The development of biological objectives for streams in a single catchment: a case study on the catchment of western port bay, Victoria, Australia

Government environment protection policies for waterways have traditionally relied on water quality indicators and their objectives. In this paper we describe the development of biological objectives based on invertebrate indicators for inclusion in a government policy for the catchment of Western Port Bay, Victoria. The first step of defining segments (areas with streams in which the same objectives are applied) was problematic, requiring two different approaches, as follows. Site groups initially based on invertebrate community composition derived using multivariate techniques (ordination and classification) proved to be unsuitable for policy segments. Segment boundaries were subsequently defined using topographical (e.g. boundary of foothills and lowland plains), climate (e.g. rainfall) and land-use (e.g. urban) features. We used information and data from reference sites inside as well outside the catchment to derive specific biological objectives based on aquatic invertebrates for these segments. Objectives were specified for the following four indicators – number of invertebrate families, the SIGNAL index, the AUSRIVAS predictive model and the number of key families.

Medical travel and the sale of human biological materials: suggestions for ethical policy development

The international medical travel industry includes patients seeking to access human biological materials (HBM) including gametes, organs and stem cells. Of the various niche markets, ‘transplant tourism’ has earned global condemnation and efforts to eradicate cross-border trade in organs, while other markets continue to expand. This article reviews the ethical issues raised by medical travel for HBM, in particular those concerning trade in HBM. It argues that a more consistent approach to the regulation of cross-border trade is imperative to ensure that the perils of ‘transplant tourism’ are not replicated in other markets. In addition, it discusses the role of the self-sufficiency model in assisting the development of ethical and practical policies regarding the procurement and use of human biological materials at a national level, thereby minimizing demand for medical travel.

Biological models of mental illness: implications for therapy development

Systems approaches are needed to recognise the complexity of the biological bases of psychiatric disease.

Development of an automated DNA purification module using a micro-fabricated pillar chip

We present a fully automated DNA purification module comprised of a micro-fabricated chip and sequential injection analysis system that is designed for use within autonomous instruments that continuously monitor the environment for the presence of biological threat agents. The chip has an elliptical flow channel containing a bed (3.5 × 3.5 mm) of silica-coated pillars with height, width and center-to-center spacing of 200, 15, and 30 µm, respectively, which provides a relatively large surface area (ca. 3 cm²) for DNA capture in the presence of chaotropic agents. We have characterized the effect of various fluidic parameters on extraction performance, including sample input volume, capture flow rate, and elution volume. The flow-through design made the pillar chip completely reusable; carryover was eliminated by flushing lines with sodium hypochlorite and deionized water between assays. A mass balance was conducted to determine the fate of input DNA not recovered in the eluent. The device was capable of purifying and recovering Bacillus anthracis genomic DNA (input masses from 0.32 to 320 pg) from spiked environmental aerosol samples, for subsequent analysis using polymerase chain reaction-based assays.

Development of monoclonal antibodies against Vibrio pathogens

Monoclonal antibodies were developed against pathogenic vibrios for use in rapid identification in disease situations of humans, fish and shellfish. Of the 12 fusions performed using V. alginolyticus, V. anguillarum, V. carchariae, V. cholerae, V. damsela, V. furnissii, V. harveyi, V. ordalii, V. parahaemolyticus and V. vulnificus, a total of 102 hybridomas were obtained. Based on cross-reactivity of a wide range of Vibrio strains and other gram-negative bacteria, three broad types of monoclonal antibodies were found. The three categories were: (1) ones that were species-specific or specific to a particular surface antigen, (2) a large number that reacted with several Vibrio species, and (3) three that reacted with most Vibrio strains but no other gram-negative bacteria. Each species-specific monoclonal antibody only recognized its corresponding Vibrio species and was used for identifying unknown species, confirming diagnosis of clinical isolates. In addition, several monoclonal antibodies only cross-reacted with similar Vibrio species, e.g. V. parahaemolyticus and V. alginolyticus which share a common H-antigen. Monoclonal antibodies reacting with several Vibrio species were not of particular use in diagnostic situations. Three monoclonal antibodies of the last group did not react with other genera of the family Vibrionaceae, namely Aeromonas, Photobacterium and Plesiomonas nor a wide range of gram-negative enteric bacteria. These data indicated the existence of an antigenic surface determinant common to Vibrio species. One monoclonal reacted with the heat-stable antigenic determinants on the cell surface as v as lipopolysaccharide extracted from all the vibrios studied, thus making it useful for large- scale screening of acute infections of vibrios. In a blind test, seven Vibrio species, isolated from 6 marine and a freshwater source were identified by two laboratories using phenetic tests. Results of immunotyping using monoclonals, three of seven were diagnosed as the same species, another three were designated as Vibrio species but could not be classified further due to the library not having the corresponding monoclonal, and one was diagnostically questionable. Two further tests were carried out. An unknown Vibrio formalin-fixed isolated from diseased marine animal was identified as V. parahaemolyticus by ELISA and FITC. Clinical human isolates of V. alginolyticus, V. parahaemolyticus and V. vulnificus were confirmed by monoclonals. Australian isolates of V. anguillarum appeared to be mostly of serotype O1. monoclonals raised to V. anguillarum AFHRL 1 reacted with only serotype O1 from Denmark but also most Australian isolates. All vibrios pathogenic to fish and shellfish, i.e. V. anguillarum, V. ordalii, V. alginolyticus, V. carchariae, V. cholerae, V. damsela, V. harveyi, V. parahaemolyticus and V. vulnificus, were used for attachment studies to fish cells using phase contrast and FITC-immunofluorescence microscopy. Of these vibrios, V. anguillarum, V. ordalii and V. perahaemolyticus, were found to adhere to different cells and tissues of rainbow trout while others did not appear to attach. However, attachment was inhibited by monoclonal antibodies specific to only these three vibrios. Lipopolysaccharide is well known as being a contributing factor in pathogenicity of gram-negative bacteria. PAGE electrophoresis of extracted LPS from 9 strains covering 6 Vibrio species showed the presence of a common 15,000 D fragment. This fragment was verified by immunoblotting with a genus-specific monoclonal antibody (i.e. F11P411F) recognizing nearly all vibrios. The common LPS fragment was separated and used to raise polyclonal antisera in mouse which reacted strongly with LPS itself, live as well as sodium azide-killed vibrios, but not with other gram-negative bacteria. This raised the possibility of developing vaccine from Vibrio LPS. Monoclonal antibodies developed in the present study enabled rapid identification of a number of pathogenic Vibrio species. There is still further work to produce monoclonal antibodies against additional vibrios that are probably pathogenic. These included V. fluvialis, V. hollisae, V. metschnikovii, V. minicus, V. salmonella and V. tubiashii. Together the application will be of significance in clinical diagnostic work, in the monitoring of vibriosis in fish farms and in quarantine.

