Organic Matter Dynamics in the Wet Tropics Under Different Sugarcane Residue Management Regimes

Retention of sugarcane leaves and tops on the soil surface after harvesting has almost completely replaced pre- and post-harvest burning of crop residues in the Australian sugar industry. Since its introduction around 25 years ago, residue retention has increased soil organic matter to improve soil fertility as well as improve harvest flexibility and reduce erosion. However, in the wet tropics residue retention also poses potential problems of prolonged waterlogging, and late-season release of nitrogen which can reduce sugar content of the crop. The objective of this project is to examine the management of sugarcane residues in the wet tropics using a systems approach. Subsidiary objectives are (a) to improve understanding of nitrogen cycling in Australian sugarcane soils in the wet tropics, and (b) to identify ways to manage crop residues to retain their advantages and limit their disadvantages. Project objectives will be addressed using several approaches. Historic farm production data recorded by sugar mills in the wet tropics will be analysed to determine the effect of residue burning or retention on crop yield and sugar content. The impact of climate on soil processes will be highlighed by development of an index of nitrogen mineralisation using the Agricultural Production Systems Simulator (APSIM) model. Increased understanding of nitrogen cycling in Australian sugarcane soils and management of crop residues will be gained through a field experiment recently established in the Australian wet tropics. From this experiment the decomposition and nitrogen dynamics of residues placed on the soil surface and incorporated will be compared. The effect of differences in temperature, soil water content and pH will be further examined on these soils under glasshouse conditions. Preliminary results show a high ammonium to nitrate ratio in tropics soils, which may be due to low rates of nitrification that increase the retention of nitrogen in a form (ammonium) that is less subject to leaching. Further results will be presented at Congress.

Oxidative modification of a specific apolipoprotein B lysine residue confers altered receptor specificity on LDL

During inflammation, many cell types release reactive oxygen species (ROS) via the respiratory burst. These ROS are potent oxidants of LDL and its major protein, apolipoprotein B. Whilst native LDL is taken up by endothelial cells via a feedback controlled receptor-regulated process, oxidative modification of LDL renders it a ligand for many scavenger receptors. Scavenger receptors include CD-36, LOX-1 and the prototypic macrophage SR A I/II, all of which are variably expressed. Uncontrolled uptake of oxidised LDL is implicated in the pathogenesis of atherosclerosis. In addition, oxidised LDL increases CCR2 protein and mRNA expression on monocytes, and thus may contribute to monocyte retention and perpetuation in inflammatory, unstable atherosclerotic lesions. However, little data are available on the effects of specific minor modifications to apolipoprotein B. In order to identify the sequence specificity and nature of oxidative modifications which confer altered properties on LDL, we have investigated the effects of modified peptides (which correspond to the putative LDLR binding domain) on LDL uptake by HUVECs and U937 monocytes.

Synthesis and expression of a gene encoding a 48-residue repeat in the Pseudomonas syringae ice nucleation protein

The aim of this work was to construct short analogues of the repetitive water-binding domain of the Pseudomonas syringae ice nucleation protein, InaZ. Structural analysis of these analogues might provide data pertaining to the protein-water contacts that underlie ice nucleation. An artificial gene coding for a 48-mer repeat sequence from InaZ was synthesized from four oligodeoxyribonucleotides and ligated into the expression vector, pGEX2T. The recombinant vector was cloned in Escherichia coli and a glutathione S-transferase fusion protein obtained. This fusion protein displayed a low level of ice-nucleating activity when tested by a droplet freezing assay. The fusion protein could be cleaved with thrombin, providing a means for future recovery of the 48-mer peptide in amounts suitable for structural analysis by nuclear magnetic resonance spectroscopy.

21-residue peptide's dynamics at and between elementary structural transitions

Elementary conformational changes of the backbone of a 21-residue peptide A5(A3RA)3A are studied using molecular dynamics simulations in explicit water. The processes of the conformational transitions and the regimes of stationary fluctuations between them are investigated using minimal perturbations of the system. The perturbations consist of a few degrees rotation of the velocity of one of the systems' atoms and keep the system on the same energy surface. It is found that (i) the system dynamics is insignificantly changed by the perturbations in the regimes between the transitions; (ii) it is very sensitive to the perturbations just before the transitions that prevents the peptide from making the transitions; and (iii) the perturbation of any atom of the system, including distant water molecules is equally effective in preventing the transition. The latter implies strongly collective dynamics of the peptide and water during the transitions.

