Metabolic and ecological study of environmental pentose utilizing bacteria (E-PUB)

Lignocellulosic materials, such as sugar cane bagasse, a waste product of the sugarcane processing industry, agricultural residues and herbaceous crops, may serve as an abundant and comparatively cheap feedstock for largescale industrial fermentation, resulting in the production of marketable end-products. However, the complex structure of lignocellulosic materials, the presence of various hexose and pentose sugars in the hemicellulose component, and the presence of various compounds that inhibit the organisms selected for the fermentation process, all constitute barriers that add to the production costs and make full scale industrial production economically less feasible. The work presented in this thesis was conducted in order to screen microorganisms for ability to utilize pentose sugars derived from the sugar mill industrial waste. A large number of individual bacterial strains were investigated from hemi-cellulose rich material collected at the Proserpine and Maryborough sugar mills, notably soil samples from the mill sites. The research conducted to isolation of six pentose-capable Gram-positive organisms from the actinomycetes group by using pentose as a sole carbon source in the cultivation process. The isolates were identified as Corynebacterium glutamicum, Actinomyces odontolyticus, Nocardia elegans, and Propionibacterium freudenreichii all of which were isolated from the hemicellulose-enriched soil. Pentose degrading microbes are very rare in the environment, so this was a significant discovery. Previous research indicated that microbes could degrade pentose after genetic modification but the microbes discovered in this research were able to naturally utilize pentose. Six isolates, identified as four different genera, were investigated for their ability to utilize single sugars as substrates (glucose, xylose, arabinose or ribose), and also dual sugars as substrates (a hexose plus a pentose). The results demonstrated that C. glutamicum, A. odontolyticus, N. elegans, and P. freudenreichii were pentose-capable (able to grow using xylose or other pentose sugar), and also showed diauxie growth characteristics during the dual-sugar (glucose, in combination with xylose, arabinose or ribose) carbon source tests. In addition, it was shown that the isolates displayed very small differences in growth rates when grown on dual sugars as compared to single sugars, whether pentose or hexose in nature. The anabolic characteristics of C. glutamicum, A. odontolyticus, N. elegans and P. freudenreichii were subsequently investigated by qualitative analysis of their end-products, using high performance liquid chromatography (HPLC). All of the organisms produced arginine and cysteine after utilization of the pentose substrates alone. In addition, P. freudenreichii produced alanine and glycine. The end-product profile arising from culture with dual carbon sources was also tested. Interestingly, this time the product was different. All of them produced the amino acid glycine, when grown on a combination substrate-mix of glucose with xylose, and also glucose with arabinose. Only N. elegans was able to break down ribose, either singly or in combination with glucose, and the end-product of metabolism of the glucose plus ribose substrate combination was glutamic acid. The ecological analysis of microbial abundance in sugar mill waste was performed using denaturing gradient gel electrophoresis (DGGE) and also the metagenomic microarray PhyloChip method. Eleven solid samples and seven liquid samples were investigated. A very complex bacterial ecosystem was demonstrated in the seven liquid samples after testing with the PhyloChip method. It was also shown that bagasse leachate was the most different, compared to all of the other samples, by virtue of its richness in variety of taxa and the complexity of its bacterial community. The bacterial community in solid samples from Proserpine, Mackay and Maryborough sugar mills showed huge diversity. The information found from 16S rDNA sequencing results was that the bacterial genera Brevibacillus, Rhodospirillaceae, Bacillus, Vibrio and Pseudomonas were present in greatest abundance. In addition, Corynebacterium was also found in the soil samples. The metagenomic studies of the sugar mill samples demonstrate two important outcomes: firstly that the bagasse leachate, as potentially the most pentose-rich sample tested, had the most complex and diverse bacterial community; and secondly that the pentose-capable isolates that were initially discovered at the beginning of this study, were not amongst the most abundant taxonomic groups discovered in the sugar mill samples, and in fact were, as suspected, very rare. As a bioprospecting exercise, therefore, the study has discovered organisms that are naturally present, but in very small numbers, in the appropriate natural environment. This has implications for the industrial application of E-PUB, in that a seeding process using a starter culture will be necessary for industrial purposes, rather than simply assuming that natural fermentation might occur.

