Relative efficiency of fishing gears and investigation of resource availability in tropical demersal scalefish fisheries FRDC REPORT – PROJECT 2006/031

This project identified that there is substantial spatial variation in the demersal fish assemblages in the NDSF with some species more abundant in the north of the fishery and others in the south. At finer scales within sites and depths there is spatial variation associated with different habitats (e.g. sand vs sponge gardens or reef)

Effects of human footprint and biophysical factors on the body-size structure of fished marine species

Marine fisheries in coastal ecosystems in many areas of the world have historically removed large-bodied individuals, potentially impairing ecosystem functioning and the long-term sustainability of fish populations. Reporting on size-based indicators that link to food-web structure can contribute to ecosystem-based management, but the application of these indicators over large (cross-ecosystem) geographical scales has been limited to either fisheries-dependent catch data or diver-based methods restricted to shallow waters (<20 m) that can misrepresent the abundance of large-bodied fished species. We obtained data on the body-size structure of 82 recreationally or commercially targeted marine demersal teleosts from 2904 deployments of baited remote underwater stereo-video (stereo-BRUV). Sampling was at up to 50 m depth and covered approximately 10,000 km of the continental shelf of Australia. Seascape relief, water depth, and human gravity (i.e., a proxy of human impacts) were the strongest predictors of the probability of occurrence of large fishes and the abundance of fishes above the minimum legal size of capture. No-take marine reserves had a positive effect on the abundance of fishes above legal size, although the effect varied across species groups. In contrast, sublegal fishes were best predicted by gradients in sea surface temperature (mean and variance). In areas of low human impact, large fishes were about three times more likely to be encountered and fishes of legal size were approximately five times more abundant. For conspicuous species groups with contrasting habitat, environmental, and biogeographic affinities, abundance of legal-size fishes typically declined as human impact increased. Our large-scale quantitative analyses highlight the combined importance of seascape complexity, regions with low human footprint, and no-take marine reserves in protecting large-bodied fishes across a broad range of species and ecosystem configurations.publishedVersio

Contribution of CXCL12 secretion to invasion of breast cancer cells

INTRODUCTION: Neu (HER2/ErbB2) is overexpressed in 25% to 30% of human breast cancer, correlating with a poor prognosis. Researchers in previous studies who used the mouse mammary tumor virus Neu-transgenic mouse model (MMTV-Neu) demonstrated that the Neu-YB line had increased production of CXCL12 and increased metastasis, whereas the Neu-YD line had decreased metastasis. In this study, we examined the role of increased production of CXCL12 in tumor cell invasion and malignancy. METHODS: We studied invasion in the tumor microenvironment using multiphoton intravital imaging, in vivo invasion and intravasation assays. CXCL12 signaling was altered by using the CXCR4 inhibitor AMD3100 or by increasing CXCL12 expression. The role of macrophage signaling in vivo was determined using a colony-stimulating factor 1 receptor (CSF-1R) blocking antibody. RESULTS: The Neu-YD strain was reduced in invasion, intravasation and metastasis compared to the Neu-YB and Neu deletion mutant (activated receptor) strains. Remarkably, in the Neu-YB strain, in vivo invasion to epidermal growth factor was dependent on both CXCL12-CXCR4 and CSF1-CSF-1R signaling. Neu-YB tumors had increased macrophage and microvessel density. Overexpression of CXCL12 in rat mammary adenocarcinoma cells increased in vivo invasion as well as microvessel and macrophage density. CONCLUSIONS: Expression of CXCL12 by tumor cells results in increased macrophage and microvessel density and in vivo invasiveness

Influence of offshore oil and gas structures on seascape ecological connectivity.

Offshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O&G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological diversity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O&G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O&G structures, although other studies provide important related information. Evidence for O&G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna; including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O&G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O&G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O&G structures contribute to extending species distributions by providing rest stops, foraging habitat, and stepping stones. These questions could be addressed with further dedicated studies of animal movement in relation to structures using telemetry, molecular techniques and movement models. Our review and these priority questions provide a roadmap for advancing research needed to support evidence-based decision making for decommissioning O&G infrastructure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Sedimentation-induced burial of subsea pipelines: observations from field data and laboratory experiments

Sediment transport-induced changes to the embedment of three 26 km long sections of subsea pipeline are analysed and subsequently explained using model scale experiments. Rather than the scour and scour-induced sinking and sagging traditionally thought to dominate post-lay pipeline spanning and embedment change, the change for these pipelines is shown to be caused by sedimentation. The pipelines traverse a range of metocean and soil conditions; the variation in embedment correlates well with the variation in metocean conditions, with most change occurring in an area where multidirectional high-velocity short-duration flows associated with internal waves propagate at near-perpendicular angles to the pipeline. To understand the mechanism driving these changes, a series of model scale tests in O-tube flumes have been completed under flow conditions mimicking those recorded in the field. Good agreement is found between the field and laboratory results, both in terms of the process timescale and the post-sedimentation profile. The consistency of the embedment changes between the pipelines, their correlation with metocean conditions, and the ability to replicate these changes in model scale tests suggests that such changes can be accounted for in more effective pipeline design. Spans are relatively rare along the pipelines but where they do occur fish rather than scour are shown to be the principal agent of span formation.</p

Comparing the effects of different coloured artificial illumination on diurnal fish assemblages in the lower mesophotic zone

Artificial illumination is required when sampling with baited remote underwater video systems (BRUVS) in the lower mesophotic zone beyond ~ 90 m depth, yet little is known of how the choice of lighting influences fish assemblages and affects survey results in this zone. Here we use BRUVS equipped with the commonly used GoPro action camera to compare the composition and abundance of diurnal fish assemblages sampled under artificial Royal blue (~ 450 nm), Deep red (~ 660 nm) and natural day white light (~ 5600 K) in the lower mesophotic zone of the north-west shelf of Australia (19° 14.724′S 117° 20.286′E). No significant differences were detected in the fish assemblage composition or the number of species when surveyed using blue, red or white light at our study location. A greater mean total abundance of fish was observed using red light compared with white and blue light, however, individual species showed varied responses to the different light colours. When using consumer-grade action cameras such as GoPros, white light was shown to be far superior in image quality (and therefore ease of fish identification) compared to red and blue light. We recommend sampling diurnal mesophotic fish assemblages using a wavelength of light based on the survey objectives and the capabilities of the camera selected

Baited Remote Underwater Video Stations (BRUVS) used in stereo configuration (A) on complex seafloor topographies and single camera configuration on flat seabeds (B).

<p>The BRUVS were deployed in fleets with marker buoys and hauling ropes to sample simultaneously (C).</p