Heat stress effects on grain sorghum productivity-biology and modelling

Heat stress can cause sterility in sorghum and the anticipated increased frequency of high temperature events implies increasing risk to sorghum productivity in Australia. Here we summarise our research on specific varietal attributes associated with heat stress tolerance in sorghum and evaluate how they might affect yield outcomes in production environments by a crop simulation analysis. We have recently conducted a range of controlled environment and field experiments to study the physiology and genetics of high temperature effects on growth and development of sorghum. Sorghum seed set was reduced by high temperature effects (>36-38oC) on pollen germination around flowering, but genotypes differed in their tolerance to high temperature stress. Effects were quantified in a manner that enabled their incorporation into the APSIM sorghum crop model. Simulation analysis indicated that risk of high temperature damage and yield loss depended on sowing date, and variety. While climate trends will exacerbate high temperature effects, avoidance by crop management and genetic tolerance seems possible.

Soil N availability, rather than N deposition, controls indirect N2O emissions

Ammonia volatilised and re-deposited to the landscape is an indirect N2O emission source. This study established a relationship between N2O emissions, low magnitude NH4 deposition (0–30  kg N ha − 1 ), and soil moisture content in two soils using in-vessel incubations. Emissions from the clay soil peaked ( < 0.002 g N [ g soil ] − 1 min − 1 ) from 85 to 93% WFPS (water filled pore space), increasing to a plateau as remaining mineral-N increased. Peak N2O emissions for the sandy soil were much lower ( < 5 × 10 − 5 μg N [ g soil ] − 1 min − 1 ) and occurred at about 60% WFPS, with an indistinct relationship with increasing resident mineral N due to the low rate of nitrification in that soil. Microbial community and respiration data indicated that the clay soil was dominated by denitrifiers and was more biologically active than the sandy soil. However, the clay soil also had substantial nitrifier communities even under peak emission conditions. A process-based mathematical denitrification model was well suited to the clay soil data where all mineral-N was assumed to be nitrified ( R 2 = 90 % ), providing a substrate for denitrification. This function was not well suited to the sandy soil where nitrification was much less complete. A prototype relationship representing mineral-N pool conversions (NO3− and NH4+) was proposed based on time, pool concentrations, moisture relationships, and soil rate constants (preliminary testing only). A threshold for mineral-N was observed: emission of N2O did not occur from the clay soil for mineral-N <70 mg ( kg of soil ) − 1 , suggesting that soil N availability controls indirect N2O emissions. This laboratory process investigation challenges the IPCC approach which predicts indirect emissions from atmospheric N deposition alone.

The biology and natural history of Tripogon loliiformis (Poaceae, Chloridoideae), an Australian resurrection grass

Tripogon loliiformis is a desiccation-tolerant grass that occurs throughout mainland Australia. There has been recent interest in this species as a model system for understanding desiccation tolerance in a native grass at the structural, molecular and physiological levels. However, not much is known about the biology and natural history of this species, despite its widespread geographic distribution and remarkable capability of withstanding prolonged drying. We provide an overview of the genus by consolidating information from a wide variety of sources. We report a variety of new and interesting observations on the general biology, ecology and desiccation response of T. loliiformis and conclude by highlighting areas for future research.

Developmental biology and prey preference of Diomus notescens Blackburn (Coleoptera: Coccinellidae): A predator of Aphis gossypii Glover (Hemiptera: Aphididae)

The minute two-spotted ladybeetle, Diomus notescens Blackburn is a common predator of aphids and other pests in Australian agricultural crops, however little is known about the biology of D. notescens. The aim of this study was to provide information on the life cycle of this predator and improve our understanding of its biological control potential, particularly against one of the major pests of cotton, Aphis gossypii Glover. In laboratory experiments, juvenile development, prey consumption, as well as adult lifespan and fecundity were studied. Results from this study revealed that D. notescens could successfully complete development on A. gossypii, which at 25 °C required 21 days and during this period they each consume 129 ± 5.2 aphids. At 25 °C adult lifespan was 77 ± 9.6 days, with a mean daily prey consumption of 28 ± 1.8 aphids and a mean daily fecundity of 8 ± 0.5 eggs. Net reproductive rate was estimated as 187 ± 25.1 females and the intrinsic rate of increase was estimated as 0.14. Juvenile development was recorded at four constant temperatures (15, 21, 26 and 27 °C) and using a linear model, the lower threshold for D. notescens development was estimated to be 10 ± 0.6 °C with 285 ± 4.7 degree days required to complete development. A prey choice experiment studying predation rates revealed a strong preference for A. gossypii nymphs compared to Bemisia tabaci Gennadius eggs.

