RNA Silencing in Plants

RNA silencing-related mechanisms have been documented in almost all living organisms and RNA silencing is now used as board term to describe the vast array of related processes involving RNA–RNA, RNA–DNA, RNA–protein or protein–protein interactions that ultimately result in the repression of gene expression. In plants, the parallel RNA silencing pathways have evolved to extraordinary levels of complexity and diversity, playing crucial roles in providing protection against invading nucleic acids derived from viruses or replicating transposons, controlling chromatin modifications as well as regulating endogenous gene expression to ensure normal plant growth and development. The aims of this chapter are (1) to provide an overview of the initial curious observations of RNA silencing-related phenomena in plants, (2) to outline the parallel gene silencing pathways of plants, and (3) to discuss current applications of RNA silencing technologies to not only study but also modify plant development

Considering research enquiry into biophilic urbanism and office worker productivity

In cities, people spend a significant portion of their time indoors, much of which is in office buildings. The quality and nature of these spaces have the potential to be a strong determinant of people’s health and wellbeing. There is a body of evidence that suggests experiences of nature increase the rate of attention recovery, reduce stress, depression and anxiety, and increase cognitive abilities. Further, the presence of nature inside buildings (such as pot plants and internal green walls) can improve indoor air quality, potentially reducing illness and increasing cognitive function. Urban design that integrates nature into the built environment to provide these benefits, among others, is called ‘biophilic urbanism’ and is the subject of growing international interest and research. The potential for these benefits to increase worker productivity in office buildings is of particular interest, as this could significantly increase the financial performance of office building-based organisations. However, productivity is a complex concept that is difficult to define, and affected by a multitude of factors, which make it difficult to measure. This inability to quantify productivity increases from investments in nature- experiences in office buildings is currently a significant barrier to such investments. Within this context, this paper considers opportunities for research to explore the relationship between office-based nature experiences and productivity, by reviewing existing research in this field and reflecting on the authors’ own experiences. This review has a particular focus on the importance of quantifying this link in order to encourage private property owners to voluntarily integrate nature into buildings to provide city-wide ecosystem service benefits. The paper begins with a contextual overview of how biophilic urbanism can potentially increase worker productivity. Existing methods of measuring and evaluating the performance of biophilic urbanism within the context of office buildings are then explored, along with a discussion of issues with such methods that are currently limiting investment in biophilic urbanism to increase worker productivity and wellbeing. This includes a summary of a survey within a Perth office building to explore the impact of views of nature through a window. Drawing on these insights, the paper makes recommendations regarding opportunities for focusing future investigations to enhance understanding of how biophilic urbanism can contribute to increased wellbeing and productivity in office buildings. This paper builds on work conducted as part of the Sustainable Built Environment National Research Centre Project 1.5, Harnessing the Potential of Biophilic Urbanism in Australia, which considered the role of nature integrated into the built environment in responding to emerging challenges of climate change, resource shortages and population pressures, while providing a host of co- benefits to a range of stakeholders.

Considering research enquiry into biophilic urbanism and office worker productivity

In cities, people spend a significant portion of their time indoors, much of which is in office buildings. The quality and nature of these spaces have the potential to be a strong determinant of people’s health and wellbeing. There is a body of evidence that suggests experiences of nature increase the rate of attention recovery, reduce stress, depression and anxiety, and increase cognitive abilities. Further, the presence of nature inside buildings (such as pot plants and internal green walls) can improve indoor air quality, potentially reducing illness and increasing cognitive function. Urban design that integrates nature into the built environment to provide these benefits, among others, is called ‘biophilic urbanism’ and is the subject of growing international interest and research. The potential for these benefits to increase worker productivity in office buildings is of particular interest, as this could significantly increase the financial performance of office building-based organisations. However, productivity is a complex concept that is difficult to define, and affected by a multitude of factors, which make it difficult to measure. This inability to quantify productivity increases from investments in nature- experiences in office buildings is currently a significant barrier to such investments. Within this context, this paper considers opportunities for research to explore the relationship between office-based nature experiences and productivity, by reviewing existing research in this field and reflecting on the authors’ own experiences. This review has a particular focus on the importance of quantifying this link in order to encourage private property owners to voluntarily integrate nature into buildings to provide city-wide ecosystem service benefits. The paper begins with a contextual overview of how biophilic urbanism can potentially increase worker productivity. Existing methods of measuring and evaluating the performance of biophilic urbanism within the context of office buildings are then explored, along with a discussion of issues with such methods that are currently limiting investment in biophilic urbanism to increase worker productivity and wellbeing. This includes a summary of a survey within a Perth office building to explore the impact of views of nature through a window. Drawing on these insights, the paper makes recommendations regarding opportunities for focusing future investigations to enhance understanding of how biophilic urbanism can contribute to increased wellbeing and productivity in office buildings. This paper builds on work conducted as part of the Sustainable Built Environment National Research Centre Project 1.5, Harnessing the Potential of Biophilic Urbanism in Australia, which considered the role of nature integrated into the built environment in responding to emerging challenges of climate change, resource shortages and population pressures, while providing a host of co- benefits to a range of stakeholders.

