Genome sequence of marine bacterium idiomarina sp. strain 28-8, isolated from Korean ark shells

Idiomarina sp. strain 28-8 is an aerobic, Gram-negative, flagellar bacterium isolated from the bodies of ark shells (Scapharca broughtonii) collected from underwater sediments in Gangjin Bay, South Korea. Here, we present the draft genome sequence of Idiomarina sp. 28-8 (2,971,606 bp, with a G+C content of 46.9%), containing 2,795 putative coding sequences.

The relationship between appetite and food preferences in British and Australian children

Background: Appetitive traits and food preferences are key determinants of children’s eating patterns but it is unclear how these behaviours relate to one another. This study explores relationships between appetitive traits and preferences for fruits and vegetables, and energy dense, nutrient poor (noncore) foods in two distinct samples of Australian and British preschool children. Methods: This study reports secondary analyses of data from families participating in the British GEMINI cohort study (n=1044) and the control arm of the Australian NOURISH RCT (n=167). Food preferences were assessed by parent-completed questionnaire when children were aged 3-4 years and grouped into three categories; vegetables, fruits and noncore foods. Appetitive traits; enjoyment of food, food responsiveness, satiety responsiveness, slowness in eating, and food fussiness were measured using the Children’s Eating Behaviour Questionnaire when children were 16 months (GEMINI) or 3-4 years (NOURISH). Relationships between appetitive traits and food preferences were explored using adjusted linear regression analyses that controlled for demographic and anthropometric covariates. Results: Vegetable liking was positively associated with enjoyment of food (GEMINI; β=0.20 ± 0.03, p<0.001, NOURISH; β=0.43 ± 0.07, p<0.001) and negatively related to satiety responsiveness (GEMINI; β=-0.19 ± 0.03, p<0.001, NOURISH; β=-0.34 ± 0.08, p<0.001), slowness in eating (GEMINI; β=-0.10 ± 0.03, p=0.002, NOURISH; β=-0.30 ± 0.08, p<0.001) and food fussiness (GEMINI; β=-0.30 ± 0.03, p<0.001, NOURISH; β=-0.60 ± 0.06, p<0.001). Fruit liking was positively associated with enjoyment of food (GEMINI; β=0.18 ± 0.03, p<0.001, NOURISH; β=0.36 ± 0.08, p<0.001), and negatively associated with satiety responsiveness (GEMINI; β=-0.13 ± 0.03, p<0.001, NOURISH; β=-0.24 ± 0.08, p=0.003), food fussiness (GEMINI; β=-0.26 ± 0.03, p<0.001, NOURISH; β=-0.51 ± 0.07, p<0.001) and slowness in eating (GEMINI only; β=-0.09 ± 0.03, p=0.005). Food responsiveness was unrelated to liking for fruits or vegetables in either sample but was positively associated with noncore food preference (GEMINI; β=0.10 ± 0.03, p=0.001, NOURISH; β=0.21 ± 0.08, p=0.010). Conclusion: Appetitive traits linked with lower obesity risk were related to lower liking for fruits and vegetables, while food responsiveness, a trait linked with greater risk of overweight, was uniquely associated with higher liking for noncore foods.

Geographical and morphological variation within and between colour phases in Coris julis (L. 1758), a protogynous marine fish

The possible differences between sexes in patterns of morphological variation in geographical space have been explored only in gonochorist freshwater species. We explored patterns of body shape variation in geographical space in a marine sequential hermaphrodite species, Coris julis (L. 1758), analyzing variation both within and between colour phases, through the use of geometric morphometrics and spatially-explicit statistical analyses. We also tested for the association of body shape with two environmental variables: temperature and chlorophyll a concentration, as obtained from time-series of satellite-derived data. Both colour phases showed a significant morphological variation in geographical space and patterns of variation divergent between phases. Although the morphological variation was qualitatively similar, individuals in the initial colour phase showed a more marked variation than individuals in the terminal phase. Body shape showed a weak but significant correlation with environmental variables, which was more pronounced in primary specimens.

