A coupled SPH-DEM model for micro-scale structural deformations of plant cells during drying

A single plant cell was modeled with smoothed particle hydrodynamics (SPH) and a discrete element method (DEM) to study the basic micromechanics that govern the cellular structural deformations during drying. This two-dimensional particle-based model consists of two components: a cell fluid model and a cell wall model. The cell fluid was approximated to a highly viscous Newtonian fluid and modeled with SPH. The cell wall was treated as a stiff semi-permeable solid membrane with visco-elastic properties and modeled as a neo-Hookean solid material using a DEM. Compared to existing meshfree particle-based plant cell models, we have specifically introduced cell wall–fluid attraction forces and cell wall bending stiffness effects to address the critical shrinkage characteristics of the plant cells during drying. Also, a moisture domain-based novel approach was used to simulate drying mechanisms within the particle scheme. The model performance was found to be mainly influenced by the particle resolution, initial gap between the outermost fluid particles and wall particles and number of particles in the SPH influence domain. A higher order smoothing kernel was used with adaptive smoothing length to improve the stability and accuracy of the model. Cell deformations at different states of cell dryness were qualitatively and quantitatively compared with microscopic experimental findings on apple cells and a fairly good agreement was observed with some exceptions. The wall–fluid attraction forces and cell wall bending stiffness were found to be significantly improving the model predictions. A detailed sensitivity analysis was also done to further investigate the influence of wall–fluid attraction forces, cell wall bending stiffness, cell wall stiffness and the particle resolution. This novel meshfree based modeling approach is highly applicable for cellular level deformation studies of plant food materials during drying, which characterize large deformations.

Differential subcellular and extracellular localisations of proteins required for insulin-like growth factor- and extracellular matrix-induced signalling events in breast cancer progression

Background: Cancer metastasis is the main contributor to breast cancer fatalities as women with the metastatic disease have poorer survival outcomes than women with localised breast cancers. There is an urgent need to develop appropriate prognostic methods to stratify patients based on the propensities of their cancers to metastasise. The insulin-like growth factor (IGF)-I:IGF binding protein (IGFBP):vitronectin complexes have been shown to stimulate changes in gene expression favouring increased breast cancer cell survival and a migratory phenotype. We therefore investigated the prognostic potential of these IGF- and extracellular matrix (ECM) interaction-induced proteins in the early identification of breast cancers with a propensity to metastasise using patient-derived tissue microarrays. Methods: Semiquantitative immunohistochemistry analyses were performed to compare the extracellular and subcellular distribution of IGF- and ECM-induced signalling proteins among matched normal, primary cancer and metastatic cancer formalin-fixed paraffin-embedded breast tissue samples. Results: The IGF- and ECM-induced signalling proteins were differentially expressed between subcellular and extracellular localisations. Vitronectin and IGFBP-5 immunoreactivity was lower while β1 integrin immunoreactivity was higher in the stroma surrounding metastatic cancer tissues, as compared to normal breast and primary cancer stromal tissues. Similarly, immunoreactive stratifin was found to be increased in the stroma of primary as well as metastatic breast tissues. Immunoreactive fibronectin and β1 integrin was found to be highly expressed at the leading edge of tumours. Based on the immunoreactivity it was apparent that the cell signalling proteins AKT1 and ERK1/2 shuffled from the nucleus to the cytoplasm with tumour progression. Conclusion: This is the first in-depth, compartmentalised analysis of the distribution of IGF- and ECM-induced signalling proteins in metastatic breast cancers. This study has provided insights into the changing pattern of cellular localisation and expression of IGF- and ECM-induced signalling proteins in different stages of breast cancer. The differential distribution of these biomarkers could provide important prognostic and predictive indicators that may assist the clinical management of breast disease, namely in the early identification of cancers with a propensity to metastasise, and/or recur following adjuvant therapy.

Three dimensional digitisation of plant leaves

Realistic plant models are important for leaf area and plant volume estimation, reconstruction of growth canopies, structure generation of the plant, reconstruction of leaf surfaces and agrichemical spray droplet modelling. This article investigates several different scanning devices for obtaining a three dimensional digitisation of plant leaves with a point cloud resolution of 200-500μm. The devices tested were a Roland mdx-20, Microsoft Kinect, Roland lpx-250, Picoscan and Artec S. The applicability of each of these devices for scanning plant leaves is discussed. The most suitable tested digitisation device for scanning plant leaves is the Artec S scanner.

Calculation of the oxygen isotope discrimination factor for studying plant respiration

Measurement of discrimination against 18O during dark respiration in plants is currently accepted as the only reliable method of estimating the partitioning of electrons between the cytochrome and alternative pathways. In this paper, we review the theory of the technique and its application to a gas-phase system. We extend it to include sampling effects and show that the isotope discrimination factor, D, is calculated as –dln(1 + δ)/dlnO*, where δ is isotopic composition of the substrate oxygen and O*=[O2]/[N2] in a closed chamber containing tissue respiring in the dark. It is not necessary to integrate the expression but, if the integrated form is used, the resultant regression should not be constrained through the origin. This is important since any error in D will have significant effects on the estimation of the flux of electrons through the two pathways.

