David Day | The University of Western Australia (original) (raw)

Papers by David Day

Advances in Photosynthesis and Respiration, 2000

The relationships between photosynthesis, carbohydrate metabolism and respiration in leaves of pl... more The relationships between photosynthesis, carbohydrate metabolism and respiration in leaves of plants are reviewed. We first provide an overview of how mitochondrial respiration relies on, and responds to, the supply of photosynthetic products in the light. The pathways by which the various substrates (glycine, oxaloacetate, malate and/or pyruvate) enter the mitochondria and are oxidized, are discussed. We also provide an overview of the pathways of mitochondrial electron transport, with particular attention being paid to the non-phosphorylating alternative oxidase (AOX). We then discuss what is known about leaf respiration rates in light versus darkness (both consumption and release). The extent to which mitochondrial consumption continues in the light is highly variable, being inhibited, not affected or even stimulated in various reports. On the other hand, non-photorespiratory mitochondrial release (R) is invariably inhibited by light (5-80% inhibition). R is sensitive to the lowest irradiance values, and is inhibited rapidly. Three methods via which R in the light is measured are outlined and mechanisms via which light might inhibit R are discussed. The effect that light to dark transitions have on respiration are also discussed: we distinguish the initial, photorespiratory postillumination burst (PIB) from the post-illumination rise in respiration (LEDR, light-enhanced-dark-respiration) which occurs following the PIB. The chapter also considers the demand for mitochondrially-derived ATP for photosynthesis and carbohydrate metabolism and the potential role of respiration during over-reduction of the chloroplast is highlighted. Mitochondrial respiration appears to be critical for the provision of ATP necessary for energy demanding processes in the light. Moreover, there is growing evidence that respiration helps a plant cope with excess photosynthetic redox equivalents, which otherwise can result in photo-oxidative stress.

Lecture Notes in Computer Science, 1995

The increasing availability of advanced-architecture computers is having a very signi cant e ect ... more The increasing availability of advanced-architecture computers is having a very signi cant e ect on all spheres of scienti c computation, including algorithm research and software development in numerical linear algebra. Linear algebra {in particular, the solution of linear systems of equations and eigenvalue problems { lies at the heart of most calculations in scienti c computing. This chapter discusses some of the recent developments in linear algebra designed to help the user on advanced-architecture computers. Much of the work in developing linear algebra software for advanced-architecture computers is motivated by the need to solve large problems on the fastest computers available. In this chapter, we focus on four basic issues: (1) the motivation for the work; (2) the development of standards for use in linear algebra and the building blocks for a library; (3) aspects of templates for the solution of large sparse systems of linear algorithm; and (4) templates for the solution of large sparse eigenvalue problems. This last project is under development and we will pay more attention to it in this chapter.

Atmospheric Chemistry and Physics Discussions, 2011

Carboxylic acids are ubiquitous in atmospheric particles, and they play an important role in the ... more Carboxylic acids are ubiquitous in atmospheric particles, and they play an important role in the physical and chemical properties of aerosol particles. During measurements in coastal California in the summer of 2009, carboxylic acid functional groups were highly associated with trajectories from an industrial region with high organic mass (OM), likely from fossil fuel combustion emissions. The concentration of carboxylic

Proceedings of the fifth conference on Applied natural language processing -, 1997

Historically, tailoring language processing systems to specific domains and languages for which t... more Historically, tailoring language processing systems to specific domains and languages for which they were not originally built has required a great deal of effort. Recent advances in corpus-based manual and automatic training methods have shown promise in reducing the time and cost of this porting process.

Approximate counting [18] is useful for data stream and database summarization. It can help in ma... more Approximate counting [18] is useful for data stream and database summarization. It can help in many settings that allow only one pass over the data, want low memory usage, and can accept some relative error. Approximate counters use fewer bits; we focus on 8-bits but our results are general. These small counters represent a sparse sequence of larger numbers. Counters are incremented probabilistically based on the spacing between the numbers they represent. Our contributions are a customized distribution of counter values and efficient strategies for deciding when to increment them. At run-time, users may independently select the spacing (accuracy) of the approximate counter for small, medium, and large values. We allow the user to select the maximum number to count up to, and our algorithm will select the exponential base of the spacing. These provide additional flexibility over both classic and Csűrös's [4] floating-point approximate counting. These provide additional structure...