Economic value of recreational fishing in Moreton Bay and the potential impact of the marine park rezoning

In 2009, the area of the Moreton Bay Marine Park was increased from 0.5 per cent of the Bay area to 16 per cent. During the planning process, opposition by commercial and recreational fishers alike was raised, arguing that loss of fishing grounds would lead to substantial loss in economic benefits. The commercial sector was compensated through a buyback of fishing effort, but the recreational sector received no compensation. In this paper, we develop a travel cost model to estimate the potential economic impact on the recreational sector from the marine park rezoning. The results suggest that, counter to initial claims, non-market recreational fishing benefits may have increased by between $1.3m and $2.5m a year, with a current total annual value of around $20m. Keywords: Travel cost model; Economic valuation; Moreton Bay Marine Park; Recreational fishing

Postglacial Early Permian (late Sakmarian-early Artinskian) shallow-marine carbonate deposition along a 2000 km transect from Timor to west Australia

Late Sakmarian to early Artinskian (Early Permian) carbonate deposition was widespread in the marine intracratonic rift basins that extended into the interior of Eastern Gondwana from Timor in the north to the northern Perth Basin in the south. These basins spanned about 20° of paleolatitude (approximately 35°S to 55°S). This study describes the type section of the Maubisse Limestone in Timor-Leste, and compares this unit with carbonate sections in the Canning Basin (Nura Nura Member of the Poole Sandstone), the Southern Carnarvon Basin (Callytharra Formation) and the northern Perth Basin (Fossil Cliff Member of the Holmwood Shale). The carbonate units have no glacial influence and formed part of a major depositional cycle that, in the southern basins, overlies glacially influenced strata and lies a short distance below mudstone containing marine fossils and scattered dropstones (perhaps indicative of sea ice). In the south marine conditions became more restricted and were replaced by coal measures at the top of the depositional sequence. In the north, the carbonate deposits are possibly bryozoan–crinoidal mounds; whereas in the southern basins they form laterally continuous relatively thin beds, deposited on a very low-gradient seafloor, at the tops of shale–limestone parasequences that thicken upward in parasequence sets. All marine deposition within the sequence took place under very shallow (inner neritic) conditions, and the limestones have similar grain composition. Bryozoan and crinoidal debris dominate the grain assemblages and brachiopod shell fragments, foraminifera and ostracod valves are usually common. Tubiphytes ranged as far south as the Southern Carnarvon Basin, albeit rarely, but is more common to the north. Gastropod and bivalve shell debris, echinoid spines, solitary rugose corals and trilobite carapace elements are rare. The uniformity of the grain assemblage and the lack of tropical elements such as larger fusulinid foraminifera, colonial corals or dasycladacean algae indicate temperate marine conditions with only a small increase in temperature to the north. The depositional cycle containing the studied carbonate deposits represents a warmer phase than the preceding glacially influenced Asselian to early Sakmarian interval and the subsequent cool phase of the “mid” Artinskian that is followed by significant warming during the late Artinskian–early Kungurian. The timing of cooler and warmer intervals in the west Australian basins seems out-of-phase with the eastern Australian succession, but this may be a problem of chronostratigraphic miscorrelation due to endemic faunas and palynofloras.

Estimating the potential impact of entry fees for marine parks on dive tourism in South East Asia

Marine reserves are increasingly being established as a mechanism to protect marine biodiversity and sensitive habitats. As well as providing conservation benefits, marine reserves provide benefits to recreational scuba divers who dive within the reserve, as well as to recreational and commercial fishers outside the reserve through spill-over effects. To ensure benefits are being realised, management of marine reserves requires ongoing monitoring and surveillance. These are not costless, and many marine reserve managers impose an entry fee. In some countries, dive tourism is major income source to coastal industries, and a concern is that high entry fees may dissuade divers. In this paper, the price elasticity of demand for dive tourism in three countries in South East Asia – Indonesia, Thailand and Malaysia – is estimated using a travel-cost model. From the model, the total non-market use value associated with diving in the area is estimated to be in the order of US$4.5 billion a year. The price elasticity of demand in the region is highly inelastic, such that increasing the cost of diving through a management levy would have little impact on total diver numbers.

Effects of PTPN22 C1858T polymorphism on susceptibility and clinical characteristics of British Caucasian rheumatoid arthritis patients

Objectives. To confirm the association of a functional single-nucleotide polymorphism (SNP), C1858T (rs2476601), in the PTPN22 gene of British Caucasian rheumatoid arthritis (RA) patients and to evaluate its influence on the RA phenotype. Methods. A total of 686 RA patients and 566 healthy volunteers, all of British Caucasian origin, were genotyped for C1858T polymorphism by PCR-restriction fragment length polymorphism assay. Data were analysed using SPSS software and the χ 2 test as applicable. Results. The PTPN22 1858T risk allele was more prevalent in the RA patients (13.9%) compared with the healthy controls (10.3%) (P = 0.008, odds ratio 1.4, 95% confidence interval 1.09-1.79). The association of the T allele was restricted to those with rheumatoid factor (RF)-positive disease (n = 524, 76.4%) (P = 0.004, odds ratio 1.5, 95% confidence interval 1.1-1.9). We found no association between PTPN22 and the presence of the HLA-DRB1 shared epitope or clinical characteristics. Conclusions. We confirmed the previously reported association of PTPN22 with RF-positive RA, which was independent from the HLA-DRB1 genotype.

