Assessing the risk of ocean acidification for scleractinian corals on the Great Barrier Reef

University of Technology, Sydney. Faculty of Science.Ocean acidification will impact the photo-physiology of reef-building corals as it can lead to dysfunction of the symbiosis and loss of productivity. The major objective of this thesis was to provide insight into the mechanism of CO₂₋induced bleaching and productivity loss across multiple life-history stages and interpret these findings in an ecological context. Chapter 1 provides a review of the literature investigating the photo-physiological impact of ocean acidification, emphasizing the experimental conditions in studies that observed Symbiodinium dysfunction and productivity loss. Chapter 2 presents a working hypothesis to describe the fundamental physiological aspects of coral bleaching under ocean acidification. This research investigates the response of Acropora aspera using pulse amplitude modulation (PAM) fluorometry and oxygen respirometry under increased pCO₂ with concomitant high light conditions. The dinoflagellate density and HPLC pigment analysis are utilised to characterise the CO₂₋induced bleaching response. We present a conceptual model linking photorespiration to CO₂₋induced bleaching and productivity loss. The impact of ocean acidification on coral reef ecosystems is likely to deviate from oceanic climate models due to diel modification of carbonate chemistry by community metabolism. Chapter 3 characterises the diurnal variation in carbonate chemistry at sites around Lizard Island and links this to the ocean acidification response of Acropora millepora collected from these sites. Furthermore, we utilise permutational multivariate statistical analyses to partition the variation in carbonate chemistry attributable to community composition at these sites. It was hypothesized that greater diurnal variation in carbonate chemistry may improve resilience of scleractinian corals to future ocean acidification conditions. This chapter highlights that site-specific physiological trade-offs may influence the response of reef-building corals to future ocean acidification scenarios. Chapter 4 reports a visual bleaching response in A. millepora juveniles under future ocean acidification conditions. The effect of ocean acidification on coral juveniles is hypothesised to impact Symbiodinium uptake and photochemical efficiency. We utilised the iPAM to align the photochemistry in the juveniles with their visual bleaching response and Symbiodnium type, as assessed by denaturing gradient gel electrophoresis (DGGE) of the internal transcribed spacer region 1 (ITS1) of the ribosomal genes. This study links the bleaching response with recruits containing a dominant population of Symbiodinium type D1 or D1-4, with potential implications for post-settlement survivorship and population dynamics. Lastly, in Chapter 5 the key findings of this thesis are discussed in light of the ecological implications for the Great Barrier Reef. The synopsis outlines the effect of ocean acidification on the photo-physiology, productivity, calcification, reproduction and symbiont acquisition of reef-building corals. Future avenues for research are suggested based on new research gaps revealed by this thesis with the aim to continue to provide up-to-date scientific information to policy makers and reef managers

Extensive horizontal gene transfer during Staphylococcus aureus co-colonization in vivo.

Staphylococcus aureus is a commensal and major pathogen of humans and animals. Comparative genomics of S. aureus populations suggests that colonization of different host species is associated with carriage of mobile genetic elements (MGE), particularly bacteriophages and plasmids capable of encoding virulence, resistance, and immune evasion pathways. Antimicrobial-resistant S. aureus of livestock are a potential zoonotic threat to human health if they adapt to colonize humans efficiently. We utilized the technique of experimental evolution and co-colonized gnotobiotic piglets with both human- and pig-associated variants of the lineage clonal complex 398, and investigated growth and genetic changes over 16 days using whole genome sequencing. The human isolate survived co-colonization on piglets more efficiently than in vitro. During co-colonization, transfer of MGE from the pig to the human isolate was detected within 4 h. Extensive and repeated transfer of two bacteriophages and three plasmids resulted in colonization with isolates carrying a wide variety of mobilomes. Whole genome sequencing of progeny bacteria revealed no acquisition of core genome polymorphisms, highlighting the importance of MGE. Staphylococcus aureus bacteriophage recombination and integration into novel sites was detected experimentally for the first time. During colonization, clones coexisted and diversified rather than a single variant dominating. Unexpectedly, each piglet carried unique populations of bacterial variants, suggesting limited transmission of bacteria between piglets once colonized. Our data show that horizontal gene transfer occurs at very high frequency in vivo and significantly higher than that detectable in vitro