Pattern analysis of the diversity of morphological plant attributes and herbage yield in a world collection of white clover (Trifolium repens L.) germplasm characterised in a summer moisture stress environment of Australia

Information on the variation available for different plant attributes has enabled germplasm collections to be effectively utilised in plant breeding. A world sourced collection of white clover germplasm has been developed at the White Clover Resource Centre at Glen Innes, New South Wales. This collection of 439 accessions was characterised under field conditions as a preliminary study of the genotypic variation for morphological attributes; stolon density, stolon branching, number of nodes. number of rooted nodes, stolon thickness, internode length, leaf length, plant height and plant spread, together with seasonal herbage yield. Characterisation was conducted on different batches of germplasm (subsets of accessions taken from the complete collection) over a period of five years. Inclusion of two check cultivars, Haifa and Huia, in each batch enabled adjustment of the characterisation data for year effects and attribute-by-year interaction effects. The component of variance for seasonal herbage yield among batches was large relative to that for accessions. Accession-by-experiment and accession-by-season interactions for herbage yield were not detected. Accession mean repeatability for herbage yield across seasons was intermediate (0.453). The components of genotypic variance among accessions for all attributes, except plant height, were larger than their respective standard errors. The estimates of accession mean repeatability for the attributes ranged from low (0.277 for plant height) to intermediate (0.544 for internode length). Multivariate techniques of clustering and ordination were used to investigate the diversity present among the accessions in the collection. Both cluster analysis and principal component analysis suggested that seven groups of accessions existed. It was also proposed from the pattern analysis results that accessions from a group characterised by large leaves, tall plants and thick stolons could be crossed with accessions from a group that had above average stolon density and stolon branching. This material could produce breeding populations to be used in recurrent selection for the development of white clover cultivars for dryland summer moisture stress environments in Australia. The germplasm collection was also found to be deficient in genotypes with high stolon density, high number of branches high number of rooted nodes and large leaves. This warrants addition of new germplasm accessions possessing these characteristics to the present germplasm collection.

Regional trade-offs between mine water and energy use : a water treatment case study

The mining industry faces concurrent pressures of reducing water use, energy consumption and greenhouse gas (GHG) emissions in coming years. However, the interactions between water and energy use, as well as GHG e missions have largely been neglected in modelling studies to date. In addition, investigations tend to focus on the unit operation scale, with little consideration of whole-of-site or regional scale effects. This paper presents an application of a hierarchical systems model (HSM) developed to represent water, energy and GHG emissions fluxes at scales ranging from the unit operation, to the site level, to the regional level. The model allows for the linkages between water use, energy use and GHG emissions to be examined in a fl exible and intuitive way, so that mine sites can predict energy and emissions impacts of water use reduction schemes and vice versa. This paper examines whether this approach can also be applied to the regional scale with multiple mine sites. The model is used to conduct a case study of several coal mines in the Bowen Basin, Australia, to compare the utility of centralised and decentralised mine water treatment schemes. The case study takes into account geographical factors (such as water pumping distances and elevations), economic factors (such as capital and operating cost curves for desalination treatment plants) and regional factors (such as regionally varying climates and associated variance in mine water volumes and quality). The case study results indicate that treatment of saline mine water incurs a trade-off between water and energy use in all cases. However, significant cost differences between centralised and decentralised schemes can be observed in a simple economic analysis. Further research will examine the possibility for deriving model up-scaling algorithms to reduce computational requirements.

