Macrophage migration inhibitory factor (MIF) family in arthropods : cloning and expression analysis of two MIF and one D-dopachrome tautomerase (DDT) homologues in Mud crabs, Scylla paramamosain

5. Acknowledgements This research was supported by grants from the National Natural Science Foundation of China (Nos. 31172438 and U1205123), the Natural Science Foundation of Fujian Province (No. 2012J06008 and 201311180002) and the projects-sponsored by SRF. TW received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.

The mechanism of ϕC31 integrase directionality : experimental analysis and computational modelling

Acknowledgments We thank Sally Rowland for helpful comments on the manuscript. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding

Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

Realisable climate change narratives in public discourse: an East/West comparative analysis of environmental, social, and corporate governance (ESG) as a response to global climate change

This thesis looks at how non-experts develop an opinion on climate change, and how those opinions could be changed by public discourse. I use Hubert Dreyfus’ account of skill acquisition to distinguish between experts and non-experts. I then use a combination of Walter Fisher’s narrative paradigm and the hermeneutics of Paul Ricœur to explore how non-experts form opinions, and how public narratives can provide a point of critique. In order to develop robust narratives, they must be financially realistic. I therefore consider the burgeoning field of environmental, social, and corporate governance (ESG) analysis as a way of informing realistic public narratives. I identify a potential problem with this approach: the Western assumptions of ESG analysis might make for public narratives that are not convincing to a non-Western audience. I then demonstrate how elements of the Chinese tradition, the Confucian, Neo-Confucian, and Daoist schools, as presented by David Hall and Roger Ames, can provide alternative assumptions to ESG analysis so that the public narratives will be more culturally adaptable. This research contributes to the discipline by bringing disparate traditions together in a unique way, into a practical project with a view towards applications. I conclude by considering avenues for further research.

Analysis of Global Compliance and Implementation of the Goals of International Environmental Treaties: A Case study of the Convention on Biodiversity (CBD)

The Convention on Biodiversity (CBD) was created in 1992 to coordinate global governments to protect biological resources. The CBD has three goals: protection of biodiversity, achievement of sustainable use of biodiversity and facilitation of equitable sharing of the benefits of biological resources. The goal of protecting biological resources has remained both controversial and difficult to implement. This study focused more on the goal of biodiversity protection. The research was designed to examine how globally constructed environmental policies get adapted by national governments and then passed down to local levels where actual implementation takes place. Effectiveness of such policies depends on the extent of actual implementation at local levels. Therefore, compliance was divided and examined at three levels: global, national and local. The study then developed various criteria to measure compliance at these levels. Both qualitative and quantitative methods were used to analyze compliance and implementation. The study was guided by three questions broadly examining critical factors that most influence the implementation of biodiversity protection policies at the global, national and local levels. Findings show that despite an overall biodiversity deficit of 0.9 hectares per person, global compliance with the CBD goals is currently at 35%. Compliance is lowest at local levels at 14%, it is slightly better at national level at 50%, and much better at the international level 64%. Compliance appears higher at both national and international levels because compliance here is paper work based and policy formulation. If implementation at local levels continues to produce this low compliance, overall conservation outcomes can only get worse than what it is at present. There are numerous weaknesses and capacity challenges countries are yet to address in their plans. In order to increase local level compliance, the study recommends a set of robust policies that build local capacity, incentivize local resource owners, and implement biodiversity protection programs that are akin to local needs and aspirations.

UTILIZATION OF GIS AND SPATIAL ANALYSIS TECHNIQUES IN ARTISANAL AND SMALL SCALE MINING TO LOCATE A CENTRALIZED PROCESSING CENTRE

One of the global phenomena with threats to environmental health and safety is artisanal mining. There are ambiguities in the manner in which an ore-processing facility operates which hinders the mining capacity of these miners in Ghana. These problems are reviewed on the basis of current socio-economic, health and safety, environmental, and use of rudimentary technologies which limits fair-trade deals to miners. This research sought to use an established data-driven, geographic information (GIS)-based system employing the spatial analysis approach for locating a centralized processing facility within the Wassa Amenfi-Prestea Mining Area (WAPMA) in the Western region of Ghana. A spatial analysis technique that utilizes ModelBuilder within the ArcGIS geoprocessing environment through suitability modeling will systematically and simultaneously analyze a geographical dataset of selected criteria. The spatial overlay analysis methodology and the multi-criteria decision analysis approach were selected to identify the most preferred locations to site a processing facility. For an optimal site selection, seven major criteria including proximity to settlements, water resources, artisanal mining sites, roads, railways, tectonic zones, and slopes were considered to establish a suitable location for a processing facility. Site characterizations and environmental considerations, incorporating identified constraints such as proximity to large scale mines, forest reserves and state lands to site an appropriate position were selected. The analysis was limited to criteria that were selected and relevant to the area under investigation. Saaty’s analytical hierarchy process was utilized to derive relative importance weights of the criteria and then a weighted linear combination technique was applied to combine the factors for determination of the degree of potential site suitability. The final map output indicates estimated potential sites identified for the establishment of a facility centre. The results obtained provide intuitive areas suitable for consideration

