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.

The biodiversity, control and genetic characterisation of the lactococcal 936 group phages

Phages belonging to the 936 group represent one of the most prevalent and frequently isolated phages in dairy fermentation processes using Lactococcus lactis as the primary starter culture. In recent years extensive research has been carried out to characterise this phage group at a genomic level in an effort to understand how the 936 group phages dominate this particular niche and cause regular problems during large scale milk fermentations. This thesis describes a large scale screening of industrial whey samples, leading to the isolation of forty three genetically different lactococcal phages. Using multiplex PCR, all phages were identified as members of the 936 group. The complete genome of thirty eight of these phages was determined using next generation sequencing technologies which identified several regions of divergence. These included the structural region surrounding the major tail protein, the replication region as well as the genes involved in phage DNA packing. For a number of phages the latter genomic region was found to harbour genes encoding putative orphan methyltransferases. Using small molecule real time (SMRT) sequencing and heterologous gene expression, the target motifs for several of these MTases were determined and subsequently shown to actively protect phage DNA from restriction endonuclease activity. Comparative analysis of the thirty eight phages with fifty two previously sequenced members of this group showed that the core genome consists of 28 genes, while the non-core genome was found to fluctuate irrespective of geographical location or time of isolation. This study highlights the continued need to perform large scale characterisation of the bacteriophage populations infecting industrial fermentation facilities in effort to further our understanding dairy phages and ways to control their proliferation.

Temporal and spatial variation in otter Lutra lutra diet in Northern Ireland

The European otter (Lutra lutra L.) has a highly specialised diet that is composed predominantly of fish. The current study investigates the percentage composition of food items in otter spraints collected in six river catchments in Northern Ireland in 1980 and again from the same locations in 2003. Spraints contained significantly more salmonids than any other prey item. The composition of spraints differed among catchments. More salmonids and three-spined stickleback (Gasterosteus aculeatus L.) were found in spraints from the Glens of Antrim, while spraints from the Lagan catchment had significantly more eel (Anguilla anguilla L.). There were significantly more spraints containing non-fish food items in 2003 compared with 1980. These non-fish items were insects, amphipods, birds, rats (Rattus norvegicus Berkenhout) and lagomorphs. Increased consumption of non-fish items was apparent in all but one of the river catchments. The mean diversity of spraint composition was significantly greater in 2003 than in 1980. Therefore, our findings indicate that otters have diversified their diet since 1980 and now eat more non-fish prey.

The effect of a healthy lifestyle programme on 8-9 year olds from social disadvantage

Aims: This study assessed the efficacy of a school-based healthy lifestyle intervention (Sport for LIFE) for increasing physical activity, decreasing sedentary behaviour, reducing screen time behaviour, encouraging healthy attitudes and behaviour to nutrition, and reducing body mass index (BMI) in 8–9-year-old primary school children from lower socioeconomic backgrounds in Northern Ireland.

Methods: A non-randomised controlled trial of 416 children from 24 schools took part. Schools were randomly assigned to one of two groups, an intervention or control group with 12 schools in each group. The intervention group received a 12-week school-based programme based on social cognitive theory. At baseline and follow-up, groups completed questionnaires assessing physical activity, screen time behaviour and dietary patterns. On each occasion anthropometric assessments of height and weight were taken. Physical activity and sedentary behaviour were measured by accelerometry.

Results Significant effects were observed for vigorous, moderate and light activity for the intervention group at follow-up. Sedentary behaviour was significantly reduced for the intervention group but not for the control group. No significant effects of the intervention on BMI, screen time behaviour or attitudes to nutrition, with the exception of non-core foods, were shown.

Conclusions: The programme was effective in increasing physical activity and reducing sedentary behaviour, however no significant changes in screen time behaviour and attitude to nutrition, with the exception of non-core foods, were observed. Future research ideas are offered for tackling low levels of physical activity in children.

Basel III: The impact of new capital requirements on profitability of Portuguese Banks

This empirical study aims to explore the impact of increased capital ratio requirements, on the ROE of the Portuguese banking sector. The paper employs both a quantitative- and qualitative approach, with the qualitative approach as the main method of research. The method adopted to conduct the qualitative research was semi structured elite interviews with banking executives. Higher capital requirements decrease the ROE of banks in Portugal, but huge impairments charges, macroeconomic factors and increased costs of deposits are clearly the dominant reasons for the reduced levels of ROE the past years. Among the measures taken to increase capital ratios, reduction of RWAs and non-core assets have been the main focus, but the issuance of CoCos is regarded as the most expensive measure due to high interest payments. However, the CoCos will not have any effect on the ROE in the long term. It is difficult to draw any conclusions on the impact of more equity in the balance sheet on the ROE of Portuguese banks, as many banks currently don’t generate enough money to pay back on shareholders´ investments.

