The use of artificial neural networks for identifying sustainable biodiesel feedstocks

Over the past few decades, biodiesel produced from oilseed crops and animal fat is receiving much attention as a renewable and sustainable alternative for automobile engine fuels, and particularly petroleum diesel. However, current biodiesel production is heavily dependent on edible oil feedstocks which are unlikely to be sustainable in the longer term due to the rising food prices and the concerns about automobile engine durability. Therefore, there is an urgent need for researchers to identify and develop sustainable biodiesel feedstocks which overcome the disadvantages of current ones. On the other hand, artificial neural network (ANN) modeling has been successfully used in recent years to gain new knowledge in various disciplines. The main goal of this article is to review recent literatures and assess the state of the art on the use of ANN as a modeling tool for future generation biodiesel feedstocks. Biodiesel feedstocks, production processes, chemical compositions, standards, physio-chemical properties and in-use performance are discussed. Limitations of current biodiesel feedstocks over future generation biodiesel feedstock have been identified. The application of ANN in modeling key biodiesel quality parameters and combustion performance in automobile engines is also discussed. This review has determined that ANN modeling has a high potential to contribute to the development of renewable energy systems by accelerating biodiesel research.

Strategies for improved disease resistance in micro-propagated bananas

Bananas (Musa sp) are one of the most important food crops in the world and provide a staple food and source of income in many households especially in Africa. Diseases are a major constraint to production with bunchy top, caused by Banana bunchy top virus (BBTV) generally considered the most important virus disease of bananas worldwide. Of the fungal diseases, Fusarium wilt, caused by the Fusarium oxysporum f.sp cubense (Foc), and black Sigatoka, caused by Mycosphaerella fijiensis, are arguably two of the most important and cause significant yield losses. The low fertility of commercially important banana cultivars has hampered efforts to generate disease resistance using conventional breeding. Possible alternative strategies to generate or increase disease resistance are through genetic engineering or by manipulation of the innate plant defence mechanisms, namely systemic acquired resistance (SAR). The first research component of this thesis describes attempts to generate BBTV-resistant banana plants using a genetic modification approach. The second research component of the thesis focused on the identification of a potential marker gene associated with SAR in banana plants and a comparison of the expression levels of the marker gene in response to biotic and abiotic stresses, and chemical inducers. Previous research at QUT CTCB showed that replication of BBTV DNA components in banana embryogenic cell suspensions (ECS) was abolished following co-bombardment with 1.1mers of mutated BBTV DNA-R. BBTV DNA-R encodes the master replication protein (Rep) and is the only viral protein essential for BBTV replication. In this study, ECS of banana were stably transformed with the same constructs, each containing a different mutation in BBTV DNA-R, namely H41G, Y79F and K187M, to examine the effect on virus replication in stably transformed plants. Cells were also transformed with a construct containing a native BBTV Rep. A total of 16, 16, 11 and five lines of stably transformed banana plants containing the Y79F, H41G, K187M and native Rep constructs, respectively, were generated. Of these, up to nine replicates from Y79F lines, four H41G lines, seven K187M lines and three native Rep lines were inoculated with BBTV by exposure to viruliferous aphids in two separate experiments. At least one replicate from each of the nine Y79F lines developed typical bunchy top symptoms and all tested positive for BBTV using PCR. Of the four H41G lines tested, at least one replicate from three of the lines showed symptoms of bunchy top and tested positive using PCR. However, none of the five replicates of one H41G line (H41G-3) developed symptoms of bunchy top and none of the plants tested positive for BBTV using PCR. Of the seven K187M lines, at least one replicate of all lines except one (K187M-1) developed symptoms of bunchy top and tested positive for BBTV. Importantly, none of the four replicates of line K187M-1 showed symptoms or tested positive for BBTV. At least one replicate from each of the three native Rep lines developed symptoms and tested positive for BBTV. The H41G-3 and K187M-1 lines possibly represent the first transgenic banana plants generated using a mutated Rep strategy. The second research component of this thesis focused on the identification of SAR-associated genes in banana and their expression levels in response to biotic and abiotic stresses and chemical inducers. The impetus for this research was the observation that tissue-cultured (TC) banana plants were more susceptible to Fusarium wilt disease (and possibly bunchy top disease) than plants grown from field-derived suckers, possibly due to decreased levels of SAR gene expression in the former. In this study, the pathogenesis-related protein 1 (PR-1) gene was identified as a potential marker