Limitations of a laboratory scale model in predicting optimal pilot scale conditions for dilute acid pretreatment of sugarcane bagasse

Pilot and industrial scale dilute acid pretreatment data can be difficult to obtain due to the significant infrastructure investment required. Consequently, models of dilute acid pretreatment by necessity use laboratory scale data to determine kinetic parameters and make predictions about optimal pretreatment conditions at larger scales. In order for these recommendations to be meaningful, the ability of laboratory scale models to predict pilot and industrial scale yields must be investigated. A mathematical model of the dilute acid pretreatment of sugarcane bagasse has previously been developed by the authors. This model was able to successfully reproduce the experimental yields of xylose and short chain xylooligomers obtained at the laboratory scale. In this paper, the ability of the model to reproduce pilot scale yield and composition data is examined. It was found that in general the model over predicted the pilot scale reactor yields by a significant margin. Models that appear very promising at the laboratory scale may have limitations when predicting yields on a pilot or industrial scale. It is difficult to comment whether there are any consistent trends in optimal operating conditions between reactor scale and laboratory scale hydrolysis due to the limited reactor datasets available. Further investigation is needed to determine whether the model has some efficacy when the kinetic parameters are re-evaluated by parameter fitting to reactor scale data, however, this requires the compilation of larger datasets. Alternatively, laboratory scale mathematical models may have enhanced utility for predicting larger scale reactor performance if bulk mass transport and fluid flow considerations are incorporated into the fibre scale equations. This work reinforces the need for appropriate attention to be paid to pilot scale experimental development when moving from laboratory to pilot and industrial scales for new technologies.

Defining the InstaBooth: Facilitating debate and content creation from situated users

Through ubiquitous computing and location-based social media, information is spreading outside the traditional domains of home and work into the urban environment. Digital technologies have changed the way people relate to the urban form supporting discussion on multiple levels, allowing more citizens to be heard in new ways (Fredericks et al. 2013; Houghton et al. 2014; Caldwell et al. 2013). Face-to-face and digitally mediated discussions, facilitated by tangible and hybrid interaction, such as multi-touch screens and media façades, are initiated through a telephone booth inspired portable structure: The InstaBooth. The InstaBooth prototype employs a multidisciplinary approach to engage local communities in a situated debate on the future of their urban environment. With it, we capture citizens’ past stories and opinions on the use and design of public places. The way public consultations are currently done often engages only a section of the population involved in a proposed development; the more vocal citizens are not necessarily the more representative of the communities (Jenkins 2006). Alternative ways to engage urban dwellers in the debate about the built environment are explored at the moment, including the use of social media or online tools (Foth 2009). This project fosters innovation by providing pathways for communities to participate in the decision making process that informs the urban form. The InstaBooth promotes dialogue and mediation between a bottom-up and a top-down approach to urban design, with the aim of promoting community connectedness with the urban environment. The InstaBooth provides an engagement and discussion platform that leverages a number of locally developed display and interaction technologies in order to facilitate a dialogue of ideas and commentary. The InstaBooth combines multiple interaction techniques into a hybrid (digital and analogue) media space. Through the InstaBooth, urban design and architectural proposals are displayed encouraging commentary from visitors. Inside the InstaBooth, visitors can activate a multi-touch screen in order to browse media, write a note, or draw a picture to provide feedback. The purpose of the InstaBooth is to engage with a broader section of society, including those who are often marginalised. The specific design of the internal and external interfaces, the mutual relationship between these interfaces with regards to information display and interaction, and the question how visitors can engage with the system, are part of the research agenda of the project.

In the Solanaceae, a hierarchy of bHLHs confer distinct target specificity to the anthocyanin regulatory complex

The anthocyanin biosynthetic pathway is regulated by a transcription factor complex consisting of an R2R3 MYB, a bHLH, and a WD40. Although R2R3 MYBs belonging to the anthocyanin-activating class have been identified in many plants, and their role well elucidated, the subgroups of bHLH implicated in anthocyanin regulation seem to be more complex. It is not clear whether these potential bHLH partners are biologically interchangeable with redundant functions, or even if heterodimers are involved. In this study, AcMYB110, an R2R3 MYB isolated from kiwifruit (Actinidia sp.) showing a strong activation of the anthocyanin pathway in tobacco (Nicotiana tabacum) was used to examine the function of interacting endogenous bHLH partners. Constitutive expression of AcMYB110 in tobacco leaves revealed different roles for two bHLHs, NtAN1 and NtJAF13. A hierarchical mechanism is shown to control the regulation of transcription factors and consequently of the anthocyanin biosynthetic pathway. Here, a model is proposed for the regulation of the anthocyanin pathway in Solanaceous plants in which AN1 is directly involved in the activation of the biosynthetic genes, whereas JAF13 is involved in the regulation of AN1 transcription.

An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in arabidopsis

Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms.

Plant biology: Coding in non-coding RNAs

The discovery of peptides encoded by what were thought to be non-coding – or 'junk' – regions of precursors to microRNA sequences reveals a new layer of gene regulation. These sequences may not be junk, after all.