Comparative analysis of the US and the EU Regulatory Models for Money Market Funds

This chapter sets out a comprehensive analysis of the regulation of money market funds in the EU and US. The theoretical framework has unique cases and examples and includes checklists to assist with the practice of fund management and legal risk analysis.

A multi vector energy analysis for interconnected power and gas systems

This paper presents the first multi vector energy analysis for the interconnected energy systems of Great Britain (GB) and Ireland. Both systems share a common high penetration of wind power, but significantly different security of supply outlooks. Ireland is heavily dependent on gas imports from GB, giving significance to the interconnected aspect of the methodology in addition to the gas and power interactions analysed. A fully realistic unit commitment and economic dispatch model coupled to an energy flow model of the gas supply network is developed. Extreme weather events driving increased domestic gas demand and low wind power output were utilised to increase gas supply network stress. Decreased wind profiles had a larger impact on system security than high domestic gas demand. However, the GB energy system was resilient during high demand periods but gas network stress limited the ramping capability of localised generating units. Additionally, gas system entry node congestion in the Irish system was shown to deliver a 40% increase in short run costs for generators. Gas storage was shown to reduce the impact of high demand driven congestion delivering a reduction in total generation costs of 14% in the period studied and reducing electricity imports from GB, significantly contributing to security of supply.

Pleiotropic Analysis of Lung Cancer and Blood Triglycerides

Epidemiologically related traits may share genetic risk factors, and pleiotropic analysis could identify individual loci associated with these traits. Because of their shared epidemiological associations, we conducted pleiotropic analysis of genome-wide association studies of lung cancer (12 160 lung cancer case patients and 16 838 control subjects) and cardiovascular disease risk factors (blood lipids from 188 577 subjects, type 2 diabetes from 148 821 subjects, body mass index from 123 865 subjects, and smoking phenotypes from 74 053 subjects). We found that 6p22.1 (rs6904596, ZNF184) was associated with both lung cancer (P = 5.50x10(-6)) and blood triglycerides (P = 1.39x10(-5)). We replicated the association in 6097 lung cancer case patients and 204 657 control subjects (P = 2.40 × 10(-4)) and in 71 113 subjects with triglycerides data (P = .01). rs6904596 reached genome-wide significance in lung cancer meta-analysis (odds ratio = 1.15, 95% confidence interval = 1.10 to 1.21 ,: Pcombined = 5.20x10(-9)). The large sample size provided by the lipid GWAS data and the shared genetic risk factors between the two traits contributed to the uncovering of a hitherto unidentified genetic locus for lung cancer.

Joint Analysis of Multiple Algorithms and Performance Measures

There has been an increasing interest in the development of new methods using Pareto optimality to deal with multi-objective criteria (for example, accuracy and time complexity). Once one has developed an approach to a problem of interest, the problem is then how to compare it with the state of art. In machine learning, algorithms are typically evaluated by comparing their performance on different data sets by means of statistical tests. Standard tests used for this purpose are able to consider jointly neither performance measures nor multiple competitors at once. The aim of this paper is to resolve these issues by developing statistical procedures that are able to account for multiple competing measures at the same time and to compare multiple algorithms altogether. In particular, we develop two tests: a frequentist procedure based on the generalized likelihood-ratio test and a Bayesian procedure based on a multinomial-Dirichlet conjugate model. We further extend them by discovering conditional independences among measures to reduce the number of parameters of such models, as usually the number of studied cases is very reduced in such comparisons. Data from a comparison among general purpose classifiers is used to show a practical application of our tests.