Comparison between analytical and 3D finite element solutions for borehole stresses in anisotropic elastic rock

We present a rigorous validation of the analytical Amadei solution for the stress concentration around an arbitrarily orientated borehole in general anisotropic elastic media. First, we revisit the theoretical framework of the Amadei solution and present analytical insights that show that the solution does indeed contain all special cases of symmetry, contrary to previous understanding, provided that the reduced strain coefficients b11 and b55 are not equal. It is shown from theoretical considerations and published experimental data that the b11 and b55 are not equal for realistic rocks. Second, we develop a 3D finite element elastic model within a hybrid analytical–numerical workflow that circumvents the need to rebuild and remesh the model for every borehole and material orientation. Third, we show that the borehole stresses computed from the numerical model and the analytical solution match almost perfectly for different borehole orientations (vertical, deviated and horizontal) and for several cases involving isotropic, transverse isotropic and orthorhombic symmetries. It is concluded that the analytical Amadei solution is valid with no restriction on the borehole orientation or the symmetry of the elastic anisotropy.

Anisotropic damage mechanics as a novel approach to improve pre-and post-failure borehole stability analysis

Anisotropic damage distribution and evolution have a profound effect on borehole stress concentrations. Damage evolution is an irreversible process that is not adequately described within classical equilibrium thermodynamics. Therefore, we propose a constitutive model, based on non-equilibrium thermodynamics, that accounts for anisotropic damage distribution, anisotropic damage threshold and anisotropic damage evolution. We implemented this constitutive model numerically, using the finite element method, to calculate stress–strain curves and borehole stresses. The resulting stress–strain curves are distinctively different from linear elastic-brittle and linear elastic-ideal plastic constitutive models and realistically model experimental responses of brittle rocks. We show that the onset of damage evolution leads to an inhomogeneous redistribution of material properties and stresses along the borehole wall. The classical linear elastic-brittle approach to borehole stability analysis systematically overestimates the stress concentrations on the borehole wall, because dissipative strain-softening is underestimated. The proposed damage mechanics approach explicitly models dissipative behaviour and leads to non-conservative mud window estimations. Furthermore, anisotropic rocks with preferential planes of failure, like shales, can be addressed with our model.

SECIS-binding protein 2 promotes cell survival by protecting against oxidative stress

Reactive oxygen species (ROS) are a primary cause of cellular damage that leads to cell death. In cells, protection from ROS-induced damage and maintenance of the redox balance is mediated to a large extent by selenoproteins, a distinct family of proteins that contain selenium in form of selenocysteine (Sec) within their active site. Incorporation of Sec requires the Sec-insertion sequence element (SECIS) in the 3'-untranslated region of selenoproteins mRNAs and the SECIS-binding protein 2 (SBP2). Previous studies have shown that SBP2 is required for the Sec-incorporation mechanism; however, additional roles of SBP2 in the cell have remained undefined. We herein show that depletion of SBP2 by using antisense oligonucleotides (ASOs) causes oxidative stress and induction of caspase- and cytochrome c-dependent apoptosis. Cells depleted of SBP2 have increased levels of ROS, which lead to cellular stress manifested as 8-oxo-7,8-dihydroguanine (8-oxo-dG) DNA lesions, stress granules, and lipid peroxidation. Small-molecule antioxidants N-acetylcysteine, glutathione, and α-tocopherol only marginally reduced ROS and were unable to rescue cells fully from apoptosis, indicating that apoptosis might be directly mediated by selenoproteins. Our results demonstrate that SBP2 is required for protection against ROS-induced cellular damage and cell survival. Antioxid. Redox Signal. 12, 797–808.

ATM is required for the cellular response to thymidine induced replication fork stress

Genetically distinct checkpoints, activated as a consequence of either DNA replication arrest or ionizing radiation-induced DNA damage, integrate DNA repair responses into the cell cycle programme. The ataxia-telangiectasia mutated (ATM) protein kinase blocks cell cycle progression in response to DNA double strand breaks, whereas the related ATR is important in maintaining the integrity of the DNA replication apparatus. Here, we show that thymidine, which slows the progression of replication forks by depleting cellular pools of dCTP, induces a novel DNA damage response that, uniquely, depends on both ATM and ATR. Thymidine induces ATM-mediated phosphorylation of Chk2 and NBS1 and an ATM-independent phosphorylation of Chk1 and SMC1. AT cells exposed to thymidine showed decreased viability and failed to induce homologous recombination repair (HRR). Taken together, our results implicate ATM in the HRR-mediated rescue of replication forks impaired by thymidine treatment.

