The Sorcerer II expedition: Intellectual property and biodiscovery

This article considers the significance of a leading marine biodiscovery initiative. In March 2004, Dr. J. Craig Venter announced the official launch of the Sorcerer II Expedition, a scientific expedition of discovery, which would survey marine and terrestrial microbial populations. The Expedition has the potential to uncover tens of thousands of new microbial species and tens of millions of new genes. Venter has disavowed that the Sorcerer II Expedition has any commercial ambitions. However, some have viewed the Sorcerer II Expedition with suspicion. Various civil society groups have accused the Expedition of engaging in 'biopiracy'. This article investigates the Convention on Biological Diversity 1992 and other relevant international treaties, various national and regional regimes to govern access to genetic resources, and benefit-sharing agreements. It considers the intersection of intellectual property law, contract law, environmental law, and international law in this field. This article provides a blueprint for a nationally consistent scheme for access to genetic resources, and a model for future international developments.

Comparative analysis and distribution of Omega-3 lcPUFA Biosynthesis genes in marine molluscs

Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs.

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.

A candidate gene association study for growth performance in an improved Giant Freshwater Prawn (Macrobrachium rosenbergii) culture line

A candidate gene approach using type I single nucleotide polymorphism (SNP) markers can provide an effective method for detecting genes and gene regions that underlie phenotypic variation in adaptively significant traits. In the absence of available genomic data resources, transcriptomes were recently generated in Macrobrachium rosenbergii to identify candidate genes and markers potentially associated with growth. The characterisation of 47 candidate loci by ABI re-sequencing of four cultured and eight wild samples revealed 342 putative SNPs. Among these, 28 SNPs were selected in 23 growth-related candidate genes to genotype in 200 animals selected for improved growth performance in an experimental GFP culture line in Vietnam. The associations between SNP markers and individual growth performance were then examined. For additive and dominant effects, a total of three exonic SNPs in glycogen phosphorylase (additive), heat shock protein 90 (additive and dominant) and peroxidasin (additive), and a total of six intronic SNPs in ankyrin repeats-like protein (additive and dominant), rolling pebbles (dominant), transforming growth factor-β induced precursor (dominant), and UTP-glucose-1-phosphate uridylyltransferase 2 (dominant) genes showed significant associations with the estimated breeding values in the experimental animals (P =0.001−0.031). Individually, they explained 2.6−4.8 % of the genetic variance (R2=0.026−0.048). This is the first large set of SNP markers reported for M. rosenbergii and will be useful for confirmation of associations in other samples or culture lines as well as having applications in marker-assisted selection in future breeding programs.

Effectiveness of on-line resources to enhance student learning and engagement

BACKGROUND For engineering graduates to be work-ready with marketable skills they must not only be well-versed with engineering science and its applications, but also able to adapt to using commercial software that is widely used in engineering practice. Hydrological/hydraulic modelling is one aspect of engineering practice which demands the ability to apply fundamentals into design and construction using software. The user manuals for such software are usually tailored for the experienced engineer but not for undergraduates who typically are novices to concepts of modelling and software tools. As the focus of a course such as Advanced Water Engineering is on the wider aspects of engineering application of hydrological and hydraulic concepts, it is ineffective for the lecturers to direct the students to user manuals as students have neither the time nor the desire to sift through numerous pages in a manual. An alternative and efficient way to demonstrate the use of the software is enabling students to develop a model to simulate real-world scenario using the tools of the software and directing them to make informed decisions based on outcomes. PURPOSE Past experience of the lecturer showed that the resources available for the students left a knowledge gap leading to numerous student queries outside contact hours. The purpose of this study is to assess how effective purpose-built video resources can be in supplementing the traditional learning resources to enhance student learning. APPROACH Short-length animated video clips comprising guided step-by-step instructions were prepared using screen capture software to capture screen activity and later edited to focus on specific features using pop-up annotations; Vocal narration was purposely excluded to avoid disturbances due to noise and allow different learning paces of individual students. The video clips were made available to the students alongside the traditional resources/approaches such as in-class demonstrations, guideline notes, and tips for efficient and error-free procedural descriptions. The number of queries the lecturer received from the student cohort outside the lecture times was recorded. An anonymous survey to assess the usefulness and adequacy of the courseware was conducted. OUTCOMES While a significant decline in the number of student queries was noted, an overwhelming majority of the survey respondents confirmed the usefulness of the purpose-developed courseware. CONCLUSIONS/RECOMMENDATIONS/SUMMARY The survey and lecturer’s experience indicated that animated demonstration video clips illustrating the various steps involved in developing hydrologic and hydraulic models and simulating design scenarios is an effective supplement for traditional learning resources. Among the many advantages of the custom-made video clips as a learning resource are that they (1) highlight the aspects that are important to undergraduate learning but not available in the software manuals as the latter are designed for more mature users/learners; (2) provide short, to-the point communication in a step-by-step manner; (3) allow students flexibility to self-learn at their own pace; (4) enhance student learning; and (5) enable time savings for the lecturer in the long term by avoiding queries of a repetitive nature. It is expected that these newly developed resources will be improved to incorporate students’ suggestions before being offered to future cohorts of students. The concept can also be expanded to other relevant courses where animated demonstrations of key modelling steps are beneficial to student learning.

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.

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.

Clarification of the low-frequency modelling concept for marine craft

This article presents some remarks on models currently used in low speed manoeuvring and dynamic positioning problems. It discusses the relationship between the classical hydrodynamic equations for manoeuvring and seakeeping, and offers insight into the models used for simulation and control system design.

Open educational resources: Enhancing education provision and practice

Open educational resources (OERs), a disruptive technology, made their appearance in early 2002 as a promising tool for enhancing the quality of and access to education generally and higher education in particular. OERs were also perceived to have the potential to reduce costs by reusing learning materials. This brief draws on a study that reviewed the uptake of OERs and related activities in six institutions in Hong Kong, China; India; Malaysia; Pakistan; and Thailand.