Priority threat management of invasive plant species in the Lake Eyre Basin

This project is led by scientists in conservation decision appraisal and brings together a group of experts working across the Lake Eyre Basin (LEB). The LEB covers a sixth of Australia, with an array of globally significant natural values that are threatened by invasive plants, among other things. Managers at various levels are investing in attempts to control, contain and eradicate these invasive plant species, under severe time and resources limitations. To date there has been no basin-wide assessment of which weed management strategies and locations provide the best investments for maximising outcomes for biodiversity per unit cost. Further, there has been no assessment of the extent of ecosystem intactness that may be lost without effective invasive plant species management strategies. Given that there are insufficient resources to manage all invasive plant species everywhere, this information has the potential to improve current investment decisions. Here, we provide a prioritisation of invasive plant management strategies in the LEB. Prioritisation was based on cost-effectiveness for biodiversity benefits. We identify the key invasive plant species to target to protect ecosystem intactness across the bioregions of the LEB, the level of investment required and the likely reduction in invasive species dominance gained per dollar spent on each strategy. Our focus is on strategies that are technically and socially feasible and reduce the likelihood that high impact invasive plant species will dominate native ecosystems, and therefore change their form and function. The outputs of this work are designed to help guide decision-making and further planning and investment in weed management for the Basin. Experts in weed management, policy-making, community engagement, biodiversity and natural values of the Basin, attended a workshop and agreed upon 12 strategies to manage invasive plants. The strategies focused primarily on 10 weeds which were considered to have a high potential for broad, significant impacts on natural ecosystems in the next 50 years and for which feasible management strategies could be defined. Each strategy consisted of one or more supporting actions, many of which were spatially linked to IBRA (Interim Biogeographical Regionalisation of Australia) bioregions. The first strategy was an over-arching recommendation for improved mapping, information sharing, education and extension efforts in order to facilitate the more specific weed management strategies. The 10 more specific weed management strategies targeted the control and/or eradication of the following high-impact exotic plants: mesquite, parkinsonia, rubber vine, bellyache bush, cacti, mother of millions, chinee apple, athel pine and prickly acacia, as well as a separate strategy for eradicating all invasive plants from one key threatened ecological community, the GAB (Great Artesian Basin dependant) mound springs. Experts estimated the expected biodiversity benefit of each strategy as the reduction in area that an invasive plant species is likely to dominate in over a 50-year period, where dominance was defined as more than 30% coverage at a site. Costs were estimated in present day terms over 50 years largely during follow up discussions post workshop. Cost-effectiveness was then calculated for each strategy in each bioregion by dividing the average expected benefit by the average annual costs. Overall, the total cost of managing 12 invasive plant strategies over the next 50 years was estimated at $1.7 billion. It was estimated that implementation of these strategies would result in a reduction of invasive plant dominance by 17 million ha (a potential 32% reduction), roughly 14% of the LEB. If only targeting Weeds of National Significance (WONS), the total cost was estimated to be $113 million over the next 50 years. Over the next 50 years, $2.3 million was estimated to eradicate all invasive plant species from the Great Artesian Basin Mound Springs threatened ecological community. Prevention and awareness programs were another key strategy targeted across the Basin and estimated at $17.5 million in total over 50 years. The cost of controlling, eradicating and containing buffel grass were the most expensive, over $1.5 billion over 50 years; this strategy was estimated to result in a reduction in buffel grass dominance of a million ha in areas where this species is identified as an environmental problem. Buffel grass has been deliberately planted across the Basin for pasture production and is by far the most widely distributed exotic species. Its management is contentious, having economic value to many graziers while posing serious threats to biodiversity and sites of high cultural and conservation interest. The strategy for containing and locally eradicating buffel grass was a challenge to cost based on expert knowledge, possibly because of the dual nature of this species as a valued pastoral grass and environmental weed. Based on our conversations with experts, it appears that control and eradication programs for this species, in conservation areas, are growing rapidly and that information on the most cost-effective strategies for this species will continue to develop over time. The top five most cost-effective strategies for the entire LEB were for the management of: 1) parkinsonia, 2) chinee apple, 3) mesquite, 4) rubber vine and 5) bellyache bush. Chinee apple and mother of millions are not WONS and have comparatively small populations within the semi-arid bioregions of Queensland. Experts felt that there was an opportunity to eradicate these species before they had the chance to develop into high-impact species within the LEB. Prickly acacia was estimated to have one of the highest benefits, but the costs of this strategy were high, therefore it was ranked 7th overall. The buffel grass strategy was ranked the lowest (10th) in terms of cost effectiveness. The top five most cost-effective strategies within and across the bioregions were the management of: 1) parkinsonia in the Channel Country, 2) parkinsonia in the Desert Uplands, 3) mesquite in the Mitchell Grass Downs, 4) parkinsonia in the Mitchell Grass Downs, and 5) mother of millions in the Desert Uplands. Although actions for several invasive plant species like parkinsonia and prickly acacia were concentrated in the Queensland part of the LEB, the actions involved investing in containment zones to prevent the spread of these species into other states. In the NT and SA bioregions of the LEB, the management of athel pine, parkinsonia and cacti were the main strategies. While outside the scientific research goals of study, this work highlighted a number of important incidental findings that led us to make the following recommendations for future research and implementation of weed management in the Basin: • Ongoing stakeholder engagement, extension and participation is required to ensure this prioritisation effort has a positive impact in affecting on-ground decision making and planning. • Short term funding for weed management was identified as a major reason for failure of current efforts, hence future funding needs to be secure and ongoing. • Improved mapping and information sharing is essential to implement effective weed management. • Due to uncertainties in the outcomes and impacts of management options, strategies should be implemented as part of an adaptive management program. The information provided in this report can be used to guide investment for controlling high-impact invasive plant species for the benefits of biodiversity conservation. We do not present a final prioritisation of invasive plant strategies for the LEB, and we have not addressed the cultural, socio-economic or spatial components necessary for an implementation plan. Cost-effectiveness depends on the objectives used; in our case we used the intactness of ecosystems as a surrogate for expected biodiversity benefits, measured by the extent that each invasive plant species is likely to dominate in a bioregion. When other relevant factors for implementation are considered the priorities may change and some actions may not be appropriate in some locations. We present the costs, ecological benefits and cost-effectiveness of preventing, containing, reducing and eradicating the dominance of high impact invasive plants through realistic management actions over the next 50 years. In doing so, we are able to estimate the size of the weed management problem in the LEB and provide expert-based estimates of the likely outcomes and benefits of implementing weed management strategies. The priorities resulting from this work provide a prospectus for guiding further investment in management and in improving information availability.

