Insertion site preference of Mu, Tn5, and Tn7 transposons

<p>Abstract</p> <p>Background</p> <p>Transposons, segments of DNA that can mobilize to other locations in a genome, are often used for insertion mutagenesis or to generate priming sites for sequencing of large DNA molecules. For both of these uses, a transposon with minimal insertion bias is desired to allow complete coverage with minimal oversampling.</p> <p>Findings</p> <p>Three transposons, Mu, Tn5, and Tn7, were used to generate insertions in the same set of fosmids containing <it>Candida glabrata </it>genomic DNA. Tn7 demonstrates markedly less insertion bias than either Mu or Tn5, with both Mu and Tn5 biased toward sequences containing guanosine (G) and cytidine (C). This preference of Mu and Tn5 yields less uniform spacing of insertions than for Tn7, in the adenosine (A) and thymidine (T) rich genome of <it>C. glabrata </it>(39% GC).</p> <p>Conclusions</p> <p>In light of its more uniform distribution of insertions, Tn7 should be considered for applications in which insertion bias is deleterious.</p

Geography and the Paris Academy of Sciences: politics and patronage in early 18th-century France

This essay considers the politics and patronage of geography in early-modern France. It examines how the Paris Academy of Sciences, widely acknowledged as the 18th century’s pre-eminent scientific society, came to recognise geography as an independent science in 1730, a century before the establishment of the first geographical societies. Although the Academy was centrally concerned with cartography from its inception in 1666, it initially afforded no official status to geography, which was viewed either as a specialised form of historical inquiry or as a minor component within the hegemonic science of astronomy. The rise of Newtonian mathematics and the associated controversy about the shape of the earth challenged the Academy’s epistemological foundations and prompted a debate about the educational and political significance of geography as a scientific practice. The death in 1726 of Guillaume Delisle, a prominent Academy astronomer-cartographer and a popular geography tutor to the young Louis XV, led to a spirited campaign to elect Philippe Buache, Delisle’s prot�eg�e, to a new Academy position as a geographer rather than an astronomer. The campaign emphasised the social and political utility of geography, though the Academy’s decision to recognise this new and distinctively modern science was ultimately facilitated by traditional networks of patronage within the French Royal Court

Reluctant empiricists: community mental health nurses and the art of evidence-based praxis

The definitive version of this article is available at www.blackwell-synergy.comThe National Service Framework for Mental Health (1999) emphasizes the need for a culture of evidence-based practice (EBP) in mental health care. However, there is relatively little research addressing EBP from the perspective of community mental health nurses and we are still unsure of why the uptake of this style of working has been slow. This paper suggests that rather than thinking in terms of ‘barriers’ to the uptake of EBP, the issue may best be conceptualized as a form of praxis on the part of nurses, as they seek to manage the diversity of ideologies and practices in their working lives. From an interview and focus group study, we identify how practitioners’ narrow definition of EBP itself, their formulation of how EBP was at odds with the nurse’s professional activity and the organizational constraints within which they work were perceived to inhibit access to information and offer little time and managerial support for information seeking. Those who attempt to further the involvement of community mental health staff in EBP will have to reconceptualize the reasons why staff have yet to incorporate it fully, and acknowledge that this does not occur because staff are simply ‘ignorant Luddites’, but that this resistance enables them to retain a sense of control over their working lives and retain a focus on work with clients. Future EBP initiatives will have to address these ideological and organizational factors in order for uptake to be accelerated. This may involve changing organizational cultures and work roles and even encouraging activism on the part of the practitioners so as to enable them to learn from each other and educate and change their work environments

Design, manufacture, modelling and testing of surface acoustic wave strain sensors

THESIS 8459There is an increasing demand for multi-sensor strain measurement systems, particularly those which incorporate wireless sensors. A possible application of such a system is the Real-Time Weigh-In-Motion (RTWIM) of heavy goods vehicles. Surface Acoustic Wave (SAW) strain sensors have been proposed for this application as they offer both wireless interrogation and passive operation, but considerable development work is required before they can be successfully deployed. This thesis details the design, manufacture, modelling and testing of SAW strain sensors for the RTWIM application. Following a discussion of surface wave theory and devices, the design and manufacture of the prototype sensors is detailed. This is achieved through a new system which integrates the design and manufacturing processes from initial sensor specifications to finished devices, thus yielding significant improvements over existing schemes. Sensor modelling is achieved through new modifications to the coupling-of-modes (COM) SAW model, which allows both the complete frequency responses of the devices, and their sensitivity to biases, to be simulated. The prototype sensors are then tested in both unstrained and strained states, thus enabling the evaluation of both the device fabrication and the COM modelling. Although issues were encountered with each of the research strands, this work successfully extends and improves the development of SAW strain sensors. It is hoped that the research can facilitate the deployment of these innovative sensors in a range of applications

Cell wall protein variation, break-induced replication, and subtelomere dynamics in Candida glabrata.

Candida glabrata is an opportunistic pathogen of humans, responsible for up to 30% of disseminated candidiasis. Adherence of C. glabrata to host cells is mediated by adhesin-like proteins (ALPs), about half of which are encoded in the subtelomeres. We performed a de novo assembly of two C. glabrata strains, BG2 and BG3993, using long single-molecule real-time (SMRT) reads, and constructed high-quality telomere-to-telomere assemblies of all 13 chromosomes to assess differences between C. glabrata strains. We documented variation between strains, and in agreement with earlier studies, found high (~0.5%-1%) frequencies of SNVs across the genome, including within subtelomeric regions. We documented changes in ALP gene structure and complement: there are large length differences in ALP genes in different strains, resulting from copy number variation in tandem repeats. We compared strains to characterize chromosome rearrangement events including within the poorly characterized subtelomeric regions. We show that rearrangements within the subtelomere regions all affect ALP-encoding genes, and 14/16 involve just the most terminal ALP gene. We present evidence that these rearrangements are mediated by break-induced replication. This study highlights the constrained nature of subtelomeric changes impacting ALP gene complement and subtelomere structure

Effects of Program Implementation on Adolescent Drug Use Behavior The Midwestern Prevention Project (MPP)

This study evaluated the relationship between level of program implementation and change in adolescent drug use behavior in the Midwestern Prevention Project (MPP), a school- and community-based program for drug abuse prevention. Trained teachers implemented the program with transition year students. Implementation was measured by teacher self-report and validated by research staff reports. Adolescent drug use was measured by student self-report; an expired air measure of smoking was used to increase the accuracy of self-reported drug use. Regression analyses were used to evaluate adherence; exposure, or amount of implementation; and reinvention. Results showed that all schools assigned to the program condition adhered to the research by implementing the program. Exposure had a significant effect on minimizing the increase in drug use from baseline to one year. Exposure also had a larger magnitude of intervention effect than experimental group assignment. Reinvention did not affect drug use. Results are discussed in terms of research assumptions about quality of program implementation, and possible school-level predictors of implementation