Generation of realistic white matter substrates with controllable morphology for diffusion MRI simulations

Numerical phantoms have played a key role in the development of diffusion MRI (dMRI) techniques seeking to estimate features of the microscopic structure of tissue by providing a ground truth for simulation experiments against which we can validate and compare techniques. One common limitation of numerical phantoms which represent white matter (WM) is that they oversimplify the true complex morphology of the tissue which has been revealed through ex vivo studies. It is important to try to generate WM numerical phantoms that capture this realistic complexity in order to understand how it impacts the dMRI signal. This thesis presents work towards improving the realism of WM numerical phantoms by generating fibres mimicking natural fibre genesis. A novel phantom generator is presented which was developed over two works, resulting in Contextual Fibre Growth (ConFiG). ConFiG grows fibres one-by-one, following simple rules motivated by real axonal guidance mechanisms. These simple rules enable ConFiG to generate phantoms with tuneable microstructural features by growing fibres while attempting to meet morphological targets such as user-specified density and orientation distribution. We compare ConFiG to the state-of-the-art approach based on packing fibres together by generating phantoms in a range of fibre configurations including crossing fibre bundles and orientation dispersion. Results demonstrate that ConFiG produces phantoms with up to 20% higher densities than the state-of-the-art, particularly in complex configurations with crossing fibres. We additionally show that the microstructural morphology of ConFiG phantoms is comparable to real tissue, producing diameter and orientation distributions close to electron microscopy estimates from real tissue as well as capturing complex fibre cross sections. ConFiG is applied to investigate the intra-axonal diffusivity and probe assumptions in a family of dMRI modelling techniques based on spherical deconvolution (SD), demonstrating that the microscopic variations in fibres’ shapes affects the diffusion within axons. This leads to variations in the per-fibre signal contrary to the assumptions inherent in SD which may have a knock-on effect in popular techniques such as tractography

Examining the effects of ontogenic microplastic transference on Culex mosquito mortality and adult weight

Microplastics (MPs) continue to proliferate and pollute aquatic and terrestrial environments globally. The impacts of MP pollution on ecosystems and their functioning remain poorly quantified, with most research hitherto focusing on marine ecosystems. There is a paucity of information on the impacts of MPs in freshwater ecosystems, despite the broad range of pathways through which MPs can proliferate and the extensive range of species which actively ingest MPs in these systems. Of particular interest are organisms that bridge aquatic and terrestrial habitats. The present study thus examines the uptake, ontogenic transference and effect of different concentrations (0, 50, 100 and 200 MPs mL-1) and sizes (2 and 15 µm) concentrations and sizes of polystyrene MPs between aquatic and terrestrial life stages of Culex pipiens complex mosquitoes. Both 2 and 15 µm MPs transferred from the aquatic larval to terrestrial adult stage of Culex mosquitoes, and uptake correlated tightly with initial exposure concentration. However, neither concentration nor size of MPs significantly influenced mortality rates between the aquatic larval and terrestrial adult stage. There was also no impact of MPs on the weight of emerging mosquito adults. We thus demonstrate that MPs can be transferred ontogenically through organisms with complex life histories, presenting a potential pathway for dispersal of MPs into terrestrial environments. We also show that MPs exposure does not affect mortality rates between life stages of freshwater Culex populations. This suggests that MPs do not impact nutritional uptakes, with unhampered development to adulthood facilitating subsequent dispersal of MPs aerially and between freshwater and terrestrial habitats

The effect of the alternative prey, Paramecium caudatum (Peniculida: Parameciidae), on the predation of Culex pipiens (Diptera: Culicidae) by the copepods Macrocyclops albidus and Megacyclops viridis (Cyclopoida: Cyclopidae)

Biological control can be an effective tool to combat public health risks associated with mosquito-borne disease. However, target impacts of biological control agents may be reduced by biotic contexts such as the presence of alternative prey. In turn, this can impede our ability to realistically assess biocontrol agent efficacy. Here, we examine the effects of alternative ciliate prey on the predation potential of two cyclopoid copepods, Macrocyclops albidus Jurine (Cyclopoida: Cyclopidae) and Megacyclops viridis Jurine (Cyclopoida: Cyclopidae), towards larvae of the West Nile virus vector mosquito Culex pipiens Linnaeus (Diptera: Culicidae). Using functional responses (FRs; resource use under different resource densities), we demonstrate that both copepods exhibit potentially destabilising Type II FRs towards mosquito prey. However, where the alternative prey was present, we observed species-specific modulations to FR form and magnitude. For M. albidus, FRs remained Type II where ciliate prey were present, however, maximum feeding rates on mosquito larvae were reduced. Conversely, for M. viridis, FRs moved towards more stabilising Type III, whilst maximum feeding rates on mosquito larvae were not significantly reduced. Whilst both species of cyclopoid copepod were able to effectively target and consume larval mosquitoes in the presence of alternative prey, we demonstrate that overall efficacies may be reduced in aquatic habitats which contain multiple prey types. We thus advocate that biotic contexts such as prey selectivity should be integrated into predatory biocontrol agent examinations for mosquitoes which vector pathogens and parasites, to more holistically assess their efficacy

