Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.

Demonstration of cellulosic ethanol production from sugarcane bagasse in Australia : the Mackay Renewable Biocommodities Pilot Plant

The ready availability of sugarcane bagasse at an existing industrial facility and the potential availability of extra fibre through trash collection make sugarcane fibre the best candidate for early stage commercialisation of cellulosic ethanol technologies. The commercialisation of cellulosic ethanol technologies in the sugar industry requires both development of novel technologies and the assessment of these technologies at a pre-commercial scale. In 2007, the Queensland University of Technology (QUT) received funding from the Australian and Queensland Governments to construct a pilot research and development facility for the production of bioethanol and other renewable biocommodities from biomass including sugarcane bagasse. This facility has been built on the site of the Racecourse Sugar Mill in Mackay, Queensland and is known as the Mackay Renewable Biocommodities Pilot Plant (MRBPP). This research facility is capable of processing cellulosic biomass by a variety of pretreatment technologies and includes equipment for enzymatic saccharification, fermentation and distillation to produce ethanol. Lignin and fermentation co-products can also be produced in the pilot facility.

Vertical growth and resonator properties of hexagonally shaped zinc oxide nanonails

We synthesized vertically aligned nail-shaped ZnO nanocrystal arrays on silicon substrates via a combination of a carbothermal reduction method and textured ZnO seeding layers that were precoated on silicon substrates by thermally decomposing zinc acetate, and studied their optical properties using cathodoluminescence (CL) and photoluminescence techniques. The ZnO nanonails show a sharp band-gap edge UV emission and a defect-related broad green emission. Monochromatic CL images of an individual ZnO nanonail show variations in spatial distributions of respective CL bands that had different origins. We attribute the spatial variation of CL images to an uneven distribution of luminescent defects and/or a structure-related light out-coupling from hexagonal ZnO nanostructures. The most distinct CL feature from the hexagonal head of an individual ZnO nanonail was the occurrence of a series of distinct resonant peaks within the visible wavelength range. It appeared that the head of a nanonail played the role of a hexagonal cavity so that polarizationdependent whispering gallery modes were stimulated by electron beam excitation.

Cellulosic ethanol from sugarcane bagasse in Australia : exploring industry feasibility through systems analysis, techno-economic assessment and pilot plant development

Overcoming many of the constraints to early stage investment in biofuels production from sugarcane bagasse in Australia requires an understanding of the complex technical, economic and systemic challenges associated with the transition of established sugar industry structures from single product agri-businesses to new diversified multi-product biorefineries. While positive investment decisions in new infrastructure requires technically feasible solutions and the attainment of project economic investment thresholds, many other systemic factors will influence the investment decision. These factors include the interrelationships between feedstock availability and energy use, competing product alternatives, technology acceptance and perceptions of project uncertainty and risk. This thesis explores the feasibility of a new cellulosic ethanol industry in Australia based on the large sugarcane fibre (bagasse) resource available. The research explores industry feasibility from multiple angles including the challenges of integrating ethanol production into an established sugarcane processing system, scoping the economic drivers and key variables relating to bioethanol projects and considering the impact of emerging technologies in improving industry feasibility. The opportunities available from pilot scale technology demonstration are also addressed. Systems analysis techniques are used to explore the interrelationships between the existing sugarcane industry and the developing cellulosic biofuels industry. This analysis has resulted in the development of a conceptual framework for a bagassebased cellulosic ethanol industry in Australia and uses this framework to assess the uncertainty in key project factors and investment risk. The analysis showed that the fundamental issue affecting investment in a cellulosic ethanol industry from sugarcane in Australia is the uncertainty in the future price of ethanol and government support that reduces the risks associated with early stage investment is likely to be necessary to promote commercialisation of this novel technology. Comprehensive techno-economic models have been developed and used to assess the potential quantum of ethanol production from sugarcane in Australia, to assess the feasibility of a soda-based biorefinery at the Racecourse Sugar Mill in Mackay, Queensland and to assess the feasibility of reducing the cost of production of fermentable sugars from the in-planta expression of cellulases in sugarcane in Australia. These assessments show that ethanol from sugarcane in Australia has the potential to make a significant contribution to reducing Australia’s transportation fuel requirements from fossil fuels and that economically viable projects exist depending upon assumptions relating to product price, ethanol taxation arrangements and greenhouse gas emission reduction incentives. The conceptual design and development of a novel pilot scale cellulosic ethanol research and development facility is also reported in this thesis. The establishment of this facility enables the technical and economic feasibility of new technologies to be assessed in a multi-partner, collaborative environment. As a key outcome of this work, this study has delivered a facility that will enable novel cellulosic ethanol technologies to be assessed in a low investment risk environment, reducing the potential risks associated with early stage investment in commercial projects and hence promoting more rapid technology uptake. While the study has focussed on an exploration of the feasibility of a commercial cellulosic ethanol industry from sugarcane in Australia, many of the same key issues will be of relevance to other sugarcane industries throughout the world seeking diversification of revenue through the implementation of novel cellulosic ethanol technologies.