Automating marine mammal detection in aerial images captured during wildlife surveys: A deep learning approach

Aerial surveys conducted using manned or unmanned aircraft with customized camera payloads can generate a large number of images. Manual review of these images to extract data is prohibitive in terms of time and financial resources, thus providing strong incentive to automate this process using computer vision systems. There are potential applications for these automated systems in areas such as surveillance and monitoring, precision agriculture, law enforcement, asset inspection, and wildlife assessment. In this paper, we present an efficient machine learning system for automating the detection of marine species in aerial imagery. The effectiveness of our approach can be credited to the combination of a well-suited region proposal method and the use of Deep Convolutional Neural Networks (DCNNs). In comparison to previous algorithms designed for the same purpose, we have been able to dramatically improve recall to more than 80% and improve precision to 27% by using DCNNs as the core approach.

Polymorphism in codon 17 of the CTLA-4 gene (+49 A/G) is not associated with susceptibility to rheumatoid arthritis in British Caucasians

The role of the CTLA-4 antigen in the development of autoimmune diseases is well documented, with several autoimmune disorders showing association or linkage with the CTLA-4 locus. Its role in the aetiology of rheumatoid arthritis (RA) however, remains unclear, as the functional studies of the B7-CTLA-4 pathway in mouse models of RA and genetic studies in humans have given contrasting results. We have studied the single nucleotide polymorphism at position +49 (A/G) of the CTLA-4 gene, in a cohort of 421 RA cases and 452 healthy controls from the UK. Despite the high statistical power to detect even a weak susceptibility effect, no significant association was found. We also analysed the distribution of the allele and genotype frequencies with respect to the presence of the shared epitope (a known RA susceptibility factor) and found no statistically significant differences. We conclude that, although the importance of the B7-CTLA-4 interaction in the development of RA can not be excluded, the CTLA-4 gene is unlikely to be a predisposing factor to this disease.

Telling tales and painting pictures: A narrative inquiry into the professional learning of Northern Territory primary teachers

This thesis narrates the professional learning experiences of seven Northern Territory teachers. It outlines the evolution from traditional professional development in schools to an active, responsive professional learning agenda. With increasing demands on teachers, standardisation and the quest for improved student outcomes, key themes in the re-storied narrative emerge about the definition and role of professional learning in complex conditions, effective teaching, quality programmes, and teacher agency. This thesis contributes to knowledge about the characteristics that teachers value in their professional learning experiences. An Ongoing Professional Enhancement Model (OPE) is proposed, highlighting directions in this field for key stakeholders.

Convergent evolution of marine mammals is associated with distinct substitutions in common genes

Phenotypic convergence is thought to be driven by parallel substitutions coupled with natural selection at the sequence level. Multiple independent evolutionary transitions of mammals to an aquatic environment offer an opportunity to test this thesis. Here, whole genome alignment of coding sequences identified widespread parallel amino acid substitutions in marine mammals; however, the majority of these changes were not unique to these animals. Conversely, we report that candidate aquatic adaptation genes, identified by signatures of likelihood convergence and/or elevated ratio of nonsynonymous to synonymous nucleotide substitution rate, are characterized by very few parallel substitutions and exhibit distinct sequence changes in each group. Moreover, no significant positive correlation was found between likelihood convergence and positive selection in all three marine lineages. These results suggest that convergence in protein coding genes associated with aquatic lifestyle is mainly characterized by independent substitutions and relaxed negative selection.

Passivity-based Trajectory-tracking for Marine Craft with Disturbance Rejection

This paper presents a Hamiltonian model of marine vehicle dynamics in six degrees of freedom in both body-fixed and inertial momentum coordinates. The model in body-fixed coordinates presents a particular structure of the mass matrix that allows the adaptation and application of passivity-based control interconnection and damping assignment design methodologies developed for robust stabilisation of mechanical systems in terms of generalised coordinates. As an example of application, we follow this methodology to design a passivity-based tracking controller with integral action for fully actuated vehicles in six degrees of freedom. We also describe a momentum transformation that allows an alternative model representation that resembles general port-Hamiltonian mechanical systems with a coordinate dependent mass matrix. This can be seen as an enabling step towards the adaptation of the theory of control of port-Hamiltonian systems developed in robotic manipulators and multi-body mechanical systems to the case of marine craft dynamics.