for SAR gene expression in banana. A quantitative real-time PCR assay was developed and optimised in order to determine the expression of PR-1, with polyubiquitin (Ubi-1) found to be the most suitable reference gene to enable relative quantification. The levels of PR-1 expression were subsequently compared in Lady Finger and Cavendish (cv. Williams) banana plants grown under three different environmental conditions, namely in the field, the glass house and in tissue-culture. PR-1 was shown to be expressed in both cultivars growing under different conditions. While PR-1 expression was highest in the field grown bananas and lowest in the TC bananas in Lady Finger cultivar, this was not the case in the Cavendish cultivar with glass house plants exhibiting the lowest PR-1 expression compared with tissue culture and field grown plants. The important outcomes of this work were the establishment of a qPCR-based assay to monitor PR-1 expression levels in banana and a preliminary assessment of the baseline PR-1 expression levels in two banana cultivars under three different growing conditions. After establishing the baseline PR-1 expression levels in Cavendish bananas, a study was done to determine whether PR-1 levels could be increased in these plants by exposure to known banana pathogens and non-pathogens, and a known chemical inducer of SAR. Cavendish banana plants were exposed to pathogenic Foc subtropical race 4 (FocSR4) and non-pathogenic Foc race 1 (Foc1), as well as two putative inducers of resistance, Fusarium lycopersici (Fol) and the chemical, acibenzolar-S-methyl (BION®). Tissue culture bananas were acclimatised under either glass house (TCS) or field (TCH) conditions and treatments were carried out in a randomised complete block design. PR-1 expression was determined using qPCR for both TCS and TCH samples for the period 12-72h post-exposure. Treatment of TCH plants using Foc1 and FocSR4 resulted in 120 and 80 times higher PR-1 expression than baseline levels, respectively. For TCS plants treated with Foc1, PR-1 expression was 30 times higher than baseline levels at 12h post-exposure, while TCS plants treated with FocSR4 showed the highest PR-1 expression (20 times higher than baseline levels) at 72h post-exposure. Interestingly, when TCS plants were treated with Fol there was a marked increase of PR-1 expression at 12 h and 48 h following treatment which was 4 and 8 times higher than the levels observed when TCS plants were treated with Foc1 and FocSR4, respectively. In contrast, when TCH plants were treated with Fol only a slight increase in PR-1 expression was observed at 12 h, which eventually returned to baseline levels. Exposure of both TCS and TCH plants to BION® resulted in no effect on PR-1 expression levels at any time-point. The major outcome of the SAR study was that the glass house acclimatised tissue culture bananas exhibited lower PR-1 gene expression compared to field acclimatised tissue culture plants and the identification of Fol as a good candidate for SAR induction in banana plants exhibiting low PR-1 levels. A number of outcomes that foster understanding of both pathogen-derived and plant innate resistance strategies in order to potentially improve banana resistance to diseases were explored in this study and include identification of potential inducers of systemic acquired resistance and a promising mutated Rep approach for BBTV resistance. The work presented in this thesis is the first report on the generation of potential BBTV resistant bananas using the mutated Rep approach. In addition, this is the first report on the status of SAR in banana grown under different conditions of exposure to the biotic and abiotic environment. Further, a robust qPCR assay for the study of gene expression using banana leaf samples was developed and a potential inducer of SAR in tissue culture bananas identified which could be harnessed to increase resistance in tissue culture bananas.

In Plant Activation: An inducible, hyperexpression platform for recombinant protein production in plants

In this study, we describe a novel protein production platform that provides both activation and amplification of transgene expression in planta. The In Plant Activation (INPACT) system is based on the replication machinery of tobacco yellow dwarf mastrevirus (TYDV) and is essentially transient gene expression from a stably transformed plant, thus combining the advantages of both means of expression. The INPACT cassette is uniquely arranged such that the gene of interest is split and only reconstituted in the presence of the TYDV-encoded Rep/RepA proteins. Rep/RepA expression is placed under the control of the AlcA:AlcR gene switch, which is responsive to trace levels of ethanol. Transgenic tobacco (Nicotiana tabacum cv Samsun) plants containing an INPACT cassette encoding the b-glucuronidase (GUS) reporter had negligible background expression but accumulated very high GUS levels (up to 10% total soluble protein) throughout the plant, within 3 d of a 1% ethanol application. The GUS reporter was replaced with a gene encoding a lethal ribonuclease, barnase, demonstrating that the INPACT system provides exquisite control of transgene expression and can be adapted to potentially toxic or inhibitory compounds. The INPACT gene expression platform is scalable, not host-limited, and has been used to express both a therapeutic and an industrial protein.