Molecular characterisation and carotenoid quantification of pro-vitamin A biofortified genetically modified bananas in Uganda

In Uganda, a significant proportion of the population depends on the micronutrient poor East African highland banana as a food staple. Consequently, micronutrient deficiencies such as vitamin A deficiency are an important health concern in the country. To reach most vulnerable rural poor populations, staple crops can be biofortified with essential micronutrients though conventional breeding or genetic engineering. This thesis provided proof of concept that genetically modified East African highland bananas with enhanced provitamin A levels can be generated and fully characterised in Uganda. In addition, provitamin A levels present in popular banana varieties was documented.

Design of a lightweight, modular robotic vehicle for the sustainable intensification of broadacre agriculture

This thesis presents the design process and the prototyping of a lightweight, modular robotic vehicle for the sustainable intensification of broadacre agriculture. Achieved by the joint operation of multiple autonomous vehicles to improve energy consumption, reduce labour, and increase efficiency in the application of inputs for the management of crops. The Small Robotic Farm Vehicle (SRFV) is a lightweight and energy efficient robotic vehicle with a configurable, modular design. It is capable of undertaking a range of agricultural tasks, including fertilising and weed management through mechanical intervention and precision spraying, whilst being more than an order of magnitude lower in weight than existing broadacre agricultural equipment.

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.

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.

Japonica rice: Intellectual property, scientific publishing and data-sharing

This article examines a series of controversies within the life sciences over data sharing. Part 1 focuses upon the agricultural biotechnology firm Syngenta publishing data on the rice genome in the journal Science, and considers proposals to reform scientific publishing and funding to encourage data sharing. Part 2 examines the relationship between intellectual property rights and scientific publishing, in particular copyright protection of databases, and evaluates the declaration of the Human Genome Organisation that genomic databases should be global public goods. Part 3 looks at varying opinions on the information function of patent law, and then considers the proposals of Patrinos and Drell to provide incentives for private corporations to release data into the public domain.

Managing milling train operation and performance

This paper discusses the main milling train management tasks necessary for maintaining good extraction performance through a season. The main activities discussed are making week by week decisions about shredder and mill setting adjustments, and selecting preseason mill settings. To maintain satisfactory milling train extraction performance, the main factors affecting extraction should be examined: cane preparation with pol in open cells or shredder torque, delivery nip compaction through the load or torque controller outputs such as roll lift, feed chute flap position or pressure feeder to mill speed ratio, and added water rate. To select mill settings for the coming season, delivery nip compaction and feed chute exit compaction can be inferred from the previous seasons.

Modelling milling train performance

This paper describes recent updates to a milling train extraction model used to assess and predict the performance of a milling train. An extension was made to the milling unit model for the bagasse mills to replace the imbibition coefficient with crushing factor and mixing efficiency. New empirical relationships for reabsorption factor, imbibition coefficient, crushing factor, mixing efficiency and purity ratio were developed. The new empirical relationships were tested against factory measurements and previous model predictions. The updated model has been implemented in the SysCAD process modelling software. New additions to the model implementation include: a shredder model to assess or predict cane preparation, mill and shredder drives for power consumption and an updated imbibition control system to add allow water to be added to intermediate mills.

SOTrain: A new program for training supervisors and operators in Australian sugar factories

The provision of effective training of supervisors and operators is essential if sugar factories are to operate profitably and in an environmentally sustainable and safe manner. The benefits of having supervisor and operator staff with a high level of operational skills are reduced stoppages, increased recovery, improved sugar quality, reduced damage to equipment, and reduced OH&S and environmental impacts. Training of new operators and supervisors in factories has traditionally relied on on-the-job training of the new or inexperienced staff by experienced supervisors and operators, supplemented by courses conducted by contractors such as Sugar Research Institute (SRI). However there is clearly a need for staff to be able to undertake training at any time, drawing on the content of online courses as required. An improved methodology for the training of factory supervisors and operators has been developed by QUT on behalf of a syndicate of mills. The new methodology provides ‘at factory’ learning via self-paced modules. Importantly, the training resources for each module are designed to support the training programs within sugar factories, thereby establishing a benchmark for training across the sugar industry. The modules include notes, training guides and session plans, guidelines for walkthrough tours of the stations, learning activities, resources such as videos, animations, job aids and competency assessments. The materials are available on the web for registered users in Australian Mills and many activities are best undertaken online. Apart from a few interactive online resources, the materials for each module can also be downloaded. The acronym SOTrain (Supervisor and Operator Training) has been applied to the new training program.

A Web-based system enabling the integration, analysis, and 3D sub-surface visualization of groundwater monitoring data and geological models

The 3D Water Chemistry Atlas is an intuitive, open source, Web-based system that enables the three-dimensional (3D) sub-surface visualization of ground water monitoring data, overlaid on the local geological model (formation and aquifer strata). This paper firstly describes the results of evaluating existing virtual globe technologies, which led to the decision to use the Cesium open source WebGL Virtual Globe and Map Engine as the underlying platform. Next it describes the backend database and search, filtering, browse and analysis tools that were developed to enable users to interactively explore the groundwater monitoring data and interpret it spatially and temporally relative to the local geological formations and aquifers via the Cesium interface. The result is an integrated 3D visualization system that enables environmental managers and regulators to assess groundwater conditions, identify inconsistencies in the data, manage impacts and risks and make more informed decisions about coal seam gas extraction, waste water extraction, and water reuse.