters

To screen for novel ribosomally synthesised antimicrobials, in-silico genome mining was performed on all publically available fully sequenced bacterial genomes. 49 novel type 1 lantibiotic clusters were identified from a number of species, genera and phyla not usually associated with lantibiotic production, and indicates high prevalence. A crucial step towards the commercialisation of fermented beverages is the characterisation of the microbial content. To achieve this goal, we applied next-generation sequencing techniques to analyse the bacterial and yeast populations of the organic, symbiotically-fermented beverages kefir, water kefir and kombucha. A number of minor components were revealed, many of which had not previously been associated with these beverages. The dominant microorganism in each of the water kefir grains and fermentates was Zymomonas, an ethanol-producing bacterium that had not previously been detected on such a scale. These studies represent the most accurate description of these populations to date, and should aid in future starter design and in determining which species are responsible for specific attributes of the beverages. Finally, high-throughput robotics was applied to screen for the presence of antimicrobial producers associated with these beverages. This revealed a low frequency of bacteriocin production amongst the bacterial isolates, with only lactococcins A, B and LcnN of lactococcin M being identified. However, a proteinaceous antimicrobial produced by the yeast Dekkera bruxellensis, isolated from kombucha, was found to be active against Lactobacillus bulgaricus. This peptide was patially purified.

Reasoning with sorted-pareto dominance and other qualitative and partially ordered preferences in soft constraints

In decision making problems where we need to choose a particular decision or alternative from a set of possible choices, we often have some preferences which determine if we prefer one decision over another. When these preferences give us an ordering on the decisions that is complete, then it is easy to choose the best or one of the best decisions. However it often occurs that the preferences relation is partially ordered, and we have no best decision. In this thesis, we look at what happens when we have such a partial order over a set of decisions, in particular when we have multiple orderings on a set of decisions, and we present a framework for qualitative decision making. We look at the different natural notions of optimal decision that occur in this framework, which gives us different optimality classes, and we examine the relationships between these classes. We then look in particular at a qualitative preference relation called Sorted-Pareto Dominance, which is an extension of Pareto Dominance, and we give a semantics for this relation as one that is compatible with any order-preserving mapping of an ordinal preference scale to a numerical one. We apply Sorted-Pareto dominance to a Soft Constraints setting, where we solve problems in which the soft constraints associate qualitative preferences to decisions in a decision problem. We also examine the Sorted-Pareto dominance relation in the context of our qualitative decision making framework, looking at the relevant optimality classes for the Sorted-Pareto case, which gives us classes of decisions that are necessarily optimal, and optimal for some choice of mapping of an ordinal scale to a quantitative one. We provide some empirical analysis of Sorted-Pareto constraints problems and examine the optimality classes that result.

Between respectability and disgrace: schismogenesis and the regeneration of inequality, stigma and social exclusion in Limerick

The thesis examines cultural processes underpinning the emergence, institutionalisation and reproduction of class boundaries in Limerick city. The research aims to bring a new understanding to the contemporary context of the city’s urban regeneration programme. Acknowledging and recognising other contemporary studies of division and exclusion, the thesis creates a distinctive approach which focuses on uncovering the cultural roots of inequality, educational disadvantage, stigma and social exclusion and the dynamics of their social reproduction. Using Bateson’s concept of schismogenesis (1953), the thesis looks to the persistent, but fragmented culture of community and develops a heuristic ‘symbolic order of the city’. This is defined as “…a cultural structure, the meaning making aspect of hierarchy, the categorical structures of world understanding, the way Limerick people understand themselves, their local and larger world” (p. 37). This provides a very different departure point for exploring the basis for urban regeneration in Limerick (and everywhere). The central argument is that if we want to understand the present (multiple) crises in Limerick we need to understand the historical, anthropological and recursive processes underpinning ‘generalised patterns of rivalry and conflict’. In addition to exploring the historical roots of status and stigma in Limerick, the thesis explores the mythopoesis of persistent, recurrent narratives and labels that mark the boundaries of the city’s identities. The thesis examines the cultural and social function of ‘slagging’ as a vernacular and highly particularised form of ironic, ritualised and, often, ‘cruel’ medium of communication (often exclusion). This is combined with an etymology of the vocabulary of Limerick slang and its mythological base. By tracing the origins of many normalised patterns of Limerick speech ‘sayings’, which have long since forgotten their roots, the thesis demonstrates how they perform a significant contemporary function in maintaining and reinforcing symbolic mechanisms of inclusion/exclusion. The thesis combines historical and archival data with biographical interviews, ethnographic data married to a deep historical hermeneutic analysis of this political community.