Effect of pretreatment on saccharification of sugarcane bagasse by complex and simple enzyme mixtures

Saccharification of sugarcane bagasse pretreated at the pilot-scale with different processes (in combination with steam-explosion) was evaluated. Maximum glucan conversion with Celluclast 1.5 L (15–25 FPU/g glucan) was in the following order: glycerol/HCl > HCl > H2SO4 > NaOH, with the glycerol system achieving ∼100% conversion. Surprisingly, the NaOH substrate achieved optimum saccharification with only 8 FPU/g glucan. Glucan conversions (3.6–6%) obtained with mixtures of endo-1,4-β-glucanase (EG) and β-glucosidase (βG) for the NaOH substrate were 2–6 times that of acid substrates. However, glucan conversions (15–60%) obtained with mixtures of cellobiohydrolase (CBH I) and βG on acidified glycerol substrate were 10–30% higher than those obtained for NaOH and acid substrates. The susceptibility of the substrates to enzymatic saccharification was explained by their physical and chemical attributes. Acidified glycerol pretreatment offers the opportunity to simplify the complexity of enzyme mixtures required for saccharification of lignocellulosics.

Bayesian modelling of surveillance and proof of freedom : the mathematical, logical & psychological challenges

Keeping exotic plant pests out of our country relies on good border control or quarantine. However with increasing globalization and mobilization some things slip through. Then the back up systems become important. This can include an expensive form of surveillance that purposively targets particular pests. A much wider net is provided by general surveillance, which is assimilated into everyday activities, like farmers checking the health of their crops. In fact farmers and even home gardeners have provided a front line warning system for some pests (eg European wasp) that could otherwise have wreaked havoc. Mathematics is used to model how surveillance works in various situations. Within this virtual world we can play with various surveillance and management strategies to "see" how they would work, or how to make them work better. One of our greatest challenges is estimating some of the input parameters : because the pest hasn't been here before, it's hard to predict how well it might behave: establishing, spreading, and what types of symptoms it might express. So we rely on experts to help us with this. This talk will look at the mathematical, psychological and logical challenges of helping experts to quantify what they think. We show how the subjective Bayesian approach is useful for capturing expert uncertainty, ultimately providing a more complete picture of what they think... And what they don't!

Tensile properties of pumpkin peel and flesh tissue and review of current testing methods

In South and Southeast Asia, postharvest loss causes material waste of up to 66% in fruits and vegetables, 30% in oilseeds and pulses, and 49% in roots and tubers. The efficiency of postharvest equipment directly affects industrial-scale food production. To enhance current processing methods and devices, it is essential to analyze the responses of food materials under loading operations. Food materials undergo different types of mechanical loading during postharvest and processing stages. Therefore, it is important to determine the properties of these materials under different types of loads, such as tensile, compression, and indentation. This study presents a comprehensive analysis of the available literature on the tensile properties of different food samples. The aim of this review was to categorize the available methods of tensile testing for agricultural crops and food materials to investigate an appropriate sample size and tensile test method. The results were then applied to perform tensile tests on pumpkin flesh and peel samples, in particular on arc-sided samples at a constant loading rate of 20 mm min-1. The results showed the maximum tensile stress of pumpkin flesh and peel samples to be 0.535 and 1.45 MPa, respectively. The elastic modulus of the flesh and peel samples was 6.82 and 25.2 MPa, respectively, while the failure modulus values were 14.51 and 30.88 MPa, respectively. The results of the tensile tests were also used to develop a finite element model of mechanical peeling of tough-skinned vegetables. However, to study the effects of deformation rate, moisture content, and texture of the tissue on the tensile responses of food materials, more investigation needs to be done in the future.

Influence of nitrogen fertiliser application and timing on greenhouse gas emissions from a lychee (Litchi chinensis) orchard in humid subtropical Australia

