J. Mar. Sci. Eng.2015, 3(2), 175-192; doi:10.3390/jmse3020175 - published 23 April 2015 Show/Hide Abstract
Abstract: Epigenetic marks affecting the expression of genes are triggered by environmental stimuli, can persist throughout life or across multiple generations and can affect an individuals phenotype. In recent years there has been a revival of interest about the possible role of epigenetics in affecting complex or quantitative traits. This growing interest is partly driven by the increasing affordability of ultra-high throughput sequencing methods for studying the epigenome. In this review we focus on some of the possible applications of epigenetic knowledge to the improvement of aquaculture. DNA methylation, in which a methyl group is added to the C5 carbon residue of a cytosine by DNA methyltransferase, has been the most widely studied epigenetic mechanism to date, and methods used to obtain and analyse genome-wide DNA methylation data are outlined. The influence of epigenetic processes on the estimation of breeding values and accuracy of genomic selection for genetic improvement of aquatic species is explored. The possibility of tightly controlling nutritional stimuli found to affect epigenetic processes in order to tailor the development of fish for aquaculture is also discussed. Complex experiments will be required in order to gain a better understanding of the role of epigenetics in affecting quantitative traits in fish.
J. Mar. Sci. Eng.2015, 3(2), 154-174; doi:10.3390/jmse3020154 - published 15 April 2015 Show/Hide Abstract
Abstract: Clay minerals have previously been used to mitigate algal blooms because of their ability to flocculate algal cells or remove nutrients, but also offer considerable potential to remove ichthyotoxins. When a barramundi farm in tropical Australia suffered substantial fish mortalities due to a bloom of the ichthyotoxic haptophyte Prymnesium parvum, the farm manager decided to manipulate pond water N:P ratios through removal of phosphorus by the addition of lanthanum-modified bentonite clay (Phoslock™) to successfully mitigate ichthyotoxic effects. We conducted Prymnesium culture experiments under a range of N:P ratios, screening 14 different clays (two zeolites, four kaolins, six bentonites and two types of Korean loess) at pH 7 and 9 for cell flocculation and removal of ichthyotoxicity assessed with the RTgill-W1 cell line assay. Application of Phoslock™ to cultures grown at different N:P effectively removed 60%–100% of water-soluble toxicity of live Prymnesium (dependent on nutritional status). While most clays efficiently flocculated Prymnesium cells (≥80% removal), cell removal proved a poor predictor of ichthyotoxin adsorption. Extensive clay screening revealed that at elevated pH, as commonly associated with dense algal blooms, most clays either exacerbated ichthyotoxicity or exhibited significantly reduced toxin adsorption. Interpretation of changes in clay zeta potential at pH 7 and 9 provided valuable insight into clay/ichthyotoxin interactions, yet further research is required to completely understand the adsorption mechanisms. Bentonite-type clays proved best suited for ichthyotoxin removal purposes (100% removal at ecologically relevant pH 9) and offer great potential for on-farm emergency response.
J. Mar. Sci. Eng.2015, 3(1), 146-153; doi:10.3390/jmse3010146 - published 20 March 2015 Show/Hide Abstract
Abstract: Disease in fish and shellfish is one of the main problems facing aquaculture production. Therefore, all attempts should be made to increase the rate of survival and, thus, reduce economic losses. Much has been done to develop vaccines and medical treatments to reduce mortality; and however, farming of aquatic species has a long way to go to optimize the environmental conditions for the animals and, thus, reduce stress and improve animal welfare. However, the good news is that there is the potential to increase disease resistance by selective breeding. By challenge-testing fingerlings from a number of families per generation, and including the rate of survival in the breeding goal, the results so far are very promising. By focusing on one disease at a time it is possible to increase the rate of survival by at least 12.5% per generation for most diseases studied. Unfortunately, selective breeding is only used to a small degree in aquatic species. In 2010, it was estimated that only 8.2% of aquaculture production was based on genetically improved stocks.
J. Mar. Sci. Eng.2015, 3(1), 128-145; doi:10.3390/jmse3010128 - published 19 March 2015 Show/Hide Abstract
Abstract: Engineers require estimates of tolerable overtopping limits for grass-covered levees, dikes, and embankments that might experience steady overflow. Realistic tolerance estimates can be used for both resilient design and risk assessment. A simple framework is developed for estimating tolerable overtopping on grass-covered slopes caused by slowly-varying (in time) overtopping discharge (e.g., events like storm surges or river flood waves). The framework adapts the well-known Hewlett curves of tolerable limiting velocity as a function of overflow duration. It has been hypothesized that the form of the Hewlett curves suggests that the grass erosion process is governed by the flow work on the slope above a critical threshold velocity (referred to as excess work), and the tolerable erosional limit is reached when the cumulative excess work exceeds a given value determined from the time-dependent Hewlett curves. The cumulative excess work is expressed in terms of overflow discharge above a critical discharge that slowly varies in time, similar to a discharge hydrograph. The methodology is easily applied using forecast storm surge hydrographs at specific locations where wave action is minimal. For preliminary planning purposes, when storm surge hydrographs are unavailable, hypothetical equations for the water level and overflow discharge hydrographs are proposed in terms of the values at maximum overflow and the total duration of overflow. An example application is given to illustrate use of the methodology.
J. Mar. Sci. Eng.2015, 3(1), 111-127; doi:10.3390/jmse3010111 - published 4 March 2015 Show/Hide Abstract
Abstract: The continuous degradation of coral reef ecosystems on a global level, the disheartening expectations of a gloomy future for reefs’ statuses, the failure of traditional conservation acts to revive most of the degrading reefs and the understanding that it is unlikely that future reefs will return to historic conditions, all call for novel management approaches. Among the most effective approaches is the “gardening” concept of active reef restoration, centered, as in silviculture, on a two-step restoration process (nursery and transplantation). In the almost two decades that passed from its first presentation, the “gardening” tenet was tested in a number of coral reefs worldwide, revealing that it may reshape coral reef communities (and associated biota) in such a way that novel reef ecosystems with novel functionalities that did not exist before are developed. Using the “gardening” approach as a climate change mediator, four novel ecosystem engineering management approaches are raised and discussed in this article. These include the take-home lessons approach, which considers the critical evaluation of reef restoration outcomes; the genetics approach; the use of coral nurseries as repositories for coral and reef species; and an approach that uses novel environmental engineering tactics. Two of these approaches (take-home lessons and using coral nurseries as repositories for reef dwelling organisms) already consider the uncertainty and the gaps in our knowledge, and they are further supported by the genetic approach and by the use of novel environmental engineering tactics as augmenting auxiliaries. Employing these approaches (combined with other novel tactics) will enhance the ability of coral reef organisms to adaptably respond to climate change.
J. Mar. Sci. Eng.2015, 3(1), 100-110; doi:10.3390/jmse3010100 - published 4 March 2015 Show/Hide Abstract
Abstract: Slides generating impulse waves are currently generated using either block models or free granular material impacting a water body. These procedures were mainly developed to study plane impulse waves, i.e., wave generation in a rectangular channel. The current VAW, ETH Zurich, research is directed to the spatial impulse wave features, i.e., waves propagating in a wave basin. The two wave generation mechanisms mentioned above complicate this process for various reasons, including experimental handling, collection of slide material in the wave basin, poor representation of prototype conditions for the block model, and excessive temporal duration for free granular slides. Impulse waves originating from slides with free granular material and mesh-packed slides are compared in this paper. Detailed test series are presented, so that the resulting main wave features can be compared. The results highlight whether the simplified procedure involving mesh-packed slides really applies in future research, and specify advantages in terms of impulse wave experimentation.