Modelling the water, energy and economic nexus

The mining industry faces three long term strategic risks in relation to its water and energy use: 1) securing enough water and energy to meet increased production; 2) reducing water use, energy consumption and emissions due to social, environmental and economic pressures; and 3) understanding the links between water and energy, so that an improvement in one area does not create an adverse effect in another. This project helps the industry analyse these risks by creating a hierarchical systems model (HSM) that represents the water and energy interactions on a sub-site, site and regional scales; which is coupled with a flexible risk framework. The HSM consists of: components that represent sources of water and energy; activities that use water and energy and off-site destinations of water and produced emissions. It can also represent more complex components on a site, with inbuilt examples including tailings dams and water treatment plants. The HSM also allows multiple sites and other infrastructure to be connected together to explore regional water and energy interactions. By representing water and energy as a single interconnected system the HSM can explore tradeoffs and synergies. For example, on a synthetic case study, which represents a typical site, simulations suggested that while a synergy in terms of water use and energy use could be made when chemical additives were used to enhance dust suppression, there were trade-offs when either thickened tailings or dry processing were used. On a regional scale, the HSM was used to simulate various scenarios, including: mines only withdrawing water when needed; achieving economics-of-scale through use of a single centralised treatment plant rather than smaller decentralised treatment plants; and capturing of fugitive emissions for energy generation. The HSM also includes an integrated risk framework for interpreting model output, so that onsite and off-site impacts of various water and energy management strategies can be compared in a managerial context. The case studies in this report explored company, social and environmental risks for scenarios of regional water scarcity, unregulated saline discharge, and the use of plantation forestry to offset carbon emissions. The HSM was able to represent the non-linear causal relationship at the regional scale, such as the forestry scheme offsetting a small percentage of carbon emissions but causing severe regional water shortages. The HSM software developed in this project will be released as an open source tool to allow industry personnel to easily and inexpensively quantify and explore the links between water use, energy use, and carbon emissions. The tool can be easily adapted to represent specific sites or regions. Case studies conducted in this project highlighted the potential complexity of these links between water, energy, and carbon emissions, as well as the significance of the cumulative effects of these links over time. A deeper understanding of these links is vital for the mining industry in order to progress to more sustainable operations, and the HSM provides an accessible, robust framework for investigating these links.

Diverse urban plantings managed with sufficient resource availability can increase plant productivity and arthropod diversity

Buildings structures and surfaces are explicitly being used to grow plants, and these “urban plantings” are generally designed for aesthetic value. Urban plantings also have the potential to contribute significant “ecological values” by increasing urban habitat for animals such as arthropods and by increasing plant productivity. In this study, we evaluated how the provision of these additional ecological values is affected by plant species richness; the availability of essential resources for plants, such as water, light, space; and soil characteristics. We sampled 33 plantings located on the exterior of three buildings in the urban center of Brisbane, Australia (subtropical climatic region) over 2, 6 week sampling periods characterized by different temperature and rainfall conditions. Plant cover was estimated as a surrogate for productivity as destructive sampling of biomass was not possible. We measured weekly light levels (photosynthetically active radiation), plant CO2 assimilation, soil CO2 efflux, and arthropod diversity. Differences in plant cover were best explained by a three-way interaction of plant species richness, management water regime and sampling period. As the richness of plant species increased in a planter, productivity and total arthropod richness also increased significantly—likely due to greater habitat heterogeneity and quality. Overall we found urban plantings can provide additional ecological values if essential resources are maintained within a planter such as water, light and soil temperature. Diverse urban plantings that are managed with these principles in mind can contribute to the attraction of diverse arthropod communities, and lead to increased plant productivity within a dense urban context.

