Mathematical Modelling of Spatially Coherent Transcription

Genetics and epigenetics are widely expected to revolutionise our understanding of health and disease. However any attempt to extract relevant information from noisy data requires a combination of modelling and statistical techniques. Given the number of genes and the complexity involved in the genome, sophisticated methods will be needed to properly capture the information that is contained. Many mechanisms and variables can affect and control the expression of a gene. In this thesis, it is specifically spatially coherent variations in transcription which are investigated. Several different areas were examined, producing a broad set of results. Important findings include the demonstration of spatial coherence as the result of epigenetic effects, the creation and validation of a technique to detect spatial coherence, and the extension of spatial modelling to epigenetic data. Other important results include the detection of spatial coherence variation due to confounding variables (PMI and neuronal concentration) and the development of new spatial modelling techniques. The results indicate that spatial modelling provides a useful approach to investigating unusual and unknown aspects of epigenetic and transcriptional regulation

Population Genetic Structure of Aldabra Giant Tortoises

Evolution of population structure on islands is the result of physical processes linked to volcanism, orogenic events, changes in sea level, as well as habitat variation. We assessed patterns of genetic structure in the giant tortoise of the Aldabra atoll, where previous ecological studies suggested population subdivisions as a result of landscape discontinuity due to unsuitable habitat and island separation. Analysis of mitochondrial DNA (mtDNA) control region sequences and allelic variation at 8 microsatellite loci were conducted on tortoises sampled in 3 locations on the 2 major islands of Aldabra. We found no variation in mtDNA sequences. This pattern corroborated earlier work supporting the occurrence of a founding event during the last interglacial period and a further reduction in genetic variability during historical time. On the other hand, significant population structure recorded at nuclear loci suggested allopatric divergence possibly due to geographical barriers among islands and ecological partitions hindering tortoise movements within islands. This is the first attempt to study the population genetics of Aldabra tortoises, which are now at carrying capacity in an isolated terrestrial ecosystem where ecological factors appear to have a strong influence on population dynamic

Mean expression of the X-chromosome is associated with neuronal density

peer reviewedBackground: Neurodegenerative diseases are characterized by key features such as loss of neurons, astrocytosis, and microglial activation/proliferation. These changes cause differences in the density of cell types between control and disease subjects, confounding results from gene expression studies. Chromosome X (ChrX) is known to be specifically important in the brain. We hypothesized the existence of a chromosomal signature of gene expression associated with the X-chromosome for neurological conditions not normally associated with that chromosome. The hypothesis was investigated using publicly available microarray datasets from studies on Parkinson's disease, Alzheimer's disease, and Huntington's disease. Data were analyzed using Chromowave, an analytical tool for detecting spatially extended expression changes along chromosomes. To examine associations with neuronal density and astrocytosis, the expression of cell specific reporter genes was extracted. The association between these genes and the expression patterns extracted by Chromowave was then analyzed. Further analyses of the X:Autosome ratios for laser dissected neurons, microglia cultures and whole tissue were performed to detect cell specific differences. Results: We observed an extended pattern of low expression of ChrX consistent in all the neurodegenerative disease brain datasets. There was a strong correlation between mean ChrX expression and the pattern extracted from the autosomal genes representing neurons, but not with mean autosomal expression. No chromosomal patterns associated with the neuron specific genes were found on other chromosomes. The chromosomal expression pattern was not present in datasets from blood cells. The X:Autosome expression ratio was also higher in neuronal cells than in tissues with a mix of cell types. Conclusions: The results suggest that neurological disorders show as a reduction in mean expression of many genes along ChrX. The most likely explanation for this finding relates to the documented general up-regulation of ChrX in brain tissue which, this work suggests, occurs primarily in neurons. If validated, this cell specific ChrX expression warrants further research as understanding the biological reasons and mechanisms for this expression, may help to elucidate a connection with the development of neurodegenerative disorders

Lessons from integrating behaviour and resource selection: activity-specific responses of African wild dogs to roads

Understanding how anthropogenic features affect species' abilities to move within landscapes is essential to conservation planning and requires accurate assessment of resource selection for movement by focal species. Yet, the extent to which an individual's behavioural state (e.g. foraging, resting, commuting) influences resource selection has largely been ignored. Recent advances in Global Positioning System (GPS) tracking technology can fill this gap by associating distinct behavioural states with location data. We investigated the role of behaviour in determining the responses of an endangered species of carnivore, the African wild dog Lycaon pictus, to one of the most widespread forms of landscape alteration globally: road systems. We collected high‐resolution GPS and activity data from 13 wild dogs in northern Botswana over a 2‐year period. We employed a step selection framework to measure resource selection across three behavioural states identified from activity data (high‐speed running, resting and travelling) and across a gradient of habitats and seasons, and compared these outputs to a full model that did not parse for behaviour. The response of wild dogs to roads varied markedly with both the behavioural and the landscape contexts in which roads were encountered. Specifically, wild dogs selected roads when travelling, ignored roads when high‐speed running and avoided roads when resting. This distinction was not evident when all movement data were considered together in the full model. When travelling, selection for roads increased in denser vegetative environments, suggesting that roads may enhance movement for this species. Our findings indicate that including behavioural information in resource selection models is critical to understanding wildlife responses to landscape features and suggest that successful application of resource selection analyses to conservation planning requires explicit examination of the behavioural contexts in which movement occurs. Thus, behaviour‐specific step selection functions offer a powerful tool for identifying resource selection patterns for animal behaviours of conservation significance

Correction: In Vivo Tumorigenesis Was Observed after Injection of In Vitro Expanded Neural Crest Stem Cells Isolated from Adult Bone Marrow.

