Deeply divergent mitochondrial lineages reveal patterns of local endemism in chironomids of the Australian Wet Tropics

The Wet Tropics bioregion of north-eastern Australia has been subject to extensive fluctuations in climate throughout the late Pliocene and Pleistocene. Cycles of rainforest contraction and expansion of dry sclerophyll forest associated with such climatic fluctuations are postulated to have played a major role in driving geographical endemism in terrestrial rainforest taxa. Consequences for the distributions of aquatic organisms, however, are poorly understood.The Australian non-biting midge species Echinocladius martini Cranston (Diptera: Chironomidae), although restricted to cool, well-forested freshwater streams, has been considered to be able to disperse among populations located in isolated rainforest pockets during periods of sclerophyllous forest expansion, potentially limiting the effect of climatic fluctuations on patterns of endemism. In this study, mitochondrial COI and 16S data were analysed for E. martini collected from eight sites spanning theWet Tropics bioregion to assess the scale and extent of phylogeographic structure. Analyses of genetic structure showed several highly divergent cryptic lineages with restricted geographical distributions. Within one of the identified lineages, strong genetic structure implied that dispersal among proximate (<1 km apart) streams was extremely restricted. The results suggest that vicariant processes, most likely due to the systemic drying of the Australian continent during the Plio-Pleistocene, might have fragmented historical E. martini populations and, hence, promoted divergence in allopatry.

Impacts of vessel capacity reduction programs on the efficiency in fisheries. The case of Australia's multispecies in northern prawn fishery

Capacity reduction programs in the form of buybacks or decommissioning programs have had relatively widespread application in fisheries in the US, Europe and Australia. A common criticism of such programs is that they remove the least efficient vessels first, resulting in an increase in average efficiency of the remaining fleet. The effective fishing power of the fleet, therefore, does not decrease in proportion to the number of vessels removed. Further, reduced crowding may increase efficiency of the remaining vessels. In this paper, the effects of a buyback program on average technical efficiency in Australia’s Northern Prawn Fishery are examined using a multi-output distance function approach with an explicit inefficiency model. The results indicate that average efficiency of the remaining vessels was greater than that of the removed vessels, and that average efficiency of remaining vessels also increased as a result of reduced crowding.

Modelling of inflatable rescue boats (IRBs) in surf conditions to reduce injuries

The Inflatable Rescue Boat (IRB) is arguably the most effective rescue tool used by the Australian surf lifesavers. The exceptional features of high mobility and rapid response have enabled it to become an icon on Australia's popular beaches. However, the IRB's extensive use within an environment that is as rugged as it is spectacular, has led it to become a danger to those who risk their lives to save others. Epidemiological research revealed lower limb injuries to be predominant, particularly the right leg. The common types of injuries were fractures and dislocations, as well as muscle or ligament strains and tears. The concern expressed by Surf Life Saving Queensland (SLSQ) and Surf Life Saving Australia (SLSA) led to a biomechanical investigation into this unique and relatively unresearched field. The aim of the research was to identify the causes of injury and propose processes that may reduce the instances and severity of injury to surf lifesavers during IRB operation. Following a review of related research, a design analysis of the craft was undertaken as an introduction to the craft, its design and uses. The mechanical characteristics of the vessel were then evaluated and the accelerations applied to the crew in the IRB were established through field tests. The data were then combined and modelled in the 3-D mathematical modelling and simulation package, MADYMO. A tool was created to compare various scenarios of boat design and methods of operation to determine possible mechanisms to reduce injuries. The results of this study showed that under simulated wave loading the boats flex around a pivot point determined by the position of the hinge in the floorboard. It was also found that the accelerations experienced by the crew exhibited similar characteristics to road vehicle accidents. Staged simulations indicated the attributes of an optimum foam in terms of thickness and density. Likewise, modelling of the boat and crew produced simulations that predicted realistic crew response to tested variables. Unfortunately, the observed lack of adherence to the SLSA footstrap Standard has impeded successful epidemiological and modelling outcomes. If uniformity of boat setup can be assured then epidemiological studies will be able to highlight the influence of implementing changes to the boat design. In conclusion, the research provided a tool to successfully link the epidemiology and injury diagnosis to the mechanical engineering design through the use of biomechanics. This was a novel application of the mathematical modelling software MADYMO. Other craft can also be investigated in this manner to provide solutions to the problem identified and therefore reduce risk of injury for the operators.