Development and parameterization of a rain- and fire-driven model for exploring elephant effects in African savannas

We describe the development and parameterization of a grid-based model of African savanna vegetation processes. The model was developed with the objective of exploring elephant effects on the diversity of savanna species and structure, and in this formulation concentrates on the relative cover of grass and woody plants, the vertical structure of the woody plant community, and the distribution of these over space. Grid cells are linked by seed dispersal and fire, and environmental variability is included in the form of stochastic rainfall and fire events. The model was parameterized from an extensive review of the African savanna literature; when available, parameter values varied widely. The most plausible set of parameters produced long-term coexistence between woody plants and grass, with the tree-grass balance being more sensitive to changes in parameters influencing demographic processes and drought incidence and response, while less sensitive to fire regime. There was considerable diversity in the woody structure of savanna systems within the range of uncertainty in tree growth rate parameters. Thus, given the paucity of height growth data regarding woody plant species in southern African savannas, managers of natural areas should be cognizant of different tree species growth and damage response attributes when considering whether to act on perceived elephant threats to vegetation. © 2007 Springer Science+Business Media B.V.

After the gold rush: Patent law and biological inventions

In response to scientific breakthroughs in biotechnology, the development of new technologies, and the demands of a hungry capitalist marketplace, patent law has expanded to accommodate a range of biological inventions. There has been much academic and public debate as to whether gene patents have a positive impact upon research and development, health-care, and the protection of the environment. In a satire of prevailing patenting practices, the English poet and part-time casino waitress, Donna MacLean, sought a patent application - GB0000180.0 - in respect of herself. She explained that she had satisfied the usual patent criteria - in that she was novel, inventive, and useful: It has taken 30 years of hard labor for me to discover and invent myself, and now I wish to protect my invention from unauthorized exploitation, genetic or otherwise. I am new: I have led a private existence and I have not made the invention of myself public. I am not obvious (2000: 18). MacLean said she had many industrial applications. ’For example, my genes can be used in medical research to extremely profitable ends - I therefore wish to have sole control of my own genetic material' (2000: 18). She observed in an interview: ’There's a kind of unpleasant, grasping, greedy atmosphere at the moment around the mapping of the human genome ... I wanted to see if a human being could protect their own genes in law' (Meek, 2000). This special issue of Law in Context charts a new era in the long-standing debate over biological inventions. In the wake of the expansion of patentable subject matter, there has been great strain placed upon patent criteria - such as ’novelty', ’inventive step', and ’utility'. Furthermore, there has been a new focus upon legal doctrines which facilitate access to patented inventions - like the defence of experimental use, the ’Bolar' exception, patent pooling, and compulsory licensing. There has been a concerted effort to renew patent law with an infusion of ethical principles dealing with informed consent and benefit sharing. There has also been a backlash against the commercialisation of biological inventions, and a call by some activists for the abolition of patents on genetic inventions. This collection considers a wide range of biological inventions - ranging from micro-organisms, plants and flowers and transgenic animals to genes, express sequence tags, and research tools, as well as genetic diagnostic tests and pharmaceutical drugs. It is thus an important corrective to much policy work, which has been limited in its purview to merely gene patents and biomedical research. This collection compares and contrasts the various approaches of a number of jurisdictions to the legal problems in respect of biological inventions. In particular, it looks at the complexities of the 1998 European Union Directive on the Legal Protection of Biotechnological Inventions, as well as decisions of member states, such as the Netherlands, and peripheral states, like Iceland. The edition considers US jurisprudence on patent law and policy, as well as recent developments in Canada. It also focuses upon recent developments in Australia - especially in the wake of parallel policy inquiries into gene patents and access to genetic resources.

Intellectual Property and Biotechnology: Biological Inventions

This book documents and evaluates the dramatic expansion of intellectual property law to accommodate various forms of biotechnology from micro-organisms, plants, and animals to human genes and stem cells. It makes a unique theoretical contribution to the controversial public debate over the commercialization of biological inventions. The author also considers the contradictions between the Supreme Court of Canada rulings in respect of the Harvard oncomouse, and genetically modified canola. He explores law, policy, and practice in both Australia and New Zealand in respect to gene patents and non-coding DNA. This study charts the rebellion against the European Union Biotechnology Directive – particularly in respect of Myriad Genetics’ BRCA1 and BRCA2 patents, and stem cell patent applications. The book also considers whether patent law will accommodate frontier technologies – such as bioinformatics, haplotype mapping, proteomics, pharmacogenomics, and nanotechnology. Intellectual Property and Biotechnology will be of prime interest to lawyers and patent attorneys, scientists and researchers, business managers and technology transfer specialists.