Organisational innovativeness : the role of strategic orientation and environmental scanning

This study examined the effects of strategic orientation and environmental scanning on a firm’s propensity to innovate (organisational innovativeness). Previous research has mostly proposed descriptive and theoretical relationships between strategic orientation, environmental scanning and organisational innovation adoption (Beal, 2000; Jennings & Lumpkin, 1992; Raymond, Julien, & Ramangalahy, 2001). However, strategic orientation and environmental scanning, as distinct constructs, have not been empirically examined directly before in relation to organisational innovativeness. Furthermore the directionality of the relationship between strategic orientation and environmental scanning on organisational innovation adoption is still unclear (Hagen, Haile, & Maghrabi, 2003). For example, does scanning the environment result in certain types of organisational strategies, and these strategies in turn influence levels of organisational innovativeness? Or do certain types of strategic orientations pre-determine the levels of environmental scanning, and then this environmental scanning influences an organisation’s propensity to innovate? Therefore, this study using a more nuanced measure of strategic orientation; the Venkatraman’s (1989) STROBE framework of analysis, defensiveness, futurity, proactiveness, aggressiveness and riskiness, examined the directional effects of strategy and environmental scanning on organisational innovativeness Specifically, two competing models of directionality between strategic orientation and environmental scanning in relation to organisational innovativeness were proposed. Model 1 (Behavioural View) proposed that certain strategic orientation dimensions affect levels of environmental scanning, which in turn influences organisational innovativeness. In contrast, Model 2 (Open Systems view) proposed that environmental scanning affects the emphasis on certain strategic orientation dimensions, which in turn influences organisational innovativeness. Data was collected from 117 industrial firms and path analyses were used to test the two competing models. The results supported both models, suggesting a bi-directional relationship, as both models had adequate fit indices and significant paths with the data. However, overall Model 2 – the Open Systems Model had the stronger fit indices and stronger indirect effect compared to Model 1 – the Behavioural Model, suggesting that overall environmental scanning does not exert a strong direct effect on innovativeness but has more of a stronger indirect effect through the analysis and proactiveness strategic orientation dimensions. In sum, the thesis results suggest that firms’ that emphasise environmental scanning – that is continually seeking information from the environment about customers, markets, industry and new technology - are more likely to emphasise strategic orientations such as proactiveness – being innovative - and also analysis – being analytical and comprehensive in decision making - and both these strategic orientations in turn greatly influence these firms’ propensity to innovate. Discussion is given to these findings and implications are drawn for organisations and future research.

A qualitative analysis of stress, uplifts and coping in the personal and professional lives of Singaporean nurses.

Aim. This paper is a report of a descriptive study of nurses’ experiences of daily stress and coping. Background. Much of the research on stress in nursing is quantitative and has focused on only work stressors. Moreover, few studies have examined the uplifting side of living and the role it may play in moderating stress. A theoretical framework on stress and coping, ‘hassles’ and ‘uplifts’ was used to examine nurses’ experiences across their personal and professional lives from a qualitative perspective. Methods. A purposive sample of Singaporean hospital nurses (n = 23) identified using a snowball sampling technique, participated in two sets of email interviews in 2009. The qualitative data were analysed using thematic analysis. Results. Three themes were identified as constituting daily hassles: (i) time pressures, (ii) nature of nursing work and (iii) multiple roles. Uplifts were expressed in relation to one main theme of feeling good extending across nurses’ personal and professional lives. Three themes were identified as ways of coping: (i) taking time out, (ii) seeking emotional support and (iii) belief systems. Conclusion. The interaction between personal and professional life plays a major role in Singaporean nurses’ experiences of stress and coping. However, stress may be ameliorated through effective management and strong familial support. Nurses and employers are recommended to use uplifts and identify ways of coping to minimize attrition and contribute to the development of a healthy workforce.

The diversity of interests in environmental governance : a challenge for the rule of law

The function of environmental governance and the principle of the rule of law are both controversial and challenging. To apply the principle of the rule of law to the function of environmental governance is perhaps even more controversial and challenging. A system of environmental governance seeks to bring together the range of competitive and potentially conflicting interests in how the environment and its resources are managed. Increasingly it is the need for economic, social and ecological sustainability that brings these interests – both public and private – together. Then there is the relevance of the principle of the rule of law. Economic, social and ecological sustainability will be achieved – if at all – by a complex series of rules of law that are capable of enforcement so as to ensure compliance with them. To what extent do these rules of law reflect the principle of the rule of law? Is the principle of the rule of law the formally unstated value that is expected to underpin the legal system or is it the normative predicate that directs the legal system both vertically and horizontally? Is sustainability an aspirational value or a normative predicate according to which the environment and its resources are managed? Let us deal sequentially with these issues by reviewing a number of examples that demonstrate the relationship between environmental governance and the rule of law.

