Numerical investigation of plant tissue porosity and its influence on cellular level shrinkage during drying

Dried plant food products are increasing in demand in the consumer market, leading to continuing research to develop better products and processing techniques. Plant materials are porous structures, which undergo large deformations during drying. For any given food material, porosity and other cellular parameters have a direct influence on the level of shrinkage and deformation characteristics during drying, which involve complex mechanisms. In order to better understand such mechanisms and their interrelationships, numerical modelling can be used as a tool. In contrast to conventional grid-based modelling techniques, it is considered that meshfree methods may have a higher potential for modelling large deformations of multiphase problem domains. This work uses a meshfree based microscale plant tissue drying model, which was recently developed by the authors. Here, the effects of porosity have been newly accounted for in the model with the objective of studying porosity development during drying and its influence on shrinkage at the cellular level. For simplicity, only open pores are modelled and in order to investigate the influence of different cellular parameters, both apple and grape tissues were used in the study. The simulation results indicated that the porosity negatively influences shrinkage during drying and the porosity decreases as the moisture content reduces (when open pores are considered). Also, there is a clear difference in the deformations of cells, tissues and pores, which is mainly influenced by the cell wall contraction effects during drying.

In silico biology : making the most of parallel computing

Biological systems are typically complex and adaptive, involving large numbers of entities, or organisms, and many-layered interactions between these. System behaviour evolves over time, and typically benefits from previous experience by retaining memory of previous events. Given the dynamic nature of these phenomena, it is non-trivial to provide a comprehensive description of complex adaptive systems and, in particular, to define the importance and contribution of low-level unsupervised interactions to the overall evolution process. In this chapter, the authors focus on the application of the agent-based paradigm in the context of the immune response to HIV. Explicit implementation of lymph nodes and the associated lymph network, including lymphatic chain structure, is a key objective, and requires parallelisation of the model. Steps taken towards an optimal communication strategy are detailed.

Complexity and high-end computing in biology and medicine

Biomedical systems involve a large number of entities and intricate interactions between these. Their direct analysis is, therefore, difficult, and it is often necessary to rely on computational models. These models require significant resources and parallel computing solutions. These approaches are particularly suited, given parallel aspects in the nature of biomedical systems. Model hybridisation also permits the integration and simultaneous study of multiple aspects and scales of these systems, thus providing an efficient platform for multidisciplinary research.

From bio-inspired computing to e-Biology

Several algorithms and techniques widely used in Computer Science have been adapted from, or inspired by, known biological phenomena. This is a consequence of the multidisciplinary background of most early computer scientists. The field has now matured, and permits development of tools and collaborative frameworks which play a vital role in advancing current biomedical research. In this paper, we briefly present examples of the former, and elaborate upon two of the latter, applied to immunological modelling and as a new paradigm in gene expression.

Numerical investigation of case hardening of plant tissue during dying and its influence on the cellular level shrinkage

Dried plant food materials are one of the major contributors to the global food industry. Widening the fundamental understanding on different mechanisms of food material alterations during drying assists the development of novel dried food products and processing techniques. In this regard, case hardening is an important phenomenon, commonly observed during the drying processes of plant food materials, which significantly influences the product quality and process performance. In this work, a recent meshfree-based numerical model of the authors is further improved and used to simulate the influence of case hardening on shrinkage characteristics of plant tissues during drying. In order to model fluid and wall mechanisms in each cell, Smoothed Particle Hydrodynamics (SPH) and the Discrete Element Method (DEM) are used. The model is fundamentally more capable of simulating large deformation of multiphase materials, when compared with conventional grid-based modelling techniques such as Finite Element Methods (FEM) or Finite Difference Methods (FDM). Case hardening is implemented by maintaining distinct moisture levels in the different cell layers of a given tissue. In order to compare and investigate different factors influencing tissue deformations under case hardening, four different plant tissue varieties (apple, potato, carrot and grape) are studied. The simulation results indicate that the inner cells of any given tissue undergo limited shrinkage and cell wall wrinkling compared to the case hardened outer cell layers of the tissues. When comparing unique deformation characteristics of the different tissues, irrespective of the normalised moisture content, the cell size, cell fluid turgor pressure and cell wall characteristics influence the tissue response to case hardening.