Journal of Interpersonal Violence, 2012

Understanding the developmental precursors of juvenile violent sex offending can contribute to th... more Understanding the developmental precursors of juvenile violent sex offending can contribute to the promotion of effective early intervention and prevention programs for high-risk children and youth. However, there is currently a lack of research on the early characteristics of adolescents who commit violent sex offenses. Drawing on the literature regarding the generalist and specialist positions of criminal behavior, the aim

We have developed a software framework that will support experiments to explore the role of trans... more We have developed a software framework that will support experiments to explore the role of translator resources and tools in the performance of translation and translation-related activities. This software environment brings together a wide range of resources and tools within a single work environment that has been instrumented to measure the actions of the translator. In this paper we present

Proceedings of the first international conference on Human language technology research - HLT '01, 2001

As part of MITRE's work under the DARPA TIDES (Translingual Information Detection, Extraction and... more As part of MITRE's work under the DARPA TIDES (Translingual Information Detection, Extraction and Summarization) program, we are preparing a series of demonstrations to showcase the TIDES Integrated Feasibility Experiment on Bio-Security (IFE-Bio).

The launching of an oceanographic expedition has its own brand of excitement, with the sound of t... more The launching of an oceanographic expedition has its own brand of excitement, with the sound of the main engines firing up, and the lifting of the gangway in a foreign port, as the team of scientists and crew sets out for a month at sea with only the resources they have aboard. Although this adventure is broadly appealing, very few have the privilege of actually joining an expedition. With the "SIOExplorer" family of projects we are now beginning to open this experience across cyberspace to a wide range of students and teachers. What began two years ago as an effort to stabilize the Scripps Institution of Oceanography (SIO) data archives from more than 700 cruises going back 50 years, has now become an operational component of the National Science Digital Library (NSDL; www.nsdl.org), complete with thousands of historic photographs, full text documents and D visualization experiences. Our initial emphasis has been on marine geology and geophysics, in particular multibeam s...

SIAM Journal on Matrix Analysis and Applications, 1999

This work presents an Adaptive Block Lanczos method for large scale non-Hermitian Eigenvalue prob... more This work presents an Adaptive Block Lanczos method for large scale non-Hermitian Eigenvalue problems (henceforth the ABLE method). The ABLE method is a block version of the non-Hermitian Lanczos algorithm. There are three innovations. First an adaptive blocksize scheme cures (near) breakdown and adapts the blocksize to the order of multiple or clustered eigenvalues. Second stopping criteria are developed that exploit the quadratic convergence property of the method. Third a well-known technique from the Hermitian Lanczos algorithm is generalized to monitor the loss of duality and maintain semi-duality among the computed Lanczos vectors. Each innovation is theoretically justi ed. Academic model problems and real application problems are solved to demonstrate the robustness and e ectiveness of this competitive method. 1 1 INTRODUCTION 2 respectively. LANCZOS 14], LASO 46, 55] and LANZ 30] are Lanczos based algorithms for solving large scale symmetric eigenvalue problems. All corresponding software can be obtained from netlib@ornl.gov, a software distribution system. Block Lanczos algorithms for Hermitian eigenvalue problems are developed in , and a state-of-the-art implementation is described in 26]. Lanczos based procedures have emerged as the methods of choice for large sparse partial Hermitian eigenvalue problems.