Patent law and biological inventions

In response to scientific breakthroughs in biotechnology, the development of new technologies, and the demands of a hungry capitalist marketplace, patent law has expanded to accommodate a range of biological inventions. There has been much academic and public debate as to whether gene patents have a positive impact upon research and development, health-care, and the protection of the environment. In a satire of prevailing patenting practices, the English poet and part-time casino waitress, Donna MacLean, sought a patent application - GB0000180.0 - in respect of herself. She explained that she had satisfied the usual patent criteria - in that she was novel, inventive, and useful: It has taken 30 years of hard labor for me to discover and invent myself, and now I wish to protect my invention from unauthorized exploitation, genetic or otherwise. I am new: I have led a private existence and I have not made the invention of myself public. I am not obvious (2000: 18). MacLean said she had many industrial applications. 'For example, my genes can be used in medical research to extremely profitable ends - I therefore wish to have sole control of my own genetic material' (2000: 18). She observed in an interview: 'There's a kind of unpleasant, grasping, greedy atmosphere at the moment around the mapping of the human genome ... I wanted to see if a human being could protect their own genes in law' (Meek, 2000). This special issue of Law in Context charts a new era in the long-standing debate over biological inventions. In the wake of the expansion of patentable subject matter, there has been great strain placed upon patent criteria - such as 'novelty', 'inventive step', and 'utility'. Furthermore, there has been a new focus upon legal doctrines which facilitate access to patented inventions - like the defence of experimental use, the 'Bolar' exception, patent pooling, and compulsory licensing. There has been a concerted effort to renew patent law with an infusion of ethical principles dealing with informed consent and benefit sharing. There has also been a backlash against the commercialisation of biological inventions, and a call by some activists for the abolition of patents on genetic inventions. This collection considers a wide range of biological inventions - ranging from micro-organisms, plants and flowers and transgenic animals to genes, express sequence tags, and research tools, as well as genetic diagnostic tests and pharmaceutical drugs. It is thus an important corrective to much policy work, which has been limited in its purview to merely gene patents and biomedical research. This collection compares and contrasts the various approaches of a number of jurisdictions to the legal problems in respect of biological inventions. In particular, it looks at the complexities of the 1998 European Union Directive on the Legal Protection of Biotechnological Inventions, as well as decisions of member states, such as the Netherlands, and peripheral states, like Iceland. The edition considers US jurisprudence on patent law and policy, as well as recent developments in Canada. It also focuses upon recent developments in Australia - especially in the wake of parallel policy inquiries into gene patents and access to genetic resources.

Mathematical modeling for improved greenhouse gas balances, agro-ecosystems, and policy development: Lessons from the Australian experience

If the land sector is to make significant contributions to mitigating anthropogenic greenhouse gas (GHG) emissions in coming decades, it must do so while concurrently expanding production of food and fiber. In our view, mathematical modeling will be required to provide scientific guidance to meet this challenge. In order to be useful in GHG mitigation policy measures, models must simultaneously meet scientific, software engineering, and human capacity requirements. They can be used to understand GHG fluxes, to evaluate proposed GHG mitigation actions, and to predict and monitor the effects of specific actions; the latter applications require a change in mindset that has parallels with the shift from research modeling to decision support. We compare and contrast 6 agro-ecosystem models (FullCAM, DayCent, DNDC, APSIM, WNMM, and AgMod), chosen because they are used in Australian agriculture and forestry. Underlying structural similarities in the representations of carbon flows though plants and soils in these models are complemented by a diverse range of emphases and approaches to the subprocesses within the agro-ecosystem. None of these agro-ecosystem models handles all land sector GHG fluxes, and considerable model-based uncertainty exists for soil C fluxes and enteric methane emissions. The models also show diverse approaches to the initialisation of model simulations, software implementation, distribution, licensing, and software quality assurance; each of these will differentially affect their usefulness for policy-driven GHG mitigation prediction and monitoring. Specific requirements imposed on the use of models by Australian mitigation policy settings are discussed, and areas for further scientific development of agro-ecosystem models for use in GHG mitigation policy are proposed.