Development of molecular techniques for the genetic analysis of abalone populations

Three DNA techniques: random amplified polymorphic DNA (RAPD), minisatellite, and microsatellite analyses, were developed for use in abalone population genetic structure studies. The techniques were assessed using sample sets of blacklip and greenlip abalone. The study identifies a potential for the application of these DNA markers in abalone fisheries management, but microsatellites are the recommended method for future studies.

Development and evaluation of an ELISA for the detection and 3D antibodies to foot and mouth disease virus

A group specific ELISA (enzyme-linked immunosorbent assay) was developed to detect virus infection associated antibodies in the serum of animals infected with any serotype of foot and mouth disease virus. The assay was developed from non-infectious sources, and is therefore suitable for use in countries where FMDV is exotic.

Characterization of high fluid strain micro contractions to study the stress on biological fluids

Microfluidics has the potential to enhance the understanding of the biological fluids under strain, due to the laminar nature of the fluid and the possibility to mimic the real conditions. We present advances on charaterization of a microfluidic platform to study high strain rate flows in the transport of biological fluids. These advances are improvements on the reproduction of a  constant extensional strain rate using micro contractions and development of 3D numerical models. The micro geometries have been fabricated in polydimethyl siloxame (PDMS) using standard soft-lithography techniques with a photolithographically patterned mold. A comparison of some microcontractions with different funnel characteristics is presented. The Micro Particle Image Velocimetry technique has been applied to validate the numerical simulations. We demonstrate the use of microfluidics in the reproduction of a large range of controllable extensional strains that can be used in the study of the effect of flow on biological fluids.

Carbon nanotubes for biological and biomedical applications

Ever since the discovery of carbon nanotubes, researchers have been exploring their potential in biological and biomedical applications. The recent expansion and availability of chemical modification and bio-functionalization methods have made it possible to generate a new class of bioactive carbon nanotubes which are conjugated with proteins, carbohydrates, or nucleic acids. The modification of a carbon nanotube on a molecular level using biological molecules is essentially an example of the 'bottom-up' fabrication principle of bionanotechnology. The availability of these biomodified carbon nanotube constructs opens up an entire new and exciting research direction in the field of chemical biology, finally aiming to target and to alter the cell's behaviour at the subcellular or molecular level. This review covers the latest advances of bio-functionalized carbon nanotubes with an emphasis on the development of functional biological nano-interfaces. Topics that are discussed herewith include methods for biomodification of carbon nanotubes, the development of hybrid systems of carbon nanotubes and biomolecules for bioelectronics, and carbon nanotubes as transporters for a specific delivery of peptides and/or genetic material to cells. All of these current research topics aim at translating these biotechnology modified nanotubes into potential novel therapeutic approaches.

The self-assembled monolayer modification of electrodes - some recent advances in biological application

The modification of an electrode surface at the molecular level using the technique of depositing self-assembled monolayers (SAM) is a typical example of the techniques used in nanotechnology, from the process "bottom up", which is to create a nanostructure by successive additions of molecular or atomic entities on a surface. This article presents some recent advances in the field, with examples: the development of systems Sat hybridized with biomolecules, nanoparticles or nanotubes in bioelectronics, the use of switchable electrodes to study the adhesion and migration of biological cells , and the integration of molecular son in the SAM to recognize and allow the transduction of a biological response allowing the practice of electrochemistry in a complex biological environment.