Germination Biology and Occurrence of Polyembryony in Two Forms of Cats Claw Creeper Vine, Dolichandra unguis-cati (Bignoniaceae): Implications for Its Invasiveness and Management

Cat’s claw creeper vine, Dolichandra unguis-cati (L.) Lohmann (syn. Macfadyena unguis-cati (L.) Gentry), is a major environmental weed in Australia. Two forms of the weed with distinctive leaf morphology and reproductive traits, including varying fruit size, occur in Queensland, Australia. The long pod form occurs in a few localities in Queensland, while the short pod form is widely distributed in Queensland and northern part of New South Wales. This investigation aimed to evaluate germination behavior and occurrence of polyembryony (production of multiple seedlings from a single seed) in the two forms of the weed. Seeds were germinated in growth chambers set to 10/20°C, 15/25°C, 20/30°C, 30/45°C and 25°C, representing ambient temperature conditions of the region. Germination and polyembryony were monitored over a period of 12 weeks. For all the treatments in this study, seeds from short pod plants exhibited significantly higher germination rates and higher occurrence of polyembryony than those from long pod plants. Seeds from long pod plants did not germinate at the lowest temperature of 10/20°C; in contrast, those of the short pod form germinated under this condition, albeit at a lower rate (reaching a maximum 45% germination at week 12). Results from this study could explain why the short pod form of D. unguis-cati is the more widely distributed plants in Australia, while the long pod is confined to a few localities. The results have implication in predicting future range of both forms of the invasive D. unguis-cati, as well as inform management decisions for control of the weed.

Semi-Classical Mechanics in Phase Space: A Study of Wigner's Function

We explore the semi-classical structure of the Wigner functions ($\Psi $(q, p)) representing bound energy eigenstates $|\psi \rangle $ for systems with f degrees of freedom. If the classical motion is integrable, the classical limit of $\Psi $ is a delta function on the f-dimensional torus to which classical trajectories corresponding to ($|\psi \rangle $) are confined in the 2f-dimensional phase space. In the semi-classical limit of ($\Psi $ ($\hslash $) small but not zero) the delta function softens to a peak of order ($\hslash ^{-\frac{2}{3}f}$) and the torus develops fringes of a characteristic 'Airy' form. Away from the torus, $\Psi $ can have semi-classical singularities that are not delta functions; these are discussed (in full detail when f = 1) using Thom's theory of catastrophes. Brief consideration is given to problems raised when ($\Psi $) is calculated in a representation based on operators derived from angle coordinates and their conjugate momenta. When the classical motion is non-integrable, the phase space is not filled with tori and existing semi-classical methods fail. We conjecture that (a) For a given value of non-integrability parameter ($\epsilon $), the system passes through three semi-classical regimes as ($\hslash $) diminishes. (b) For states ($|\psi \rangle $) associated with regions in phase space filled with irregular trajectories, ($\Psi $) will be a random function confined near that region of the 'energy shell' explored by these trajectories (this region has more than f dimensions). (c) For ($\epsilon \neq $0, $\hslash $) blurs the infinitely fine classical path structure, in contrast to the integrable case ($\epsilon $ = 0, where $\hslash $ )imposes oscillatory quantum detail on a smooth classical path structure.