Fast and sensitive aflatoxin B1 and total aflatoxins ELISAs for analysis of peanuts, maize and feed ingredients

Aflatoxins are a group of carcinogenic compounds produced by Aspergillus fungi that can grow on different agricultural crops. Both acute and chronic exposure to these mycotoxins can cause serious illness. Due to the high occurrence of aflatoxins in crops worldwide fast and cost-effective analytical methods are required for the identification of contaminated agricultural commodities before they are processed into final products and placed on the market. In order to provide new tools for aflatoxin screening two prototype fast ELISA methods: one for the detection of aflatoxin B₁ and the other for total aflatoxins were developed. Seven monoclonal antibodies with unique high sensitivity and at the same time good cross-reactivity profiles were produced. The monoclonal antibodies were characterized and two antibodies showing IC₅₀ of 0.037 ng/mL and 0.031 ng/mL for aflatoxin B₁ were applied in simple and fast direct competitive ELISA tests. The methods were validated for peanut matrix as this crop is one of the most affected by aflatoxin contamination. The detection capabilities of aflatoxin B₁ and total aflatoxins ELISAs were 0.4 μg/kg and 0.3 μg/kg for aflatoxin B₁, respectively, which are one of the lowest reported values. Total aflatoxins ELISA was also validated for the detection of aflatoxins B₂, G₁ and G₂. The application of the developed tests was demonstrated by screening 32 peanut samples collected from the UK retailers. Total aflatoxins ELISA was further applied to analyse naturally contaminated maize porridge and distiller's dried grain with solubles samples and the results were correlated with these obtained by UHPLC-MS/MS method.

Can the European Union build a bridge over troubled waters? An analysis of the politicised and depoliticised legal approach between the European Union and Cyprus

The Cyprus dispute accurately portrays the evolution of the conflict from ‘warfare to lawfare’ enriched in politics; this research has proven that the Cyprus problem has been and will continue to be one of the most judicialised disputes across the globe. Notwithstanding the ‘normalisation’ of affairs between the two ethno-religious groups on the island since the division in 1974, the Republic of Cyprus’ (RoC) European Union (EU) membership in 2004 failed to catalyse reunification and terminate the legal, political and economic isolation of the Turkish Cypriot community. So the question is; why is it that the powerful legal order of the EU continuously fails to tame the tiny troublesome island of Cyprus? This is a thesis on the interrelationship of the EU legal order and the Cyprus problem. A literal and depoliticised interpretation of EU law has been maintained throughout the EU’s dealings with Cyprus, hence, pre-accession and post-accession. The research has brought to light that this literal interpretation of EU law vis-à-vis Cyprus has in actual fact deepened the division on the island. Pessimists outnumber optimists so far as resolving this problem is concerned, and rightly so if you look back over the last forty years of failed attempts to do just that, a diplomatic combat zone scattered with the bones of numerous mediators. This thesis will discuss how the decisions of the EU institutions, its Member States and specifically of the European Court of Justice, despite conforming to the EU legal order, have managed to disregard the principle of equality on the divided island and thus prevent the promised upgrade of the status of the Turkish Cypriot community since 2004. Indeed, whether a positive or negative reading of the Union’s position towards the Cyprus problem is adopted, the case remains valid for an organisation based on the rule of law to maintain legitimacy, democracy, clarity and equality to the decisions of its institutions. Overall, the aim of this research is to establish a link between the lack of success of the Union to build a bridge over troubled waters and the right of self-determination of the Turkish Cypriot community. The only way left for the EU to help resolve the Cyprus problem is to aim to broker a deal between the two Cypriot communities which will permit the recognition of the Turkish Republic of Northern Cyprus (TRNC) or at least the ‘Taiwanisation’ of Northern Cyprus. Albeit, there are many studies that address the impact of the EU on the conflict or the RoC, which represents the government that has monopolised EU accession, the argument advanced in this thesis is that despite the alleged Europeanisation of the Turkish Cypriot community, they are habitually disregarded because of the EU’s current legal framework and the Union’s lack of conflict transformation strategy vis-à-vis the island. Since the self-declared TRNC is not recognised and EU law is suspended in northern Cyprus in accordance with Protocol No 10 on Cyprus of the Act of Accession 2003, the Turkish-Cypriots represent an idiomatic partner of Brussels but the relations between the two resemble the experience of EU enlargement: the EU’s relevance to the community has been based on the prospects for EU accession (via reunification) and assistance towards preparation for potential EU integration through financial and technical aid. Undeniably, the pre-accession and postaccession strategy of Brussels in Cyprus has worsened the Cyprus problem and hindered the peace process. The time has come for the international community to formally acknowledge the existence of the TRNC.