The urban littoral frontier : land reclamation in the history of human settlements

The urban waterfront may be regarded as the littoral frontier of human settlement. Typically, over the years, it advances, sometimes retreats, where terrestrial and aquatic processes interact and frequently contest this margin of occupation. Because most towns and cities are sited beside water bodies, many of these urban centers on or close to the sea, their physical expansion is constrained by the existence of aquatic areas in one or more directions from the core. It is usually much easier for new urban development to occur along or inland from the waterfront. Where other physical constraints, such as rugged hills or mountains, make expansion difficult or expensive, building at greater densities or construction on steep slopes is a common response. This kind of development, though technically feasible, is usually more expensive than construction on level or gently sloping land, however. Moreover, there are many reasons for developing along the shore or riverfront in preference to using sites further inland. The high cost of developing existing dry land that presents serious construction difficulties is one reason for creating new land from adjacent areas that are permanently or periodically under water. Another reason is the relatively high value of artificially created land close to the urban centre when compared with the value of existing developable space at a greater distance inland. The creation of space for development is not the only motivation for urban expansion into aquatic areas. Commonly, urban places on the margins of the sea, estuaries, rivers or great lakes are, or were once, ports where shipping played an important role in the economy. The demand for deep waterfronts to allow ships to berth and for adjacent space to accommodate various port facilities has encouraged the advance of the urban land area across marginal shallows in ports around the world. The space and locational demands of port related industry and commerce, too, have contributed to this process. Often closely related to these developments is the generation of waste, including domestic refuse, unwanted industrial by-products, site formation and demolition debris and harbor dredgings. From ancient times, the foreshore has been used as a disposal area for waste from nearby settlements, a practice that continues on a huge scale today. Land formed in this way has long been used for urban development, despite problems that can arise from the nature of the dumped material and the way in which it is deposited. Disposal of waste material is a major factor in the creation of new urban land. Pollution of the foreshore and other water margin wetlands in this way encouraged the idea that the reclamation of these areas may be desirable on public health grounds. With reference to examples from various parts of the world, the historical development of the urban littoral frontier and its effects on the morphology and character of towns and cities are illustrated and discussed. The threat of rising sea levels and the heritage value of many waterfront areas are other considerations that are addressed.

Sustainable urban stormwater management : water sensitive urban design perceptions, drivers and barriers

Stormwater has been recognised as one of the main culprits of aquatic ecosystem pollution and as a significant threat to the goal of ecological sustainable development. Water sensitive urban design is one of the key responses to the need to better manage urban stormwater runoff, the objectives of which go beyond rapid and efficient conveyance. Underpinned by the concepts of sustainable urban development, water sensitive urban design has proven to be an efficient and environmentally-friendly approach to urban stormwater management, with the necessary technical know-how and skills already available. However, large-scale implementation of water sensitive urban design is still lacking in Australia due to significant impediments and negative perceptions. Identification of the issues, barriers and drivers that affect sustainability outcomes of urban stormwater management is one of the first steps towards encouraging the wide-scale uptake of water sensitive urban design features which integrate sustainable urban stormwater management. This chapter investigates key water sensitive urban design perceptions, drivers and barriers in order to improve sustainable urban stormwater management efforts.

Investigating challenges and opportunities of water sensitive urban design for knowledge based development of Australian cities

A new approach that is slowly replacing neoclassical models of economic growth and commodity based industrial activities, knowledge based urban development (KBUD) aims to provide opportunities for citiesw to foster knowledge creation, exchange and innovation, and is based on the concepts of both sustainable urban development and economic prosperity; sustainable uses and protection of natural resources are therefore integral parts of KBUD. As such, stormwater, which has been recognised as one of the main culprits of aquatic ecosystem pollution and as therefore a significant threat to the goal of sustainable urban development, needs to be managed in a manner that produces ecologically sound outcomes. Water sensitive urban design (WSUD) is one of the key responses to the need to better management urban stormwater runoff and supports KBUD by providing an alternative, innovative and effective strategy to traditional stormwater management.

Engineering an Ecosystem : Taking Cues from Nature’s Paradigm to Build Tissue in the Lab and the Body