[This corrects the article DOI: 10.1371/journal.pone.0046425.]

The Welfare Implications of Using Exotic Tortoises as Ecological Replacements

<div><h3>Background</h3><p>Ecological replacement involves the introduction of non-native species to habitats beyond their historical range, a factor identified as increasing the risk of failure for translocations. Yet the effectiveness and success of ecological replacement rely in part on the ability of translocatees to adapt, survive and potentially reproduce in a novel environment. We discuss the welfare aspects of translocating captive-reared non-native tortoises, <em>Aldabrachelys gigantea</em> and <em>Astrochelys radiata</em>, to two offshore Mauritian islands, and the costs and success of the projects to date.</p> <h3>Methodology/Principal Findings</h3><p>Because tortoises are long-lived, late-maturing reptiles, we assessed the progress of the translocation by monitoring the survival, health, growth, and breeding by the founders. Between 2000 and 2011, a total of 26 <em>A. gigantea</em> were introduced to Ile aux Aigrettes, and in 2007 twelve sexually immature <em>A. gigantea</em> and twelve male <em>A. radiata</em> were introduced to Round Island, Mauritius. Annual mortality rates were low, with most animals either maintaining or gaining weight. A minimum of 529 hatchlings were produced on Ile aux Aigrettes in 11 years; there was no potential for breeding on Round Island. Project costs were low. We attribute the success of these introductions to the tortoises’ generalist diet, habitat requirements, and innate behaviour.</p> <h3>Conclusions/Significance</h3><p>Feasibility analyses for ecological replacement and assisted colonisation projects should consider the candidate species’ welfare during translocation and in its recipient environment. Our study provides a useful model for how this should be done. In addition to serving as ecological replacements for extinct Mauritian tortoises, we found that releasing small numbers of captive-reared <em>A. gigantea</em> and <em>A. radiata</em> is cost-effective and successful in the short term. The ability to release small numbers of animals is a particularly important attribute for ecological replacement projects since it reduces the potential risk and controversy associated with introducing non-native species.</p> </div

What is carbon? Conceptualising carbon and capabilities in the context of community sequestration projects in the global South

Carbon has been described as a ‘surreal commodity.’ While carbon trading, storage, sequestration, and emissions have become a part of the contemporary climate lexicon, how carbon is understood, valued, and interpreted by actors responsible for implementing carbon sequestration projects is still unclear. In this review paper, we are concerned with how carbon has come to take on a range of meanings. In particular, we appraise what is known about the situated meanings that people involved in delivering, and participating in, carbon sequestration projects in the global South assign to this complex element. There has been some reflection on the new meanings conferred on carbon via the neoliberal processes of marketisation and on how these processes interact with historical and contemporary narratives of environmental change. But less is known about how these meanings are (re)produced and (re)interpreted locally. We review how carbon has been defined both as a chemical element and as a tradable, marketable commodity. We discuss the implications these global meanings might have for situated understandings, particularly linked to climate change narratives, among communities in the global South. We consider how the concept of carbon capabilities, alongside theoretical notions of networks, assemblages, and local knowledges of the environment and nature, might be useful in beginning to understand how communities engage with abstract notions of carbon. We discuss the implications of specific values attributed to carbon, and therefore to different ecologies, for wider conceptualizations of how nature is valued, and climate is understood. We review in particular how this may impact on community interactions with carbon sequestration projects. Knowing more about how people understand, value, and know carbon allows policies to be better informed and practices more effectively targeted at engaging local populations meaningfully in carbon-related projects

Step by step: reconstruction of terrestrial animal movement paths by dead-reckoning

Background: Research on wild animal ecology is increasingly employing GPS telemetry in order to determine animal movement. However, GPS systems record position intermittently, providing no information on latent position or track tortuosity. High frequency GPS have high power requirements, which necessitates large batteries (often effectively precluding their use on small animals) or reduced deployment duration. Dead-reckoning is an alternative approach which has the potential to ‘fill in the gaps’ between less resolute forms of telemetry without incurring the power costs. However, although this method has been used in aquatic environments, no explicit demonstration of terrestrial dead-reckoning has been presented.Results: We perform a simple validation experiment to assess the rate of error accumulation in terrestrial dead-reckoning. In addition, examples of successful implementation of dead-reckoning are given using data from the domestic dog Canus lupus, horse Equus ferus, cow Bos taurus and wild badger Meles meles.Conclusions: This study documents how terrestrial dead-reckoning can be undertaken, describing derivation of heading from tri-axial accelerometer and tri-axial magnetometer data, correction for hard and soft iron distortions on the magnetometer output, and presenting a novel correction procedure to marry dead-reckoned paths to ground-truthed positions. This study is the first explicit demonstration of terrestrial dead-reckoning, which provides a workable method of deriving the paths of animals on a step-by-step scale. The wider implications of this method for the understanding of animal movement ecology are discussed