Drivers and Barriers of Collaboration in the Value Chain of Paperboard-Packed Consumer Goods

Value chain collaboration has been a prevailing topic for research, and there is a constantly growing interest in developing collaborative models for improved efficiency in logistics. One area of collaboration is demand information management, which enables improved visibility and decrease of inventories in the value chain. Outsourcing of non-core competencies has changed the nature of collaboration from intra-enterprise to cross-enterprise activity, and this together with increasing competition in the globalizing markets have created a need for methods and tools for collaborative work. The retailer part in the value chain of consumer packaged goods (CPG) has been studied relatively widely, proven models have been defined, and there exist several best practice collaboration cases. The information and communications technology has developed rapidly, offering efficient solutions and applications to exchange information between value chain partners. However, the majority of CPG industry still works with traditional business models and practices. This concerns especially companies operating in the upstream of the CPG value chain. Demand information for consumer packaged goods originates at retailers' counters, based on consumers' buying decisions. As this information does not get transferred along the value chain towards the upstream parties, each player needs to optimize their part, causing safety margins for inventories and speculation in purchasing decisions. The safety margins increase with each player, resulting in a phenomenon known as the bullwhip effect. The further the company is from the original demand information source, the more distorted the information is. This thesis concentrates on the upstream parts of the value chain of consumer packaged goods, and more precisely the packaging value chain. Packaging is becoming a part of the product with informative and interactive features, and therefore is not just a cost item needed to protect the product. The upstream part of the CPG value chain is distinctive, as the product changes after each involved party, and therefore the original demand information from the retailers cannot be utilized as such – even if it were transferred seamlessly. The objective of this thesis is to examine the main drivers for collaboration, and barriers causing the moderate adaptation level of collaborative models. Another objective is to define a collaborative demand information management model and test it in a pilot business situation in order to see if the barriers can be eliminated. The empirical part of this thesis contains three parts, all related to the research objective, but involving different target groups, viewpoints and research approaches. The study shows evidence that the main barriers for collaboration are very similar to the barriers in the lower part of the same value chain; lack of trust, lack of business case and lack of senior management commitment. Eliminating one of them – the lack of business case – is not enough to eliminate the two other barriers, as the operational model in this thesis shows. The uncertainty of the future, fear of losing an independent position in purchasing decision making and lack of commitment remain strong enough barriers to prevent the implementation of the proposed collaborative business model. The study proposes a new way of defining the value chain processes: it divides the contracting and planning process into two processes, one managing the commercial parts and the other managing the quantity and specification related issues. This model can reduce the resistance to collaboration, as the commercial part of the contracting process would remain the same as in the traditional model. The quantity/specification-related issues would be managed by the parties with the best capabilities and resources, as well as access to the original demand information. The parties in between would be involved in the planning process as well, as their impact for the next party upstream is significant. The study also highlights the future challenges for companies operating in the CPG value chain. The markets are becoming global, with toughening competition. Also, the technology development will most likely continue with a speed exceeding the adaptation capabilities of the industry. Value chains are also becoming increasingly dynamic, which means shorter and more agile business relationships, and at the same time the predictability of consumer demand is getting more difficult due to shorter product life cycles and trends. These changes will certainly have an effect on companies' operational models, but it is very difficult to estimate when and how the proven methods will gain wide enough adaptation to become standards.

Criteria for the validation of specialized verb equivalents : application in bilingual terminography

