This thesis addresses the need for environmentally and socially responsible sources of energy. Biofuels, made from organic matter, have recently become a viable alternative to petroleum-based fossil fuel. Sugar and starch make up the majority of feedstock used in biofuel production as it is easily digested. However, the use of these feedstocks is problematic as they consume resources with negative implications. By using a bacterium able to utilise five and six carbon sugars, such as the thermophile Geobacillus thermoglucosidans, organic lignocellulosic waste material can be used as a feedstock. The aim of this project was to investigate and utilise key genetic regulators of fermentation in G. thermoglucosidans and to construct genetic engineering tools that enable strain development for second generation biofuel production. We have focused on the redox-sensing transcriptional regulator Rex, widespread in Grampositive bacteria, which controls the major fermentation pathways in response to changes in cellular NAD+/NADH ratio. Following the identification of several members of the Rex regulon via bioinformatics analysis, ChIP-seq and qRT-PCR experiments were performed to locate genome-wide binding sites and controlled genes in G. thermoglucosidans. Initial electromobility shift assay experiments were performed to demonstrate the potential for use of Rex from Clostridium thermocellum as an orthogonal regulator. To further this research, novel in vivo synthetic regulatory switches were designed and tested with the aim of controlling gene expression in response to changes in cellular redox state. In addition, new tools for the efficient genetic engineering of G. thermoglucosidans were produced and optimised, including an E. coli-G. thermoglucosidans conjugation method for plasmid transfer and gene disruption.

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Vigorous debates have taken place in many European countries, and between the EU and the USA, about regulatory policy regimes covering the assessment and approval of GM crops. In such countries the debates have, to a large extent, taken place in public arenas and with the active participation of broadcast and print media. In Iran, a very vigorous and hotly-contested policy debate concerning legislation covering GM crops took place between 2004 and 2009, but it was almost entirely confined within the Government with no public debate and minimal media coverage. From early 2006 to late 2008 a protracted dispute occurred between different parts of the Iranian regime, which was characterised by an apparent stalemate. In 2008-2009, conspicuous policy shifts occurred, which culminated in the passage of a Biosafety Law by the Iranian Parliament (or Majlis). This thesis describes, analyses and explains the policy-making process from 2006 to 2009. It explains firstly how and why a stalemate arose in the disputes between ministries and departments. It then explains how that impasse was overcome, and how a particular policy regime came to be adopted. The chosen analytical framework draws mainly on two bodies of literature, namely the regulation of technological risk, and the analysis of public policymaking. A task-specific analytical framework is developed which uses the concept of the ‘framing assumptions', which underpin the particular positions taken by the diverse protagonists in the debate, to analyse the characteristics of the seemingly irresolvable dispute. The differences between those framing assumptions are used to provide an explanation of why the stalemate arose and remained unresolved for several years. The explanation of the eventual policy outcome takes account of those framing assumptions, but on their own they are not sufficient to explain the eventual policy decisions. To provide that explanation, considerations of the unequal division of political power between parts of the Iranian regime are required. The Iranian case study, despite some of its unique characteristics, can support several general conclusions about the dynamics of risk policy making, the conditions under which disputes can arise and those under which they may be resolved.

At the core of any effort by a nation state to regulate new technologies for public release is an implicit navigation of uncertainty. The case of Bt cotton in India presents a very timely and pragmatic example of how nation states grapple with uncertainty in a regulatory context. While much attention has been given to how government actors form regulation, far less is given to how actors outside of the government spheres act as catalysts for regulatory reform. In practice, it is often these parties that drive regulation as a process. The question is how. This paper outlines the findings of fieldwork conducted in India between March 2007 and July 2009 in addressing this central question: what does regulation really mean in a context where new technologies burdened with uncertain consequences are introduced? How do preferences, decisions, and regulatory norms adapt to this introduction based on the interactions of a multitude of parties acting on multiple framings of understanding what risk means? The conclusion is that regulation – in the context of Bt cotton in India - is far from a set of government policies derived from scientific measures of risk assessment. Civil society, firms, and farmers themselves all have tremendous influence on how a nation state navigates uncertainty in a regulatory context. It is a process forged on risk interfaces, where constructions of risk both complement and oppose one another. The actors involved enter these spaces, invited or otherwise. What the government may have initially imagined as ‘regulation' is subject to multiple technical, economic, and political framings of risk from each actor. As a result, regulation is a coevolutionary, co-constructed process. This process of negotiating these spaces is what regulation really means.

