Human threats to sandy beaches: a meta-analysis of ghost crabs illustrates global anthropogenic impacts

Beach and coastal dune systems are increasingly subjected to a broad range of anthropogenic pressures that on many shorelines require significant conservation and mitigation interventions. But these interventions require reliable data on the severity and frequency of adverse ecological impacts. Such evidence is often obtained by measuring the response of 'indicator species'.Ghost crabs are the largest invertebrates inhabiting tropical and subtropical sandy shores and are frequently used to assess human impacts on ocean beaches. Here we present the first global meta-analysis of these impacts, and analyse the design properties and metrics of studies using ghost-crabs in their assessment. This was complemented by a gap analysis to identify thematic areas of anthropogenic pressures on sandy beach ecosystems that are under-represented in the published literature.Our meta-analysis demonstrates a broad geographic reach, encompassing studies on shores of the Pacific, Indian, and Atlantic Oceans, as well as the South China Sea. It also reveals what are, arguably, two major limitations: i) the near-universal use of proxies (i.e. burrow counts to estimate abundance) at the cost of directly measuring biological traits and bio-markers in the organism itself; and ii) descriptive or correlative study designs that rarely extend beyond a simple 'compare and contrast approach', and hence fail to identify the mechanistic cause(s) of observed contrasts.Evidence for a historically narrow range of assessed pressures (i.e., chiefly urbanisation, vehicles, beach nourishment, and recreation) is juxtaposed with rich opportunities for the broader integration of ghost crabs as a model taxon in studies of disturbance and impact assessments on ocean beaches. Tangible advances will most likely occur where ghost crabs provide foci for experiments that test specific hypotheses associated with effects of chemical, light and acoustic pollution, as well as the consequences of climate change (e.g. species range shifts).

A computational framework for nucleic acid sub-sequence identification

Identification of nucleic acid sub-sequences within larger background sequences is a fundamental need of the biology community. The applicability correlates to research studies looking for homologous regions, diagnostic purposes and many other related activities. This paper serves to detail the approaches taken leading to sub-sequence identification through the use of hidden Markov models and associated scoring optimisations. The investigation of techniques for locating conserved basal promoter elements correlates to promoter thus gene identification techniques. The case study centred on the TATA box basal promoter element, as such the background is a gene sequence with the TATA box the target. Outcomes from the research conducted, highlights generic algorithms for sub-sequence identification, as such these generic processes can be transposed to any case study where identification of a target sequence is required. Paths extending from the work conducted in this investigation have led to the development of a generic framework for the future applicability of hidden Markov models to biological sequence analysis in a computational context.

Multiagent framework for bio-data mining

This paper proposes to apply multiagent based data mining technologies to biological data analysis. The rationale is justified from multiple perspectives with an emphasis on biological context. Followed by that, an initial multiagent based bio-data mining framework is presented. Based on the framework, we developed a prototype system to demonstrate how it helps the biologists to perform a comprehensive mining task for answering biological questions. The system offers a new way to reuse biological datasets and available data mining algorithms with ease.

Multifaceted role of nitric oxide in an in vitro mouse neuronal injury model: transcriptomic profiling defines the temporal recruitment of death signalling cascades

Nitric oxide is implicated in the pathogenesis of various neuropathologies characterized by oxidative stress. Although nitric oxide has been reported to be involved in the exacerbation of oxidative stress observed in several neuropathologies, existent data fail to provide a holistic description of how nitrergic pathobiology elicits neuronal injury. Here we provide a comprehensive description of mechanisms contributing to nitric oxide induced neuronal injury by global transcriptomic profiling. Microarray analyses were undertaken on RNA from murine primary cortical neurons treated with the nitric oxide generator DETA-NONOate (NOC-18, 0.5 mM) for 8–24 hrs. Biological pathway analysis focused upon 3672 gene probes which demonstrated at least a ±1.5-fold expression in a minimum of one out of three time-points and passed statistical analysis (one-way anova, P < 0.05). Numerous enriched processes potentially determining nitric oxide mediated neuronal injury were identified from the transcriptomic profile: cell death, developmental growth and survival, cell cycle, calcium ion homeostasis, endoplasmic reticulum stress, oxidative stress, mitochondrial homeostasis, ubiquitin-mediated proteolysis, and GSH and nitric oxide metabolism. Our detailed time-course study of nitric oxide induced neuronal injury allowed us to provide the first time a holistic description of the temporal sequence of cellular events contributing to nitrergic injury. These data form a foundation for the development of screening platforms and define targets for intervention in nitric oxide neuropathologies where nitric oxide mediated injury is causative.