The endless search for SA: spiritual ideology in Hindustāni music

This dissertation centres on philosophical attitudes presented by North Indian classical musicians in relation to the concept and experience of rāga improvisation. In Hindustāni music, there is a dynamic tension ideology and pragmatism, devotion and entertainment, fixity and improvisational freedom, and cognition and visceral experience. On one hand, rāga is an embodied methodological template for the creation of music. On the other hand, rāga improvisation is conceptualised as a path to metaphysical experience and as an evocation of an ineffable divine presence. A masterful rendition of rāga is both a re-enactment of a systematic prescribed formula and a spontaneous flow of consciousness. This study presents these apparent dichotomies to highlight ideological concerns, while simultaneously contextualising philosophical idealism in relation to pragmatic realities. A central paradigm is the manner in which pragmatic concerns are elevated in status and given spiritual significance. The dissertation begins with a view into historical and religious context. The discussion continues with a speculative investigation positing co-relations between Hindustāni music and central tenets of Indian philosophy, considering how rāga improvisation may manifest as a philosophy of sound. The study then explores the concept of rāga, a modal and conceptual construct that forms the heart of Indian classical music. The final three sections ground the subject of spiritual ideology within the life experience of Hindustāni musicians: ‘Transmission’ looks at the learning and enculturation process, which encapsulates values intrinsic to the ethos of Hindustāni music culture. ‘Practice’ explores the discipline, science and experience of musical practice, revealing core ideological concerns connecting spirituality to musical experience; and ‘Performance’ examines the live presentation of rāga improvisation, and the relationship between music as ‘entertainment’ and music as ‘devotion’. Both ethnographic and musicological, this research is the culmination of various fieldtrips to India, extensive interviews with Hindustāni musicians, fifteen year’s sitār training, and the study of relevant musicological and philosophical texts.

Religion, the study of religion and other products of transnational and colonial imaginings

The category of ‘religion’ as contemporary scholarship has demonstrated is a fairly recent innovation, dating back only a few hundred years in Western thought, and ‘world religions’ as we think of it and as we teach it is an even more recent category, emerging out of European colonialism. Thus the academic study of religion is both the product and, at times, the agent of colonial modes of knowledge. And yet, it is perhaps because ‘religion’ continues to be invented and reinvented through connections across cultures that investigating the work of religious ideas and practices offers such fruitful possibilities for understanding the work of culture and power. This article investigates religion and the study of religion as a mode of anti-colonial practice, seeking to understand how each have the potential to cross boundaries, build bridges and produce critical insights into assumptions and worldviews too often taken for granted.

Monstrative acts and becoming-monster: on identity, bodies, and the feminine other

Using two examples of literary monsters, the Creature in Mary Shelley’s Frankenstein (1818), and Grendel’s Mother in Beowulf, this thesis demonstrates the bearing fictional identities have on “real” bodies, through an examination of two further literary texts, David Henry Hwang’s play, M. Butterfly (1986) and J. M. Coetzee’s novel, Disgrace (1999). Western definitions of Being have historically divided body and mind, favouring the mind as formative of subjective experience and denigrating the body as secondary and impure. This thesis demonstrates that this mind/body binary is symptomatic of the masculine ontological imperative to disown the body and its effects on Being, simultaneously ridding itself of the feminine it believes is its irrational opposite. Using recent feminist reviews of the canon, which emphasise the body’s importance to ontology and demonstrate the conceptual association between the feminine and the corporeal, this thesis links performative identity practices to theories of monstrosity, explaining how fictional qualities adhere to monstrous bodies by proposing a new theoretical category, the “monstrative.” The monstrative is a performative force that makes the Other into a living sign of Otherness; however, unlike earlier theories of Othering, the monstrative accounts for the Other’s being other to herself. This thesis also attempts to read the misrepresented body of the Other as a possible site for more empowered identity performances, where the monstrous “I” is interpreted as a potentially positive model for identity practice, through the conceptualisation of identity as a process of Becoming rather than Being. The transferal from a noun to a verb not only emphasises the performativity of identity, but also suggests fluidity and multiplicity in identity practice, which always already indicates a monstrosity at work. Thus, while monstrative acts constitute bodies as monstrous, Becoming-monster is an empathetic response to the Other’s monstrosity.

