Ecosystem Approach to Fisheries Management (Essential EAFM) training and TOT in Sri Lanka

This report presents presentations from representatives of 12 countries, key outcomes and recommendations for the future.

Live food: a lesser known essential

This article is a short discussion of the requirements for live food production in aquaculture and a brief presentation of the processes involved.

Optical tweezing beam control using liquid crystal adaptive optical elements

Liquid crystal (LC) adaptive optical elements are described, which provide an alternative to existing micropositioning technologies in optical tweezing. A full description of this work is given in [1]. An adaptive LC prism supplies tip/tilt to the phase profile of the trapping beam, giving rise to an available steering radius within the x-y plane of 10 μm. Additionally, a modally addressed adaptive LC lens provides defocus, offering a z-focal range for the trapping site of 100 μm. The result is full three-dimensional positional control of trapped particle(s) using a simple and wholly electronic control system. Compared to competing technologies, these devices provide a lower degree of controllability, but have the advantage of simplicity, cost and light efficiency. Furthermore, due to their birefringence, LC elements offer the opportunity of the creation of dual optical traps with controllable depth and separation.

Subdivision-stabilised immersed b-spline finite elements for moving boundary flows

An immersed finite element method is presented to compute flows with complex moving boundaries on a fixed Cartesian grid. The viscous, incompressible fluid flow equations are discretized with b-spline basis functions. The two-scale relation for b-splines is used to implement an elegant and efficient technique to satisfy the LBB condition. On non-grid-aligned fluid domains and at moving boundaries, the boundary conditions are enforced with a consistent penalty method as originally proposed by Nitsche. In addition, a special extrapolation technique is employed to prevent the loss of numerical stability in presence of arbitrarily small cut-cells. The versatility and accuracy of the proposed approach is demonstrated by means of convergence studies and comparisons with previous experimental and computational investigations.

The bacterial cytoskeleton modulates motility, type 3 secretion, and colonization in Salmonella.

Although there have been great advances in our understanding of the bacterial cytoskeleton, major gaps remain in our knowledge of its importance to virulence. In this study we have explored the contribution of the bacterial cytoskeleton to the ability of Salmonella to express and assemble virulence factors and cause disease. The bacterial actin-like protein MreB polymerises into helical filaments and interacts with other cytoskeletal elements including MreC to control cell-shape. As mreB appears to be an essential gene, we have constructed a viable ΔmreC depletion mutant in Salmonella. Using a broad range of independent biochemical, fluorescence and phenotypic screens we provide evidence that the Salmonella pathogenicity island-1 type three secretion system (SPI1-T3SS) and flagella systems are down-regulated in the absence of MreC. In contrast the SPI-2 T3SS appears to remain functional. The phenotypes have been further validated using a chemical genetic approach to disrupt the functionality of MreB. Although the fitness of ΔmreC is reduced in vivo, we observed that this defect does not completely abrogate the ability of Salmonella to cause disease systemically. By forcing on expression of flagella and SPI-1 T3SS in trans with the master regulators FlhDC and HilA, it is clear that the cytoskeleton is dispensable for the assembly of these structures but essential for their expression. As two-component systems are involved in sensing and adapting to environmental and cell surface signals, we have constructed and screened a panel of such mutants and identified the sensor kinase RcsC as a key phenotypic regulator in ΔmreC. Further genetic analysis revealed the importance of the Rcs two-component system in modulating the expression of these virulence factors. Collectively, these results suggest that expression of virulence genes might be directly coordinated with cytoskeletal integrity, and this regulation is mediated by the two-component system sensor kinase RcsC.

