title: Modelling epistasis in genetic disease using Petri nets, evolutionary computation and frequent itemset mining

authors: Mayo, Michael

subjects: Petri net

abstract: Petri nets are useful for mathematically modelling disease-causing genetic epistasis. A Petri net model of an interaction has the potential to lead to biological insight into the cause of a genetic disease. However, defining a Petri net by hand for a particular interaction is extremely difficult because of the sheer complexity of the problem and degrees of freedom inherent in a Petri net’s architecture.
We propose therefore a novel method, based on evolutionary computation and data mining, for automatically constructing Petri net models of non-linear gene interactions. The method comprises two main steps. Firstly, an initial partial Petri net is set up with several repeated sub-nets that model individual genes and a set of constraints, comprising relevant common sense and biological knowledge, is also defined. These constraints characterise the class of Petri nets that are desired. Secondly, this initial Petri net structure and the constraints are used as the input to a genetic algorithm. The genetic algorithm searches for a Petri net architecture that is both a superset of the initial net, and also conforms to all of the given constraints. The genetic algorithm evaluation function that we employ gives equal weighting to both the accuracy of the net and also its parsimony.
We demonstrate our method using an epistatic model related to the presence of digital ulcers in systemic sclerosis patients that was recently reported in the literature. Our results show that although individual “perfect” Petri nets can frequently be discovered for this interaction, the true value of this approach lies in generating many different perfect nets, and applying data mining techniques to them in order to elucidate common and statistically significant patterns of interaction.

text: Modelling epistasis in genetic disease using Petri nets, evolutionary computation and frequent itemset mining Petri nets are useful for mathematically modelling disease-causing genetic epistasis. A Petri net model of an interaction has the potential to lead to biological insight into the cause of a genetic disease. However, defining a Petri net by hand for a particular interaction is extremely difficult because of the sheer complexity of the problem and degrees of freedom inherent in a Petri net’s architecture.
We propose therefore a novel method, based on evolutionary computation and data mining, for automatically constructing Petri net models of non-linear gene interactions. The method comprises two main steps. Firstly, an initial partial Petri net is set up with several repeated sub-nets that model individual genes and a set of constraints, comprising relevant common sense and biological knowledge, is also defined. These constraints characterise the class of Petri nets that are desired. Secondly, this initial Petri net structure and the constraints are used as the input to a genetic algorithm. The genetic algorithm searches for a Petri net architecture that is both a superset of the initial net, and also conforms to all of the given constraints. The genetic algorithm evaluation function that we employ gives equal weighting to both the accuracy of the net and also its parsimony.
We demonstrate our method using an epistatic model related to the presence of digital ulcers in systemic sclerosis patients that was recently reported in the literature. Our results show that although individual “perfect” Petri nets can frequently be discovered for this interaction, the true value of this approach lies in generating many different perfect nets, and applying data mining techniques to them in order to elucidate common and statistically significant patterns of interaction.

year: 2010

title: Implications of sea-level rise on estuarine benthic biodiversity and ecosystem functioning

authors: Dixon, Olivia Jane

abstract: Estuarine habitats are among the most productive ecosystems around the globe. The macroinvertebrate communities within these habitats underpin ecosystem functioning and therefore the provision of ecosystem services valued by society. Due to their geographic positioning, coastal areas represent a human-ocean interface and are consequently at the forefront of anthropogenic pressure. Sea-level rise (SLR) is one major consequence of anthropogenic climate change that poses a great threat to coastal environments and will result in extensive intertidal area loss. There is an evident bias within coastal SLR research towards the implications for the abiotic environment such as impacts on geomorphology but the ecological implications however, have been largely overlooked despite their likely significance. In this thesis, I aim to address this knowledge gap by investigating how benthic macroinvertebrate communities and their contributions to ecosystem function will respond to SLR within a large temperate estuary. To explore how benthic macroinvertebrate community structure will respond to future SLR, I employed a space-for-time approach. In this study, I considered site depth as a proxy for SLR to gauge how macroinvertebrate communities may shift with increasing depth as sea level is elevated. This study was based on data obtained from 119 unvegetated soft-sediment sampling locations throughout Tauranga Harbour. An initial hierarchical cluster analysis was performed on the macroinvertebrate abundance data to reveal groups of sites that shared significantly similar community structure. Three clusters of sites were identified at a > 34% similarity level with significantly different macroinvertebrate community structure. Clustered groups were generally characterised by different depth ranges that we could consider representative of intertidal, shallow subtidal and deep subtidal habitats. Similarly, depth was identified as the most important environmental variable for predicting variation in macroinvertebrate community structure using distance-based linear modelling (explaining 12%) and gradient forest analysis indicated it is important in explaining rates of compositional turnover (6%). Chl-a, mud content and average current speed were among the next most important predictors explaining variation in community structure (5%, 4% and 2%, respectively) and compositional turnover (6%, 3%, 4%, respectively). Functional trait analysis indicated low functional redundancy for a key intertidal suspension-feeding bivalve (Austrovenus stutchburyi) and the lack of a shallow subtidal functional replacement should intertidal habitats become inundated by SLR. The findings of this thesis strongly suggest SLR and the associated environmental changes will significantly alter estuarine macroinvertebrate communities, indicating implications for ecosystem function and resilience. Key findings of this thesis will complement management strategies of coastal areas and encourage they are not treated as static systems as ecological shifts are predicted to occur with SLR over time. Well- informed management of important estuarine habitats that recognises their spatial and temporal dynamicity will be critical for ensuring ecosystem functions and services they deliver will be conserved for future generations.

