Development of a pilot-scale bacterial fermentation for plasmid-based biopharmaceutical production using a stoichiometric medium

The recognition of the potential efficacy of plasmid DNA (pDNA) molecules as vectors in the treatment and prevention of emerging diseases has birthed the confidence to combat global pandemics. This is due to the close-to-zero safety concern associated with pDNA vectors compared to viral vectors in cell transfection and targeting. Considerable attention has been paid to the potential of pDNA vectors but comparatively less thought has been given to the practical challenges in producing large quantities to meet current rising demands. A pilot-scale fermentation scheme was developed by employing a stoichiometrically-designed growth medium whose exceptional plasmid yield performance was attested in a shake flask environment for pUC19 and pEGFP-N1 transformed into E. coliDH5α and E. coliJM109, respectively. Batch fermentation of E. coliDH5α-pUC19 employing the stoichiometric medium displayed a maximum plasmid volumetric and specific yield of 62.6 mg/L and 17.1 mg/g (mg plasmid/g dry cell weight), respectively. Fed-batch fermentation of E. coliDH5α-pUC19 on a glycerol substrate demonstrated one of the highest ever reported pilot-scale plasmid specific yield of 48.98 mg/g and a volumetric yield of 0.53 g/L. The attainment of high plasmid specific yields constitutes a decrease in plasmid manufacturing cost and enhances the effectiveness of downstream processes by reducing the proportion of intracellular impurities. The effect of step-rise temperature induction was also considered to maximize ColE1-origin plasmid replication.

Large-scale habitat mapping using vision-based AUVs : experiences, challenges & vehicle design

This paper overviews the development of a vision-based AUV along with a set of complementary operational strategies to allow reliable autonomous data collection in relatively shallow water and coral reef environments. The development of the AUV, called Starbug, encountered many challenges in terms of vehicle design, navigation and control. Some of these challenges are discussed with focus on operational strategies for estimating and reducing the total navigation error when using lower-resolution sensing modalities. Results are presented from recent field trials which illustrate the ability of the vehicle and associated operational strategies to enable rapid collection of visual data sets suitable for marine research applications.

Scale adaptive tracking using mean shift and efficient feature matching

The mean shift tracker has achieved great success in visual object tracking due to its efficiency being nonparametric. However, it is still difficult for the tracker to handle scale changes of the object. In this paper, we associate a scale adaptive approach with the mean shift tracker. Firstly, the target in the current frame is located by the mean shift tracker. Then, a feature point matching procedure is employed to get the matched pairs of the feature point between target regions in the current frame and the previous frame. We employ FAST-9 corner detector and HOG descriptor for the feature matching. Finally, with the acquired matched pairs of the feature point, the affine transformation between target regions in the two frames is solved to obtain the current scale of the target. Experimental results show that the proposed tracker gives satisfying results when the scale of the target changes, with a good performance of efficiency.

Green criminology : reflections, connections, horizons

This paper traces aspects of the development of a ‘green’ criminology. It starts with personal reflections and then describes the emergence of explicit statements of a green criminological perspective. Initially these statements were independently voiced, in different parts of the world but they reflected shared concerns. These works have found unification as a ‘green’, ‘eco-global’ or ‘conservation’ criminology. The paper reviews the classifications available when talking about not only legally-defined crimes but also legally perpetrated harms, as well as typologies of such harms and crimes. It then looks at the integration of ‘green’ and ‘traditional’ criminological thinking before briefly exploring four dimensions of concern for today and the future.

Green Cultural Criminology : Constructions of Environmental Harm, Consumerism, and Resistance to Ecocide

Over the last two decades, "green criminology" has emerged as a unique area of study, bringing together criminologists and sociologists from a wide range of research backgrounds and varying theoretical orientations. It spans the micro to the macro—from individual-level environmental crimes and victimization to business/corporate violations and state transgressions. There have been few attempts, however, to explicitly or implicitly integrate cultural criminology into green criminology (or vice versa). This book moves towards articulating a green cultural criminological perspective. Brisman and South examine existing overlapping research and offer a platform to support future excursions by green criminologists into cultural criminology’s concern with media images and representations, consumerism and consumption, and resistance. At the same time, they offer an invitation to cultural criminologists to adopt a green view of the consumption landscape and the growth (and depictions) of environmental harms.