The combination of plant-expressed cellobiohydrolase and low dosages of cellulases for the hydrolysis of sugar cane bagasse

Background The expression of biomass-degrading enzymes (such as cellobiohydrolases) in transgenic plants has the potential to reduce the costs of biomass saccharification by providing a source of enzymes to supplement commercial cellulase mixtures. Cellobiohydrolases are the main enzymes in commercial cellulase mixtures. In the present study, a cellobiohydrolase was expressed in transgenic corn stover leaf and assessed as an additive for two commercial cellulase mixtures for the saccharification of pretreated sugar cane bagasse obtained by different processes. Results Recombinant cellobiohydrolase in the senescent leaves of transgenic corn was extracted using a simple buffer with no concentration step. The extract significantly enhanced the performance of Celluclast 1.5 L (a commercial cellulase mixture) by up to fourfold on sugar cane bagasse pretreated at the pilot scale using a dilute sulfuric acid steam explosion process compared to the commercial cellulase mixture on its own. Also, the extracts were able to enhance the performance of Cellic CTec2 (a commercial cellulase mixture) up to fourfold on a range of residues from sugar cane bagasse pretreated at the laboratory (using acidified ethylene carbonate/ethylene glycol, 1-butyl-3-methylimidazolium chloride, and ball-milling) and pilot (dilute sodium hydroxide and glycerol/hydrochloric acid steam explosion) scales. We have demonstrated using tap water as a solvent (under conditions that mimic an industrial process) extraction of about 90% recombinant cellobiohydrolase from senescent, transgenic corn stover leaf that had minimal tissue disruption. Conclusions The accumulation of recombinant cellobiohydrolase in senescent, transgenic corn stover leaf is a viable strategy to reduce the saccharification cost associated with the production of fermentable sugars from pretreated biomass. We envisage an industrial-scale process in which transgenic plants provide both fibre and biomass-degrading enzymes for pretreatment and enzymatic hydrolysis, respectively.

Product stability and sequestration mechanisms in Solanum tuberosum engineered to biosynthesize high value ketocarotenoids

To produce commercially valuable ketocarotenoids in Solanum tuberosum, the 4, 4′ β-oxygenase (crtW) and 3, 3′ β-hydroxylase (crtZ) genes from Brevundimonas spp. have been expressed in the plant host under constitutive transcriptional control. The CRTW and CRTZ enzymes are capable of modifying endogenous plant carotenoids to form a range of hydroxylated and ketolated derivatives. The host (cv. Désirée) produced significant levels of nonendogenous carotenoid products in all tissues, but at the apparent expense of the economically critical metabolite, starch. Carotenoid levels increased in both wild-type and transgenic tubers following cold storage; however, stability during heat processing varied between compounds. Subcellular fractionation of leaf tissues revealed the presence of ketocarotenoids in thylakoid membranes, but not predominantly in the photosynthetic complexes. A dramatic increase in the carotenoid content of plastoglobuli was determined. These findings were corroborated by microscopic analysis of chloroplasts. In tuber tissues, esterified carotenoids, representing 13% of the total pigment found in wild-type extracts, were sequestered in plastoglobuli. In the transgenic tubers, this proportion increased to 45%, with esterified nonendogenous carotenoids in place of endogenous compounds. Conversely, nonesterified carotenoids in both wild-type and transgenic tuber tissues were associated with amyloplast membranes and starch granules.

Evaluating unmanned aircraft systems for deployment in plant biosecurity

This report provides a qualitative evaluation of Unmanned Aircraft Systems (UAS) and on-board sensor technology for use in plant biosecurity in the Australian context. The more general term UAS describes both the Unmanned Aerial Vehicle (UAV) and all supporting components required to operate it. This may include a ground station, operator or pilot, and a launch and recovery device for example. The focus is to identify how and under what circumstances UAS may be useful for plant biosecurity. This can be used to help guide future decisions regarding investment in UAS for plant biosecurity.

An Australian native plant: A novel antimicrobial for the treatment of MRSA

Chronic wounds, often associated with venous and arterial ulcers, diabetes and pressure sores, is an area of great concern. In Australia, the cost of treating chronic wounds is conservatively estimated at $285 million/annum for the treatment of pressure ulcers and $654 million annually for the treatment and management of leg ulcers. Current figures indicate that more than seven million people suffer from chronic wounds worldwide with Australians accounting for approximately 600,000 of this number. Bacterial infection of the wound site is a major issue as contamination of a chronic wound with methicillin-resistant Staphylococcus aureus (MRSA) significantly delays wound healing. Further, once systemic, current antibiotic therapies capable of treating the infection are limited. Aboriginal bush medicine has been used for thousands of years for the treatment of wounds and sores. Hence, we selected a native Australian plant to evaluate its bactericidal activity against MRSA.