Decentralised off-grid electricity generation in India using intermediate pyrolysis of residue straws

Use of agricultural residues, like wheat or rice straw for energy generation, is the most effective measure in terms of costs and availability. The present paper focuses the need of such measure, its impact on the environment as practiced today (open burning). The application of intermediate pyrolysis technology for straw conversion in India is discussed herein. A 20 kg/h Pyroformer has been coupled to a direct quenching system without filtration. The process temperature was around 360 ?C and the yields for the product fractions, char pyrolysis oil, and non-condensable gas fractions were, 32%, 35%, and 33% respectively. The pyrolysis oil was condensed in a quenching unit using bio-diesel or diesel. The blend produced was 30 % pyrolysis liquid and 70 % bio-diesel. The engine has been tested with the pyro-oil/biooil mixture over a long term (75 hours). An overall economic analysis of the process has been carried out.

The coupling mechanism of P-glycoprotein involves residue L339 in the sixth membrane spanning segment

The transmembrane (TM) domains in P-glycoprotein (P-gp) contain the drug binding sites and undergo conformational changes driven by nucleotide catalysis to effect translocation. However, our understanding of exactly which regions are involved in such events remains unclear. A site-directed labelling approach was used to attach thiol-reactive probes to cysteines introduced into transmembrane segment 6 (TM6) in order to perturb function and infer involvement of specific residues in drug binding and/or interdomain communication. Covalent attachment of coumarin-maleimide at residue 339C within TM6 resulted in impaired ATP hydrolysis by P-gp. The nature of the effect was to reduce the characteristic modulation of basal activity caused by transported substrates, modulators and the potent inhibitor XR9576. Photoaffinity labelling of P-gp with [(3)H]-azidopine indicated that residue 339C does not alter drug binding per se. However, covalent modification of this residue appears to prevent conformational changes that lead to drug stimulation of ATP hydrolysis.

Communication between the nucleotide binding domains of P-glycoprotein occurs via conformational changes that involve residue 508

Our aim is to provide molecular understanding of the mechanisms underlying the (i) interaction between the two nucleotide binding domains (NBDs) and (ii) coupling between NBDs and transmembrane domains within P-glycoprotein (Pgp) during a transport cycle. To facilitate this, we have introduced a number of unique cysteine residues at surface exposed positions (E393C, S452C, I500C, N508C, and K578C) in the N-terminal NBD of Pgp, which had previously been engineered to remove endogenous cysteines. Positions of the mutations were designed using a model based on crystallographic features of prokaryotic NBDs. The single cysteine mutants were expressed in insect cells using recombinant baculovirus and the proteins purified by metal affinity chromatography by virtue of a polyhistidine tag. None of the introduced cysteine residues perturbed the function of Pgp as judged by the characteristics of drug stimulated ATP hydrolysis. The role of residues at each of the introduced sites in the catalytic cycle of Pgp was investigated by the effect of covalent conjugation with N-ethyl-maleimide (NEM). All but one mutation (K578C) was accessible to labeling with [3H]-NEM. However, perturbation of ATPase activity was only observed for the derivitized N508C isoform. The principle functional manifestation was a marked inhibition of the "basal" rate of ATP hydrolysis. Neither the extent nor potency to which a range of drugs could affect the ATPase activity were altered in the NEM conjugated N508C isoform. The results imply that the accessibility of residue 508, located in the alpha-helical subdomain of NBD1 in Pgp, is altered by the conformational changes that occur during ATP hydrolysis.