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Tests for conceptual design of 6.6 kV class superconducting fault current limiter with YBCO thin film elements

A superconducting fault current limiter (SFCL) for 6.6 kV and 400 A installed in a cubicle for a distribution network substation was conceptually designed. The SFCL consists of parallel- and series-connected superconducting YBCO elements and a limiting resistor. Before designing the SFCL, some tests were carried out. The width and length of each element used in the tests are 30 mm and 210 mm, respectively. The element consists of YBCO thin film of about 200 nm in thickness on cerium dioxide (CeO2) as a cap-layer on a sapphire substrate by metal-organic deposition with a protective metal coat. In the tests, characteristics of each element, such as over-current, withstand-voltage, and so on, were obtained. From these characteristics, series and parallel connections of the elements, called units, were considered. The characteristics of the units were obtained by tests. From the test results, a single phase prototype SFCL was manufactured and tested. Thus, an SFCL rated at 6.6 kV and 400 A can be designed. © 2009 IEEE.

Detection of large-scale concrete columns for automated bridge inspection

There are over 600,000 bridges in the US, and not all of them can be inspected and maintained within the specified time frame. This is because manually inspecting bridges is a time-consuming and costly task, and some state Departments of Transportation (DOT) cannot afford the essential costs and manpower. In this paper, a novel method that can detect large-scale bridge concrete columns is proposed for the purpose of eventually creating an automated bridge condition assessment system. The method employs image stitching techniques (feature detection and matching, image affine transformation and blending) to combine images containing different segments of one column into a single image. Following that, bridge columns are detected by locating their boundaries and classifying the material within each boundary in the stitched image. Preliminary test results of 114 concrete bridge columns stitched from 373 close-up, partial images of the columns indicate that the method can correctly detect 89.7% of these elements, and thus, the viability of the application of this research.

Seismic analyses of shallow tunnels by dynamic centrifuge tests and finite elements

The increments of internal forces induced in a tunnel lining during earthquakes can be assessed with several procedures at different levels of complexity. However, the substantial lack of well-documented case histories still represents a difficulty in order to validate any of the methods proposed in literature. To bridge this gap, centrifuge model tests were carried out on a circular aluminium tunnel located at two different depths in dense and loose dry sand. Each model has been instrumented for measuring soil motion and internal loads in the lining and tested under several dynamic input signals. The tests performed represented an experimental benchmark to calibrate dynamic analyses with different approaches to account for soil-tunnel kinematic interaction. © 2009 IOS Press.

Thylakoid terminal oxidases are essential for the cyanobacterium Synechocystis sp. PCC 6803 to survive rapidly changing light intensities.

Cyanobacteria perform photosynthesis and respiration in the thylakoid membrane, suggesting that the two processes are interlinked. However, the role of the respiratory electron transfer chain under natural environmental conditions has not been established. Through targeted gene disruption, mutants of Synechocystis sp. PCC 6803 were generated that lacked combinations of the three terminal oxidases: the thylakoid membrane-localized cytochrome c oxidase (COX) and quinol oxidase (Cyd) and the cytoplasmic membrane-localized alternative respiratory terminal oxidase. All strains demonstrated similar growth under continuous moderate or high light or 12-h moderate-light/dark square-wave cycles. However, under 12-h high-light/dark square-wave cycles, the COX/Cyd mutant displayed impaired growth and was completely photobleached after approximately 2 d. In contrast, use of sinusoidal light/dark cycles to simulate natural diurnal conditions resulted in little photobleaching, although growth was slower. Under high-light/dark square-wave cycles, the COX/Cyd mutant suffered a significant loss of photosynthetic efficiency during dark periods, a greater level of oxidative stress, and reduced glycogen degradation compared with the wild type. The mutant was susceptible to photoinhibition under pulsing but not constant light. These findings confirm a role for thylakoid-localized terminal oxidases in efficient dark respiration, reduction of oxidative stress, and accommodation of sudden light changes, demonstrating the strong selective pressure to maintain linked photosynthetic and respiratory electron chains within the thylakoid membrane. To our knowledge, this study is the first to report a phenotypic difference in growth between terminal oxidase mutants and wild-type cells and highlights the need to examine mutant phenotypes under a range of conditions.