Plant programmed cell death : Can't live with it; Can't live without it

The decision of whether a cell should live or die is fundamental for the wellbeing of all organisms. Despite intense investigation into cell growth and proliferation, only recently has the essential and equally important idea that cells control/programme their own demise for proper maintenance of cellular homeostasis gained recognition. Furthermore, even though research into programmed cell death (PCD) has been an extremely active area of research there are significant gaps in our understanding of the process in plants. In this review, we discuss PCD during plant development and pathogenesis, and compare/contrast this with mammalian apoptosis. © 2008 Blackwell Publishing Ltd.

The Profiling of Property, Plant & Equipment (PPE) Contributions in Australia and Malaysia Public Listed Construction Companies

The purpose of this paper is to study the profiling of property, plant and equipment (PPE) contributions in Australia and Malaysia construction companies. A company’s worth is usually based on the listed share price on the stock exchange. In arriving at the net profit, the contribution of PPE in the company’s assets is somehow being neglected. This paper will investigate the followings; firstly the level of PPE contribution in the construction firms by comparing the PPE contributions to the company’s asset as a whole which includes fixed (non-current) assets and current assets. This will determine the true strength of the companies, rather than relying on the share prices alone. Secondly, the paper will determine the trend of company’s asset ownership to show the company’s performance of the PPE ownership during the period of study. The data is based on the selected construction companies listed on the Australian Stock Exchange (ASX) and Malaysian Stock Exchange, known as Bursa Malaysia. The profiling will help to determine the strength of the construction firms based on the PPE holding, and the level of PPE ownerships in the two countries construction firms during the period of study.

Functionalised zinc oxide nanowire gas sensors : enhanced NO2 gas sensor response by chemical modification of nanowire surfaces

Surface coating with an organic self-assembled monolayer (SAM) can enhance surface reactions or the absorption of specific gases and hence improve the response of a metal oxide (MOx) sensor toward particular target gases in the environment. In this study the effect of an adsorbed organic layer on the dynamic response of zinc oxide nanowire gas sensors was investigated. The effect of ZnO surface functionalisation by two different organic molecules, tris(hydroxymethyl)aminomethane (THMA) and dodecanethiol (DT), was studied. The response towards ammonia, nitrous oxide and nitrogen dioxide was investigated for three sensor configurations, namely pure ZnO nanowires, organic-coated ZnO nanowires and ZnO nanowires covered with a sparse layer of organic-coated ZnO nanoparticles. Exposure of the nanowire sensors to the oxidising gas NO2 produced a significant and reproducible response. ZnO and THMA-coated ZnO nanowire sensors both readily detected NO2 down to a concentration in the very low ppm range. Notably, the THMA-coated nanowires consistently displayed a small, enhanced response to NO2 compared to uncoated ZnO nanowire sensors. At the lower concentration levels tested, ZnO nanowire sensors that were coated with THMA-capped ZnO nanoparticles were found to exhibit the greatest enhanced response. ΔR/R was two times greater than that for the as-prepared ZnO nanowire sensors. It is proposed that the ΔR/R enhancement in this case originates from the changes induced in the depletion-layer width of the ZnO nanoparticles that bridge ZnO nanowires resulting from THMA ligand binding to the surface of the particle coating. The heightened response and selectivity to the NO2 target are positive results arising from the coating of these ZnO nanowire sensors with organic-SAM-functionalised ZnO nanoparticles.