Environmental education through listening to children

Environmental education centres contribute to schools and communities in Environmental Education and Education for Sustainability through nature and urban -based, experiential learning and action learning approaches. An underlying assumption of these centres is that intensive, short-term, outdoor/environmental education experiences can change key attitudes and/or actions leading to positive environmental behaviour. This study reflects the interests of a researching professional who investigated aspects of a program that he designed and implemented as principal of an environmental education centre. Most evaluations of similar programs have used quasi-experimental designs to measure the program outcomes. However, this study considered the experiences of the program from the perspectives of a group of key stakeholders often overlooked in the literature; the children who participated in the program. This study examined children’s accounts of their own experiences in order to contribute new understandings of children’s perspectives and how they can be considered when designing and implementing environmental education programs. This research drew on key theoretical assumptions derived from the sociology of childhood. Within sociology of childhood, children are considered to be competent practitioners within their social worlds, who, through their talk and interaction, participate actively in the construction of their own social situations. This approach also views children as capable and competent learners who construct their knowledge through everyday participation in social experiences. This study set out to generate children’s own accounts of their experiences of a five day residential program at the Centre. In total, 54 children participated in the study that used a multi-faceted data collection approach that included conversations, drawings, photographs and journal writing. Using content analysis, data were analysed by means of an inductive approach to develop themes related to the children’s perspectives of their experiences. Three interrelated and co-dependent components of the experience emerged from the analysis; space and place; engagement and participation; and responsiveness and reflection. These components co-exist and construct the conditions for effective experiences in environmental education at the Centre. The first key finding was the emphasis that the children placed on being provided with somewhere where they could feel safe and comfortable to interact with their environment and engage in a range of outdoor experiences. The children identified that place was an outdoor classroom where they could participate in first-hand experiences and, at times, explore out-of-bound spaces; that is, a place where they had previously been limited, often by adults, in their opportunities to interact with nature. A second key finding was the emphasis that the children placed on engagement and participation in environmental experience. The children described participating in a range of new primary experiences that involved first-hand, experiences and also described participating in collaborative experiences that involved interacting with peers and with teachers, who appeared to behave differently to how they behaved at school. Finally, the children described a different type of interactional relationship with teachers, comparing the active educational role they played on camp to a more passive role at school where they sat at a table and the teacher wrote on the board. The final key finding was the emphasis that the children placed on responsiveness and reflection in the experience. In responding to their experiences, the children described the fun and excitement, confidence and satisfaction that they gained from the experience. The children also identified how their experiences contributed to the development of a caring-for-nature attitude and the value of a disorienting dilemma in promoting responsiveness to the environment. This disorienting dilemma was an event that caused the children to reassess their own beliefs and attitudes. From the three main findings, a theoretical framework that represented the children’s accounts of their experiences and a pedagogic approach that respected their accounts was developed. This pedagogic approach showed how a disorienting dilemma could create a disequilibrium in relation to a child’s existing ideas and experiences. As a result, children were challenged to reflect upon their existing environmental beliefs and practices. The findings of this research have implications for the field of environmental education. Adopting sociology of childhood provides an alternative foundation to research and can present a deeper understanding of what children believe, than an approach that relies solely on using scientific methods to undercover and analyse these understandings. This research demonstrates the value of gaining children’s accounts to assist educators to design environmental education programs as it can offer more than adult and educator perspectives. This study also provides understandings of environmental education practice by describing how the children engaged with informal learning situations. Finally, two sets of recommendations, drawn from this study, are made. The first set considers nine recommendations about and for future research and the second relates to redesigning of the environmental educational program at the research site, with six recommendations made.

Environmental pollution from shipbreaking industry : international law and national legal response

The international legal regime on shipbreaking is in its formative years. At the international level, the shipbreaking industry is partially governed by the Basel Convention on the Control of Transboundary Movements of Hazardous Wastes and their Disposal. However, how far this convention will be applicable for all aspects of transboundary movement of end-of-life ships is still, at least in the view of some scholars, a debatable issue. Against this backdrop, the International Maritime Organisation (IMO) has adopted a new, legally binding convention for shipbreaking. There is a rising voice from the developing countries that the convention is likely to impose more obligations on recycling facilities in the developing countries than on shipowners from rich nations. This may be identified as a clear derogation from the globally recognized international environmental law principle of common but differentiated treatment. This article will examine in detail major international conventions regulating transboundary movement and environmentally sound disposal of obsolete ships, as well as the corresponding laws of Bangladesh for implementing these conventions in the domestic arena. Moreover this article will examine in detail the recently adopted IMO Ship Recycling Convention.

