Are in vitro estimates of cell diffusivity and cell proliferation rate sensitive to assay geometry?

Cells respond to various biochemical and physical cues during wound–healing and tumour progression. In vitro assays used to study these processes are typically conducted in one particular geometry and it is unclear how the assay geometry affects the capacity of cell populations to spread, or whether the relevant mechanisms, such as cell motility and cell proliferation, are somehow sensitive to the geometry of the assay. In this work we use a circular barrier assay to characterise the spreading of cell populations in two different geometries. Assay 1 describes a tumour–like geometry where a cell population spreads outwards into an open space. Assay 2 describes a wound–like geometry where a cell population spreads inwards to close a void. We use a combination of discrete and continuum mathematical models and automated image processing methods to obtain independent estimates of the effective cell diffusivity, D, and the effective cell proliferation rate, λ. Using our parameterised mathematical model we confirm that our estimates of D and λ accurately predict the time–evolution of the location of the leading edge and the cell density profiles for both assay 1 and assay 2. Our work suggests that the effective cell diffusivity is up to 50% lower for assay 2 compared to assay 1, whereas the effective cell proliferation rate is up to 30% lower for assay 2 compared to assay 1.

Analysis of expressed sequence tags from Actinidia : Applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening

Background Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs). Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.

Quality aspects in service ecosystems : areas for exploitation and exploration

Service Science, Management, and Engineering (SSME) is a research area with significant relevance to research and practice. Networked systems of web services are a field of service science that enjoys growing interest from researchers. The complex and dynamic environment of these service ecosystems poses new requirements on quality management that are insufficiently addressed by current approaches that focus mainly on the technical aspects of quality. This focus is a severe limitation for the development of service networks because it neglects perceived service quality from the viewpoint of service consumers. In this paper we propose a reference model for quality management in service ecosystems. This reference model is linked in particular to innovation and new service development. Towards the end we propose premises for the implementation and outline a future research agenda.

Protocol : A highly sensitive RT-PCR method for detection and quantification of microRNAs

MicroRNAs (miRNAs) are a class of small non-coding RNAs with a critical role in development and environmental responses. Efficient and reliable detection of miRNAs is an essential step towards understanding their roles in specific cells and tissues. However, gel-based assays currently used to detect miRNAs are very limited in terms of throughput, sensitivity and specificity. Here we provide protocols for detection and quantification of miRNAs by RT-PCR. We describe an end-point and real-time looped RT-PCR procedure and demonstrate detection of miRNAs from as little as 20 pg of plant tissue total RNA and from total RNA isolated from as little as 0.1 l of phloem sap. In addition, we have developed an alternative real-time PCR assay that can further improve specificity when detecting low abundant miRNAs. Using this assay, we have demonstrated that miRNAs are differentially expressed in the phloem sap and the surrounding vascular tissue. This method enables fast, sensitive and specific miRNA expression profiling and is suitable for facilitation of high-throughput detection and quantification of miRNA expression.

The rurality of sex : community resistance and objection to prostitution in rural and regional areas throughout Queensland

Queensland legislation currently defines two legally recognised forms of prostitution: sex work conducted in a licensed brothel; or, sex work conducted privately by a sole operator.Despite prostitution’s legality in these contexts, it continues to be heavily controlled and restricted by authorities, while also being rejected by surrounding communities. Such resistance towards prostitution is demonstrated in Queensland where over 200 towns with populations of less than 25,000 have been successful in applying for exemption from the development of licensed brothels in those jurisdictions (Prostitution Licensing Authority 2012). Queensland’s legislative acknowledgement of prostitution as a legal act, while simultaneously allowing small communities to reject such activity, seems somewhat contradictory. This paper will provide a theoretical examination of common community objections to prostitution in modern society, determining whether such attitudes are applicable to communities in rural and regional Queensland towns. Additionally, this paper will incorporate an analysis of rural and urban areas via the ‘gemeinschaft‐gesellschaft’ dichotomy to understand the potential justification for opposing areas being subject to differential treatment under the law.