ConFiG: Contextual Fibre Growth to generate realistic axonal packing for diffusion MRI simulation

This paper presents Contextual Fibre Growth (ConFiG), an approach to generate white matter numerical phantoms by mimicking natural fibre genesis. ConFiG grows fibres one-by-one, following simple rules motivated by real axonal guidance mechanisms. These simple rules enable ConFiG to generate phantoms with tuneable microstructural features by growing fibres while attempting to meet morphological targets such as user-specified density and orientation distribution. We compare ConFiG to the state-of-the-art approach based on packing fibres together by generating phantoms in a range of fibre configurations including crossing fibre bundles and orientation dispersion. Results demonstrate that ConFiG produces phantoms with up to 20% higher densities than the state-of-the-art, particularly in complex configurations with crossing fibres. We additionally show that the microstructural morphology of ConFiG phantoms is comparable to real tissue, producing diameter and orientation distributions close to electron microscopy estimates from real tissue as well as capturing complex fibre cross sections. Signals simulated from ConFiG phantoms match real diffusion MRI data well, showing that ConFiG phantoms can be used to generate realistic diffusion MRI data. This demonstrates the feasibility of ConFiG to generate realistic synthetic diffusion MRI data for developing and validating microstructure modelling approaches

Differential interaction strengths and prey preferences across larval mosquito ontogeny by a cohabiting predatory midge

Abstract Understandings of natural enemy efficacy are reliant on robust quantifications of interaction strengths under context-dependencies. For medically important mosquitoes, rapid growth during aquatic larval stages could impede natural enemy impacts through size refuge effects. The identification of biocontrol agents which are unimpeded by ontogenic size variability of prey is therefore vital. We use functional response and prey preference experiments to examine the interaction strengths and selectivity traits of larvae of the cohabiting predatory midge Chaoborus flavicans (Meigen 1830) (Diptera: Chaoboridae) towards larval stages of the Culex pipiens (Diptera: Culicidae) mosquito complex. Moreover, we examine the influence of search area variation on selectivity traits, given its importance in consumer-resource interactions. Chaoborids were able to capture and consume mosquito prey across their larval ontogeny. When prey types were available individually, a destabilizing Type II functional response was exhibited towards late instar mosquito prey, whereas a more stabilizing Type III functional response was displayed towards early instars. Accordingly, search efficiencies were lowest towards early instar prey, whereas, conversely, maximum feeding rates were highest towards this smaller prey type. However, when the prey types were present simultaneously, C. flavicans exhibited a significant positive preference for late instar prey, irrespective of water volume. Our results identify larval chaoborids as efficacious natural enemies of mosquito prey, with which they frequently coexist in aquatic environments. In particular, an ability to prey on mosquitoes across their larval stages, coupled with a preference for late instar prey, could enable high population-level offtake rates and negate compensatory reductions in intraspecific competition through size refuge

Impact of within-voxel heterogeneity in fibre geometry on spherical deconvolution

Axons in white matter have been shown to have varying geometries within a bundle using ex vivo imaging techniques, but what does this mean for diffusion MRI (dMRI) based spherical deconvolution (SD)? SD attempts to estimate the fibre orientation distribution function (fODF) by assuming a single dMRI fibre response function (FRF) for all white matter populations and deconvolving this FRF from the dMRI signal at each voxel to estimate the fODF. Variable fibre geometry within a bundle however suggests the FRF might not be constant even within a single voxel. We test what impact realistic fibre geometry has on SD by simulating the dMRI signal in a range of realistic white matter numerical phantoms, including synthetic phantoms and real axons segmented from electron microscopy. We demonstrate that variable fibre geometry leads to a variable FRF across axons and that in general no single FRF is effective to recover the underlying fibre orientation distribution function (fODF). This finding suggests that assuming a single FRF can lead to misestimation of the fODF, causing further downstream errors in techniques such as tractography

Up and away: ontogenic transference as a pathway for aerial dispersal of microplastics

Microplastics (MPs) are ubiquitous pollutants found in marine, freshwater and terrestrial ecosystems. With so many MPs in aquatic systems it is inevitable that they will be ingested by aquatic organisms, and be transferred up through the food chain. However, to date, no study has considered whether MPs can be transmitted by means of ontogenic transference i.e. between life stages that utilise different habitats. Here, we determine whether fluorescent polystyrene beads could transfer between Culex mosquito life stages and, particularly, could move into the flying adult stage. We show for the first time that MPs can be transferred ontogenically from a feeding (larva) into a non-feeding (pupa) life stage and subsequently into the adult terrestrial life stage. However, transference is dependent on particle size, with smaller 2 µm MPs transferring readily into pupae and adult stages, whilst 15 µm MPs transferred at a significantly reduced rate. Microplastics appear to accumulate in the Malpighian tubule renal excretion system. The transfer of MPs to the adults represents a potential aerial pathway to contamination of new environments. Thus, any organism that feeds on terrestrial life phases of freshwater insects could be impacted by MPs found in aquatic ecosystems

