The analysis of plasmid rearrangements observed in the soil bacterium OR168 after the introduction of transposon Tn5 : a thesis presented in fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University

Transposon Tn5 mutagenesis has been used extensively in Escherichia coli and various other Gram-negative bacteria to produce both random and site directed mutants. The popularity of Tn5 as a mutagen stems from its apparent random insertion into the genome, leading to non-leaky polar mutations. It also confers on many bacteria resistance to aminoglycosides, providing a strong selectable marker. The site of insertion can be mapped by Southern DNA hybridisation against a specific Tn5 probe. Tn5-containing derivatives of the Rhizobia-like soil isolate, OR168, were produced using the broad host-range suicide plasmid vector pSUP1011. After the transfer of pSUP1011 to OR168 via heterogeneric bacterial conjugation, stable OR168::Tn5 exconjugants were selectively isolated at frequencies of approximately 10-4 per recipient. None of the 53 OR168::Tn5 exconjugants screened showed the parental plasmid profile. Visible alterations to the plasmid profile were common with respect to the native plasmid profile. These events generally showed large deletions from, or additions to, the native replicons of OR168. The alterations also included a low incidence of a decrease in plasmid number. Analysis of the exconjugant population shows that the insertion of Tn5 into the genome of OR168 may not be strictly random. It was shown that 66% of OR168::Tn5 exconjugants screened contain a plasmid-borne Tn5 element, with 90% of those involving Tn5 insertion in the same episome. There is evidence that events other than classical conservative transposition have occurred after the introduction of pSUP1011 into the OR168 genome. Screening of the isolated OR168::Tn5 population for pSUP1011 vector sequences revealed the presence of the pSUP1011-derived RP4-mob fragment in 33 of 35 OR168::Tn5 exconjugants containing a plasmid-borne Tn5 element. Analysis also revealed the acquisition of Tn5 alone, presumably by conservative transposition, occurred only twice in the 35 events involving a plasmid target. This suggests that another site within the RP4 fragment can act as a surrogate transposase recognition site. Alternatively, the insertion of the RP4-mob::Tn5 sequence into a plasmid target may involve a site specific recombination process peculiar to the OR168 isolate. No mechanism was elucidated for the formation of many of the alterations in plasmid mobility. Restriction fragment lengths in the immediate vicinity of the anomalous RP4-mob::Tn5 insertion arc identical in different plasmids. This may indicate sequence duplication among the OR 168 plasmids. Such duplication may precipitate, through homologous recombination processes, the plasmid instability observed

Impact Of Curve Construction And Community Dynamics On The Species–Time Relationship

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117224/1/ecy20078892145.pd

Undergraduate Accounts of the Impact of Lockdown on Their Self-Managed Reflective Development of Graduate Abilities

This account is mostly written by students in the first year of their discipline-based study of civil engineering. It features their self-managed development of graduate abilities in the second semester of an undergraduate Irish course in problem-based civil engineering. The principal abilities were creativity, problem-solving, presentations and teamwork. The case-study paper concentrates upon four students’ reports and reflections on their experiences concerning their second (partially locked-down) semester. Their accounts complement the review of the early weeks of their first semester experience, that has already been published elsewhere. They are joined by the tutor who was an external facilitator of their early drafts of reviews. He suggested the compilation and structure of this paper, and has assisted with the assembly of the condensed individual contributions

Consumption-Based Conservation Targeting: Linking Biodiversity Loss to Upstream Demand through a Global Wildlife Footprint.

Although most conservation efforts address the direct, local causes of biodiversity loss, effective long-term conservation will require complementary efforts to reduce the upstream economic pressures, such as demands for food and forest products, which ultimately drive these downstream losses. Here, we present a wildlife footprint analysis that links global losses of wild birds to consumer purchases across 57 economic sectors in 129 regions. The United States, India, China, and Brazil have the largest regional wildlife footprints, while per-person footprints are highest in Mongolia, Australia, Botswana, and the United Arab Emirates. A US$100 purchase of bovine meat or rice products occupies approximately 0.1 km2 of wild bird ranges, displacing 1-2 individual birds, for 1 year. Globally significant importer regions, including Japan, the United Kingdom, Germany, Italy, and France, have large footprints that drive wildlife losses elsewhere in the world and represent important targets for consumption-focused conservation attention

Energy-aware dynamic route management for THAWS

In this research we focus on the Tyndall 25mm and 10mm nodes energy-aware topology management to extend sensor network lifespan and optimise node power consumption. The two tiered Tyndall Heterogeneous Automated Wireless Sensors (THAWS) tool is used to quickly create and configure application-specific sensor networks. To this end, we propose to implement a distributed route discovery algorithm and a practical energy-aware reaction model on the 25mm nodes. Triggered by the energy-warning events, the miniaturised Tyndall 10mm data collector nodes adaptively and periodically change their association to 25mm base station nodes, while 25mm nodes also change the inter-connections between themselves, which results in reconfiguration of the 25mm nodes tier topology. The distributed routing protocol uses combined weight functions to balance the sensor network traffic. A system level simulation is used to quantify the benefit of the route management framework when compared to other state of the art approaches in terms of the system power-saving