A robust methodology for developing an operational systems view of mine water interactions

The Minerals Council of Australia’s (MCA) Water Accounting Framework (WAF) is an industry lead initiative to enable cross company communication and comparisons of water management performance. The WAF consists of two models, the Input-Output Model that represents water interactions between an operation and its surrounding environment and the Operational Model that represents water interactions within an operation. Recently, MCA member companies have agreed to use the Input-Output Model to report on their external water interactions in Australian operations, with some adopting it globally. The next step will be to adopt the Operational Model. This will expand the functionality of the WAF from corporate reporting to allowing widespread identification of inefficiencies and to connect internal and external interactions. Implementing the WAF, particularly the Operational Model, is non-trivial. It can be particularly difficult for operations that are unfamiliar with the WAF definitions and methodology, lack information pertaining to flow volumes or contain unusual configurations. Therefore, there is a need to help industry with its implementation. This work presents a step-by-step guide to producing the Operational Model. It begins by describing a methodology for implementing the Operational Model by describing the identification of pertinent objects (stores, tasks and treatments), quantification of flows, aggregation of objects and production of reports. It then discusses how the Operational Model can represent a series of challenging scenarios and how it can be connected with Input-Output Model to improve water management.

Determinants of plant performance dynamics : empirical analysis of the manufacturing sector in Indonesia, 1990-2000

We identify determinants of plant dynamics and find their differences before, during, and after the Asian financial crisis. The results show that the distinction of the crisis is important and the effects of the crisis do not seem to persist after 1998. Furthermore, we reject Gibrat's law as the right functional form to describe plant growth. We are not able to support empirically the theoretical results that smaller and efficient plants tend to grow faster than larger and inefficient plants with the exception of the crisis period. The results reflect that there was a trickle down effect of economic development.

An integrated modeling and risk analysis tool for mine water interactions

Poor mine water management can lead to corporate, environmental and social risks. These risks become more pronounced as mining operations move into areas of water scarcity and/or increase climatic variability while also managing increased demand, lower ore grades and increased strip ratios. Therefore, it is vital that mine sites better understand these risks in order to implement management practices to address them. Systems models provide an effective approach to understand complex networks, particularly across multiple scales. Previous work has represented mine water interactions using systems model on a mine site scale. Here, we expand on that work by present an integrated tool that uses a systems modeling approach to represent mine water interactions on a site and regional scale and then analyses the risks associated with events stemming from those interactions. A case study is presented to represent three indicative corporate, environmental and social risks associated with a mine site that exists in a water scarce region. The tool is generic and flexible, and can be used in many scenarios to provide significant potential utility to the mining industry.

miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.

