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Thesis (Ph. D.)--Massachusetts Institute of Technology, Microbiology Graduate Program, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 91-96). / Integrative and conjugative elements (ICEs) are widespread mobile genetic elements that are integrated in bacterial chromosomes, but can excise and transfer to a recipient through conjugation. ICEs are important agents of evolution, contributing to the acquisition of new traits, including antibiotic resistance. Many ICEs are site-specific in that they integrate preferentially into a primary attachment site in the bacterial chromosome. Site-specific ICEs can integrate into secondary locations, but little is known about the consequences of integration. Using ICEBs1, a site-specific ICE from Bacillus subtilis, I found that integration into secondary attachment sites is detrimental to both ICEBs1 and the host cell. Integration at secondary locations is detrimental to ICEBsJ. Once integrated in the chromosome, excision of ICEBs1 from all secondary attachment sites analyzed was either reduced (4 sites) or undetectable (3 sites) compared to ICEBs1 excision from the primary site. Additionally, from two of the four secondary sites that exhibited reduced but detectable excision, the excised, circular form of ICEBs1 was present at lower levels than expected, indicating that circular ICEBs1 may be unstable. Defects in excision and stability of ICEBs] severely limit its ability to spread to other cells. Integration at secondary locations is detrimental to the host cell. Induction of ICEBs1 gene expression in secondary integration sites resulted in a defect in cell proliferation and/or viability, as well as induction of the SOS response. These effects are likely due to DNA damage resulting from plasmid-like, rolling-circle replication of the excision-defective ICEBs1 in the chromosome. Consistent with this model, deletion of ICEBs] replication genes (nicK and helP) alleviated the proliferation and viability defects. Implications for the evolution of ICEs. These previously unrecognized detrimental effects may provide selective pressure against propagation of ICEBs1 in secondary attachment sites. Such detrimental effects could explain the maintenance and prevalence of site-specific integration among ICEs. / by Kayla L. Menard. / Ph.D.

Nature and scope of enquiry This thesis explores how emotional dimensions of supervising doctoral students are accommodated in supervisory identities. It aims to answer two key questions: What is the nature of the emotional labour involved in doctoral supervision? To what extent does an acknowledgement of emotional labour in the supervisory process have implications for the academic development of doctoral supervisors? The conceptual framework for the study is developed from Woods' (2010) definition of emotions as physical responses to situations involving an element of risk to self, Butler's (2005) notion of accounting for oneself, and Archer's (1995; 2000; 2003; 2012) model of identity formation based on the ability of human beings to reflect on their social situation through internal conversations. Archer states that identities are formed through the way we monitor, prioritise and accommodate our concerns about our social reality. It is on the basis of this priority of concerns that we embark on our life-projects and it is these concerns that shape our behaviour and actions. It is believed that all humans strive towards a modus vivendi which Archer defines as a set of practices which at the same time respects what is unavoidable and privileges what matters most to the person concerned (Archer 2003: 149). In this study I apply Archer's theory to doctoral supervision by viewing the supervisory process as a project and exploring the nature of the emotional labour involved in this project. Based on interviews with doctoral supervisors, I identify three supervisory identities from Archer's typology of reflexivity – the autonomous reflexive supervisor, the meta-reflexive supervisor and the communicative reflexive supervisor. These identities are constructed around the ways in which individual supervisors accommodate emotional labour in their practice. The thesis goes on to consider appropriate ways of supporting academics in dealing with emotional dimensions of doctoral supervision. Contribution to knowledge and practice This thesis makes a contribution to knowledge in two ways. First, it identifies the nature of the emotional labour that is invested in supervising doctoral students, and by doing so adds empirical evidence to the small number of studies that exist in the field. Second, it develops a conceptual framework that includes emotional dimensions and accounting for one's own practice. This framework can be applied as a theoretical foundation for discussing supervisory practice in an academic development context. The study contributes to practice within the context of academic development. Conventional academic development for doctoral supervisors focuses on procedural and managerial aspects of the supervisory process. This study proposes addressing emotional dimensions as well in such development. Method The thesis is based on interviews with fourteen supervisors from five universities – three post-92 and two pre-92 institutions. Between them they represent eleven disciplines, three from the social sciences, six from the sciences and five from arts and humanities. All interviews were transcribed and analysed through close reading and thematic analysis. Principal arguments in this thesis are that: emotional labour is a key feature of doctoral supervision emotional dimensions of doctoral supervision should be included in academic development for doctoral supervisors timely completion is increasingly becoming a performance indicator for supervisors, and a need may arise for structures to be set in place to provide better support for academics, in particular, in the early stages of their supervisory practice Conclusions The findings suggest that the doctoral supervisors interviewed in this study invest considerable effort in managing emotions – their own, those of their students and those of their colleagues - as part of the supervisory process. Three supervisory identities can be mapped against Archer's typology according to how doctoral supervisors accommodate and manage these emotions in order to achieve a modus vivendi. The thesis concludes that acknowledging, articulating and addressing emotional dimensions of doctoral supervision should be included as part of the academic development offered to staff planning to supervise doctoral projects.

The purpose of this thesis is to explore the field of influences on the occupational trajectories of physics graduates in the United Kingdom. My research examines the assumptions by government and policy makers that school education holds the key to providing more physicists available for employment in physics-related occupations. The research analyses qualitative data from current and recently graduated students to explore the field of influences on their decisions to take physics, and how these experiences influence their identity as a scientist. My hypothesis tests these assumptions by examining the significant events, or critical incidents, during the educational experience on a physics degree. The research design is a case study of the physics departments of two UK institutions. A series of interviews provides insight into the educational journeys of current and recently graduated physics students and the consequent analysis identifies emergent themes. These themes include how the influences of school education and social and individual expectations engage people into enrolling on a physics degree. Further analysis explores how events occurring on the degree courses may influence occupational trajectories. My findings identify attitudes to laboratory work and institutional feedback as significant influences to this sample of individuals during their degree experience. This work has implications for highlighting the significance of laboratory work in future science education policies, as well as contributing to the extant research on STEM education.