Teaching the conflicts

PhD ThesisI read Neal Town Stephenson’s Cryptonomicon and The Baroque Cycle to interrogate what types of links they make to US countercultural writing, postmodern discourse in American culture, and perceived uninterrogated links to the term America itself in images of modern progressive liberalism. Postmodernist readings of literary texts came under increasing public scrutiny in intellectual debates of the 80s and 90s. My analysis is to situate and reconsider these fictions within debates happening in the North American academy at this time and the more recent one concerning the demise of poststructuralism in the humanities. Linking together works of Sean McCann, Michael Szalay, John Guillory and Mark McGurl I locate Cryptonomicon as constitutive of the postwar drift from the modernist aesthetic yet simultaneously developing within Sacvan Bercovitch’s model of dissensus. Through reference to McGurl’s work in particular, my thesis will offer the first sustained critical reading of Cryptonomicon relevant to the University’s new teaching standards of diversity and research excellence. Through Lauren Berlant’s concept of an intimate public I argue The Baroque Cycle develops a richly aesthetic form of criticism that challenges the consensus view of culturally affirming alternatives to American sociopolitical and economic life. In addition, each chapter charts specific aspects of the impact of European critical theories that presided over the marriage of intellectualism and professionalism in the North American academy. More specifically, and throwing particular focus on resistances to theory and canon change, I discuss how the politics of the classroom developed within the literary culture wars brought with it a renewed emphasis on what postwar professors taught in the classroom

Systems Mapping

This open access book explores a range of new and older systems mapping methods focused on representing causal relationships in systems. In a practical manner, it describes the methods and considers the differences between them; describes how to use them yourself; describes how to choose between and combine them; considers the role of data, evidence, and stakeholder opinion; and describes how they can be useful in a range of policy and research settings. This book provides a key starting point and general-purpose resource for understanding complex adaptive systems in practical, actionable, and participatory ways. The book successfully meets the growing need in a range of social, environmental, and policy challenges for a richer more nuanced, yet actionable and participatory understanding of the world. The authors provide a clear framework to alleviate any confusion about the use of appropriate terms and methods, enhance the appreciation of the value they can bring, and clearly explain the differences between approaches and the resulting outputs of mapping processes and analysis

The Chloroplast Genome of a Symbiodinium sp. Clade C3 Isolate

Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as ‘minicircles’. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any ‘empty’ minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic

The genetic intractability of Symbiodinium microadriaticum to standard algal transformation methods.

Modern transformation and genome editing techniques have shown great success across a broad variety of organisms. However, no study of successfully applied genome editing has been reported in a dinoflagellate despite the first genetic transformation of Symbiodinium being published about 20 years ago. Using an array of different available transformation techniques, we attempted to transform Symbiodinium microadriaticum (CCMP2467), a dinoflagellate symbiont of reef-building corals, with the view to performing subsequent CRISPR-Cas9 mediated genome editing. Plasmid vectors designed for nuclear transformation containing the chloramphenicol resistance gene under the control of the CaMV p35S promoter as well as several putative endogenous promoters were used to test a variety of transformation techniques including biolistics, electroporation and agitation with silicon carbide whiskers. Chloroplast-targeted transformation was attempted using an engineered Symbiodinium chloroplast minicircle encoding a modified PsbA protein expected to confer atrazine resistance. We report that we have been unable to confer chloramphenicol or atrazine resistance on Symbiodinium microadriaticum strain CCMP2467

The replication of plastid minicircles involves rolling circle intermediates

Plastid genomes of peridinin-containing dinoflagellates are unique in that its genes are found on multiple circular DNA molecules known as ‘minicircles’ of ∼2–3 kb in size, carrying from one to three genes. The non-coding regions (NCRs) of these minicircles share a conserved core region (250–500 bp) that are AT-rich and have several inverted or direct repeats. Southern blot analysis using an NCR probe, after resolving a dinoflagellate whole DNA extract in pulsed-field gel electrophoresis (PFGE), revealed additional positive bands (APBs) of 6–8 kb in size. APBs preferentially diminished from cells treated with the DNA-replication inhibitor aphidicolin, when compared with 2–3 kb minicircles, implicating they are not large minicircles. The APBs are also exonuclease III-sensitive, implicating the presence of linear DNA. These properties and the migration pattern of the APBs in a 2D-gel electrophoresis were in agreement with a rolling circle type of replication, rather than the bubble-forming type. Atomic force microscopy of 6–8 kb DNA separated by PFGE revealed DNA intermediates with rolling circle shapes. Accumulating data thus supports the involvement of rolling circle intermediates in the replication of the minicircles

The replication of plastid minicircles involves rolling circle intermediates

Plastid genomes of peridinin-containing dinoflagellates are unique in that its genes are found on multiple circular DNA molecules known as ‘minicircles’ of ∼2–3 kb in size, carrying from one to three genes. The non-coding regions (NCRs) of these minicircles share a conserved core region (250–500 bp) that are AT-rich and have several inverted or direct repeats. Southern blot analysis using an NCR probe, after resolving a dinoflagellate whole DNA extract in pulsed-field gel electrophoresis (PFGE), revealed additional positive bands (APBs) of 6–8 kb in size. APBs preferentially diminished from cells treated with the DNA-replication inhibitor aphidicolin, when compared with 2–3 kb minicircles, implicating they are not large minicircles. The APBs are also exonuclease III-sensitive, implicating the presence of linear DNA. These properties and the migration pattern of the APBs in a 2D-gel electrophoresis were in agreement with a rolling circle type of replication, rather than the bubble-forming type. Atomic force microscopy of 6–8 kb DNA separated by PFGE revealed DNA intermediates with rolling circle shapes. Accumulating data thus supports the involvement of rolling circle intermediates in the replication of the minicircles