Nitrous oxide emissions from intensive, fertilised agricultural systems have been identified as significant contributors to both Australia's and the global greenhouse gas (GHG) budget. This is expected to increase as rates of agriculture intensification and land use change accelerate to support population growth and food production. Limited data exists on N2O trace gas fluxes from subtropical or tropical tree cropping soils critical for the development of effective mitigation strategies.This study aimed to quantify GHG emissions over two consecutive years (March 2007 to March 2009) from a 30 year (lychee) orchard in the humid subtropical region of Australia. GHG fluxes were measured using a combination of high temporal resolution automated sampling and manually sampled chambers. No fertiliser was added to the plots during the 2007 measurement season. A split application of nitrogen fertiliser (urea) was added at the rate of 265kgNha-1 during the autumn and spring of 2008. Emissions of N2O were influenced by rainfall events and seasonal temperatures during 2007 and the fertilisation events in 2008. Annual N2O emissions from the lychee canopy increased from 1.7kgN2O-Nha-1yr-1 for 2007, to 7.6kgN2O-Nha-1yr-1 following fertiliser application in 2008. This represented an emission factor of 1.56%, corrected for background emissions. The timing of the split application was found to be critical to N2O emissions, with over twice as much lost following an application in spring (2.44%) compared to autumn (EF: 1.10%). This research suggests that avoiding fertiliser application during the hot and moist spring/summer period can reduce N2O losses without compromising yields.

Low temperature pretreatment of sugarcane bagasse at atmospheric pressure using mixtures of ethylene carbonate and ethylene glycol

A low temperature lignocellulose pretreatment process was developed using acid-catalysed mixtures of alkylene carbonate and alkylene glycol. Pretreatment of sugarcane bagasse with mixtures of ethylene carbonate (EC) and ethylene glycol (EG) was more effective than that with mixtures of propylene carbonate (PC) and propylene glycol (PG). These mixtures were more effective than the individual components in making bagasse cellulose more amenable to cellulase digestion. Glucan digestibilities of ≥87% could be achieved with a wide range of EC to EG ratios from 9:1 to 1:1 (w/w). Pretreatment of bagasse by the EC/EG mixture with a ratio of 4:1 in the presence of 1.2% H2SO4 at 90 °C for 30 min led to the highest glucan enzymatic digestibility of 93%. The high glucan digestibilities obtained under these acidic conditions were due to (a) the ability of alkylene carbonate to cause significant biomass size reduction, (b) the ability of alkylene glycol to cause biomass defibrillation, (c) the ability of alkylene carbonate and alkylene glycol to remove xylan and lignin, and (d) the magnified above attributes in the mixtures of alkylene carbonate and alkylene glycol.

Modeling the co-precipitation of silica and calcium oxalate in sugar solutions

Solution chemistry plays a significant role in the rate and type of foulant formed on heated industrial surfaces. This paper describes the effect of sucrose, silica (SiO2), Ca2+ and Mg2+ ions, and trans-aconitic acid on the kinetics and solubility of SiO2 and calcium oxalate monohydrate (COM) in mixed salt solutions containing sucrose and refines models previously proposed. The developed SiO2 models show that sucrose and SiO2 concentrations are the main parameters that determine apparent order (n) and apparent rate of reaction (k) and SiO2 solubility over a 24 h period. The calcium oxalate solubility model shows that while increasing [Mg2+] increases COM solubility, the reverse is so with increasing sucrose concentrations. The role of solution species on COM crystal habit is discussed and the appearance of the uncommon (001) face is explained.

Understanding mild acid pretreatment of sugarcane bagasse through particle scale modeling

Sugarcane bagasse is an abundant and sustainable resource, generated as a by-product of sugarcane milling. The cellulosic material within bagasse can be broken down into glucose molecules and fermented to produce ethanol, making it a promising feedstock for biofuel production. Mild acid pretreatment hydrolyses the hemicellulosic component of biomass, thus allowing enzymes greater access to the cellulosic substrate during saccharification. A particle-scale mathematical model describing the mild acid pretreatment of sugarcane bagasse has been developed, using a volume averaged framework. Discrete population-balance equations are used to characterise the polymer degradation kinetics, and diffusive effects account for mass transport within the cell wall of the bagasse. As the fibrous material hydrolyses over time, variations in the porosity of the cell wall and the downstream effects on the reaction kinetics are accounted for using conservation of volume arguments. Non-dimensionalization of the model equations reduces the number of parameters in the system to a set of four dimensionless ratios that compare the timescales of different reaction and diffusion events. Theoretical yield curves are compared to macroscopic experimental observations from the literature and inferences are made as to constraints on these “unknown” parameters. These results enable connections to be made between experimental data and the underlying thermodynamics of acid pretreatment. Consequently, the results suggest that data-fitting techniques used to obtain kinetic parameters should be carefully applied, with prudent consideration given to the chemical and physiological processes being modeled.