Afro-Cuban Bata Drum Aesthetics: Developing Individual and Group Technique, Sound and Identity

The Lucumi religion (also Santeria and Regla de Ocha) developed in 19th-century colonial Cuba, by syncretizing elements of Catholicism with the Yoruba worship of orisha. When fully initiated, santeros (priests) actively participate in religious ceremonies by periodically being possessed or "mounted" by a patron saint or orisha, usually within the context of a drumming ritual, known as a toque de santo, bembe, or tambor. Within these rituals, there is a clearly defined goal of trance possession, though its manifestation is not the sole measure of success or failure. Rather than focusing on the fleeting, exciting moments that immediately precede the arrival of an orisha in the form of a possession trance, this thesis investigates the entire four- to six-hour musical performance that is central to the ceremony. It examines the brief pauses, the moments of reduced intensity, the slow but deliberate build-ups of energy and excitement, and even the periods when novices are invited to perform the sacred bata drums, and places these moments on an equal footing with the more dynamic periods where possession is imminent or in progress. This document approaches Lucumi ritual from the viewpoint of bata drummers, ritual specialists who, during the course of a toque de santo, exercise wide latitude in determining the shape of the event. Known as omo Ana (children of the orisha Ana who is manifest in drums and rhythms), bata drummers comprise a fraternity that is accessible only through ritual initiation. Though they are sensitive to the desires of the many participants during a toque de santo, and indeed make their living by satisfying the expectations of their hosts, many of the drummers' activities are inwardly focused on the cultivation and preservation of this fraternity. Occasionally interfering with spirit possession, and other expectations of the participants, these aberrant activities include teaching and learning, developing group identity or signature sound, and achieving a state of intimacy among the musicians known as "communitas."

Burning a hole in the budget: tobacco spending and its crowd-out of other goods.

Smoking is an expensive habit. Smoking households spend, on average, more than $US1000 annually on cigarettes. When a family member quits, in addition to the former smoker's improved long-term health, families benefit because savings from reduced cigarette expenditures can be allocated to other goods. For households in which some members continue to smoke, smoking expenditures crowd-out other purchases, which may affect other household members, as well as the smoker. We empirically analyse how expenditures on tobacco crowd-out consumption of other goods, estimating the patterns of substitution and complementarity between tobacco products and other categories of household expenditure. We use the Consumer Expenditure Survey data for the years 1995-2001, which we complement with regional price data and state cigarette prices. We estimate a consumer demand system that includes several main expenditure categories (cigarettes, food, alcohol, housing, apparel, transportation, medical care) and controls for socioeconomic variables and other sources of observable heterogeneity. Descriptive data indicate that, comparing smokers to nonsmokers, smokers spend less on housing. Results from the demand system indicate that as the price of cigarettes rises, households increase the quantity of food purchased, and, in some samples, reduce the quantity of apparel and housing purchased.

Trade-offs between cancer and other diseases: do they exist and influence longevity?

Relationships between aging, disease risks, and longevity are not yet well understood. For example, joint increases in cancer risk and total survival observed in many human populations and some experimental aging studies may be linked to a trade-off between cancer and aging as well as to the trade-off(s) between cancer and other diseases, and their relative impact is not clear. While the former trade-off (between cancer and aging) received broad attention in aging research, the latter one lacks respective studies, although its understanding is important for developing optimal strategies of increasing both longevity and healthy life span. In this paper, we explore the possibility of trade-offs between risks of cancer and selected major disorders. First, we review current literature suggesting that the trade-offs between cancer and other diseases may exist and be linked to the differential intensity of apoptosis. Then we select relevant disorders for the analysis (acute coronary heart disease [ACHD], stroke, asthma, and Alzheimer disease [AD]) and calculate the risk of cancer among individuals with each of these disorders, and vice versa, using the Framingham Study (5209 individuals) and the National Long Term Care Survey (NLTCS) (38,214 individuals) data. We found a reduction in cancer risk among old (80+) men with stroke and in risk of ACHD among men (50+) with cancer in the Framingham Study. We also found an increase in ACHD and stroke among individuals with cancer, and a reduction in cancer risk among women with AD in the NLTCS. The manifestation of trade-offs between risks of cancer and other diseases thus depended on sex, age, and study population. We discuss factors modulating the potential trade-offs between major disorders in populations, e.g., disease treatments. Further study is needed to clarify possible impact of such trade-offs on longevity.

Alternative splicing in multiple sclerosis and other autoimmune diseases.

Alternative splicing is a general mechanism for regulating gene expression that affects the RNA products of more than 90% of human genes. Not surprisingly, alternative splicing is observed among gene products of metazoan immune systems, which have evolved to efficiently recognize pathogens and discriminate between "self" and "non-self", and thus need to be both diverse and flexible. In this review we focus on the specific interface between alternative splicing and autoimmune diseases, which result from a malfunctioning of the immune system and are characterized by the inappropriate reaction to self-antigens. Despite the widespread recognition of alternative splicing as one of the major regulators of gene expression, the connections between alternative splicing and autoimmunity have not been apparent. We summarize recent findings connecting splicing and autoimmune disease, and attempt to find common patterns of splicing regulation that may advance our understanding of autoimmune diseases and open new avenues for therapy.