PROTEOMICS, 2007

Redox active proteins in plant mitochondria were examined using 2-D oxidant/reductant diagonal-SD... more Redox active proteins in plant mitochondria were examined using 2-D oxidant/reductant diagonal-SDS-PAGE to separate and identify proteins with intermolecular or intramolecular disulphide bonds using diamide in the first dimension and DTT in the second dimension. Eighteen proteins spots were resolved either above or below the diagonal and these were in-gel digested and identified by MS/MS. This analysis revealed intermolecular disulphide bonds in alternative oxidase, O-acetylserine (thiol) lyase, citrate synthase and between subunits of the ATP synthase. Intramolecular disulphide bonds were observed in a range of mitochondrial dehydrogenases, elongation factor Tu, adenylate kinase and the phosphate translocator. Many of the soluble proteins found were known glutaredoxin/thioredoxin targets in other plants, but the membrane proteins were not found by these methods nor were the nature of the disulphides able to be investigated. The accessibility of thiols involved in disulphide bonds to modification by a lipid derived aldehyde gave an insight into the potential impact of Cys modification on redoxfunctions in mitochondria during lipid peroxidation. Comparison of the protein sequences of the identified proteins with homologs from other species has identified specific Cys residues that may be responsible for plant-specific redox modulations of mitochondrial proteins.

Plant, Cell & Environment, 2008

We examined the effect of short-and long-term changes in temperature on gene expression, protein ... more We examined the effect of short-and long-term changes in temperature on gene expression, protein abundance, and the activity of the alternative oxidase and cytochrome oxidase pathways (AOP and COP, respectively) in Arabidopsis thaliana. The AOP was more sensitive to short-term changes in temperature than the COP, with partitioning to the AOP decreasing significantly below a threshold temperature of 20°C. AOP activity was increased in leaves, which had been shifted to the cold for several days, but this response was transient, with AOP activity subsiding (and COP activity increasing) following the development of leaves in the cold. The transient increase in AOP activity in 10-d cold-shifted leaves was not associated with an increase in alternative oxidase (AOX) protein or AOX1a transcript abundance. By contrast, the amount of uncoupling protein was significantly increased in cold-developed leaves. In conjunction with this, transcript levels of the uncoupling protein-encoding gene UCP1 and the external NAD(P)H dehydrogenase-encoding gene NDB2 exhibited sustained increases following growth in the cold. The data suggest a role for each of these alternative non-phosphorylating bypasses of mitochondrial electron transport at different points in time following exposure to cold, with increased AOP activity being important only in the early stages of cold treatment.

PLANT PHYSIOLOGY, 1997

The alternative oxidase (AOX) of the soybean (Glycine max 1.) inner mitochondrial membrane is enc... more The alternative oxidase (AOX) of the soybean (Glycine max 1.) inner mitochondrial membrane is encoded by a multigene family (Aox) with three known members. Here, the Aox2 and Aox3 primary translation products, deduced from cDNA analysis, were found to be 38.1 and 36.4 kD, respectively. Direct N-terminal sequencing of partially purified AOX from cotyledons demonstrates that the mature proteins are 31.8 and 31.6 kD, respectively, implying that processing occurs upon import of these proteins into the mitochondrion. Sequence comparisons show that the processing of plant AOX proteins occurs ata characteristic site and that the AOX2 and AOX3 proteins are more similar to one another than to other AOX proteins, including soybean AOXl . Transcript analysis using a Abbreviations: AOX, alternative oxidase; ORF, open reading frame; RACE, rapid amplification of cDNA ends; RT-PCR, reverse transcriptase PCR; SMP, submitochondrial particle; UQ, ubiquinone. 455 www.plant.org on August 5, 2015 -Published by www.plantphysiol.org Downloaded from

PLANT PHYSIOLOGY, 1998

Changes in the respiratory rate and the contribution of the cytochrome (Cyt) c oxidase and altern... more Changes in the respiratory rate and the contribution of the cytochrome (Cyt) c oxidase and alternative oxidase (COX and AOX, respectively) were investigated in soybean (Glycine max L. cv Stevens) root seedlings using the 18 O-discrimination method. In 4-d-old roots respiration proceeded almost entirely via COX, but by d 17 more than 50% of the flux occurred via AOX. During this period the capacity of COX, the theoretical yield of ATP synthesis, and the root relative growth rate all decreased substantially. In extracts from whole roots of different ages, the ubiquinone pool was maintained at 50% to 60% reduction, whereas pyruvate content fluctuated without a consistent trend. In whole-root immunoblots, AOX protein was largely in the reduced, active form at 7 and 17 d but was partially oxidized at 4 d. In isolated mitochondria, Cyt pathway and succinate dehydrogenase capacities and COX I protein abundance decreased with root age, whereas both AOX capacity and protein abundance remained unchanged. The amount of mitochondrial protein on a dry-mass basis did not vary significantly with root age. It is concluded that decreases in whole-root respiration during growth of soybean seedlings can be largely explained by decreases in maximal rates of electron transport via COX. Flux via AOX is increased so that the ubiquinone pool is maintained in a moderately reduced state.

