Barriers to fieldwork in undergraduate geoscience degrees

Fieldwork is an integral part of geoscience subjects, but changing career pathways and student demographics have major implications for the future of compulsory fieldwork. The ways in which fieldwork is taught and the learning outcomes it fulfils urgently need updating.<br/

In Vitro Recombination Catalyzed by Bacterial Class 1 Integron Integrase IntI1 Involves Cooperative Binding and Specific Oligomeric Intermediates

Gene transfer via bacterial integrons is a major pathway for facilitating the spread of antibiotic resistance genes across bacteria. Recently the mechanism underlying the recombination catalyzed by class 1 integron recombinase (IntI1) between attC and attI1 was highlighted demonstrating the involvement of a single-stranded intermediary on the attC site. However, the process allowing the generation of this single-stranded substrate has not been determined, nor have the active IntI1•DNA complexes been identified. Using the in vitro strand transfer assay and a crosslink strategy we previously described we demonstrated that the single-stranded attC sequences could be generated in the absence of other bacterial proteins in addition to IntI. This suggests a possible role for this protein in stabilizing and/or generating this structure. The mechanism of folding of the active IntI•DNA complexes was further analyzed and we show here that it involves a cooperative binding of the protein to each recombination site and the emergence of different oligomeric species specific for each DNA substrate. These findings provide further insight into the recombination reaction catalyzed by IntI1

Marine integrons containing novel integrase genes, attachment sites, attI, and associated gene cassettes in polluted sediments from Suez and Tokyo Bays

In order to understand the structure and biological significance of integrons and associated gene cassettes in marine polluted sediments, metagenomic DNAs were extracted from sites at Suez and Tokyo Bays. PCR amplicons containing new integrase genes, intI, linked with novel gene cassettes, were recovered and had sizes from 1.8 to 2.5 kb. This approach uncovered, for the first time, the structure and diversity of both marine integron attachment site, attI, and the first gene cassette, the most efficiently expressed integron-associated gene cassette. The recovered 13 and 20 intI phylotypes, from Suez and Tokyo Bay samples, respectively, showed a highly divergence, suggesting a difference in integron composition between the sampling sites. Some intI phylotypes showed similarity with that from Geobacter metallireducens, belonging to Deltaproteobacteria, the dominant class in both sampling sites, as determined by 16S rRNA gene analysis. Thirty distinct families of putative attI site, as determined by the presence of an attI-like simple site, were recovered. A total of 146 and 68 gene cassettes represented Suez and Tokyo Bay unsaturated cassette pools, respectively. Gene cassettes, including a first cassette, from both sampling sites encoded two novel families of glyoxalase/bleomycin antibiotic-resistance protein. Gene cassettes from Suez Bay encoded proteins similar to haloacid dehalogenases, protein disulfide isomerases and death-on-curing and plasmid maintenance system killer proteins. First gene cassettes from Tokyo Bay encoded a xenobiotic-degrading protein, cardiolipin synthetase, esterase and WD40-like β propeller protein. Many of the first gene cassettes encoded proteins with no ascribable function but some of them were duplicated and possessed signal functional sites, suggesting efficient adaptive functions to their bacterial sources. Thus, each sampling site had a specific profile of integrons and cassette types consistent with the hypothesis that the environment shapes the genome

Inverse Correlation between Promoter Strength and Excision Activity in Class 1 Integrons

Class 1 integrons are widespread genetic elements that allow bacteria to capture and express gene cassettes that are usually promoterless. These integrons play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria. They typically consist of a gene (intI) encoding an integrase (that catalyzes the gene cassette movement by site-specific recombination), a recombination site (attI1), and a promoter (Pc) responsible for the expression of inserted gene cassettes. The Pc promoter can occasionally be combined with a second promoter designated P2, and several Pc variants with different strengths have been described, although their relative distribution is not known. The Pc promoter in class 1 integrons is located within the intI1 coding sequence. The Pc polymorphism affects the amino acid sequence of IntI1 and the effect of this feature on the integrase recombination activity has not previously been investigated. We therefore conducted an extensive in silico study of class 1 integron sequences in order to assess the distribution of Pc variants. We also measured these promoters' strength by means of transcriptional reporter gene fusion experiments and estimated the excision and integration activities of the different IntI1 variants. We found that there are currently 13 Pc variants, leading to 10 IntI1 variants, that have a highly uneven distribution. There are five main Pc-P2 combinations, corresponding to five promoter strengths, and three main integrases displaying similar integration activity but very different excision efficiency. Promoter strength correlates with integrase excision activity: the weaker the promoter, the stronger the integrase. The tight relationship between the aptitude of class 1 integrons to recombine cassettes and express gene cassettes may be a key to understanding the short-term evolution of integrons. Dissemination of integron-driven drug resistance is therefore more complex than previously thought

Quantum Measurement Theory in Gravitational-Wave Detectors

The fast progress in improving the sensitivity of the gravitational-wave (GW) detectors, we all have witnessed in the recent years, has propelled the scientific community to the point, when quantum behaviour of such immense measurement devices as kilometer-long interferometers starts to matter. The time, when their sensitivity will be mainly limited by the quantum noise of light is round the corner, and finding the ways to reduce it will become a necessity. Therefore, the primary goal we pursued in this review was to familiarize a broad spectrum of readers with the theory of quantum measurements in the very form it finds application in the area of gravitational-wave detection. We focus on how quantum noise arises in gravitational-wave interferometers and what limitations it imposes on the achievable sensitivity. We start from the very basic concepts and gradually advance to the general linear quantum measurement theory and its application to the calculation of quantum noise in the contemporary and planned interferometric detectors of gravitational radiation of the first and second generation. Special attention is paid to the concept of Standard Quantum Limit and the methods of its surmounting.Comment: 147 pages, 46 figures, 1 table. Published in Living Reviews in Relativit