Inventing life: Intellectual property and the new biology

In 2009, the National Research Council of the National Academies released a report on A New Biology for the 21st Century. The council preferred the term ‘New Biology’ to capture the convergence and integration of the various disciplines of biology. The National Research Council stressed: ‘The essence of the New Biology, as defined by the committee, is integration—re-integration of the many sub-disciplines of biology, and the integration into biology of physicists, chemists, computer scientists, engineers, and mathematicians to create a research community with the capacity to tackle a broad range of scientific and societal problems.’ They define the ‘New Biology’ as ‘integrating life science research with physical science, engineering, computational science, and mathematics’. The National Research Council reflected: 'Biology is at a point of inflection. Years of research have generated detailed information about the components of the complex systems that characterize life––genes, cells, organisms, ecosystems––and this knowledge has begun to fuse into greater understanding of how all those components work together as systems. Powerful tools are allowing biologists to probe complex systems in ever greater detail, from molecular events in individual cells to global biogeochemical cycles. Integration within biology and increasingly fruitful collaboration with physical, earth, and computational scientists, mathematicians, and engineers are making it possible to predict and control the activities of biological systems in ever greater detail.' The National Research Council contended that the New Biology could address a number of pressing challenges. First, it stressed that the New Biology could ‘generate food plants to adapt and grow sustainably in changing environments’. Second, the New Biology could ‘understand and sustain ecosystem function and biodiversity in the face of rapid change’. Third, the New Biology could ‘expand sustainable alternatives to fossil fuels’. Moreover, it was hoped that the New Biology could lead to a better understanding of individual health: ‘The New Biology can accelerate fundamental understanding of the systems that underlie health and the development of the tools and technologies that will in turn lead to more efficient approaches to developing therapeutics and enabling individualized, predictive medicine.’ Biological research has certainly been changing direction in response to changing societal problems. Over the last decade, increasing awareness of the impacts of climate change and dwindling supplies of fossil fuels can be seen to have generated investment in fields such as biofuels, climate-ready crops and storage of agricultural genetic resources. In considering biotechnology’s role in the twenty-first century, biological future-predictor Carlson’s firm Biodesic states: ‘The problems the world faces today – ecosystem responses to global warming, geriatric care in the developed world or infectious diseases in the developing world, the efficient production of more goods using less energy and fewer raw materials – all depend on understanding and then applying biology as a technology.’ This collection considers the roles of intellectual property law in regulating emerging technologies in the biological sciences. Stephen Hilgartner comments that patent law plays a significant part in social negotiations about the shape of emerging technological systems or artefacts: 'Emerging technology – especially in such hotbeds of change as the life sciences, information technology, biomedicine, and nanotechnology – became a site of contention where competing groups pursued incompatible normative visions. Indeed, as people recognized that questions about the shape of technological systems were nothing less than questions about the future shape of societies, science and technology achieved central significance in contemporary democracies. In this context, states face ongoing difficulties trying to mediate these tensions and establish mechanisms for addressing problems of representation and participation in the sociopolitical process that shapes emerging technology.' The introduction to the collection will provide a thumbnail, comparative overview of recent developments in intellectual property and biotechnology – as a foundation to the collection. Section I of this introduction considers recent developments in United States patent law, policy and practice with respect to biotechnology – in particular, highlighting the Myriad Genetics dispute and the decision of the Supreme Court of the United States in Bilski v. Kappos. Section II considers the cross-currents in Canadian jurisprudence in intellectual property and biotechnology. Section III surveys developments in the European Union – and the interpretation of the European Biotechnology Directive. Section IV focuses upon Australia and New Zealand, and considers the policy responses to the controversy of Genetic Technologies Limited’s patents in respect of non-coding DNA and genomic mapping. Section V outlines the parts of the collection and the contents of the chapters.

Climate-ready crops: Intellectual property, agriculture, and climate change

In The Climate Change Review, Ross Garnaut emphasised that ‘Climate change and climate change mitigation will bring about major structural change in the agriculture, forestry and other land use sectors’. He provides this overview of the effects of climate change on food demand and supply: ‘Domestic food production in many developing countries will be at immediate risk of reductions in agricultural productivity due to crop failure, livestock loss, severe weather events and new patterns of pests and diseases.’ He observes that ‘Changes to local climate and water availability will be key determinants of where agricultural production occurs and what is produced.’ Gert Würtenberger has commented that modern plant breeding is particularly concerned with addressing larger issues about nutrition, food security and climate change: ‘Modern plant breeding has an increasing importance with regard to the continuously growing demand for plants for nutritional and feeding purposes as well as with regard to renewal energy sources and the challenges caused by climate changes.’ Moreover, he notes that there is a wide array of scientific and technological means of breeding new plant varieties: ‘Apart from classical breeding, technologies have an important role in the development of plants that satisfy the various requirements that industrial and agricultural challenges expect to be fulfilled.’ He comments: ‘Plant variety rights, as well as patents which protect such results, are of increasingly high importance to the breeders and enterprises involved in plant development programmes.’ There has been larger interest in the intersections between sustainable agriculture, environmental protection and food security. The debate over agricultural intellectual property is a polarised one, particularly between plant breeders, agricultural biotechnology companies and a range of environmentalist groups. Susan Sell comments that there are complex intellectual property battles surrounding agriculture: 'Seeds are at the centre of a complex political dynamic between stakeholders. Access to seeds concerns the balance between private rights and public obligations, private ownership and the public domain, and commercial versus humanitarian objectives.' Part I of this chapter considers debates in respect of plant breeders’ rights, food security and climate change in relation to the UPOV Convention 1991. Part II explores efforts by agricultural biotechnology companies to patent climate-ready crops. Part III considers the report of the Special Rapporteur for Food, Olivier De Schutter. It looks at a variety of options to encourage access to plant varieties with climate adaptive or mitigating properties.