PLANT PHYSIOLOGY, 2004

Lipoic acid-dependent pathways of ␣-keto acid oxidation by mitochondria were investigated in pea ... more Lipoic acid-dependent pathways of ␣-keto acid oxidation by mitochondria were investigated in pea (Pisum sativum), rice (Oryza sativa), and Arabidopsis. Proteins containing covalently bound lipoic acid were identified on isoelectric focusing/ sodium dodecyl sulfate-polyacrylamide gel electrophoresis separations of mitochondrial proteins by the use of antibodies raised to this cofactor. All these proteins were identified by tandem mass spectrometry. Lipoic acid-containing acyltransferases from pyruvate dehydrogenase complex and ␣-ketoglutarate dehydrogenase complex were identified from all three species. In addition, acyltransferases from the branched-chain dehydrogenase complex were identified in both Arabidopsis and rice mitochondria. The substrate-dependent reduction of NAD ϩ was analyzed by spectrophotometry using specific ␣-keto acids. Pyruvate-and ␣-ketoglutarate-dependent reactions were measured in all three species. Activity of the branched-chain dehydrogenase complex was only measurable in Arabidopsis mitochondria using substrates that represented the ␣-keto acids derived by deamination of branched-chain amino acids (Val [valine], leucine, and isoleucine). The rate of branched-chain amino acid-and ␣-keto acid-dependent oxygen consumption by intact Arabidopsis mitochondria was highest with Val and the Val-derived ␣-keto acid, ␣-ketoisovaleric acid. Sequencing of peptides derived from trypsination of Arabidopsis mitochondrial proteins revealed the presence of many of the enzymes required for the oxidation of all three branched-chain amino acids. The potential role of branched-chain amino acid catabolism as an oxidative phosphorylation energy source or as a detoxification pathway during plant stress is discussed. fax 61-8 -9380 -1148.

PLANT PHYSIOLOGY, 1991

External NADH and succinate were oxidized at similar rates by soybean (Glycine max) cotyledon and... more External NADH and succinate were oxidized at similar rates by soybean (Glycine max) cotyledon and leaf mitochondria when the cytochrome chain was operating, but the rate of NADH oxidation via the alternative oxidase was only half that of succinate. However, measurements of the redox poise of the endogenous quinone pool and reduction of added quinones revealed that external NADH reduced them to the same, or greater, extent than did succinate. A kinetic analysis of the relationship between alternative oxidase activity and the redox state of ubiquinone indicated that the degree of ubiquinone reduction during extemal NADH oxidation was sufficient to fully engage the altemative oxidase. Measurements of NADH oxidation in the presence of succinate showed that the two substrates competed for cytochrome chain activity but not for altemative oxidase activity. Both reduced 0-1 and duroquinone were readily oxidized by the cytochrome oxidase pathway but only slowly by the alternative oxidase pathway in soybean mitochondria. In mitochondria isolated from the thermogenic spadix of Philodendron selloum, on the other hand, quinol oxidation via the altemative oxidase was relatively rapid; in these mitochondria, external NADH was also oxidized readily by the alternative oxidase. Antibodies raised against alternative oxidase proteins from Sauromatum guttatum cross-reacted with proteins of similar molecular size from soybean mitochondria, indicating similarities between the two alternative oxidases. However, it appears that the organization of the respiratory chain in soybean is different, and we suggest that some segregation of electron transport chain components may exist in mitochondria from nonthermogenic plant tissues.