A novel mutation of the ACADM gene (c.145C>G) associated with the common c.985A>G mutation on the other ACADM allele causes mild MCAD deficiency: a case report.

A female patient, with normal familial history, developed at the age of 30 months an episode of diarrhoea, vomiting and lethargy which resolved spontaneously. At the age of 3 years, the patient re-iterated vomiting, was sub-febrile and hypoglycemic, fell into coma, developed seizures and sequels involving right hemi-body. Urinary excretion of hexanoylglycine and suberylglycine was low during this metabolic decompensation. A study of pre- and post-prandial blood glucose and ketones over a period of 24 hours showed a normal glycaemic cycle but a failure to form ketones after 12 hours fasting, suggesting a mitochondrial β-oxidation defect. Total blood carnitine was lowered with unesterified carnitine being half of the lowest control value. A diagnosis of mild MCAD deficiency (MCADD) was based on rates of 1-14C-octanoate and 9, 10-3H-myristate oxidation and of octanoyl-CoA dehydrogenase being reduced to 25% of control values. Other mitochondrial fatty acid oxidation proteins were functionally normal. De novo acylcarnitine synthesis in whole blood samples incubated with deuterated palmitate was also typical of MCADD. Genetic studies showed that the patient was compound heterozygous with a sequence variation in both of the two ACADM alleles; one had the common c.985A>G mutation and the other had a novel c.145C>G mutation. This is the first report for the ACADM gene c.145C>G mutation: it is located in exon 3 and causes a replacement of glutamine to glutamate at position 24 of the mature protein (Q24E). Associated with heterozygosity for c.985A>G mutation, this mutation is responsible for a mild MCADD phenotype along with a clinical story corroborating the emerging literature view that patients with genotypes representing mild MCADD (high residual enzyme activity and low urinary levels of glycine conjugates), similar to some of the mild MCADDs detected by MS/MS newborn screening, may be at risk for disease presentation.

The Aesthetics of Motion in Musics for the Mevlana Celal ed-Din Rumi

This dissertation investigates the concept of motion as a fundamental aesthetic element in the devotional music, dance, and rituals performed in honor of the celebrated thirteenth-century Persian mystic poet and saint, the Mevlana Celal ed-Din Muhammad Rumi. The main focus of the study is threefold. First, it investigates the prevalence of the notion of movement in Islamic music and culture, specifically within the Sufi communities of Turkey, in order to arrive at a broader understanding of the relationship between music, aesthetics, and worldview. Secondly, it explores how musical performance functions as a form of devotion or religious worship by focusing on the musical repertories performed in honor of a single holy figure, the Mevlana Rumi. Finally, it provides an ethnographic account of contemporary developments in Sufi musical culture in Turkey and across the world by describing the recent activities of the Mevlana's devotees, which includes members of the Mevlevi Order of Islamic mystics as well as adherents of other Sufi brotherhoods and followers of so-called New Religions or New Age. The primary research for this study involved two short one-month field trips to Turkey and India in 2002 and 2003, respectively, and a longer one year expedition to Turkey in 2004 and 2005, which also included shorter stays in Cyprus, Syria, and Egypt. Additionally, the dissertation draws directly from critical theories advanced in the fields of ethnomusicology, cultural anthropology, and ethnochoreology and focuses on the kinesthetic parameters of music, dance, trance, and ritual as well as on broader forms of socio-cultural movement including pilgrimage, cultural tourism, and globalization. These forms of movement are analyzed in four broad categories of music used in worship, including classical Mevlevi music, music of the zikr ceremony, popular musics, and non-Turkish musics.

Cholera in Haiti and other Caribbean regions, 19th century.

Medical journals and other sources do not show evidence that cholera occurred in Haiti before 2010, despite the devastating effect of this disease in the Caribbean region in the 19th century. Cholera occurred in Cuba in 1833-1834; in Jamaica, Cuba, Puerto Rico, St. Thomas, St. Lucia, St. Kitts, Nevis, Trinidad, the Bahamas, St. Vincent, Granada, Anguilla, St. John, Tortola, the Turks and Caicos, the Grenadines (Carriacou and Petite Martinique), and possibly Antigua in 1850-1856; and in Guadeloupe, Cuba, St. Thomas, the Dominican Republic, Dominica, Martinique, and Marie Galante in 1865-1872. Conditions associated with slavery and colonial military control were absent in independent Haiti. Clustered populations, regular influx of new persons, and close quarters of barracks living contributed to spread of cholera in other Caribbean locations. We provide historical accounts of the presence and spread of cholera epidemics in Caribbean islands.