Find my office: Navigating real space from semantic descriptions

This paper shows that by using only symbolic language phrases, a mobile robot can purposefully navigate to specified rooms in previously unexplored environments. The robot intelligently organises a symbolic language description of the unseen environment and “imagines” a representative map, called the abstract map. The abstract map is an internal representation of the topological structure and spatial layout of symbolically defined locations. To perform goal-directed exploration, the abstract map creates a high-level semantic plan to reason about spaces beyond the robot’s known world. While completing the plan, the robot uses the metric guidance provided by a spatial layout, and grounded observations of door labels, to efficiently guide its navigation. The system is shown to complete exploration in unexplored spaces by travelling only 13.3% further than the optimal path.

Structural and Functional Studies on Trimeric Autotransporters

Trimeric autotransporters are a family of secreted outer membrane proteins in Gram-negative bacteria. These obligate homotrimeric proteins share a conserved C-terminal region, termed the translocation unit. This domain consists of an integral membrane β-barrel anchor and associated α-helices which pass through the pore of the barrel. The α-helices link to the extracellular portion of the protein, the passenger domain. Autotransportation refers to the way in which the passenger domain is secreted into the extracellular space. It appears that the translocation unit mediates the transport of the passenger domain across the outer membrane, and no external factors, such as ATP, ion gradients nor other proteins, are required. The passenger domain of autotransporters contains the specific activities of each protein. These are usually related to virulence. In trimeric autotransporters, the main function of the proteins is to act as adhesins. One such protein is the Yersinia adhesin YadA, found in enteropathogenic species of Yersinia. The main activity of YadA from Y. enterocolitica is to bind collagen, and it also mediates adhesion to other molecules of the extracellular matrix. In addition, YadA is involved in serum resistance, phagocytosis resistance, binding to epithelial cells and autoagglutination. YadA is an essential virulence factor of Y. enterocolitica, and removal of this protein from the bacteria leads to avirulence. In this study, I investigated the YadA-collagen interaction by studying the binding of YadA to collagen-mimicking peptides by several biochemical and biophysical methods. YadA bound as tightly to the triple-helical model peptide (Pro-Hyp-Gly)10 as to native collagen type I. However, YadA failed to bind a similar peptide that does not form a collagenous triple helix. As (Pro-Hyp-Gly)10 does not contain a specific sequence, we concluded that a triple-helical conformation is necessary for YadA binding, but no specific sequence is required. To further investigate binding determinants for YadA in collagens, I examined the binding of YadA to a library of collagen-mimicking peptides that span the entire triple-helical sequences of human collagens type II and type III. YadA bound promiscuously to many but not all peptides, indicating that a triple-helical conformation alone is not sufficient for binding. The high-binding peptides did not share a clear binding motif, but these peptides were rich in hydroxyproline residues and contained a low number of charged residues. YadA thus binds collagens without sequence specificity. This strategy of promiscuous binding may be advantageous for pathogenic bacteria. The Eib proteins from Escherichia coli are immunoglobulin (Ig)-binding homologues of YadA. I showed conclusively that recombinant EibA, EibC, EibD and EibF bind to IgG Fc. I crystallised a fragment of the passenger domain of EibD, which binds IgA in addition to IgG. The structure has a YadA-like head domain and an extended coiled-coil stalk. The top half of the coiled-coil is right-handed with hendecad periodicity, whereas the lower half is a canonical left-handed coiled-coil. At the transition from right- to left-handedness, a small β-sheet protrudes from each monomer. I was able to map the binding regions for IgG and IgA using truncations and site-directed mutagenesis to the coiled-coil stalk and identified residues critical for Ig binding.

Denitrification losses from an intensively managed sub-tropical pasture: Impact of soil moisture on the partitioning of N2 and N2O emissions