Traditional knowledge, biological resources and intellectual property rights in Asia : the example of the Philippines

The relationship between traditional knowledge and intellectual property rights has become a topic for intensive debates at the national level, in various international settings and within and among different UN agencies, including the World Intellectual Property Organisation (WIPO), the UN Food and Agriculture Organisation (FAO), UNESCO, UNCTAD and the United Nations Environment Programme (UNEP). However, a consensus on a definition of traditional knowledge has yet to emerge due to persistent differences in perception. On the one hand, indigenous communities hold locally specific and holistic views of traditional knowledge, which are difficult to place within the framework of current intellectual property rights. Governments of developing countries, on the other hand, mostly focus on clearly defined aspects of traditional knowledge and their interpretation in the national interest and as expressions of national culture. Asian governments, in particular, have advocated the latter view. The Philippines provide an exception due to a tradition of recognising indigenous people as separate "cultural communities". However, the practical implementation of so-called "community intellectual rights" thus far is largely confined to access and benefit sharing rules, compensation requirements for traditional farmers and defensive protection measures such as digital libraries documenting traditional knowledge.

Evolution of JAK-STAT pathway components : mechanisms and role in immune system development

Background
Lying downstream of a myriad of cytokine receptors, the Janus kinase (JAK) – Signal transducer and activator of transcription (STAT) pathway is pivotal for the development and function of the immune system, with additional important roles in other biological systems. To gain further insight into immune system evolution, we have performed a comprehensive bioinformatic analysis of the JAK-STAT pathway components, including the key negative regulators of this pathway, the SH2-domain containing tyrosine phosphatase (SHP), Protein inhibitors against Stats (PIAS), and Suppressor of cytokine signaling (SOCS) proteins across a diverse range of organisms.

Results
Our analysis has demonstrated significant expansion of JAK-STAT pathway components co-incident with the emergence of adaptive immunity, with whole genome duplication being the principal mechanism for generating this additional diversity. In contrast, expansion of upstream cytokine receptors appears to be a pivotal driver for the differential diversification of specific pathway components.

Conclusion
Diversification of JAK-STAT pathway components during early vertebrate development occurred concurrently with a major expansion of upstream cytokine receptors and two rounds of whole genome duplications. This produced an intricate cell-cell communication system that has made a significant contribution to the evolution of the immune system, particularly the emergence of adaptive immunity.

Functional imaging to understand biomechanics : a critical tool for the study of biology, pathology and the development of pharmacological solutions

We present four case studies of the literature discussing the effects of physical forces on biological function. While the field of biomechanics has existed for many decades, it may be considered by some a poor cousin to biochemistry and other traditional fields of medical research. In these case studies, including cardiovascular and respiratory systems, we demonstrate that, in fact, many systems historically believed to be controlled by biochemistry are dominated by biomechanics. We discuss both the previous paradigms that have advanced research in these fields and the changing paradigms that will define the progressions of these fields for decades to come. In the case of biomechanical effects of flowing blood on the endothelium, this has been well understood for decades. In the cases of platelet activation and liquid clearance from the lungs during birth, these discoveries are far more recent and perhaps not as universally accepted. While only a few specific examples are examined here, it is clear that not enough attention is paid to the possible mechanical links to biological function. The continued development of these research areas, with the inclusion of physical effects, will hopefully provide new insight into disease development, progression, diagnosis and effective therapies.

Book review: Understanding human development:a multi-dimensional approach (2nd ed.)

Book review: This book has much to offer social work and human services students. It covers many key theories, ideas, and debates relevant to a wide range of practice fields in a comprehensive, clearly organised, and engaging fashion. The author proposes, as on overarching premise, a “multidimensional” approach to understanding lifespan development and experiences of trauma, stress, and grief, as well as responses of adaptation and resilience across the life course. Consistent with social work values, the multidimensional approach “places an emphasis on the constant interaction of the biological, psychological, and spiritual dimensions of our inner worlds with the relational, social, structural, and cultural dimensions of our outer worlds” (p. 394).

Integrating biological and social values when prioritizing places for biodiversity conservation

The consideration of information on social values in conjunction with biological data is critical for achieving both socially acceptable and scientifically defensible conservation planning outcomes. However, the influence of social values on spatial conservation priorities has received limited attention and is poorly understood. We present an approach that incorporates quantitative data on social values for conservation and social preferences for development into spatial conservation planning. We undertook a public participation GIS survey to spatially represent social values and development preferences and used species distribution models for 7 threatened fauna species to represent biological values. These spatially explicit data were simultaneously included in the conservation planning software Zonation to examine how conservation priorities changed with the inclusion of social data. Integrating spatially explicit information about social values and development preferences with biological data produced prioritizations that differed spatially from the solution based on only biological data. However, the integrated solutions protected a similar proportion of the species' distributions, indicating that Zonation effectively combined the biological and social data to produce socially feasible conservation solutions of approximately equivalent biological value. We were able to identify areas of the landscape where synergies and conflicts between different value sets are likely to occur. Identification of these synergies and conflicts will allow decision makers to target communication strategies to specific areas and ensure effective community engagement and positive conservation outcomes.