Biological control agent selection under environmental change using functional responses, abundances and fecundities; the Relative Control Potential (RCP) metric

We currently lack the capacity to rapidly and reliably predict the efficacy of biological control agents due to inadequate consistency in derivations of functional and numerical responses and potential effects of context-dependencies. Here, we propose and apply a novel metric, Relative Control Potential (RCP), which combines the functional response (FR, per capita effect) with proxies for the numerical response (NR, agent population response) to compare agent efficacies, where RCP = FR × abundance (or other proxies e.g. fecundity). The RCP metric is a comparative ratio between potential biocontrol agents, where values > 1 indicate higher relative control efficacy. Further, RCP can compare the efficacy of agents under environmental contexts, such as temperature change. We thus derived the RCP for two predatory cyclopoid copepods, Macrocyclops albidus (Cyclopoida: Cyclopidae) and Megacyclops viridis (Cyclopoida: Cyclopidae), towards larvae of the mosquito Culex pipiens (Diptera: Culicidae) under temperatures representative of current and future climate. Both copepods exhibited potentially population destabilising Type II FRs, with increasing temperatures inducing greater magnitude FRs through increased attack rates and decreased handling times. Attack rates by M. albidus were higher than M. viridis, yet handling times and maximum feeding rates were similar between the species across all temperatures. The inclusion of abundance data drives an elevated RCP of M. albidus and the integration of fecundity drives greater RCP of M. albidus at peak temperatures. Q10 values are indicative of increased feeding activity by both copepods with temperature increases, however relative feeding level increases of M. viridis slowed towards the peak temperature. We present RCP calculations and biplots that represent the comparative efficacies of the two biological control agents across temperatures. The Relative Control Potential (RCP) metric thus provides a new tool for practitioners to better assess the potential efficacy of biocontrol agents before their integration into management approaches for pests, vectors and invasive species

Elusive enemies: consumptive and ovipositional effects on mosquitoes by predatory midge larvae are enhanced in dyed environments

Mosquito-borne disease incidences continue to proliferate and cause enormous mortality and debilitation rates. Predatory natural enemies can be effective in population management strategies targeting medically-important mosquito species. However, context-dependencies and target organism behavioural responses can impede or facilitate biological control agents. Black pond dye has been shown to be a strong mosquito oviposition attractant, and could potentially be used alongside predatory agents to create mosquito population sink effects. Here, we thus examine the predatory impact of larvae of the non-biting chaoborid midge Chaoborus flavicans towards larvae of the West Nile virus vector mosquito complex Culex pipiens in the presence and absence of black pond dye. We then examine the ovipositional responses of C. pipiens to predation risk and dye in laboratory-, semi-field- and field-based trials. Larval C. flavicans exhibited potentially population destabilising type II functional responses towards mosquito larvae irrespective of the presence of pond dye. Neither consumption rates nor functional response parameters (attack rates, handling times) were significantly influenced by the presence of dye, indicating a use of hydromechanics to detect mosquito prey by chaoborids. Wild-caught adult C. pipiens did not avoid predatory chaoborids when ovipositing, however they were significantly more attracted to oviposit in dye-treated water regardless of the presence of predators. We thus demonstrate high predatory impact towards mosquito larvae by non-biting chaoborid midges during their predaceous aquatic larval stages, and proliferations of such predators may assist or augment control efforts for mosquitoes. Our results suggest a lack of influence of predatory dipterans on oviposition selectivity by C. pipiens mosquitoes, and that pond dye may enhance the efficacy of select predatory biological control agents through the creation of population sinks, characterised by high rates of oviposition and subsequent predation

The influence of microplastics on trophic interaction strengths and oviposition preferences of dipterans

Microplastic (MP) pollution continues to proliferate in freshwater, marine and terrestrial environments, but with their biotic implications remaining poorly understood. Biotic interactions such as predation can profoundly influence ecosystem structuring, stability and functioning. However, we currently lack quantitative understandings of how trophic interaction strengths and associated behaviours are influenced by MP pollution, and how transference of MPs between trophic levels relates to consumptive traits. We also lack understanding of key life-history effects of MPs, for example, reproductive strategies such as oviposition. The present study examines the predatory ability of non-biting midge larvae, Chaoborus flavicans, towards larvae of Culex pipiens mosquitoes when the latter are exposed to MPs, using a functional response (FR) approach. Transfer of MPs occurred from larval mosquitoes to larval midges via predation. Microplastics transfer was significantly positively related to predation rates. Predation by C. flavicans followed a Type II FR, with average maximum feeding rates of 6.2 mosquito larvae per hour. These and other FR parameters (attack rates and handling times) were not significantly influenced by the presence of MPs. Further, C. pipiens adults did not avoid ovipositing in habitats with high concentrations of MPs. We thus demonstrate that MPs can move readily through freshwater food webs via biotic processes such as predation, and that uptake correlates strongly with consumption rates. Further, as MPs do not deter adult mosquitoes from ovipositing, our experiments reveal high potential for MP exposure and transference through ecosystems