Differences in physical activity between black and white girls living in rural and urban areas

This study examined the relationship of race and rural/urban setting to physical, behavioral, psychosocial, and environmental factors associated with physical activity. Subjects included 1,668 eighth-grade girls from 31 middle schools: 933 from urban settings, and 735 from rural settings. Forty-six percent of urban girls and 59% of rural girls were Black. One-way and two-way ANOVAs with school as a covariate were used to analyze the data. Results indicated that most differences were associated with race rather than setting. Black girls were less active than White girls, reporting significantly fewer 30-minute blocks of both vigorous and moderate-to-vigorous physical activity. Black girls also spent more time watching television, and had higher BMIs and greater prevalence of overweight than White girls. However, enjoyment of physical education and family involvement in physical activity were greater among Black girls titan White girls. Rural White girls and urban Black girls had more favorable attitudes toward physical activity. Access to sports equipment, perceived safety of neighborhood, and physical activity self-efficacy were higher in White girls than Black girls.

DDT resistance and transformation by different microbial strains isolated from DDT-contaminated soils and compost materials

Bioremediation is a potential option to treat 1, 1, 1-trichloro-2, 2 bis (4-chlorophenyl) ethane (DDT) contaminated sites. In areas where suitable microbes are not present, the use of DDT resistant microbial inoculants may be necessary. It is vital that such inoculants do not produce recalcitrant breakdown products e.g. 1, 1-dichloro-2, 2-bis (4-chlorophenyl) ethylene (DDE). Therefore, this work aimed to screen DDT-contaminated soil and compost materials for the presence of DDT-resistant microbes for use as potential inoculants. Four compost amended soils, contaminated with different concentrations of DDT, were used to isolate DDT-resistant microbes in media containing 150 mg I -1 DDT at three temperatures (25, 37 and 55°C). In all soils, bacteria were more sensitive to DDT than actinomycetes and fungi. Bacteria isolated at 55°C from any source were the most DDT sensitive. However DDT-resistant bacterial strains showed more promise in degrading DDT than isolated fungal strains, as 1, 1-dichloro 2, 2-bis (4-chlorophenyl) ethane (DDD) was a major bacterial transformation product, while fungi tended to produce more DDE. Further studies on selected bacterial isolates found that the most promising bacterial strain (Bacillus sp. BHD-4) could remove 51% of DDT from liquid culture after 7 days growth. Of the amount transformed, 6% was found as DDD and 3% as DDE suggesting that further transformation of DDT and its metabolites occurred.

Conceptualising, evaluating and reporting social resilience in vulnerable regional and remote communities facing climate change in tropical Queensland : marine and tropical sciences research facility transition project final report