Spatially explicit perceptions of ecosystem services and land cover change in forested regions of Borneo

Spatially explicit information on local perceptions of ecosystem services is needed to inform land use planning within rapidly changing landscapes. In this paper we spatially modelled local people's use and perceptions of benefits from forest ecosystem services in Borneo, from interviews of 1837 people in 185 villages. Questions related to provisioning, cultural/spiritual, regulating and supporting ecosystem services derived from forest, and attitudes towards forest conversion. We used boosted regression trees (BRTs) to combine interview data with social and environmental predictors to understand spatial variation of perceptions across Borneo. Our results show that people use a variety of products from intact and highly degraded forests. Perceptions of benefits from forests were strongest: in human-altered forest landscapes for cultural and spiritual benefits; in human-altered and intact forests landscapes for health benefits; intact forest for direct health benefits, such as medicinal plants; and in regions with little forest and extensive plantations, for environmental benefits, such as climatic impacts from deforestation. Forest clearing for small scale agriculture was predicted to be widely supported yet less so for large-scale agriculture. Understanding perceptions of rural communities in dynamic, multi-use landscapes is important where people are often directly affected by the decline in ecosystem services.

Field evaluation of micropropagated and conventionally propagated ginger in subtropical Queensland

The growth and performance of micropropagated ginger (Zingiber officinale Roscoe) was compared with 'seed'-derived plants in field trials conducted in south-eastern Queensland. In the first generation ex vitro, micropropagated plants had significantly (P<0.01) reduced rhizome yield with smaller knobs and more roots. Micropropagated plants had a greater (P<0.01) shoot: root (rhizome) ratio compared with seed-derived plants. Shoots from micropropagated plants were also significantly (P<0.01) smaller with a greater number of shoots per plant. The unusual shoot morphology of the micropropagated plants did not appear to be related to the presence of benzylaminopurine, a plant growth hormone added to the multiplication medium, as plants subcultured for 3 cycles on a hormone-free medium also exhibited similar characteristics. Seed collected from the micropropagated plants and seed-derived plants was harvested and, despite the micropropagated seed being significantly (P<0.01) smaller, by the second generation ex vitro there were no significant differences between the treatments. Factors that can improve rhizome size, while reducing production costs, need to be identified before micropropagated plants can be recommended for routine use in the ginger industry as a source of disease and pest-free planting material.

Characterisation and early detection of an offtype from micropropagated Lady Finger bananas

An offtype has been identified from micropropagated Lady Finger bananas (Musa spp., AAB group, Pome subgroup) that is characterised by its slow growth and poor bunch size. Bunch weights were approximately 25% those of normal Lady Finger plants and all of the fruit produced was unmarketable. This particular offtype is the most commonly encountered from micropropagated Lady Finger plants and, in 2 instances, blocks of 3000 and 1500 plants were entirely comprised of this single offtype. Detection of offtype plants was possible during establishment and growth of plants in the glasshouse by the presence of chlorotic streaks in the leaves. In more severe cases the streaks coalesced into chlorotic patches that developed thin, necrotic areas that eventually produced holes or splits in the leaves. Symptom expression was not ameliorated by the addition of fertiliser and even though symptoms were similar to severe Ca and B deficiency, both normal and offtype plants had similar levels of these elements in the leaves. The offtype plants were also slow growing in the glasshouse and produced significantly (P<0.05) smaller pseudostems and leaves than normal plants. Offtype plants could be readily detected after 4 weeks deflasking using the presence of chlorotic streaks in the leaves as the main selection criterion. Maximum discrimination was possible between weeks 5–7 and at the 6-leaf stage when all of the offtypes could be detected.