RNAi for insect-proof plants

RNA interference induced in insects after ingestion of plant-expressed hairpin RNA offers promise for managing devastating crop pests

Comparison of the coat protein, movement protein and RNA polymerase gene sequences of Australian, Chinese, and American isolates of barley yellow dwarf virus transmitted by Rhopalosiphum padi

Barley yellow dwarf luteovirus-GPV (BYDV-GPV) is a common problem in Chinese wheat crops but is unrecorded elsewhere. A defining characteristic of GPV is its capacity to be transmitted efficiently by both Schizaphis graminum and Rhopaloshiphum padi. This dual aphid species transmission contrasts with those of BYDV-RPV and BYDV-SGV, globally distributed viruses, which are efficiently transmitted only by Rhopaloshiphum padi and Schizaphis graminum respectively. The viral RNA sequences encoding the coat protein (22K) gene, the movement protein (17K) gene, the region surrounding the conserved GDD motif of the polymerase gene and the intergenic sequences between these genes were determined for GPV and an Australian isolate of BYDV-RPV (RPVa). In all three genes, the sequences of GPV and RPVa were more similar to those of an American isolate of BYDV-RPV (RPVu) than to any other luteovirus for which there is data available. RPVa and RPVu were very similar, especially their coat proteins which had 97% identity at the amino acid level. The coat protein of GPV had 76% and 78% amino acid identity with RPVa and RPVu respectively. The data suggest that RPVu and RPVa are correctly named as strains of the same serotype and that GPV is sufficiently different from either RPV strain to be considered a distinct BYDV type. The coat protein and movement protein genes of GPV are very dissimilar to SGV. The polymerase sequences of RPVu, RPVa and GPV show close affinities with those of the sobemo-like luteoviruses and little similarity with those of the carmo-like luteoviruses. The sequences of the coat proteins, movement proteins and the polymerase segments of BYDV serotypes, other than RPV and GPV, form a cluster that is separate from their counterpart sequences from dicot-infecting luteoviruses. The RPV and GPV isolates consistently fall within a dicot-infecting cluster. This suggests that RPV and GPV evolved from within this group of viruses. Since these other viruses all infect dicots it seems likely that their common ancestor infected a dicot and that RPV and GPV evolved from a virus that switched hosts from a dicot to a monocot.

Geologic map of the Valley Mountain 15’ quadrangle, San Bernardino and Riverside Counties, California: U.S. Geological Survey Geologic Quadrangle Map GQ–1767, scale 1:62,500

The Valley Mountain 15’ quadrangle straddles the Pinto Mountain Fault, which bounds the eastern Transverse Ranges in the south against the Mojave Desert province in the north. The Pinto Mountains, part of the eastern Transverse Ranges in the south part of the quadrangle expose a series of Paleoproterozoic gneisses and granite and the Proterozoic quartzite of Pinto Mountain. Early Triassic quartz monzonite intruded the gneisses and was ductiley deformed prior to voluminous Jurassic intrusion of diorite, granodiorite, quartz monzonite, and granite plutons. The Jurassic rocks include part of the Bullion Mountains Intrusive Suite, which crops out prominently at Valley Mountain and in the Bullion Mountains, as well as in the Pinto Mountains. Jurassic plutons in the southwest part of the quadrangle are deeply denuded from midcrustal emplacement levels in contrast to supracrustal Jurassic limestone and volcanic rocks exposed in the northeast. Dikes inferred to be part of the Jurassic Independence Dike Swarm intrude the Jurassic plutons and Proterozoic rocks. Late Cretaceous intrusion of the Cadiz Valley Batholith in the northeast caused contact metamorphism of adjacent Jurassic plutonic rocks...

Global indigenous studies in the first world: some reflections and epistemological matters

Indigenous studies in First World nation states such as Australia, Canada, New Zealand, the United States of America and Hawaii, appear to have acquired the status of a discipline, although the accounts of its formation vary. Indigenous studies is formally recognised as part of university curricula in these countries and is included in inter‐disciplinary contexts and degree programs or is offered as a program and a degree in its own right. Indigenous scholarship is being published in unprecedented numbers with publishing houses competing for manuscripts. Indigenous studies journals have proliferated having emerged in the 1970s though most were, and continue to be, edited by non‐Indigenous people. In addition, Indigenous studies professional associations have been established organising research related activities as well as convening conferences to enable intellectual engagement and the formation of national and international networks. The nature and extent of this institutionalisation and the conditions of existence, though often marginalised and under resourced, may allude to the coherence of Indigenous Studies as a discipline with global reach but what remains unclear are its epistemological boundaries and the degree to which it perpetuates cultural entrapment . This paper will reflect on some of these epistemological matters.