Cross-scale biophysics modelling of F-actin cytoskeleton in cell

This thesis is a comparative study of the modelling of mechanical behaviours of F-actin cytoskeleton which is an important structural component in living cells. A new granular model was developed for F-actin cytoskeleton based on the concept of multiscale modelling. This framework overcomes difficulties encountered in physical modelling of cytoskeleton in conventional continuum mechanics modelling, and the computational challenges in all-atom molecular dynamics simulation. The thermostat algorithm was further modified to better predict the thermodynamic properties of F-actin cytoskeleton in modelling. This multiscale modelling framework was applied in explaining the physical mechanisms of cytoskeleton responses to external mechanical loads.

Green-fluorescent protein facilitates rapid in vivo detection of genetically transformed plant cells

Early detection of plant transformation events is necessary for the rapid establishment and optimization of plant transformation protocols. We have assessed modified versions of the green fluorescent protein (GFP) from Aequorea victoria as early reporters of plant transformation using a dissecting fluorescence microscope with appropriate filters. Gfp-expressing cells from four different plant species (sugarcane, maize, lettuce, and tobacco) were readily distinguished, following either Agrobacterium-mediated or particle bombardment-mediated transformation. The identification of gfp-expressing sugarcane cells allowed for the elimination of a high proportion of non-expressing explants and also enabled visual selection of dividing transgenic cells, an early step in the generation of transgenic organisms. The recovery of transgenic cell clusters was streamlined by the ability to visualize gfp-expressing tissues in vitro.

Development and validation of the Self-Gifting Consumer Behaviour scale

Self-gifting consumer behaviour (SGCB) is on the rise as consumers seek reward and therapeutic benefits from their shopping experiences. SGCB is defined as personally symbolic, self-communication through special indulgences, which tend to be premeditated and highly context bound. Prior research into the measurement of this growing behavioural phenomenon has been fragmented because of differences in conceptualisation. This research builds upon the prior literature and through a series of qualitative and quantitative studies, develops a valid, multidimensional measure of SGCB that will be useful for future quantitative inquiry into self-gifting consumption.

The validity of personal disturbance scale (DSSI/sAD) in people with diabetes mellitus, using longitudinal data

Despite being used since 1976, Delusions-Symptoms-States-Inventory/states of Anxiety and Depression (DSSI/sAD) has not yet been validated for use among people with diabetes. The aim of this study was to examine the validity of the personal disturbance scale (DSSI/sAD) among women with diabetes using Mater-University of Queensland Study of Pregnancy (MUSP) cohort data. The DSSI subscales were compared against DSM-IV disorders, the Mental Component Score of the Short Form 36 (SF-36 MCS), and Center for Epidemiologic Studies Depression Scale (CES-D). Factor analyses, odds ratios, receiver operating characteristic (ROC) analyses and diagnostic efficiency tests were used to report findings. Exploratory factor analysis and fit indices confirmed the hypothesized two-factor model of DSSI/sAD. We found significant variations in the DSSI/sAD domain scores that could be explained by CES-D (DSSI-Anxiety: 55%, DSSI-Depression: 46%) and SF-36 MCS (DSSI-Anxiety: 66%, DSSI-Depression: 56%). The DSSI subscales predicted DSM-IV diagnosed depression and anxiety disorders. The ROC analyses show that although the DSSI symptoms and DSM-IV disorders were measured concurrently the estimates of concordance remained only moderate. The findings demonstrate that the DSSI/sAD items have similar relationships to one another in both the diabetes and non-diabetes data sets which therefore suggest that they have similar interpretations.