This manuscript took a 'top down' approach to understanding survival of inhabitant cells in the ecosystem bone, working from higher to lower length and time scales through the hierarchical ecosystem of bone. Our working hypothesis is that nature “engineered” the skeleton using a 'bottom up' approach,where mechanical properties of cells emerge from their adaptation to their local me-chanical milieu. Cell aggregation and formation of higher order anisotropic struc- ture results in emergent architectures through cell differentiation and extracellular matrix secretion. These emergent properties, including mechanical properties and architecture, result in mechanical adaptation at length scales and longer time scales which are most relevant for the survival of the vertebrate organism [Knothe Tate and von Recum 2009]. We are currently using insights from this approach to har-ness nature’s regeneration potential and to engineer novel mechanoactive materials [Knothe Tate et al. 2007, Knothe Tate et al. 2009]. In addition to potential applications of these exciting insights, these studies may provide important clues to evolution and development of vertebrate animals. For instance, one might ask why mesenchymal stem cells condense at all? There is a putative advantage to self-assembly and cooperation, but this advantage is somewhat outweighed by the need for infrastructural complexity (e.g., circulatory systems comprised of specific differentiated cell types which in turn form conduits and pumps to overcome limitations of mass transport via diffusion, for example; dif-fusion is untenable for multicellular organisms larger than 250 microns in diameter. A better question might be: Why do cells build skeletal tissue? Once cooperatingcells in tissues begin to deplete local sources of food in their aquatic environment, those that have evolved a means to locomote likely have an evolutionary advantage. Once the environment becomes less aquarian and more terrestrial, self-assembled organisms with the ability to move on land might have conferred evolutionary ad-vantages as well. So did the cytoskeleton evolve several length scales, enabling the emergence of skeletal architecture for vertebrate animals? Did the evolutionary advantage of motility over noncompliant terrestrial substrates (walking on land) favor adaptations including emergence of intracellular architecture (changes in the cytoskeleton and upregulation of structural protein manufacture), inter-cellular con- densation, mineralization of tissues, and emergence of higher order architectures?How far does evolutionary Darwinism extend and how can we exploit this knowl- edge to engineer smart materials and architectures on Earth and new, exploratory environments?[Knothe Tate et al. 2008]. We are limited only by our ability to imagine. Ultimately, we aim to understand nature, mimic nature, guide nature and/or exploit nature’s engineering paradigms without engineer-ing ourselves out of existence.

Planning and implementing trajectories for autonomous underwater vehicles to track evolving ocean processes based on predictions from a regional ocean model

Path planning and trajectory design for autonomous underwater vehicles (AUVs) is of great importance to the oceanographic research community because automated data collection is becoming more prevalent. Intelligent planning is required to maneuver a vehicle to high-valued locations to perform data collection. In this paper, we present algorithms that determine paths for AUVs to track evolving features of interest in the ocean by considering the output of predictive ocean models. While traversing the computed path, the vehicle provides near-real-time, in situ measurements back to the model, with the intent to increase the skill of future predictions in the local region. The results presented here extend prelim- inary developments of the path planning portion of an end-to-end autonomous prediction and tasking system for aquatic, mobile sensor networks. This extension is the incorporation of multiple vehicles to track the centroid and the boundary of the extent of a feature of interest. Similar algorithms to those presented here are under development to consider additional locations for multiple types of features. The primary focus here is on algorithm development utilizing model predictions to assist in solving the motion planning problem of steering an AUV to high-valued locations, with respect to the data desired. We discuss the design technique to generate the paths, present simulation results and provide experimental data from field deployments for tracking dynamic features by use of an AUV in the Southern California coastal ocean.

Autonomous underwater vehicle trajectory design coupled with predictive ocean models : a case study

Data collection using Autonomous Underwater Vehicles (AUVs) is increasing in importance within the oceano- graphic research community. Contrary to traditional moored or static platforms, mobile sensors require intelligent planning strategies to manoeuvre through the ocean. However, the ability to navigate to high-value locations and collect data with specific scientific merit is worth the planning efforts. In this study, we examine the use of ocean model predictions to determine the locations to be visited by an AUV, and aid in planning the trajectory that the vehicle executes during the sampling mission. The objectives are: a) to provide near-real time, in situ measurements to a large-scale ocean model to increase the skill of future predictions, and b) to utilize ocean model predictions as a component in an end-to-end autonomous prediction and tasking system for aquatic, mobile sensor networks. We present an algorithm designed to generate paths for AUVs to track a dynamically evolving ocean feature utilizing ocean model predictions. This builds on previous work in this area by incorporating the predicted current velocities into the path planning to assist in solving the 3-D motion planning problem of steering an AUV between two selected locations. We present simulation results for tracking a fresh water plume by use of our algorithm. Additionally, we present experimental results from field trials that test the skill of the model used as well as the incorporation of the model predictions into an AUV trajectory planner. These results indicate a modest, but measurable, improvement in surfacing error when the model predictions are incorporated into the planner.