Soleus Muscle as a Surrogate for Health Status in Human Heart Failure

We propose the hypothesis that soleus muscle function may provide a surrogate measure of functional capacity in patients with heart failure. We summarize literature pertaining to skeletal muscle as a locus of fatigue and present our recent findings, using in vivo imaging in combination with biomechanical experimentation and modeling, to reveal novel structure-function relationships in chronic heart failure skeletal muscle and gait

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression.

The unintended consequences of gene targeting in mouse models have not been thoroughly studied and a more systematic analysis is needed to understand the frequency and characteristics of off-target effects. Using RNA-seq, we evaluated targeted and neighboring gene expression in tissues from 44 homozygous mutants compared with C57BL/6N control mice. Two allele types were evaluated: 15 targeted trap mutations (TRAP); and 29 deletion alleles (DEL), usually a deletion between the translational start and the 3' UTR. Both targeting strategies insert a bacterial beta-galactosidase reporter (LacZ) and a neomycin resistance selection cassette. Evaluating transcription of genes in +/- 500 kb of flanking DNA around the targeted gene, we found up-regulated genes more frequently around DEL compared with TRAP alleles, however the frequency of alleles with local down-regulated genes flanking DEL and TRAP targets was similar. Down-regulated genes around both DEL and TRAP targets were found at a higher frequency than expected from a genome-wide survey. However, only around DEL targets were up-regulated genes found with a significantly higher frequency compared with genome-wide sampling. Transcriptome analysis confirms targeting in 97% of DEL alleles, but in only 47% of TRAP alleles probably due to non-functional splice variants, and some splicing around the gene trap. Local effects on gene expression are likely due to a number of factors including compensatory regulation, loss or disruption of intragenic regulatory elements, the exogenous promoter in the neo selection cassette, removal of insulating DNA in the DEL mutants, and local silencing due to disruption of normal chromatin organization or presence of exogenous DNA. An understanding of local position effects is important for understanding and interpreting any phenotype attributed to targeted gene mutations, or to spontaneous indels

Measuring Coverage of Prolog Programs Using Mutation Testing

Testing is an important aspect in professional software development, both to avoid and identify bugs as well as to increase maintainability. However, increasing the number of tests beyond a reasonable amount hinders development progress. To decide on the completeness of a test suite, many approaches to assert test coverage have been suggested. Yet, frameworks for logic programs remain scarce. In this paper, we introduce a framework for Prolog programs measuring test coverage using mutations. We elaborate the main ideas of mutation testing and transfer them to logic programs. To do so, we discuss the usefulness of different mutations in the context of Prolog and empirically evaluate them in a new mutation testing framework on different examples.Comment: 16 pages, Accepted for presentation in WFLP 201

Muscle size explains low passive skeletal muscle force in heart failure patients.

BACKGROUND: Alterations in skeletal muscle function and architecture have been linked to the compromised exercise capacity characterizing chronic heart failure (CHF). However, how passive skeletal muscle force is affected in CHF is not clear. Understanding passive force characteristics in CHF can help further elucidate the extent to which altered contractile properties and/or architecture might affect muscle and locomotor function. Therefore, the aim of this study was to investigate passive force in a single muscle for which non-invasive measures of muscle size and estimates of fiber force are possible, the soleus (SOL), both in CHF patients and age- and physical activity-matched control participants. METHODS: Passive SOL muscle force and size were obtained by means of a novel approach combining experimental data (dynamometry, electromyography, ultrasound imaging) with a musculoskeletal model. RESULTS: We found reduced passive SOL forces (∼30%) (at the same relative levels of muscle stretch) in CHF vs. healthy individuals. This difference was eliminated when force was normalized by physiological cross sectional area, indicating that reduced force output may be most strongly associated with muscle size. Nevertheless, passive force was significantly higher in CHF at a given absolute muscle length (non length-normalized) and likely explained by the shorter muscle slack lengths and optimal muscle lengths measured in CHF compared to the control participants. This later factor may lead to altered performance of the SOL in functional tasks such gait. DISCUSSION: These findings suggest introducing exercise rehabilitation targeting muscle hypertrophy and, specifically for the calf muscles, exercise that promotes muscle lengthening