Research and technological development processes increasingly entail inter-organisational collaboration for the access and integration of external complementary knowledge, especially within emergent technological innovation systems and small developing countries. Collaborative efforts aggregate capabilities of individual actors into system-level innovation capacity, fostering technological and innovation outcomes from both individual organisations and the technological system as a whole. Significant understanding of these interactive processes has been achieved by previous research on innovation systems, inter-organisational collaboration and networks, and studies of interdisciplinary scientific research. Nevertheless, further knowledge is required on how and why organisations may differ in their ability to collaboratively exploit potential complementarities. Consequently, this thesis examines institutional and organisational factors that influence the actual extent of knowledge integration achieved by public research organisations through collaborative research endeavours, within the agri-biotechnology innovation system in Uruguay. The research followed a mixed empirical method. Exploratory interviews with members of public R&D groups and firms were conducted in order to reach a preliminary understanding of the main forces affecting collaboration and knowledge integration. Quantitative indicators of the degree of knowledge-integration achieved by R&D groups' collaborative links were designed and computed using data gathered through a survey of R&D group members. Indicators were also developed to statistically assess how the extent of collaborative knowledge-integration achieved by an R&D group is influenced by system-level incentive institutions, by the absorptive and relational capacities of the group, and by the compliance of the group with local scientific assessment and reward mechanisms. This thesis makes various theoretical contributions and draws relevant policy implications. The results show that members of R&D groups may exert differing levels of influence on knowledge-integration. Specifically, postgraduate students were found to play a relevant bridging role, enhancing the ability of the group to access knowledge from complementary disciplines. The study also found consistent evidence of a negative relation between an R&D group's compliance with local scientific incentives, and the group's ability to collaboratively integrate complementary knowledge-assets. Therefore, formal incentive institutions are presumably affecting the exploitation of potential synergies among local knowledge resources and hence the learning and innovation capabilities and the cohesion of the entire agri-biotechnology innovation system. As a methodological contribution, this thesis develops novel indicators to assess the degree of inter-organisational complementarity that go beyond those used in previous research.

This dissertation, by comparing the agricultural biotechnology sector in the Netherlands and the UK, aims to understand the advantages and disadvantages posed by intermediary organisations for the promotion of knowledge exchange between universities and industry. An original conceptual framework has been constructed to allow a systematic analysis of intermediaries according to the functions they fulfil. The framework suggests that intermediaries can fulfil one or more of the following functions: access to human resources, access to the knowledge base, opportunities for commercialisation, access to facilities and other infrastructure, and access to networks. In order to move beyond the limitations brought about by differing nomenclature for intermediaries, the framework also proposes four ideal types of intermediaries derived from an analysis of existing intermediaries. The results of the empirical study reported here show that the roles of intermediaries are dependent on the characteristics of the sector as well as the history and configuration of existing national institutions. The policy implications of this study are several-fold. It is shown in this dissertation that application of certain dominant models of intermediaries can result in disadvantages for sectors like agricultural biotechnology that differ in important respects from the more frequently studied sectors, where these intermediaries seem to work better. This study of the agricultural biotechnology sector showed that there is space for new configurations of intermediaries such as sectoral technology transfer companies. The study highlighted that the crucial element for knowledge exchange is the production of knowledge itself. After identifying certain weaknesses in the UK agricultural sector and strengths within the Netherlands, the dissertation finds that large collaborative programs tend to facilitate knowledge exchange, while collaborative research and training can be a path for overcoming weaknesses in the system. By comparing the Netherlands and the UK, this study also showed that the presence of a strong industry is necessary for the uptake of knowledge originating from the research base.