CO2 laser manufacturing of miniaturised lenses for lab-on-a-chip systems

This article describes the manufacturing and characterisation of plano-convex miniaturised lenses using a CO2 laser engraving process in PMMA substrates. The technique allows for lenses to be fabricated rapidly and in a reproducible manner at depths of over 200 µm and for lens diameters of more than 3 mm. Experimental characterisation of the lens focal lengths shows good correlation with theory. The plano-convex lenses have been successfully embedded into capillary microfluidic systems alongside planar microlenses, allowing for a significant reduction of ancillary optics without a loss of detection sensitivity when performing fluorescence measurements. Such technology provides a significant step forward towards the portability of fluorescence- or luminescence-based systems for biological/chemical analysis.

Genetic analyses reveal limited dispersal and recovery potential in the large freshwater crayfish Euastacus armatus from the southern Murray-Darling Basin

Understanding dispersal traits and adaptive potential is critically important when assessing the vulnerability of freshwater species in highly modified ecosystems. The present study investigates the population genetic structure of the Murray crayfish Euastacus armatus in the southern Murray–Darling Basin. This species has suffered significant population declines in sections of the Murray River in recent years, prompting the need for information on natural recruitment processes to help guide conservation. We assessed allele frequencies from 10 polymorphic microsatellite loci across 20 sites encompassing the majority of the species’ range. Low levels of gene flow were observed throughout hydrologically connected waterways, but significant spatial autocorrelation and low migration rate estimates reflect local genetic structuring and dispersal limitations, with home ranges limited to distances <50-km. Significant genetic differentiation of headwater populations upstream of barriers imposed by impoundments were also observed; however, population simulations demonstrate that these patterns likely reflect historical limitations to gene flow rather than contemporary anthropogenic impacts. Dispersal limitations, coupled with its biological traits, suggest that local populations are vulnerable to environmental disturbance with limited potential for natural recolonisation following population decline. We discuss the implications of these findings in the context of managing the recovery of the species.

Genetic analysis along an invasion pathway reveals endemic cryptic taxa, but a single species with little population structure in the introduced range

The invasion pathways of pest arthropods can be traced using genetic tools to develop an understanding of the processes that have shaped successful invasions and to inform both pest management and conservation strategies in their non-native and native ranges, respectively. The redlegged earth mite, Halotydeus destructor, is a major economic pest in Australia, successfully establishing and spreading after arrival from South Africa more than 100 years ago. Halotydeus destructor has recently expanded its range and evolved resistance to numerous pesticides in Australia, raising questions around its origin and spread. Location: South Africa and Australia. Methods: We sampled H. destructor populations in South Africa and Australia and developed a microsatellite marker library. We then examined genetic variation using mtDNA and microsatellite markers across both native and invasive ranges to determine endemic genetic diversity within South Africa, identify the likely origin of invasive populations and test genetic divergence across Australia. Results: The data show that H. destructor comprises a cryptic species complex in South Africa, with putative climatic/host plant associations that may correspond to regional variation. A lineage similar to that found near Cape Town has spread throughout Western and eastern Australia, where populations remain genetically similar. Main conclusions: Tracing the invasion pathway of this economically important pest revealed cryptic lineages in South Africa which points to the need for a taxonomic revision. The absence of significant genetic structure across the wide invasive range of H. destructor within Australia has implications for the development (and spread) of pesticide resistance and also points to recent local adaptation in physiological traits.

Towards powerful experimental and statistical approaches to study intraindividual variability in labile traits

There is a long-standing interest in behavioural ecology, exploring the causes and correlates of consistent individual differences in mean behavioural traits ('personality') and the response to the environment ('plasticity'). Recently, it has been observed that individuals also consistently differ in their residual intraindividual variability (rIIV). This variation will probably have broad biological and methodological implications to the study of trait variation in labile traits, such as behaviour and physiology, though we currently need studies to quantify variation in rIIV, using more standardized and powerful methodology. Focusing on activity rates in guppies (Poecilia reticulata), we provide a model example, from sampling design to data analysis, in how to quantify rIIV in labile traits. Building on the doubly hierarchical generalized linear model recently used to quantify individual differences in rIIV, we extend the model to evaluate the covariance between individual mean values and their rIIV. After accounting for time-related change in behaviour, our guppies substantially differed in rIIV, and it was the active individuals that tended to be more consistent (lower rIIV). We provide annotated data analysis code to implement these complex models, and discuss how to further generalize the model to evaluate covariances with other aspects of phenotypic variation.

ANNODA: tool for integrating molecular-biological annotation data

Collecting, analyzing, and making Molecularbiological annotation data accessible in different public data sources is still an ongoing project. Integration of such data from these data sources might lead to valuable biological knowledge. There are numerous annotation data and only some of those are structured. The number and contents of related sources are continuously increasing. In addition, the existing data sources have their own storage structure and implementation. As a result, these could lead to a limitation in the combining of annotation. Here, we proposed a tool, called ANNODA, for integrating Molecular-biological annotation data. Unlike the past work on database interoperation in the bioinformatics community, this database design uses web-links which are very useful for interactive navigation and meanwhile it also supports automated large-scale analysis tasks.

