How well-connected is the surface of the global ocean?

The Ekman dynamics of the ocean surface circulation is known to contain attracting regions such as the great oceanic gyres and the associated garbage patches. Less well-known are the extents of the basins of attractions of these regions and how strongly attracting they are. Understanding the shape and extent of the basins of attraction sheds light on the question of the strength of connectivity of different regions of the ocean, which helps in understanding the flow of buoyant material like plastic litter. Using short flow time trajectory data from a global ocean model, we create a Markov chain model of the surface ocean dynamics. The surface ocean is not a conservative dynamical system as water in the ocean follows three-dimensional pathways, with upwelling and downwelling in certain regions. Using our Markov chain model, we easily compute net surface upwelling and downwelling, and verify that it matches observed patterns of upwelling and downwelling in the real ocean. We analyze the Markov chain to determine multiple attracting regions. Finally, using an eigenvector approach, we (i) identify the five major ocean garbage patches, (ii) partition the ocean into basins of attraction for each of the garbage patches, and (iii) partition the ocean into regions that demonstrate transient dynamics modulo the attracting garbage patches

The separation of the East Australian Current: A Lagrangian approach to potential vorticity and upstream control

The East Australian Current (EAC) is the western boundary current flowing along the east coast of Australia separating from the coast at approximately 34°S. After the separation two main pathways can be distinguished, the eastward flowing Tasman Front and the extension of the EAC flowing southward. The area south of the separation latitude is eddy-rich and the separation latitude of the EAC is variable. Little is known of the properties of the water masses that separate at the bifurcation of the EAC. This paper presents new insights from the Lagrangian perspective, where the water masses that veer east and those that continue south are tracked in an eddy-permitting numerical model. The transport along the two pathways is computed, and a 1:3 ratio between transport in the EAC extension and transport in the Tasman Front is found. The results show that the "fate" of the particles is to first order already determined by the particle distribution within the EAC current upstream of the separation latitude, where 85% of the particles following the EAC extension originate from below 460 m and 90% of the particles following the Tasman Front originate from the top 460 m depth at 28°S. The separation and pathways are controlled by the structure of the isopycnals in this region. Analysis of anomalies in potential vorticity show that in the region where the two water masses overlap, the fate of the water depends on the presence of anticyclonic eddies that push isopycnals down and therefore enable particles to travel further south

Relating Agulhas leakage to the Agulhas Current retroflection location

The relation between the Agulhas Current retroflection location and the magnitude of Agulhas leakage, the transport of water from the Indian to the Atlantic Ocean, is investigated in a high-resolution numerical ocean model. Sudden eastward retreats of the Agulhas Current retroflection loop are linearly related to the shedding of Agulhas rings, where larger retreats generate larger rings. Using numerical Lagrangian floats a 37 year time series of the magnitude of Agulhas leakage in the model is constructed. The time series exhibits large amounts of variability, both on weekly and annual time scales. A linear relation is found between the magnitude of Agulhas leakage and the location of the Agulhas Current retroflection, both binned to three month averages. In the relation, a more westward location of the Agulhas Current retroflection corresponds to an increased transport from the Indian Ocean to the Atlantic Ocean. When this relation is used in a linear regression and applied to almost 20 years of altimetry data, it yields a best estimate of the mean magnitude of Agulhas leakage of 13.2 Sv. The early retroflection of 2000, when Agulhas leakage was probably halved, can be identified using the regression

Threat of plastic pollution to seabirds is global, pervasive, and increasing

Plastic pollution in the ocean is a global concern; concentrations reach 580,000 pieces per km(2) and production is increasing exponentially. Although a large number of empirical studies provide emerging evidence of impacts to wildlife, there has been little systematic assessment of risk. We performed a spatial risk analysis using predicted debris distributions and ranges for 186 seabird species to model debris exposure. We adjusted the model using published data on plastic ingestion by seabirds. Eighty of 135 (59%) species with studies reported in the literature between 1962 and 2012 had ingested plastic, and, within those studies, on average 29% of individuals had plastic in their gut. Standardizing the data for time and species, we estimate the ingestion rate would reach 90% of individuals if these studies were conducted today. Using these results from the literature, we tuned our risk model and were able to capture 71% of the variation in plastic ingestion based on a model including exposure, time, study method, and body size. We used this tuned model to predict risk across seabird species at the global scale. The highest area of expected impact occurs at the Southern Ocean boundary in the Tasman Sea between Australia and New Zealand, which contrasts with previous work identifying this area as having low anthropogenic pressures and concentrations of marine debris. We predict that plastics ingestion is increasing in seabirds, that it will reach 99% of all species by 2050, and that effective waste management can reduce this threat

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model.