Assessment of the centre of pressure pattern and moments about S2 in scoliotic subjects during normal walking

Background Context: Research employing gait measurements indicate asymmetries in ground reaction forces and suggest relationships between these asymmetries, neurological dysfunction and spinal deformity. Although, studies have documented the use of centre of pressure (CoP) and net joint moments in gait assessment and have assessed centre of mass (CoM)-CoP distance relationships in clinical conditions, there is a paucity of information relating to the moments about CoM. It is commonly considered that CoM is situated around S2 vertebra in normal upright posture and hence this study uses S2 vertebral prominence as reference point relative to CoM. Purpose: To assess and establish asymmetry in the CoP pattern and moments about S2 vertebral prominence during level walking and its relationship to spinal deformity in adolescents with scoliosis. Patient sample: Nine Adolescent Idiopathic Scoliosis subjects (8 females and 1 male with varying curve magnitudes and laterality) scheduled for surgery within 2-3 days after data collection, took part in this study. Outcome measures: Kinetic and Kinematic Gait assessment was performed with an aim to estimate the CoP displacement and the moments generated by the ground reaction force about the S2 vertebral prominence during left and right stance during normal walking. Methods: The study employed a strain gauge force platform to estimate the medio-lateral and anterior-posterior displacement of COP and a six camera motion analysis system to track the reflective markers to assess the kinematics. The data were recorded simultaneously. Results: Results indicate wide variations in the medio lateral direction CoP, which could be related to the laterality of both the main and compensation curves. This variation is not evident in the anterior-posterior direction. Similar results were recorded for moments about S2 vertebral prominence. Subjects with higher left compensation curve had greater displacement to the left. Conclusion: Although further longitudinal studies are needed, results indicate that the variables identified in this study are applicable to initial screening and surgical evaluation of scoliosis. © 2008 Chockalingam et al; licensee BioMed Central Ltd

What explains electoral responses to the 'Great Recession in Europe?

The ?Great Recession? in Europe started in early 2008 and was the greatest economic crisis facing the continent since the Great Depression of the 1930s. It produced a largescale loss of support for many incumbent parties. The purpose of this paper is to explain responses to the crisis among European electorates with the assistance of three rival models of electoral choice. The first is the cleavages model associated with Rokkan and Lipset which highlights the importance of social groups as the sources of electoral support. The second is the spatial model of party competition which focuses on the ideological distance between voters and parties in relation to divisive issues in society. The third is the valence model which argues that voters will support parties that deliver policies over which there is widespread agreement about what should be done. The paper models electoral support for incumbent parties using data from the European Social Surveys of 2006, conducted prior to the recession, and again in 2012 some four years into the crisis. The results show that all three models are relevant for understanding mass political responses to the crisis. It is also apparent that an ideological shift to the right occurred in electoral support between the two periods and this happened among both the voters and also the incumbent parties in Europe

Measurement of vertebral rotation in adolescent idiopathic scoliosis with low-dose CT in prone position - method description and reliability analysis

<p>Abstract</p> <p>Background</p> <p>To our knowledge there is no report in the literature on measurements of vertebral rotation with low-dose computed tomography (CT) in prone position.</p> <p>Aims</p> <p>To describe and test the reliability of this new method, compare it with other methods in use and evaluate the influence of body position on the degree of vertebral rotation measured by different radiological methods.</p> <p>Study design</p> <p>Retrospective study.</p> <p>Methods</p> <p>25 consecutive patients with adolescent idiopathic scoliosis scheduled for surgery (17 girls, 8 boys) aged 15 ± 2 years (mean ± SD) were included in the analysis of this study. The degree of the vertebral rotation was in all patients measured according to the method of Perdriolle on standing plain radiographs and on supine CT scanogram, and according to the method of Aaro and Dahlborn on axial CT images in prone position and on magnetic resonance imaging (MRI) in supine position. The measurements were done by one neuroradiologist at two different occasions. Bland and Altman statistical approach was used in the reliability assessment.</p> <p>Results</p> <p>The reliability of measuring vertebral rotation by axial CT images in prone position was almost perfect with an intraclass correlation coefficient of 0.95, a random error of the intraobserver differences of 2.3°, a repeatability coefficient of 3.2° and a coefficient of variation of 18.4%. Corresponding values for measurements on CT scanogram were 0.83, 5.1°, 7.2°, and 32.8%, respectively, indicating lower reliability of the latter modality and method. The degree of vertebral rotation measured on standing plain radiographs, prone CT scanogram, axial images on CT in prone position and on MRI in supine position were 25.7 ± 9.8°, 21.9 ± 8.3°, 17.4 ± 7.1°, and 16.1 ± 6.5°, respectively. The vertebral rotation measured on axial CT images in prone position was in average 7.5% larger than that measured on axial MRI in supine position.</p> <p>Conclusions</p> <p>This study has shown that measurements of vertebral rotation in prone position were more reliable on axial CT images than on CT scanogram. The measurement of vertebral rotation on CT (corrected to the pelvic tilt) in prone position imposes lower impact of the recumbent position on the vertebral rotation than did MRI in supine position. However, the magnitude of differences is of doubtful clinical significance.</p