Web mediated market interactions and enterprise software

With increased consolidation and a few large vendors dominating the market, how can software vendors distinguish themselves in order to maintain profitability and gain market share? Increasingly customers are becoming more proactive in selecting a vendor and a product, drawing upon various publications, market surveys, mailing lists, and, of course, other users. In particular, though, a company's Web site is the obvious place to begin information gathering. In sum, it may seem that the days of the uninformed customer prepared to be "sold to" are potentially all but gone.

Understanding Heliothine (Lepidoptera: Heliothinae) pests: What is a host plant?

Heliothine moths (Lepidoptera: Heliothinae) include some of the world's most devastating pest species. Whereas the majority of nonpest heliothinae specialize on a single plant family, genus, or species, pest species are highly polyphagous, with populations often escalating in size as they move from one crop species to another. Here, we examine the current literature on heliothine host-selection behavior with the aim of providing a knowledge base for research scientists and pest managers. We review the host relations of pest heliothines, with a particular focus on Helicoverpa armigera (Hubner), the most economically damaging of all heliothine species. We then consider the important question of what constitutes a host plant in these moths, and some of the problems that arise when trying to determine host plant status from empirical studies on host use. The top six host plant families in the two main Australian pest species (H. armigera and Helicoverpa punctigera Wallengren) are the same and the top three (Asteraceae, Fabaceae, and Malvaceae) are ranked the same (in terms of the number of host species on which eggs or larvae have been identified), suggesting that these species may use similar cues to identify their hosts. In contrast, for the two key pest heliothines in the Americas, the Fabaceae contains approximate to 1/3 of hosts for both. For Helicoverpa zea (Boddie), the remaining hosts are more evenly distributed, with Solanaceae next, followed by Poaceae, Asteraceae, Malvaceae, and Rosaceae. For Heliothis virescens (F.), the next highest five families are Malvaceae, Asteraceae, Solanaceae, Convolvulaceae, and Scrophulariaceae. Again there is considerable overlap in host use at generic and even species level. H. armigera is the most widely distributed and recorded from 68 plant families worldwide, but only 14 families are recorded as a containing a host in all geographic areas. A few crop hosts are used throughout the range as expected, but in some cases there are anomalies, perhaps because host plant relation studies are not comparable. Studies on the attraction of heliothines to plant odors are examined in the context of our current understanding of insect olfaction, with the aim of better understanding the connection between odor perception and host choice. Finally, we discuss research into sustainable management of pest heliothines using knowledge of heliothine behavior and ecology. A coordinated international research effort is needed to advance our knowledge on host relations in widely distributed polyphagous species instead of the localized, piecemeal approaches to understanding these insects that has been the norm to date.

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.

Application of meshfree methods to numerically simulate microscale deformations of different plant food materials during drying

Plant food materials have a very high demand in the consumer market and therefore, improved food products and efficient processing techniques are concurrently being researched in food engineering. In this context, numerical modelling and simulation techniques have a very high potential to reveal fundamentals of the underlying mechanisms involved. However, numerical modelling of plant food materials during drying becomes quite challenging, mainly due to the complexity of the multiphase microstructure of the material, which undergoes excessive deformations during drying. In this regard, conventional grid-based modelling techniques have limited applicability due to their inflexible grid-based fundamental limitations. As a result, meshfree methods have recently been developed which offer a more adaptable approach to problem domains of this nature, due to their fundamental grid-free advantages. In this work, a recently developed meshfree based two-dimensional plant tissue model is used for a comparative study of microscale morphological changes of several food materials during drying. The model involves Smoothed Particle Hydrodynamics (SPH) and Discrete Element Method (DEM) to represent fluid and solid phases of the cellular structure. Simulation are conducted on apple, potato, carrot and grape tissues and the results are qualitatively and quantitatively compared and related with experimental findings obtained from the literature. The study revealed that cellular deformations are highly sensitive to cell dimensions, cell wall physical and mechanical properties, middle lamella properties and turgor pressure. In particular, the meshfree model is well capable of simulating critically dried tissues at lower moisture content and turgor pressure, which lead to cell wall wrinkling. The findings further highlighted the potential applicability of the meshfree approach to model large deformations of the plant tissue microstructure during drying, providing a distinct advantage over the state of the art grid-based approaches.

Numerical simulation of micro-scale morphological changes of plant food materials during drying - a meshfree approach

This thesis developed a high preforming alternative numerical technique to investigate microscale morphological changes of plant food materials during drying. The technique is based on a novel meshfree method, and is more capable of modeling large deformations of multiphase problem domains, when compared with conventional grid-based numerical modeling techniques. The developed cellular model can effectively replicate dried tissue morphological changes such as shrinkage and cell wall wrinkling, as influenced by moisture reduction and turgor loss.