Kinetic study of the pyrolysis of miscanthus and its acid hydrolysis residue by thermogravimetric analysis

The kinetic parameters of the pyrolysis of miscanthus and its acid hydrolysis residue (AHR) were determined using thermogravimetric analysis (TGA). The AHR was produced at the University of Limerick by treating miscanthus with 5 wt.% sulphuric acid at 175 °C as representative of a lignocellulosic acid hydrolysis product. For the TGA experiments, 3 to 6 g of sample, milled and sieved to a particle size below 250 μm, were placed in the TGA ceramic crucible. The experiments were carried out under non-isothermal conditions heating the samples from 50 to 900 °C at heating rates of 2.5, 5, 10, 17 and 25 °C/min. The activation energy (EA) of the decomposition process was determined from the TGA data by differential analysis (Friedman) and three isoconversional methods of integral analysis (Kissinger–Akahira–Sunose, Ozawa–Flynn–Wall, Vyazovkin). The activation energy ranged from 129 to 156 kJ/mol for miscanthus and from 200 to 376 kJ/mol for AHR increasing with increasing conversion. The reaction model was selected using the non-linear least squares method and the pre-exponential factor was calculated from the Arrhenius approximation. The results showed that the best fitting reaction model was the third order reaction for both feedstocks. The pre-exponential factor was in the range of 5.6 × 1010 to 3.9 × 10+ 13 min− 1 for miscanthus and 2.1 × 1016 to 7.7 × 1025 min− 1 for AHR.

Residue-specific investigation of the relationship between oxidation and activity of a dual specificity phosphatase by mass spectrometry

Redox regulation of signalling pathways is critical in proliferation and apoptosis; redox imbalance can lead to pathologies such as inflammation and cancer. Vaccinia H1-related protein (VHR; DUSP3) is a dual-specificity phosphatase important in controlling MAP kinase activity during cell cycle. the active-site motif contains a cysteine that acts as a nucleophile during catalysis. We used VHR to investigate the effect of oxidation in vitro on phosphatase activity, with the aim of determining how the profile of site-specific modification related to catalytic activity. Recombinant human VHR was expressed in E. coli and purified using a GST-tag. Protein was subjected to oxidation with various concentrations of SIN-1 or tetranitromethane (TNM) as nitrating agents, or HOCl. the activity was assayed using either 3-O-methylfluorescein phosphate with fluorescence detection or PIP3 by phosphate release with malachite green. the sites of oxidation were mapped using HPLC coupled to tandem mass spectrometry on an ABSciex 5600TripleTOF following in-gel digestion. More than 25 different concentration-dependent oxidative modifications to the protein were detected, including oxidations of methionine, cysteine, histidine, lysine, proline and tyrosine, and the % oxidized peptide (versus unmodified peptide) was determined from the extracted ion chromatograms. Unsurprisingly, methionine residues were very susceptible to oxidation, but there was a significant different in the extent of their oxidation. Similarly, tyrosine residues varied greatly in their modifications: Y85 and Y138 were readily nitrated, whereas Y38, Y78 and Y101 showed little modification. Y138 must be phosphorylated for MAPK phosphatase activity, so this susceptibility impacts on signalling pathways. Di- and tri- oxidations of cysteine residues were observed, but did not correlate directly with loss of activity. Overall, the catalytic activity did not correlate with redox state of any individual residue, but the total oxidative load correlated with treatment concentration and activity. This study provides the first comprehensive analysis of oxidation modifications of VHR, and demonstrates both heterogenous oxidant effects and differential residue susceptibility in a signalling phosphatase.

Method development for the analysis of smokeless powders and organic gunshot residue by ultra performance liquid chromatography with tandem mass spectrometry

The goal of this project was to develop a rapid separation and detection method for analyzing organic compounds in smokeless powders and then test its applicability on gunshot residue (GSR) samples. In this project, a total of 20 common smokeless powder additives and their decomposition products were separated by ultra performance liquid chromatography (UPLC) and confirmed by tandem mass spectrometry (MS/MS) using multiple reaction monitoring mode (MRM). Some of the targeted compounds included diphenylamines, centralites, nitrotoluenes, nitroglycerin, and various phthalates. The compounds were ionized in the MS source using simultaneous positive and negative electrospray ionization (ESI) with negative atmospheric pressure chemical ionization (APCI) in order to detect all compounds in a single analysis. The developed UPLC/MS/MS method was applied to commercially available smokeless powders and gunshot residue samples recovered from the hands of shooters, spent cartridges, and smokeless powder retrieved from unfired cartridges. Distinct compositions were identified for smokeless powders from different manufacturers and from separate manufacturing lots. The procedure also produced specific chemical profiles when tested on gunshot residues from different manufacturers. Overall, this thesis represents the development of a rapid and reproducible procedure capable of simultaneously detecting the widest possible range of components present in organic gunshot residue.^