Regional and remote communities in tropical Queensland are among Australia’s most vulnerable in the face of climate change. At the same time, these socially and economically vulnerable regions house some of Australia’s most significant biodiversity values. Past approaches to terrestrial biodiversity management have focused on tackling biophysical interventions through the use of biophysical knowledge. An equally important focus should be placed on building regional-scale community resilience if some of the worst biodiversity impacts of climate change are to be avoided or mitigated. Despite its critical need, more systemic or holistic approaches to natural resource management have been rarely trialed and tested in a structured way. Currently, most strategic interventions in improving regional community resilience are ad hoc, not theory-based and short term. Past planning approaches have not been durable, nor have they been well informed by clear indicators. Research into indicators for community resilience has been poorly integrated within adaptive planning and management cycles. This project has aimed to resolve this problem by: * Reviewing the community and social resilience and adaptive planning literature to reconceptualise an improved framework for applying community resilience concepts; * Harvesting and extending work undertaken in MTSRF Phase 1 to identifying the learnings emerging from past MTSRF research; * Distilling these findings to identify new theoretical and practical approaches to the application of community resilience in natural resource use and management; * Reconsidering the potential interplay between a region’s biophysical and social planning processes, with a focus on exploring spatial tools to communicate climate change risk and its consequent environmental, economic and social impacts, and; * Trialling new approaches to indicator development and adaptive planning to improve community resilience, using a sub-regional pilot in the Wet Tropics. In doing so, we also looked at ways to improve the use and application of relevant spatial information. Our theoretical review drew upon the community development, psychology and emergency management literature to better frame the concept of community resilience relative to aligned concepts of social resilience, vulnerability and adaptive capacity. Firstly, we consider community resilience as a concept that can be considered at a range of scales (e.g. regional, locality, communities of interest, etc.). We also consider that overall resilience at higher scales will be influenced by resilience levels at lesser scales (inclusive of the resilience of constituent institutions, families and individuals). We illustrate that, at any scale, resilience and vulnerability are not necessarily polar opposites, and that some understanding of vulnerability is important in determining resilience. We position social resilience (a concept focused on the social characteristics of communities and individuals) as an important attribute of community resilience, but one that needs to be considered alongside economic, natural resource, capacity-based and governance attributes. The findings from the review of theory and MTSRF Phase 1 projects were synthesized and refined by the wider project team. Five predominant themes were distilled from this literature, research review and an expert analysis. They include the findings that: 1. Indicators have most value within an integrated and adaptive planning context, requiring an active co-research relationship between community resilience planners, managers and researchers if real change is to be secured; 2. Indicators of community resilience form the basis for planning for social assets and the resilience of social assets is directly related the longer term resilience of natural assets. This encourages and indeed requires the explicit development and integration of social planning within a broader natural resource planning and management framework; 3. Past indicator research and application has not provided a broad picture of the key attributes of community resilience and there have been many attempts to elicit lists of “perfect” indicators that may never be useful within the time and resource limitations of real world regional planning and management. We consider that modeling resilience for proactive planning and prediction purposes requires the consideration of simple but integrated clusters of attributes; 4. Depending on time and resources available for planning and management, the combined use of well suited indicators and/or other lesser “lines of evidence” is more flexible than the pursuit of perfect indicators, and that; 5. Index-based, collaborative and participatory approaches need to be applied to the development, refinement and reporting of indicators over longer time frames. We trialed the practical application of these concepts via the establishment of a collaborative regional alliance of planners and managers involved in the development of climate change adaptation strategies across tropical Queensland (the Gulf, Wet Tropics, Cape York and Torres Strait sub-regions). A focus on the Wet Tropics as a pilot sub-region enabled other Far North Queensland sub-region’s to participate and explore the potential extension of this approach. The pilot activities included: * Further exploring ways to innovatively communicate the region’s likely climate change scenarios and possible environmental, economic and social impacts. We particularly looked at using spatial tools to overlay climate change risks to geographic communities and social vulnerabilities within those communities; * Developing a cohesive first pass of a State of the Region-style approach to reporting community resilience, inclusive of regional economic viability, community vitality, capacitybased and governance attributes. This framework integrated a literature review, expert (academic and community) and alliance-based contributions; and * Early consideration of critical strategies that need to be included in unfolding regional planning activities with Far North Queensland. The pilot assessment finds that rural, indigenous and some urban populations in the Wet Tropics are highly vulnerable and sensitive to climate change and may require substantial support to adapt and become more resilient. This assessment finds that under current conditions (i.e. if significant adaptation actions are not taken) the Wet Tropics as a whole may be seriously impacted by the most significant features of climate change and extreme climatic events. Without early and substantive action, this could result in declining social and economic wellbeing and natural resource health. Of the four attributes we consider important to understanding community resilience, the Wet Tropics region is particularly vulnerable in two areas; specifically its economic vitality and knowledge, aspirations and capacity. The third and fourth attributes, community vitality and institutional governance are relatively resilient but are vulnerable in some key respects. In regard to all four of these attributes, however, there is some emerging capacity to manage the possible shocks that may be associated with the impacts of climate change and extreme climatic events. This capacity needs to be carefully fostered and further developed to achieve broader community resilience outcomes. There is an immediate need to build individual, household, community and sectoral resilience across all four attribute groups to enable populations and communities in the Wet Tropics region to adapt in the face of climate change. Preliminary strategies of importance to improve regional community resilience have been identified. These emerging strategies also have been integrated into the emerging Regional Development Australia Roadmap, and this will ensure that effective implementation will be progressed and coordinated. They will also inform emerging strategy development to secure implementation of the FNQ 2031 Regional Plan. Of most significance in our view, this project has taken a co-research approach from the outset with explicit and direct importance and influence within the region’s formal planning and management arrangements. As such, the research: * Now forms the foundations of the first attempt at “Social Asset” planning within the Wet Tropics Regional NRM Plan review; * Is assisting Local government at regional scale to consider aspects of climate change adaptation in emerging planning scheme/community planning processes; * Has partnered the State government (via the Department of Infrastructure and Planning and Regional Managers Coordination Network Chair) in progressing the Climate Change adaptation agenda set down within the FNQ 2031 Regional Plan; * Is informing new approaches to report on community resilience within the GBRMPA Outlook reporting framework; and * Now forms the foundation for the region’s wider climate change adaptation priorities in the Regional Roadmap developed by Regional Development Australia. Through the auspices of Regional Development Australia, the outcomes of the research will now inform emerging negotiations concerning a wider package of climate change adaptation priorities with State and Federal governments. Next stage research priorities are also being developed to enable an ongoing alliance between researchers and the region’s climate change response.

