Towards a verified mechanistic model of plankton population dynamics

Plankton are a signicant component of the biogeochemical cycles that impact on the global climate. Plankton ecosystems constitute around 40 % of the annual global primary productivity, and the sinking of plankton to the deep ocean (the so-called biological pump) is the largest permanent loss of carbon from the coupled atmosphere-surface ocean-land system. The biological pump need only increase by 25 % to cancel the anthropogenically-released ux of CO2 into the atmosphere. Mechanistic models of atmosphere-ocean dynamics have proved to have superior predictive capabilities on climate phenomena, such as the El Ni~no, than empirical models. Mechanistic models are based on fundamental laws describing the underlying processes controlling a particular system. Existing plankton population models are primarily empirical, raising doubts to their ability to forecast the behaviour of the plankton system, especially in an altered global climate. This thesis works towards a mechanistic model of plankton population dynamics based primarily on physical laws, and using laboratory-determined parameters. The processes modelled include: diusion and convection to the cell surface, light capture by photosynthetic pigments, sinking and encounter rates of predators and prey. The growth of phytoplankton cells is modelled by analogy to chemical kinetics. The equations describing each process are veried by comparison to existing laboratory experiments. Process-based model verication is proposed as a superior diagnostic tool for model validation than verication based on the changing state of the system over time. To increase our ability to undertake process-based verication, a model of stable isotope fractionation during phytoplankton growth is developed and tested. The developed model has been written to complement other process-based models of biogeochemical cycles. A suite of process-based, biogeochemical models, coupled to an atmosphere-ocean circulation model, will have superior predictive capabilities compared with present global climate models

Differential spontaneous folding of mycolic acids from Mycobacterium tuberculosis

AbstractMycolic acids are structural components of the mycobacterial cell wall that have been implicated in the pathogenicity and drug resistance of certain mycobacterial species. They also offer potential in areas such as rapid serodiagnosis of human and animal tuberculosis. It is increasingly recognized that conformational behavior of mycolic acids is very important in understanding all aspects of their function. Atomistic molecular dynamics simulations, in vacuo, of stereochemically defined Mycobacterium tuberculosis mycolic acids show that they fold spontaneously into reproducible conformational groupings. One of the three characteristic mycolate types, the keto-mycolic acids, behaves very differently from either α-mycolic acids or methoxy-mycolic acids, suggesting a distinct biological role. However, subtle conformational behavioral differences between all the three mycolic acid types indicate that cooperative interplay of individual mycolic acids may be important in the biophysical properties of the mycobacterial cell envelope and therefore in pathogenicity

The effect of natural and anthropogenic nutrient and sediment loads on coral oxidative stress on runoff-exposed reefs

Recently, corals on the Great Barrier (GBR) have suffered mass bleaching. The link between ocean warming and coral bleaching is understood to be due to temperature-dependence of complex physiological processes in the coral host and algal symbiont. Here we use a coupled catchment-hydrodynamic-biogeochemical model, with detailed zooxanthellae photophysiology including photoadaptation, photoacclimation and reactive oxygen build-up, to investigate whether natural and anthropogenic catchment loads impact on coral bleaching on the GBR. For the wet season of 2017, simulations show the cross-shelf water quality gradient, driven by both natural and anthropogenic loads, generated a contrasting zooxanthellae physiological state on inshore versus mid-shelf reefs. The relatively small catchment flows and loads delivered during 2017, however, generated small river plumes with limited impact on water quality. Simulations show the removal of the anthropogenic fraction of the catchment loads delivered in 2017 would have had a negligible impact on bleaching rates

Oral mucosal injury caused by mammalian target of rapamycin inhibitors: emerging perspectives on pathobiology and impact on clinical practice.

In recent years oral mucosal injury has been increasingly recognized as an important toxicity associated with mammalian target of rapamycin (mTOR) inhibitors, including in patients with breast cancer who are receiving everolimus. This review addresses the state-of-the-science regarding mTOR inhibitor-associated stomatitis (mIAS), and delineates its clinical characteristics and management. Given the clinically impactful pain associated with mIAS, this review also specifically highlights new research focusing on the study of the molecular basis of pain. The incidence of mIAS varies widely (2-78%). As reported across multiple mTOR inhibitor clinical trials, grade 3/4 toxicity occurs in up to 9% of patients. Managing mTOR-associated oral lesions with topical oral, intralesional, and/or systemic steroids can be beneficial, in contrast to the lack of evidence supporting steroid treatment of oral mucositis caused by high-dose chemotherapy or radiation. However, steroid management is not uniformly efficacious in all patients receiving mTOR inhibitors. Furthermore, technology does not presently exist to permit clinicians to predict a priori which of their patients will develop these lesions. There thus remains a strategic need to define the pathobiology of mIAS, the molecular basis of pain, and risk prediction relative to development of the clinical lesion. This knowledge could lead to novel future interventions designed to more effectively prevent mIAS and improve pain management if clinically significant mIAS lesions develop

A REPEATED MEASURES ANALYSIS OF THE EFFECT OF VEGETATIVE BUFFERS ON CONTAMINANT RUNOFF FROM BERMUDAGRASS TURF

A repeated measures analysis was conducted on a set of data from a multi-year study to assess the effect of vegetative buffers on the surface runoff of selected herbicides and nutrients. Multiplicative models describing the observed behavior of runoff concentration over time for buffered and non-buffered plots were fitted on a log-transformed scale using linear mixed models with PROC MIXED in PC SAS version 6.11. A spatial power covariance structure was used. Additional models for contaminant mass flow rates were fitted to evaluate the effect of buffers on total runoff mass

Impact of catchment-derived nutrients and sediments on marine water quality on the Great Barrier Reef: an application of the eReefs marine modelling system

Water quality of the Great Barrier Reef (GBR) is determined by a range of natural and anthropogenic drivers that are resolved in the eReefs coupled hydrodynamic - biogeochemical marine model forced by a process-based catchment model, GBR Dynamic SedNet. Model simulations presented here quantify the impact of anthropogenic catchment loads of sediments and nutrients on a range of marine water quality variables. Simulations of 2011–2018 show that reduction of anthropogenic catchment loads results in improved water quality, especially within river plumes. Within the 16 resolved river plumes, anthropogenic loads increased chlorophyll concentration by 0.10 (0.02–0.25) mg Chl m−3. Reductions of anthropogenic loads following proposed Reef 2050 Water Quality Improvement Plan targets reduced chlorophyll concentration in the plumes by 0.04 (0.01–0.10) mg Chl m−3. Our simulations demonstrate the impact of anthropogenic loads on GBR water quality and quantify the benefits of improved catchment management