text: Implications of sea-level rise on estuarine benthic biodiversity and ecosystem functioning Estuarine habitats are among the most productive ecosystems around the globe. The macroinvertebrate communities within these habitats underpin ecosystem functioning and therefore the provision of ecosystem services valued by society. Due to their geographic positioning, coastal areas represent a human-ocean interface and are consequently at the forefront of anthropogenic pressure. Sea-level rise (SLR) is one major consequence of anthropogenic climate change that poses a great threat to coastal environments and will result in extensive intertidal area loss. There is an evident bias within coastal SLR research towards the implications for the abiotic environment such as impacts on geomorphology but the ecological implications however, have been largely overlooked despite their likely significance. In this thesis, I aim to address this knowledge gap by investigating how benthic macroinvertebrate communities and their contributions to ecosystem function will respond to SLR within a large temperate estuary. To explore how benthic macroinvertebrate community structure will respond to future SLR, I employed a space-for-time approach. In this study, I considered site depth as a proxy for SLR to gauge how macroinvertebrate communities may shift with increasing depth as sea level is elevated. This study was based on data obtained from 119 unvegetated soft-sediment sampling locations throughout Tauranga Harbour. An initial hierarchical cluster analysis was performed on the macroinvertebrate abundance data to reveal groups of sites that shared significantly similar community structure. Three clusters of sites were identified at a > 34% similarity level with significantly different macroinvertebrate community structure. Clustered groups were generally characterised by different depth ranges that we could consider representative of intertidal, shallow subtidal and deep subtidal habitats. Similarly, depth was identified as the most important environmental variable for predicting variation in macroinvertebrate community structure using distance-based linear modelling (explaining 12%) and gradient forest analysis indicated it is important in explaining rates of compositional turnover (6%). Chl-a, mud content and average current speed were among the next most important predictors explaining variation in community structure (5%, 4% and 2%, respectively) and compositional turnover (6%, 3%, 4%, respectively). Functional trait analysis indicated low functional redundancy for a key intertidal suspension-feeding bivalve (Austrovenus stutchburyi) and the lack of a shallow subtidal functional replacement should intertidal habitats become inundated by SLR. The findings of this thesis strongly suggest SLR and the associated environmental changes will significantly alter estuarine macroinvertebrate communities, indicating implications for ecosystem function and resilience. Key findings of this thesis will complement management strategies of coastal areas and encourage they are not treated as static systems as ecological shifts are predicted to occur with SLR over time. Well- informed management of important estuarine habitats that recognises their spatial and temporal dynamicity will be critical for ensuring ecosystem functions and services they deliver will be conserved for future generations.

year: 2022

title: Introduction: Recognition, redistribution and reconciliation in postcolonial settler societies

authors: van Meijl, Toon

subjects: multiculturalism

abstract: Various questions are addressed regarding recognition of special rights for indigenous minorities in postcolonial nation-states, redistributing resources to redress longstanding indigenous grievances about the history of colonial dispossession and strategy of reconciliation between the immigrant majority of settlers and their descendants against a backdrop of multiculturalism.

text: Introduction: Recognition, redistribution and reconciliation in postcolonial settler societies Various questions are addressed regarding recognition of special rights for indigenous minorities in postcolonial nation-states, redistributing resources to redress longstanding indigenous grievances about the history of colonial dispossession and strategy of reconciliation between the immigrant majority of settlers and their descendants against a backdrop of multiculturalism.

year: 2003-09-01