The doomsday vault: Seed banks, food security, and climate change

"It could easily provide the back-drop for a James Bond movie. Deep inside a mountain near the North Pole, down a fortified tunnel, and behind airlocked doors in a vault frozen to -18 degrees Celsius, scientists are squirreling away millions of seed samples. The samples constitute the very foundation of agriculture, the biological diversity needed so the world's major food crops can adapt to the next pest or disease, or to climate change. It's little wonder that the Svalbard Global Seed Vault has captured the public's imagination more than almost any agricultural topic in recent years. Popular press reports about the ‘Doomsday Vault,’ however, typically mask the complexity of the endeavor and, if anything, underestimate its practical utility." Cary Fowler This chapter considers the use of seed banks to address concerns about intellectual property, climate change and food security. It has a number of themes. First of all, it is interested in the use of ‘Big Science’ projects to address pressing global scientific concerns and Millennium Development Goals. Second, it highlights the increasing use of banks as a means of managing both property and intellectual property across a wide range of fields of agriculture and biotechnology. Third, it considers the linkage of intellectual property, access to genetic resources and benefit sharing. There are a variety of positions in this debate. Some see requirements in respect of access to genetic resources and benefit sharing as an inconvenient burden for science and commerce. Others defend access to genetic resources and benefit sharing as meaningful and productive. Those inclined to somewhat more conspiratorial views suggest that access to genetic resources and benefit sharing are a ruse to facilitate biopiracy. This chapter has a number of components. Section I focuses upon the Consultative Group on International Agricultural Research (CGIAR) network – often raised as a model for Climate Innovation Centres. Section II considers the Svalbard Global Seed Vault – the so-called Doomsday Vault. After a consideration of the World Summit on Food Security in 2009, it is concluded in this chapter that any future international agreement on climate change needs to address intellectual property, plant genetic resources and food security.

Franklin Barley: Patent law and plant breeders’ rights

This paper considers the relationship between patent law and plant breeders' rights in light of modern developments in biotechnology. It examines how a number of superior courts have sought to manage the tensions and conflicts between these competing schemes of intellectual property protection. Part 1 considers the High Court of Australia case of Grain Pool of Western Australia v the Commonwealth dealing with Franklin barley. Part 2 examines the significance of the Supreme Court of the United States decision in JEM Ag Supply Inc v Pioneer Hi-Bred International Inc with respect to utility patents and hybrid seed. Part 3 considers the Supreme Court of Canada case of Harvard College v the Commissioner of Patents dealing with the transgenic animal, oncomouse, and discusses its implications for the forthcoming appeal from the Federal Court case of Percy Schmeiser v Monsanto.

Plant species’ origin predicts dominance and response to nutrient enrichment and herbivores in global grasslands

Exotic species dominate many communities; however the functional significance of species’ biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental nutrient addition increases the cover and richness of exotic species, nutrients decrease native diversity and cover. Native and exotic species also differ in their response to vertebrate consumer exclusion. These results suggest that species origin has functional significance, and that eutrophication will lead to increased exotic dominance in grasslands.

Inventing life: Patent law and synthetic biology

With promises of improved medical treatments, greener energy and even artificial life, the field of synthetic biology has captured the public imagination and attracted significant government and commercial investment. This excitement reached a crescendo on 21 May 2010, when scientists at the J Craig Venter Institute in the United States announced that they had made a “self-replicating synthetic bacterial cell”. This was the first living cell to have an entirely human-made genome, which means that all of the cell’s characteristics were controlled by a DNA sequence designed by scientists. This achievement in biological engineering was made possible by combining molecular biotechnology, gene synthesis technology and information technology.