Managed livestock grazing is compatible with the maintenance of plant diversity in semidesert grasslands

Even when no baseline data are available, the impacts of 150 years of livestock grazing on natural grasslands can be assessed using a combined approach of grazing manipulation and regional-scale assessment of the flora. Here, we demonstrate the efficacy of this method across 18 sites in the semidesert Mitchell grasslands of northeastern Australia. Fifteen-year-old exclosures (ungrazed and macropod grazed) revealed that the dominant perennial grasses in the genus Astrebla do not respond negatively to grazing disturbance typical of commercial pastoralism. Neutral, positive, intermediate, and negative responses to grazing disturbance were recorded amongst plant species with no single life-form group associated with any response type. Only one exotic species, Cenchrus ciliaris, was recorded at low frequency. The strongest negative response was from a native annual grass, Chionachne hubbardiana, an example of a species that is highly sensitive to grazing disturbance. Herbarium records revealed only scant evidence that species with a negative response to grazing have declined through the period of commercial pastoralism. A regional analysis identified 14 from a total of 433 plant species in the regional flora that may be rare and potentially threatened by grazing disturbance. However, a targeted survey precluded grazing as a cause of decline for seven of these based on low palatability and positive responses to grazing and other disturbance. Our findings suggest that livestock grazing of semidesert grasslands with a short evolutionary history of ungulate grazing has altered plant composition, but has not caused declines in the dominant perennial grasses or in species richness as predicted by the preceding literature. The biggest impact of commercial pastoralism is the spread of woody leguminous trees that can transform grassland to thorny shrubland. The conservation of plant biodiversity is largely compatible with commercial pastoralism provided these woody weeds are controlled, but reserves strategically positioned within water remote areas are necessary to protect grazing-sensitive species. This study demonstrates that a combination of experimental studies and regional surveys can be used to understand anthropogenic impacts on natural ecosystems where reference habitat is not available.

Ultra sensitive label free surface enhanced Raman spectroscopy method for the detection of biomolecules

We present a proof of concept for a novel nanosensor for the detection of ultra-trace amounts of bio-active molecules in complex matrices. The nanosensor is comprised of gold nanoparticles with an ultra-thin silica shell and antibody surface attachment, which allows for the immobilization and direct detection of bio-active molecules by surface enhanced Raman spectroscopy (SERS) without requiring a Raman label. The ultra-thin passive layer (~1.3 nm thickness) prevents competing molecules from binding non-selectively to the gold surface without compromising the signal enhancement. The antibodies attached on the surface of the nanoparticles selectively bind to the target molecule with high affinity. The interaction between the nanosensor and the target analyte result in conformational rearrangements of the antibody binding sites, leading to significant changes in the surface enhanced Raman spectra of the nanoparticles when compared to the spectra of the un-reacted nanoparticles. Nanosensors of this design targeting the bio-active compounds erythropoietin and caffeine were able to detect ultra-trace amounts the analyte to the lower quantification limits of 3.5×10−13 M and 1×10−9 M, respectively.