Zinc aluminium layered double hydroxides for the removal of iodine and iodide from aqueous solutions

129I is a radioactive isotope of iodine that is readily absorbed by the body. In this paper we investigated the potential of a 3:1 Zn/Al layered double hydroxide (LDH) as a sorbent for the removal of iodine and iodide from water. Synthetic Zn6Al2(OH)16(CO3)∙4H2O was prepared by the co-precipitation before thermal activation. The LDH was treated with solutions containing iodide and iodine. It was found that iodine could be more easily removed from solution than iodide. Powder X-ray diffraction revealed the destruction of the LDH structure during thermal activation and the successful reformation of a similar LDH material after treatment with the iodide or iodine solution. Thermal decomposition of all samples studied by thermogravimetry appeared to be similar. A new decomposition mechanism similar to one previously described in the literature was proposed for the Zn/Al LDH. The total mass loss of samples treated with iodide and iodine was significantly lower than that of the original LDH indicating that iodine species may form non-removable anions when intercalated into the LDH structure. Evolved gas mass spectrometry failed to detect any iodine species lost as gases during the decomposition of iodide treated LDH however, small quantities of iodine species were observed during decomposition of samples treated with iodine solution.

Gold coating of silica and zinc oxide nanoparticles by the surface reduction of gold(I) chloride

The possibility of a surface inner sphere electron transfer mechanism leading to the coating of gold via the surface reduction of gold(I) chloride on metal and semi-metal oxide nanoparticles was investigated. Silica and zinc oxide nanoparticles are known to have very different surface chemistry, potentially leading to a new class of gold coated nanoparticles. Monodisperse silica nanoparticles were synthesised by the well known Stöber protocol in conjunction with sonication. The nanoparticle size was regulated solely by varying the amount of ammonia solution added. The presence of surface hydroxyl groups was investigated by liquid proton NMR. The resultant nanoparticle size was directly measured by the use of TEM. The synthesised silica nanoparticles were dispersed in acetonitrile (MeCN) and added to a bis acetonitrile gold(I) co-ordination complex [Au(MeCN)2]+ in MeCN. The silica hydroxyl groups were deprotonated in the presence of MeCN generating a formal negative charge on the siloxy groups. This allowed the [Au(MeCN)2]+ complex to undergo ligand exchange with the silica nanoparticles, which formed a surface co-ordination complex with reduction to gold(0), that proceeded by a surface inner sphere electron transfer mechanism. The residual [Au(MeCN)2]+ complex was allowed to react with water, disproportionating into gold(0) and gold(III) respectively, with gold(0) being added to the reduced gold already bound on the silica surface. The so-formed metallic gold seed surface was found to be suitable for the conventional reduction of gold(III) to gold(0) by ascorbic acid. This process generated a thin and uniform gold coating on the silica nanoparticles. This process was modified to include uniformly gold coated composite zinc oxide nanoparticles (Au@ZnO NPs) using surface co-ordination chemistry. AuCl dissolved in acetonitrile (MeCN) supplied chloride ions which were adsorbed onto ZnO NPs. The co-ordinated gold(I) was reduced on the ZnO surface to gold(0) by the inner sphere electron transfer mechanism. Addition of water disproportionated the remaining gold(I) to gold(0) and gold(III). Gold(0) bonded to gold(0) on the NP surface with gold(III) was reduced to gold(0) by ascorbic acid (ASC), which completed the gold coating process. This gold coating process of Au@ZnO NPs was modified to incorporate iodide instead of chloride. ZnO NPs were synthesised by the use of sodium oxide, zinc iodide and potassium iodide in refluxing basic ethanol with iodide controlling the presence of chemisorbed oxygen. These ZnO NPs were treated by the addition of gold(I) chloride dissolved in acetonitrile leaving chloride anions co-ordinated on the ZnO NP surface. This allowed acetonitrile ligands in the added [Au(MeCN)2]+ complex to surface exchange with adsorbed chloride from the dissolved AuCl on the ZnO NP surface. Gold(I) was then reduced by the surface inner sphere electron transfer mechanism. The presence of the reduced gold on the ZnO NPs allowed adsorption of iodide to generate a uniform deposition of gold onto the ZnO NP surface without the use of additional reducing agents or heat.