A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection

Empirical Lagrangian parametrization for wind-driven mixing of buoyant particles at the ocean surface

Turbulent mixing is a vital component of vertical particulate transport, but ocean global circulation models (OGCMs) generally have low-resolution representations of near-surface mixing. Furthermore, turbulence data are often not provided in OGCM model output. We present 1D parametrizations of wind-driven turbulent mixing in the ocean surface mixed layer that are designed to be easily included in 3D Lagrangian model experiments. Stochastic transport is computed by Markov-0 or Markov-1 models, and we discuss the advantages and disadvantages of two vertical profiles for the vertical diffusion coefficient Kz. All vertical diffusion profiles and stochastic transport models lead to stable concentration profiles for buoyant particles, which for particles with rise velocities of 0.03 and 0.003 m s−1 agree relatively well with concentration profiles from field measurements of microplastics when Langmuir-circulation-driven turbulence is accounted for. Markov-0 models provide good model performance for integration time steps of Δt≈30 s and can be readily applied when studying the behavior of buoyant particulates in the ocean. Markov-1 models do not consistently improve model performance relative to Markov-0 models and require an additional parameter that is poorly constrained

The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the Thermohaline Circulation

The subtropical ocean gyres are recognized as greatmarine accummulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Oceanwas extensively sampled for floating plastic debris fromthe TaraOceans circumpolar expedition. Although plastic debris was scarce or absent in most of the Arctic waters, it reached high concentrations (hundreds of thousands of pieces per square kilometer) in the northernmost and easternmost areas of the Greenland and Barents seas. The fragmentation and typology of the plastic suggested an abundant presence of aged debris that originated from distant sources. This hypothesis was corroborated by the relatively high ratios of marine surface plastic to local pollution sources. Surface circulation models and field data showed that the poleward branch of the Thermohaline Circulation transfers floating debris from the North Atlantic to the Greenland and Barents seas, which would be a dead end for this plastic conveyor belt. Given the limited surface transport of the plastic that accumulated here and the mechanisms acting for the downward transport, the seafloor beneath this Arctic sector is hypothesized as an important sink of plastic debris

Paleo Agulhas rings enter the subtropical gyre during the penultimate deglaciation

A maximum in the strength of Agulhas leakage has been registered at the interface between the Indian and South Atlantic oceans during glacial Termination II (T-II). This presumably transported the salt and heat necessary for maintaining the Atlantic circulation at rates similar to the present day. However, it was never shown whether these waters were effectively incorporated into the South Atlantic gyre, or whether they retroflected into the Indian and/or Southern oceans. To resolve this question, we investigate the presence of paleo Agulhas rings from a sediment core on the central Walvis Ridge, almost 1800 km farther into the Atlantic Basin than previously studied. Analysis of a 60 yr data set from the global-nested INALT01 model allows us to relate density perturbations at the depth of the thermocline to the passage of individual rings over the core site. Using this relation from the numerical model as the basis for a proxy, we generate a time series of variability of individual Globorotalia truncatulinoides delta O-18. We reveal high levels of pycnocline depth variability at the site, suggesting enhanced numbers of Agulhas rings moving into the South Atlantic Gyre around T-II. Our record closely follows the published quantifications of Agulhas leakage from the east of the Cape Basin, and thus shows that Indian Ocean waters entered the South Atlantic circulation. This provides crucial support for the view of a prominent role of the Agulhas leakage in the shift from a glacial to an interglacial mode of the Atlantic circulation

Characterisation and Treatment of Pan-Human Epidermal Receptor Tyrosine Kinase Inhibitor-Induced Gastrointestinal Toxicity

The format of my thesis is as follows: two literature reviews, three research chapters, a general discussion, references and appendices. During my candidature, I made a significant effort to publish my research findings. Each chapter is presented in its original publication format, with the exception of spelling changes to keep consistent English spelling, and the references which are listed in the final chapter. This may result in slight repetition between chapters arising from the same study. My thesis has two distinct themes relating to the pathobiology of gastrointestinal toxicity second to targeted cancer treatment. The first theme aims to characterise gastrointestinal toxicity induced by dacomitinib, a pan-human epidermal receptor (HER) tyrosine kinase inhibitor (TKI) associated with high levels of diarrhoea. This theme gives rise to the first four chapters. Chapter 1 was an invited review introducing dacomitinib, highlighting the increasing incidence of gastrointestinal toxicity seen with second generation small molecule HER-TKIs and incorporating basic information required for understanding of subsequent chapters. Chapter 2 is a detailed literature review proposing chloride secretion as a mechanistic hypothesis for development of HER TKI-induced diarrhoea. Chapter 3 is my first original research chapter, which characterised dacomitinib-induced gastrointestinal toxicity in a novel rat model. Chapter 4, my second original research chapter, advances on this characterisation, and introduces crofelemer, a chloride channel blocker as a therapeutic intervention for the prevention of dacomitinib-induced diarrhoea. During my candidature, I had the opportunity to work with Assistant Professor Tom Carney from the Institute of Molecular and Cell Biology (IMCB), Biopolis, Singapore. This collaboration comprises Chapter 5, the second theme of this thesis. This chapter attempted to address the need for an innovative model for the study of gastrointestinal toxicity, investigating transgenic zebrafish reporter lines as a novel model for the study of chemotherapy and targeted therapy-induced gastrointestinal toxicity. Parts of this thesis were funded by Pfizer Pharmaceuticals under an unrestricted investigator-initiated grant (Reference #WI175212). The report I generated for this grant, which partly formed the basis of the publications presented in Chapters 3 and 4, is included as an appendix in this thesis.Thesis (Ph.D.) -- University of Adelaide, Adelaide Medical School, 201