Highly NO2 sensitive caesium doped graphene oxide conductometric sensors

Here we report on the synthesis of caesium doped graphene oxide (GO-Cs) and its application to the development of a novel NO2 gas sensor. The GO, synthesized by oxidation of graphite through chemical treatment, was doped with Cs by thermal solid-state reaction. The samples, dispersed in DI water by sonication, have been drop-casted on standard interdigitated Pt electrodes. The response of both pristine and Cs doped GO to NO2 at room temperature is studied by varying the gas concentration. The developed GO-Cs sensor shows a higher response to NO2 than the pristine GO based sensor due to the oxygen functional groups. The detection limit measured with GO-Cs sensor is ≈90 ppb.

A control theoretic paradigm for cell signaling networks : a simple complexity for a sensitive robustness

The fields of molecular biology and cell biology are being flooded with complex genomic and proteomic datasets of large dimensions. We now recognize that each molecule in the cell and tissue can no longer be viewed as an isolated entity. Instead, each molecule must be considered as one member of an interacting network. Consequently, there is an urgent need for mathematical models to understand the behavior of cell signaling networks in health and in disease.

Effective control of ion fluxes over large areas by magnetic fields : from narrow beams to highly uniform fluxes

An effective control of the ion current distribution over large-area (up to 103 cm2) substrates with the magnetic fields of a complex structure by using two additional magnetic coils installed under the substrate exposed to vacuum arc plasmas is demonstrated. When the magnetic field generated by the additional coils is aligned with the direction of the magnetic field generated by the guiding and focusing coils of the vacuum arc source, a narrow ion density distribution with the maximum current density 117 A m-2 is achieved. When one of the additional coils is set to generate the magnetic field of the opposite direction, an area almost uniform over the substrate of 103 cm2 ion current distribution with the mean value of 45 A m-2 is achieved. Our findings suggest that the system with the vacuum arc source and two additional magnetic coils can be effectively used for the effective, high throughput, and highly controllable plasma processing.

Nanoparticle manipulation in the near-substrate areas of low-temperature, high-density rf plasmas

Manipulation of a single nanoparticle in the near-substrate areas of high-density plasmas of low-temperature glow discharges is studied. It is shown that the nanoparticles can be efficiently manipulated by the thermophoretic force controlled by external heating of the substrate stage. Particle deposition onto or repulsion from nanostructured carbon surfaces critically depends on the values of the neutral gas temperature gradient in the near-substrate areas, which is directly measured in situ in different heating regimes by originally developed temperature gradient probe. The measured values of the near-surface temperature gradient are used in the numerical model of nanoparticle dynamics in a variable-length presheath. Specific conditions enabling the nanoparticle to overcome the repulsive potential and deposit on the substrate during the discharge operation are investigated. The results are relevant to fabrication of various nanostructured films employing structural incorporation of the plasma-grown nanoparticles, in particular, to nanoparticle deposition in the plasma-enhanced chemical-vapor deposition of carbon nanostructures in hydrocarbon-based plasmas.

Compatibility of stormwater treatment performance data between different geographical areas

Using a case study approach, this paper presents a robust methodology for assessing the compatibility of stormwater treatment performance data between two geographical regions in relation to a treatment system. The desktop analysis compared data derived from a field study undertaken in Florida, USA, with South East Queensland (SEQ) rainfall and pollutant characteristics. The analysis was based on the hypothesis that when transposing treatment performance information from one geographical region to another, detailed assessment of specific rainfall and stormwater quality parameters is required. Accordingly, characteristics of measured rainfall events and stormwater quality in the Florida study were compared with typical characteristics for SEQ. Rainfall events monitored in the Florida study were found to be similar to events that occur in SEQ in terms of their primary characteristics of depth, duration and intensity. Similarities in total suspended solids (TSS) and total nitrogen (TN) concentration ranges for Florida and SEQ suggest that TSS and TN removal performances would not be very different if the treatment system is installed in SEQ. However, further investigations are needed to evaluate the treatment performance of total phosphorus (TP). The methodology presented also allows comparison of other water quality parameters.