PLANT PHYSIOLOGY, 2008

Mitochondrial complex I is a major avenue for reduced NAD oxidation linked to oxidative phosphory... more Mitochondrial complex I is a major avenue for reduced NAD oxidation linked to oxidative phosphorylation in plants. However, the plant enzyme has structural and functional features that set it apart from its counterparts in other organisms, raising questions about the physiological significance of this complex in plants. We have developed an experimental model in which rotenone, a classic complex I inhibitor, has been applied to Arabidopsis (Arabidopsis thaliana) cell suspension cultures in order to dissect early metabolic adjustments involved in cell acclimation to mitochondrial dysfunction. Rotenone induced a transitory decrease in cellular respiration (0-4 h after treatment). Cell respiration then progressively recovered and reached a steady state at 10 to 12 h after treatment. Complex I inhibition by rotenone did not induce obvious oxidative stress or cell death but affected longer term cell growth. Integrated analyses of gene expression, the mitochondrial proteome, and changes in primary metabolism indicated that rotenone treatment caused changes in mitochondrial function via alterations in specific components. A physical disengagement of glycolytic activities associated with the mitochondrial outer membrane was observed, and the tricarboxylic acid cycle was altered. Amino acid and organic acid pools were also modified by rotenone treatment, with a marked early decrease of 2-oxoglutarate, aspartate, and glutamine pools. These data demonstrate that, in Arabidopsis cells, complex I inhibition by rotenone induces significant remodeling of metabolic pathways involving the mitochondria and other compartments and point to early metabolic changes in response to mitochondrial dysfunction.

PLANT PHYSIOLOGY, 2005

The effect of water stress on respiration and mitochondrial electron transport has been studied i... more The effect of water stress on respiration and mitochondrial electron transport has been studied in soybean (Glycine max) leaves, using the oxygen-isotope-fractionation technique. Treatments with three levels of water stress were applied by irrigation to replace 100%, 50%, and 0% of daily water use by transpiration. The levels of water stress were characterized in terms of lightsaturated stomatal conductance (g s ): well irrigated (g s . 0.2 mol H 2 O m 22 s 21 ), mildly water stressed ( g s between 0.1 and 0.2 mol H 2 O m 22 s 21 ), and severely water stressed (g s , 0.1 mol H 2 O m 22 s 21 ). Although net photosynthesis decreased by 40% and 70% under mild and severe water stress, respectively, the total respiratory oxygen uptake (V t ) was not significantly different at any water-stress level. However, severe water stress caused a significant shift of electrons from the cytochrome to the alternative pathway. The electron partitioning through the alternative pathway increased from 10% to 12% under well-watered or mild water-stress conditions to near 40% under severe water stress. Consequently, the calculated rate of mitochondrial ATP synthesis decreased by 32% under severe water stress. Unlike many other stresses, water stress did not affect the levels of mitochondrial alternative oxidase protein. This suggests a biochemical regulation (other than protein synthesis) that causes this mitochondrial electron shift. fax 34-971-173184.

Plant Molecular Biology, 2005

Plant mitochondria contain non-phosphorylating bypasses of the respiratory chain, catalysed by th... more Plant mitochondria contain non-phosphorylating bypasses of the respiratory chain, catalysed by the alternative oxidase (AOX) and alternative NADH dehydrogenases (NDH), as well as uncoupling (UCP) protein. Each of these components either circumvents or short-circuits proton translocation pathways, and each is encoded by a small gene family in Arabidopsis. Whole genome microarray experiments were performed with suspension cell cultures to examine the effects of various 3 h treatments designed to induce abiotic stress. The expression of over 60 genes encoding components of the classical, phosphorylating respiratory chain and tricarboxylic acid cycle remained largely constant when cells were subjected to a broad range of abiotic stresses, but expression of the alternative components responded differentially to the various treatments. In detailed time-course quantitative PCR analysis, specific members of both AOX and NDH gene families displayed coordinated responses to treatments. In particular, the co-expression of AOXla and NDB2 observed under a number of treatments suggested co-regulation that may be directed by common sequence elements arranged hierarchically in the upstream promoter regions of these genes. A series of treatment sets were identified, representing the response of specific AOX and NDH genes to mitochondrial inhibition, plastid inhibition and abiotic stresses. These treatment sets emphasise the multiplicity of pathways affecting alternative electron transport components in plants.