Analyzing inconsistency toward enhancing integration of biological molecular databases

The rapid growth of biological databases not only provides biologists with abundant data but also presents a big challenge in relation to the analysis of data. Many data analysis approaches such as data mining, information retrieval and machine learning have been used to extract frequent patterns from diverse biological databases. However, the discrepancies, due to the differences in the structure of databases and their terminologies, result in a significant lack of interoperability. Although ontology-based approaches have been used to integrate biological databases, the inconsistent analysis of biological databases has been greatly disregarded. This paper presents a method by which to measure the degree of inconsistency between biological databases. It not only presents a guideline for correct and efficient database integration, but also exposes high quality data for data mining and knowledge discovery.

Enhancing the effectiveness of clustering with spectra analysis

For many clustering algorithms, such as K-Means, EM, and CLOPE, there is usually a requirement to set some parameters. Often, these parameters directly or indirectly control the number of clusters, that is, k, to return. In the presence of different data characteristics and analysis contexts, it is often difficult for the user to estimate the number of clusters in the data set. This is especially true in text collections such as Web documents, images, or biological data. In an effort to improve the effectiveness of clustering, we seek the answer to a fundamental question: How can we effectively estimate the number of clusters in a given data set? We propose an efficient method based on spectra analysis of eigenvalues (not eigenvectors) of the data set as the solution to the above. We first present the relationship between a data set and its underlying spectra with theoretical and experimental results. We then show how our method is capable of suggesting a range of k that is well suited to different analysis contexts. Finally, we conclude with further  empirical results to show how the answer to this fundamental question enhances the clustering process for large text collections.

Effect of dietary modificatio of muscle long-chainN-3 fatty acid on plasma insulin and lipid metabolite, carcass traits, and fat deposition in lambs

In a previous study we showed that feeding fish meal significantly increased muscle long chain n-3 fatty acids (FA) and hot carcass weight. In this study we compared the effect of fish meal and fish oil on increasing muscle long-chain FA. We also investigated whether the increase in carcass weight was due to the effect of dietary enrichment of muscle long-chain n-3 FA on muscle membrane phospholipids and(or) to rumen by-pass protein provided by fish meal. Forty crossbred ([Merino x Border Leicester] x Poll Dorset) wether lambs between 26 and 33 kg BW were randomly assigned to one of five treatments: 1) basal diet of oaten:lucerne chaff (Basal); 2) Basal + fish meal (9% DM) = FM; 3) Basal + fish oil (1.5% DM) with protected sunflower meal (9% DM ) = FOSMP; 4) Basal + fish oil (1.5% DM) = FO; or 5) Basal + protected sunflower meal (10.5% DM) = SMP. Daily intake of ME (9.60 - 10.5 MJ ME/d) and CP (150 to 168 g/d) in all treatments was kept similar by varying the ratio of oaten:lucerne chaff and by feeding the animals at 90% ad libitum intake. Blood samples were collected at the start of the experiment and on the day (d 42) prior to slaughter. Lambs were then slaughtered at a commercial abattoir. At 24 h postmortem carcass traits were measured and longis-simus thoracis muscle taken for analysis of FA of phospholipid and triglyceride fractions. Lambs fed FO and FOSMP showed a marked increase in muscle longchain n-3 FA (P < 0.001) and a reduction in magnitude of the rise in insulin concentration (P < 0.001) after feeding compared with lambs fed Basal and SMP diets. Lambs in FM had a moderate increase (P < 0.001) in muscle long-chain n-3 FA content. Compared with Basal diet, both plasma total cholesterol (P < 0.02) and high-density lipoprotein cholesterol (P < 0.001) levels were greater in SMP and less in FO and FOSMP treat- ments. The i.m. fat content was reduced (P < 0.05) in FM and FO treatments, but carcass weight was increased only with fish meal (P < 0.03). Adding SMP to FO produced muscle with an intermediate level of i.m. fat, whereas muscle long-chain n-3 FA, i.m. fat, and insulin concentration were unchanged with SMP treatment. These results indicate that an increase in carcass weight in FM may be due to the supply of ruminally undegraded protein. They also suggest that fish oil along with fish meal can increase long-chain n-3 FA content in phospholipid of muscle membrane. This may be associated with reduced i.m. fat content and altered insulin action and lipoprotein metabolism.

Survey commentaries and analysis on Singapore biotechnology venture capital, intellectual and property regulatory law

The article presents survey commentaries and analysis on biotechnology venture capital, intellectual and property regulatory law in Singapore as of April 2006. The survey revealed that the financial sector and venture capitalists lack the ability to evaluate and understand biotechnology. Some major concerns for stakeholders are the lack of experience in the litigation of cases by Singaporean law firms and the lack of strategic management of portfolios for biomedical and pharmaceutical companies and the government. Stakeholders cited the need for Singaporean laws to be amended to accommodate developments in medical devices, herbal medicine, some biological areas and pre-clinical and clinical trials.