The time course of in vivo recovery of transverse strain in high-stress tendons following exercise

Objective To evaluate the time course of the recovery of transverse strain in the Achilles and patellar tendon following a bout of resistance exercise. Methods Seventeen healthy adults underwent sonographic examination of the right patellar (n=9) and Achilles (n=8) tendons immediately prior to and following 90 repetitions of weight-bearing quadriceps and gastrocnemius-resistance exercise performed against an effective resistance of 175% and 250% body weight, respectively. Sagittal tendon thickness was determined 20 mm from the enthesis and transverse strain, as defined by the stretch ratio, was repeatedly monitored over a 24 h recovery period. Results Resistance exercise resulted in an immediate decrease in Achilles (t7=10.6, p<0.01) and patellar (t8=8.9, p<0.01) tendon thickness, resulting in an average transverse stretch ratio of 0.86±0.04 and 0.82±0.05, which was not significantly different between tendons. The magnitude of the immediate transverse strain response, however, was reduced with advancing age (r=0.63, p<0.01). Recovery in transverse strain was prolonged compared with the duration of loading and exponential in nature. The average primary recovery time was not significantly different between the Achilles (6.5±3.2 h) and patellar (7.1±3.2 h) tendons. Body weight accounted for 62% and 64% of the variation in recovery time, respectively. Conclusions Despite structural and biochemical differences between the Achilles and patellar tendon, the mechanisms underlying transverse creep recovery in vivo appear similar and are highly time dependent. These novel findings have important implications concerning the time required for the mechanical recovery of high-stress tendons following an acute bout of exercise.

Transcriptome analysis of neutrophils after endurance exercise reveals novel signaling mechanisms in the immune response to physiological stress

Neutrophils serve as an intriguing model for the study of innate immune cellular activity induced by physiological stress. We measured changes in the transcriptome of circulating neutrophils following an experimental exercise trial (EXTRI) consisting of 1 h of intense cycling immediately followed by 1 h of intense running. Blood samples were taken at baseline, 3 h, 48 h, and 96 h post-EXTRI from eight healthy, endurance-trained, male subjects. RNA was extracted from isolated neutrophils. Differential gene expression was evaluated using Illumina microarrays and validated with quantitative PCR. Gene set enrichment analysis identified enriched molecular signatures chosen from the Molecular Signatures Database. Blood concentrations of muscle damage indexes, neutrophils, interleukin (IL)-6 and IL-10 were increased (P < 0.05) 3 h post-EXTRI. Upregulated groups of functionally related genes 3 h post-EXTRI included gene sets associated with the recognition of tissue damage, the IL-1 receptor, and Toll-like receptor (TLR) pathways (familywise error rate, P value < 0.05). The core enrichment for these pathways included TLRs, low-affinity immunoglobulin receptors, S100 calcium binding protein A12, and negative regulators of innate immunity, e.g., IL-1 receptor antagonist, and IL-1 receptor associated kinase-3. Plasma myoglobin changes correlated with neutrophil TLR4 gene expression (r = 0.74; P < 0.05). Neutrophils had returned to their nonactivated state 48 h post-EXTRI, indicating that their initial proinflammatory response was transient and rapidly counterregulated. This study provides novel insight into the signaling mechanisms underlying the neutrophil responses to endurance exercise, suggesting that their transcriptional activity was particularly induced by damage-associated molecule patterns, hypothetically originating from the leakage of muscle components into the circulation.

The politics and poetics of coexistence : experiments at the intersection of art and environmental engineering

This research project explores how interdisciplinary art practices can provide ways for questioning and envisaging alternative modes of coexistence between humans and the non-humans who together, make up the environment. As a practiceled project, it combines a body of creative work (50%) and this exegesis (50%). My interdisciplinary artistic practice appropriates methods and processes from science and engineering and merges them into artistic contexts for critical and poetic ends. By blending pseudo-scientific experimentation with creative strategies like visual fiction, humour, absurd public performance and scripted audience participation, my work engages with a range of debates around ecology. This exegesis details the interplay between critical theory relating to these debates, the work of other creative practitioners and my own evolving artistic practice. Through utilising methods and processes drawn from my prior career in water engineering, I present an interdisciplinary synthesis that seeks to promote improved understandings of the causes and consequences of our ecological actions and inactions.