Dynamic agent composition for large-scale agent-based models

PURPOSE: This paper describes dynamic agent composition, used to support the development of flexible and extensible large-scale agent-based models (ABMs). This approach was motivated by a need to extend and modify, with ease, an ABM with an underlying networked structure as more information becomes available. Flexibility was also sought after so that simulations are set up with ease, without the need to program. METHODS: The dynamic agent composition approach consists in having agents, whose implementation has been broken into atomic units, come together at runtime to form the complex system representation on which simulations are run. These components capture information at a fine level of detail and provide a vast range of combinations and options for a modeller to create ABMs. RESULTS: A description of the dynamic agent composition is given in this paper, as well as details about its implementation within MODAM (MODular Agent-based Model), a software framework which is applied to the planning of the electricity distribution network. Illustrations of the implementation of the dynamic agent composition are consequently given for that domain throughout the paper. It is however expected that this approach will be beneficial to other problem domains, especially those with a networked structure, such as water or gas networks. CONCLUSIONS: Dynamic agent composition has many advantages over the way agent-based models are traditionally built for the users, the developers, as well as for agent-based modelling as a scientific approach. Developers can extend the model without the need to access or modify previously written code; they can develop groups of entities independently and add them to those already defined to extend the model. Users can mix-and-match already implemented components to form large-scales ABMs, allowing them to quickly setup simulations and easily compare scenarios without the need to program. The dynamic agent composition provides a natural simulation space over which ABMs of networked structures are represented, facilitating their implementation; and verification and validation of models is facilitated by quickly setting up alternative simulations.

Reconceptualizing green infrastructure for climate change adaptation: Barriers to adoption and drivers for uptake by spatial planners

Urban green infrastructure can help cities adapt to climate change. Spatial planning can play an important role in utilizing green infrastructure for adaptation. Yet climate change risks represent a different sort of challenge for planning institutions. This paper aims to address two issues arising from this challenge. First, it defines the concept of green infrastructure within the context of climate adaptation. Second, it identifies and puts into perspective institutional barriers to adopting green infrastructure for climate adaptation, including path dependence. We begin by arguing that there is growing confusion among planners and policy makers about what constitutes green infrastructure. Definitional ambiguity may contribute to inaction on climate change adaptation, because it muddies existing programs and initiatives that are to do with green-space more broadly, which in turn feeds path dependency. We then report empirical findings about how planners perceive the institutional challenge arising from climate change and the adoption of green infrastructure as an adaptive response. The paper concludes that spatial planners generally recognize multiple rationales associated with green infrastructure. However they are not particularly keen on institutional innovation and there is a tendency for path dependence. We propose a conceptual model that explicitly recognizes such institutional factors. This paper contributes to the literature by showing that agency and institutional dimensions are a limiting factor in advancing the concept of green infrastructure within the context of climate change adaptation.

Building cross-scale models of epigenetic mechanisms

Epigenetic changes correspond to heritable modifications of the chromosome structure, which do not involve alteration of the DNA sequence but do affect gene expression. These mechanisms play an important role in normal cell differentiation, but aberration is associated also with several diseases, including cancer and neural disorders. In consequence, despite intensive studies in recent years, the contribution of modifications remains largely unquantified due to overall system complexity and insufficient data. Computational models can provide powerful auxiliary tools to experimentation, not least as scales from the sub-cellular through cell populations (or to networks of genes) can be spanned. In this paper, the challenges to development, of realistic cross-scale models, are discussed and illustrated with respect to current work.

Bioaerosols associated with industrial green waste composting facilities and optimal microbiological indicators

This project developed and assessed a standard operating procedure for monitoring microbiological aerosol levels and dispersal from Australian industrial composting facilities. Development occurred via seasonal monitoring of such operations with evaluation of optimal microbial indicator organisms, sampling and analysis logistics. The resultant procedure allows practical end-user assessment of compost-associated bioaerosol levels, and potential health risks to proximal residential populations encroaching on such composting facilities and on-site industrial operations personnel.

Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens-to-hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma, and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and 7 control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/mL sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and inter-laboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy isotope labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an inter-laboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality c`ontrol measures, enables sensitive, specific, reproducible and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

Impact of agricultural chemicals on the environment and human health in Asia: Are there solutions?

Modern commercial agricultural practices in Asia during the last three to four decades involving chemicals (fertilisers and pesticides) have been associated with large increases in food production never witnessed before, especially under the Green Revolution technology in South Asia. This also involves large-scale increases in commercial vegetable crops. However, the high reliance on chemical inputs to bring about these increases in food production is not without problems. A visible, parallel correlation between higher productivity, high artificial input use and environmental degradation and human ill-health is evident in many countries where commercial agriculture is widespread. In this chapter, we focus on the impact of chemical inputs, in particular the impact of pesticides on the environment and on human health in South Asia with special reference to Sri Lanka...