Intensively managed pastures in subtropical Australia under dairy production are nitrogen (N) loaded agro-ecosystems, with an increased pool of N available for denitrification. The magnitude of denitrification losses and N2:N2O partitioning in these agro-ecosystems is largely unknown, representing a major uncertainty when estimating total N loss and replacement. This study investigated the influence of different soil moisture contents on N2 and N2O emissions from a subtropical dairy pasture in Queensland, Australia. Intact soil cores were incubated over 15 days at 80% and 100% water-filled pore space (WFPS), after the application of 15N labelled nitrate, equivalent to 50 kg N ha−1. This setup enabled the direct quantification of N2 and N2O emissions following fertilisation using the 15N gas flux method. The main product of denitrification in both treatments was N2. N2 emissions exceeded N2O emissions by a factor of 8 ± 1 at 80% WFPS and a factor of 17 ± 2 at 100% WFPS. The total amount of N-N2 lost over the incubation period was 21.27 kg ± 2.10 N2-N ha−1 at 80% WFPS and 25.26 kg ± 2.79 kg ha−1 at 100% WFPS respectively. N2 emissions remained high at 100% WFPS, while related N2O emissions decreased. At 80% WFPS, N2 emissions increased constantly over time while N2O fluxes declined. Consequently, N2/(N2 + N2O) product ratios increased over the incubation period in both treatments. N2/(N2 + N2O) product ratios responded significantly to soil moisture, confirming WFPS as a key driver of denitrification. The substantial amount of fertiliser lost as N2 reveals the agronomic significance of denitrification as a major pathway of N loss for sub-tropical pastures at high WFPS and may explain the low fertiliser N use efficiency observed for these agro-ecosystems.

Chemistry and biology of DNA methyltransferases

Recognition of a specific DNA sequence by a protein is probably the best example of macromolecular interactions leading to various events. It is a prerequisite to understanding the basis of protein-DNA interactions to obtain a better insight into fundamental processes such as transcription, replication, repair, and recombination. DNA methyltransferases with varying sequence specificities provide an excellent model system for understanding the molecular mechanism of specific DNA recognition. Sequence comparison of cloned genes, along with mutational analyses and recent crystallographic studies, have clearly defined the functions of various conserved motifs. These enzymes access their target base in an elegant manner by flipping it out of the DNA double helix. The drastic protein-induced DNA distortion, first reported for HhaI DNA methyltransferase, appears to be a common mechanism employed by various proteins that need to act on bases. A remarkable feature of the catalytic mechanism of DNA (cytosine-5) methyltransferases is the ability of these enzymes to induce deamination of the target cytosine in the absence of S-adenosyl-L-methionine or its analogs. The enzyme-catalyzed deamination reaction is postulated to be the major cause of mutational hotspots at CpG islands responsible for various human genetic disorders. Methylation of adenine residues in Escherichia coli is known to regulate various processes such as transcription, replication, repair, recombination, transposition, and phage packaging.

Ecological communities in variable environments : dynamics and diversity under coloured environmental stochasticity

While environmental variation is an ubiquitous phenomenon in the natural world which has for long been appreciated by the scientific community recent changes in global climatic conditions have begun to raise consciousness about the economical, political and sociological ramifications of global climate change. Climate warming has already resulted in documented changes in ecosystem functioning, with direct repercussions on ecosystem services. While predicting the influence of ecosystem changes on vital ecosystem services can be extremely difficult, knowledge of the organisation of ecological interactions within natural communities can help us better understand climate driven changes in ecosystems. The role of environmental variation as an agent mediating population extinctions is likely to become increasingly important in the future. In previous studies population extinction risk in stochastic environmental conditions has been tied to an interaction between population density dependence and the temporal autocorrelation of environmental fluctuations. When populations interact with each other, forming ecological communities, the response of such species assemblages to environmental stochasticity can depend, e.g., on trophic structure in the food web and the similarity in species-specific responses to environmental conditions. The results presented in this thesis indicate that variation in the correlation structure between species-specific environmental responses (environmental correlation) can have important qualitative and quantitative effects on community persistence and biomass stability in autocorrelated (coloured) environments. In addition, reddened environmental stochasticity and ecological drift processes (such as demographic stochasticity and dispersal limitation) have important implications for patterns in species relative abundances and community dynamics over time and space. Our understanding of patterns in biodiversity at local and global scale can be enhanced by considering the relevance of different drift processes for community organisation and dynamics. Although the results laid out in this thesis are based on mathematical simulation models, they can be valuable in planning effective empirical studies as well as in interpreting existing empirical results. Most of the metrics considered here are directly applicable to empirical data.