Multilingual terminological resources do not always include valid equivalents of legal terms for two main reasons. Firstly, legal systems can differ from one language community to another and even from one country to another because each has its own history and traditions. As a result, the non-isomorphism between legal and linguistic systems may render the identification of equivalents a particularly challenging task. Secondly, by focusing primarily on the definition of equivalence, a notion widely discussed in translation but not in terminology, the literature does not offer solid and systematic methodologies for assigning terminological equivalents. As a result, there is a lack of criteria to guide both terminologists and translators in the search and validation of equivalent terms. This problem is even more evident in the case of predicative units, such as verbs. Although some terminologists (L‘Homme 1998; Lerat 2002; Lorente 2007) have worked on specialized verbs, terminological equivalence between units that belong to this part of speech would benefit from a thorough study. By proposing a novel methodology to assign the equivalents of specialized verbs, this research aims at defining validation criteria for this kind of predicative units, so as to contribute to a better understanding of the phenomenon of terminological equivalence as well as to the development of multilingual terminography in general, and to the development of legal terminography, in particular. The study uses a Portuguese-English comparable corpus that consists of a single genre of texts, i.e. Supreme Court judgments, from which 100 Portuguese and 100 English specialized verbs were selected. The description of the verbs is based on the theory of Frame Semantics (Fillmore 1976, 1977, 1982, 1985; Fillmore and Atkins 1992), on the FrameNet methodology (Ruppenhofer et al. 2010), as well as on the methodology for compiling specialized lexical resources, such as DiCoInfo (L‘Homme 2008), developed in the Observatoire de linguistique Sens-Texte at the Université de Montréal. The research reviews contributions that have adopted the same theoretical and methodological framework to the compilation of lexical resources and proposes adaptations to the specific objectives of the project. In contrast to the top-down approach adopted by FrameNet lexicographers, the approach described here is bottom-up, i.e. verbs are first analyzed and then grouped into frames for each language separately. Specialized verbs are said to evoke a semantic frame, a sort of conceptual scenario in which a number of mandatory elements (core Frame Elements) play specific roles (e.g. ARGUER, JUDGE, LAW), but specialized verbs are often accompanied by other optional information (non-core Frame Elements), such as the criteria and reasons used by the judge to reach a decision (statutes, codes, previous decisions). The information concerning the semantic frame that each verb evokes was encoded in an xml editor and about twenty contexts illustrating the specific way each specialized verb evokes a given frame were semantically and syntactically annotated. The labels attributed to each semantic frame (e.g. [Compliance], [Verdict]) were used to group together certain synonyms, antonyms as well as equivalent terms. The research identified 165 pairs of candidate equivalents among the 200 Portuguese and English terms that were grouped together into 76 frames. 71% of the pairs of equivalents were considered full equivalents because not only do the verbs evoke the same conceptual scenario but their actantial structures, the linguistic realizations of the actants and their syntactic patterns were similar. 29% of the pairs of equivalents did not entirely meet these criteria and were considered partial equivalents. Reasons for partial equivalence are provided along with illustrative examples. Finally, the study describes the semasiological and onomasiological entry points that JuriDiCo, the bilingual lexical resource compiled during the project, offers to future users.

Sistemas de gestión para el control de la cadena de abastecimiento que apropie características de los cubos OLAP como marco de aplicación en una empresa colombiana del sector de alimentos.

Se basa en un análisis teórico de los sistemas de información como lo es el almacenaje de datos, cubos OLAP e inteligencia de negocios. Seguidamente, se hace un análisis de los sectores económicos de Colombia con un especial interés sobre el sector de alimentos, de esta manera conceptualizar la empresa sobre la cual este trabajo se enfocara. Se encontrará un análisis del caso de éxito Summerwood Corporation, el cual brindará una justificación para la propuesta final presentada a la empresa Dipsa Food, Pyme dedicada a la producción de alimentos no perecederos ubicada en la ciudad de Bogotá D.C –Colombia, la cual tiene gran interés en cuanto al desarrollo de nuevas tecnologías que brinden información fidedigna para la toma de decisiones

Bayesian estimation of willingness-to-pay where respondents mis-report their preferences

We introduce a modified conditional logit model that takes account of uncertainty associated with mis-reporting in revealed preference experiments estimating willingness-to-pay (WTP). Like Hausman et al. [Journal of Econometrics (1988) Vol. 87, pp. 239-269], our model captures the extent and direction of uncertainty by respondents. Using a Bayesian methodology, we apply our model to a choice modelling (CM) data set examining UK consumer preferences for non-pesticide food. We compare the results of our model with the Hausman model. WTP estimates are produced for different groups of consumers and we find that modified estimates of WTP, that take account of mis-reporting, are substantially revised downwards. We find a significant proportion of respondents mis-reporting in favour of the non-pesticide option. Finally, with this data set, Bayes factors suggest that our model is preferred to the Hausman model.