Trajectory design for autonomous underwater vehicles based on ocean model predictions for feature tracking

Trajectory design for Autonomous Underwater Vehicles (AUVs) is of great importance to the oceanographic research community. Intelligent planning is required to maneuver a vehicle to high-valued locations for data collection. We consider the use of ocean model predictions to determine the locations to be visited by an AUV, which then provides near-real time, in situ measurements back to the model to increase the skill of future predictions. The motion planning problem of steering the vehicle between the computed waypoints is not considered here. Our focus is on the algorithm to determine relevant points of interest for a chosen oceanographic feature. This represents a first approach to an end to end autonomous prediction and tasking system for aquatic, mobile sensor networks. We design a sampling plan and present experimental results with AUV retasking in the Southern California Bight (SCB) off the coast of Los Angeles.

Hydrodynamic and thruster model validation for autonomous underwater vehicles

From Pontryagin’s Maximum Principle to the Duke Kahanamoku Aquatic Complex; we develop the theory and generate implementable time efficient trajectories for a test-bed autonomous underwater vehicle (AUV). This paper is the beginning of the journey from theory to implementation. We begin by considering pure motion trajectories and move into a rectangular trajectory which is a concatenation of pure surge and pure sway. These trajectories are tested using our numerical model and demonstrated by our AUV in the pool. In this paper we demonstrate that the above motions are realizable through our method, and we gain confidence in our numerical model. We conclude that using our current techniques, implementation of time efficient trajectories is likely to succeed.

Genetic analysis reveals two stocks of skipjack tuna (Katsuwonus pelamis) in the north western Indian Ocean

Skipjack (SJT) (Katsuwonus pelamis) is a medium sized, pelagic, highly dispersive tuna species that occurs widely across tropical and subtropical waters. SJT constitute the largest tuna fishery in the Indian Ocean, and are currently managed as a single stock. Patterns of genetic variation in a mtDNA gene and 6 microsatellite loci were examined to test for stock structure in the northwestern Indian Ocean. 324 individuals were sampled from five major fishing grounds around Sri Lanka, and single sites in the Maldive Islands and the Laccadive Islands. Phylogenetic reconstruction of mtDNA revealed two coexisting divergent clades in the region. AMOVA (Analysis of Molecular Variance) of mtDNA data revealed significant genetic differentiation among sites (ΦST = 0.2029, P < 0.0001), also supported by SAMOVA results. AMOVA of microsatellite data also showed significant differentiation among most sampled sites (FST = 0.0256, P<0.001) consistent with the mtDNA pattern. STRUCTURE analysis of the microsatellite data revealed two differentiated stocks. While the both two marker types examined identified two genetic groups, microsatellite analysis indicates that the sampled SJT are likely to represent individuals sourced from discrete breeding grounds that are mixed in feeding grounds in Sri Lankan waters.

Investigation into the introduction of clonal strains of Pseudomonas aeruginosa to the cystic fibrosis population by consumption of raw salad vegetables

Most salad vegetables are eaten fresh by consumers. However, raw vegetables may pose a risk of transmitting opportunistic bacteria to immunocompromised people, including cystic fibrosis (CF) patients. In particular, CF patients are vulnerable to chronic Pseudomonas aeruginosa lung infections and this organism is the primary cause of morbidity and mortality in this group. Clonal variants of P. aeruginosa have been identified as emerging threats to people afflicted with CF; however it has not yet been proven from where these clones originate or how they are transmitted. Due to the organisms‟ aquatic environmental niche, it was hypothesised that vegetables may be a source of these clones. To test this hypothesis, lettuce, tomatoes, mushrooms and bean sprout packages (n = 150) were analysed from a green grocer, supermarket and farmers‟ market within the Brisbane region, availability permitting. The internal and external surfaces of the vegetables were separately analysed for the presence of clonal strains of P. aeruginosa using washings and homogenisation techniques, respectively. This separation was in an attempt to establish which surface was contaminated, so that recommendations could be made to decrease or eliminate P. aeruginosa from these foods prior to consumption. Soil and water samples (n = 17) from local farms were also analysed for the presence of P. aeruginosa. Presumptive identification of isolates recovered from these environmental samples was made based on growth on Cetrimide agar at 42°C, presence of the cytochrome-oxidase enzyme and inability to ferment lactose. P. aeruginosa duplex real-time polymerase chain reaction assay (PAduplex) was performed on all bacterial isolates presumptively identified as P. aeruginosa. Enterobacterial repetitive intergenic consensus strain typing PCR (ERIC-PCR) was subsequently performed on confirmed bacterial isolates. Although 72 P. aeruginosa were isolated, none of these proved to be clonal strains. The significance of these findings is that vegetables may pose a risk of transmitting sporadic strains of P. aeruginosa to people afflicted with CF and possibly, other immunocompromised people.