Mitigating undesirable impacts in the marine environment: A review of market-based management measures

Internationally, marine biodiversity conservation objectives are having an increasing influence on the management of commercial fisheries. While this is largely being implemented through Marine Protected Areas (MPAs) other management measures, such as market based instruments (MBIs), have proved to be effective at managing target species catch in fisheries and reducing environmental impacts in industries such as mining and tourism. Market-based management measures aim to mitigate the impacts of activities by better aligning the incentives their participants face with the objectives of management, changing their behavior as a consequence. In this paper, we review the potential of MBIs as management tools to mitigate undesirable environmental impacts associated with commercial fishing. Where they exist, examples of previous applications are described and the factors that influence their applicability and effectiveness are discussed. Several fishing methods and impacts are considered and suggest that whilst no single approach is most appropriate in all circumstances either replacing or complementing existing management arrangements with MBIs has the potential to improve environmental performance. This has a number of implications. From the environmental perspective they should enable levels of undesirable impacts such as damage to sensitive habitat or the bycatch of protected species of turtles, marine mammals, and seabirds to be reduced. The increased flexibility MBIs allow industry when developing solutions also has the potential to reduce costs to both the industry and managers, improving the cost-effectiveness of regulation as a result. Further, in the increasingly relevant case of MPAs the need for publicly funded compensation, often paid to industry when vessels are excluded from grounds, may also be significantly reduced if improved environmental performance makes it possible for some industry members to continue operating.

Strike Hard, Strike Sure - Operation Musketeer : British Military Planning during the Suez Crisis, 1956

This study analyses British military planning and actions during the Suez Crisis in 1956. It seeks to find military reasons for the change of concepts during the planning and compares these reasons with the tactical doctrines of the time. The thesis takes extensive advantage of military documents preserved in the National Archives, London. In order to expand the understanding of the exchange of views during the planning process, the private papers of high ranking military officials have also been consulted. French military documents preserved in the Service Historique de la Defence, Paris, have provided an important point of comparison. The Suez Crisis caught the British armed forces in the middle of a transition phase. The main objective of the armed forces was to establish a credible deterrence against the Soviet Union. However, due to overseas commitments the Middle East playing a paramount role because of its economic importance the armed forces were compelled to also prepare for Limited War and the Cold War. The armed forces were not fully prepared to meet this demand. The Middle Eastern garrison was being re-organised after the withdrawal from the Canal Base and the concept for a strategic reserve was unimplemented. The tactical doctrines of the time were based on experiences from the Second World War. As a result, the British view of amphibious operations and the subsequent campaigns emphasised careful planning, mastery of the sea and the air, sufficient superiority in numbers and firepower, centralised command and extensive administrative preparations. The British military had realized that Nasser could nationalise the Suez Canal and prepared an outline plan to meet this contingency. Although the plan was nothing more than a concept, it was accepted as a basis for further planning when the Canal was nationalised at the end of July. This plan was short-lived. The nominated Task Force Commanders shifted the landing site from Port Said to Alexandria because it enabled faster expansion of the bridgehead. In addition, further operations towards Cairo the hub of Nasser s power would be easier to conduct. The operational concept can be described as being traditional and was in accordance with the amphibious warfare doctrine. This plan was completely changed at the beginning of September. Apparently, General Charles Keightley, the Commander-in-Chief, and the Chairman of the Chiefs of Staff Committee developed the idea of prolonged aerial operations. The essence of the concept was to break the Egyptian will to resist by attacking the oil facilities, the transportation system and the armed forces. This victory through air concept would be supported by carefully planned psychological operations. This concept was in accordance with the Royal Air Force doctrine, which promoted a bomber offensive against selected target categories. General Keightley s plan was accepted despite suspicions at every planning level. The Joint Planning Staff and the Task Force Commanders opposed the concept from the beginning to the end because of its unpredictability. There was no information that suggested the bombing would persuade the Egyptians to submit. This problem was worsened by the fact that British intelligence was unable to provide reliable strategic information. The Task Force Commanders, who were responsible for the tactical plans, were not able to change Keightley s mind, but the concept was expanded to include a traditional amphibious assault on Port Said due to their resistance. The bombing campaign was never tested as the Royal Air Force was denied authorisation to destroy the transportation and oil targets. The Chiefs of Staff and General Keightley were too slow to realise that the execution of the plan depended on the determination of the Prime Minister. However, poor health, a lack of American and domestic support and the indecisiveness of the military had ruined Eden s resolve. In the end, a very traditional amphibious assault, which was bound to succeed at the tactical level but fail at the strategic level, was launched against Port Said.