Probiotics and prebiotics in female health

Functional foods such as probiotics, prebiotics and nutraceuticals are of extreme interest to researchers. There is growing evidence that these food ingredients may improve and in some cases treat certain conditions that are implicated in women's health. The use of probiotics (live, beneficial bacteria) in improving gastrointestinal and non-gastrointestinal tract conditions such as irritable bowel syndrome, candidiasis and other female urogenital tract conditions are reviewed. Emphasis is also given to the importance of prebiotics (non-digestible food ingredients) in osteoporosis management and alleviation of menopausal symptoms and reducing the onset of cancer.

Prebiotics

In nutritional sciences there is much interest in dietary modulation of the human gut. The gastrointestinal tract, particularly the colon, is very heavily populated with bacteria. Most bacteria are benign; however, certain gut species are pathogenic and may be involved in the onset of acute and chronic disorders. Bifidobacteria and lactobacilli are thought to be beneficial and are common targets for dietary intervention. Prebiotic is a non-viable food ingredient selectively metabolized by beneficial intestinal bacteria. Dietary modulation of the gut microflora by prebiotics is designed to improve health by stimulating numbers and/or activities of the bifidobacteria and lactobacilli. Having an 'optimal' gut microflora can increase resistance to pathogenic bacteria, lower blood ammonia, increase stimulation of the immune response and reduce the risk of cancer. This chapter examines how prebiotics are being applied to the improvement of human health and reviews the scientific evidence behind their use.

Monetary integration and real estate markets: an investigation of the impact of the introduction of a single currency on real estate performance

This paper assesses the impact of the monetary integration on different types of stock returns in Europe. In order to isolate European factors, the impact of global equity integration and small cap factors are investigated. European countries are sub-divided according to the process of monetary convergence. Analysis shows that national equity indices are strongly influenced by global market movements, with a European stock factor providing additional explanatory power. The global and European factors explain small cap and real estate stocks much less well –suggesting an increased importance of ‘local’ drivers. For real estate, there are notable differences between core and non-core countries. Core European countries exhibit convergence – a convergence to a European rather than a global factor. The non-core countries do not seem to exhibit common trends or movements. For the non-core countries, monetary integration has been associated with increased dispersion of returns, lower correlation and lower explanatory power of a European factor. It is concluded that this may be explained by divergence in underlying macro-economic drivers between core and non-core countries in the post-Euro period.

Probiotics and prebiotics

The human large intestine is an intensively colonised area containing bacteria that are health promoting, as well as pathogenic - This has led to functional food developments that fortify the former at the expense of the latter - Probiotics have a long history of use in humans as live microbial feed additions - In contrast, a prebiotic is a non digestible food ingredient that beneficially affects the host by targeting indigenous components thought to be positive - Dietary carbohydrates, such as fibres are candidate prebiotics but most promise has been realised with oligosaccharides - As prebiotics exploit non-viable food ingredients, their applicability in diets is wide ranging - As gastrointestinal disorders are prevalent in terms of human health, both probiotics and prebiotics serve an important role in the prophylactic management of various acute and chronic gut derived conditions - Examples include protection from gastroenteritis and some inflammatory conditions.

Extensive and intensive globalizations: explicating the low connectivity puzzle of U.S. cities using a city-dyad analysis

This article reports an experiment in world city network analysis focusing on city-dyads. Results are derived from an unusual principal components analysis of 27,966 city-dyads across 5 advanced producer service sectors. A 2-component solution is found that identifies different forms of globalization: extensive and intensive. The latter is characterized by very high component scores and describes the more important city-dyads focused upon London-New York (NYLON). The extensive globalization component heavily features London and New York but with each linked to less important cities. U.S. cities score relatively high on the intensive globalization component and we use this finding to explain the low connectivities of U.S. cities in previous studies of the world city network. The two components are tentatively interpreted in world-systems terms: intensive globalization is the process of core-making through city-dyads; extensive globalization is the process of linking core with non-core through city-dyads.

Recent developments in prebiotics to selectively impact beneficial microbes and promote intestinal health

Prebiotics are non-digestible food ingredients that have a specific stimulatory effect upon selected populations of gut bacteria. The usual target microorganisms for prebiotic approaches are bifidobacteria. Numerous human feeding studies have shown the prebiotic influences that galactans and fructans can exert. Other candidate prebiotics are under investigation. The field is now moving towards identifying the health aspect associated with their use. Many avenues of gut related health are being researched, including reduction of diarrhoea, immune stimulation, and improved mineral bioavailability. Most current emphasis appears to be towards various parameters associated with metabolic syndrome. These include markers of insulin resistance, appetite, satiety, blood lipids and inflammatory status.