Mean first-passage times of non-Markovian random walkers in confinement

The first-passage time (FPT), defined as the time a random walker takes to reach a target point in a confining domain, is a key quantity in the theory of stochastic processes. Its importance comes from its crucial role to quantify the efficiency of processes as varied as diffusion-limited reactions, target search processes or spreading of diseases. Most methods to determine the FPT properties in confined domains have been limited to Markovian (memoryless) processes. However, as soon as the random walker interacts with its environment, memory effects can not be neglected. Examples of non Markovian dynamics include single-file diffusion in narrow channels or the motion of a tracer particle either attached to a polymeric chain or diffusing in simple or complex fluids such as nematics \cite{turiv2013effect}, dense soft colloids or viscoelastic solution. Here, we introduce an analytical approach to calculate, in the limit of a large confining volume, the mean FPT of a Gaussian non-Markovian random walker to a target point. The non-Markovian features of the dynamics are encompassed by determining the statistical properties of the trajectory of the random walker in the future of the first-passage event, which are shown to govern the FPT kinetics.This analysis is applicable to a broad range of stochastic processes, possibly correlated at long-times. Our theoretical predictions are confirmed by numerical simulations for several examples of non-Markovian processes including the emblematic case of the Fractional Brownian Motion in one or higher dimensions. These results show, on the basis of Gaussian processes, the importance of memory effects in first-passage statistics of non-Markovian random walkers in confinement.Comment: Submitted version. Supplementary Information can be found on the Nature website : http://www.nature.com/nature/journal/v534/n7607/full/nature18272.htm

Topics in Quantum Computers

I provide an introduction to quantum computers, describing how they might be realized using language accessible to a solid state physicist. A listing of the minimal requirements for creating a quantum computer is given. I also discuss several recent developments in the area of quantum error correction, a subject of importance not only to quantum computation, but also to some aspects of the foundations of quantum theory.Comment: 22 pages, Latex, 1 eps figure, Paper to be published in "Mesoscopic Electron Transport", edited by L. Kowenhoven, G. Schoen and L. Sohn, NATO ASI Series E, Kluwer Ac. Publ., Dordrecht. v2: typos in refrences fixe

Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine

D-cycloserine is an antibiotic which targets sequential bacterial cell wall peptidoglycan biosynthesis enzymes: alanine racemase and D-alanine:D-alanine ligase. By a combination of structural, chemical and mechanistic studies here we show that the inhibition of D-alanine:D-alanine ligase by the antibiotic D-cycloserine proceeds via a distinct phosphorylated form of the drug. This mechanistic insight reveals a bimodal mechanism of action for a single antibiotic on different enzyme targets and has significance for the design of future inhibitor molecules based on this chemical structure

Dynamics of multi-stage infections on networks

This paper investigates the dynamics of infectious diseases with a nonexponentially distributed infectious period. This is achieved by considering a multistage infection model on networks. Using pairwise approximation with a standard closure, a number of important characteristics of disease dynamics are derived analytically, including the final size of an epidemic and a threshold for epidemic outbreaks, and it is shown how these quantities depend on disease characteristics, as well as the number of disease stages. Stochastic simulations of dynamics on networks are performed and compared to output of pairwise models for several realistic examples of infectious diseases to illustrate the role played by the number of stages in the disease dynamics. These results show that a higher number of disease stages results in faster epidemic outbreaks with a higher peak prevalence and a larger final size of the epidemic. The agreement between the pairwise and simulation models is excellent in the cases we consider