Developing an estuarine planning support system : a case study for the Humber Estuary, UK

Estuaries are often challenging to manage, as management must strike a balance between the needs of the users and the ecological and economic values within the context of multiple legislative drivers. To help facilitate integrated management, a novel Estuarine Planning Support System (EPSS) framework, using the Humber Estuary in Eastern England as a case study, has been developed. This integrated EPSS framework goes beyond previous approaches as it brings together the legislative drivers, management tools and other mechanisms for controlling plans (formal/legal management, action or work plans (e.g. shoreline management plans) and projects (a new structure or activity such as extending a port). It thereby enables managers and users to assess and address both the current environmental state, and the way in which the new project could impact an estuary in an accessible and understandable tool. This study has been primarily completed by desk based research using peer reviewed literature, technical and research reports, marine licence applications and legislation, with correspondence to several sources to determine the baseline information and existing knowledge gaps. Further to the framework, an EPSS tool was developed to provide a practical application of these requirements. The GIS-based tool ensures that the information is accessible for regulators, managers, the scientific community, developers and the public. Whilst the tool is adaptable for regions within and outside the United Kingdom (UK), the research presented in this thesis focussed on the Humber Estuary. The successful application of the tool for a complex socio-economic and environmental system such as the Humber Estuary shows that the tool can efficiently guide users through the complex administrative requirements needed to implement a management plan, and therefore support sustainable development. In addition, the tool can be used as a scoping mechanism to identify potential stressors which are to be addressed in an environmental impact assessment (EIA). The tool was validated against four case studies and was also tested by a number of stakeholders to determine the utility and accuracy of the tool. The tool was subsequently updated to reflect feedback from the stakeholders. This project should be viewed as a ‘proof of concept’ in that its primary purpose is to demonstrate the potential for developing and operationalizing an approach in the field. The method has the potential to integrate highly technical knowledge from scientists, and the views of non-scientists, to make better-informed management and planning decisions and to provide reasonable assurance to justify those decisions. The tool can be used to prevent conflicts among stakeholders and/or between uses and users and the environment, and makes it possible to integrate all the existing background data in thematic maps and identifies the human activities that use the areas, resources and services. The EPSS tool can save time and resources, aid in the decision-making process and make the decision process more transparent and consistent. It has the potential to make the governance of the marine area more logical, simple, fast and therefore more cost effective. The tool has been developed to be flexible in its approach, this means that it can be easily adapted to be used internationally and to allow for it to be adaptable to future changes. It combines the many aspects required for a holistic approach to marine management, from the inclusion of governance and stakeholder views, to the need for, and use of, monitoring information. In marine management, there will always be a need for robust and scientifically and legally defendable science to inform management. The increasingly large spatial scales that are addressed by policy makers, and the reduction in funding, means that new methods are needed to provide the evidence base which this tool helps to provide, and can be applied worldwide. The developed toolbox is an important step towards such an integrated, holistic ecosystem based approach for marine management, demonstrating that a single tool can bring together the legislative, environmental and economic considerations. The tool is a method to undertake the assessments that are currently being carried out by separate organisations, to combine in a single process that is consistent and transparent and on a quicker timescale helping to reduce costs

The potential alternative uses of dredged material in the Humber Estuary

The Humber Estuary handles around 16% of the UK’s maritime trade. It is important for Economic reasons with a number ports and wharves as well as for the environment, with local, national and international designations applied to numerous species and habitats. Associated British Ports (ABP) (as well as other port operators) routinely dredges parts of the estuary for the safe navigation of vessels. Occasionally developer’s capitals dredge new areas to create new or deeper channels or berth pockets in order to remain economically competitive.This study has investigated the alternative uses of the maintenance and capital dredged material which is usually disposed of within the estuary, to alternative suitable locations within the Humber Estuary whilst taking into account the sediment composition and hydrodynamics, as well as the local need, economics and adherence to the 7 tenets of sustainable development.The potential use locations were based primarily on the sites that have been identified by the Environment Agency (EA) has having flood defences in less than favourable condition. These locations were characterised by the sediment type, quantity of material needed to ensure protection, average flow velocities at the sites and distance from the dredge site.By disposing of this sediment within the estuary, it keeps it available to maintain the equilibrium; however this material could potentially be used as a resource to reduce erosion and protect the flood defences behind along the banks of the Humber.Maintenance dredging involves the removal of the recently settled sediment that contributes to the sediment budget (sediment within a system at one time including the sources, sinks and processes). Therefore only those options that allow the sediment to remain part of the budget have been considered. After taking into account the considerations identified above, this study has indicated that the maintenance dredge arisings could potentially be used for the creation of berm breakwaters within the estuary in order to protect the shore and flood defences behind from erosion and the continuation of disposal within the estuary.Capital dredging occurs rarely in order to create new channels or berths for new or expanding ports. As capital dredge arisings do not contribute to the sediment budget more options were available to investigate. Dependant on the material type, quantity and distance between the dredge and disposal sites, the alternative uses include the construction of berm breakwaters, intertidal enhancement and also the continuation of disposal within the estuary.Potential alternative uses for the maintenance and the proposed capital dredge arisings from the Humber Estuary have been identified taking the considerations above into account. The organisations that carry out the dredging operations however are different to those who would require the material for the potential uses identified; therefore there would be difficulties in combining the projects. From this study it appears that due to the designations of the estuary and the characteristics of the dredged material, the continuation of within estuary disposal is the most suitable method of disposal at this time. As it has fewer constraints associated with it, requires less monitoring and also appears to have more neutral than detrimental effects on the estuary than other identified potential uses. From monitoring past published charts and the dynamics of the estuary, historically there is no evidence to prove that this method of disposal negatively affects the estuary’s functioning.Further work including a detailed field investigation to determine the local and estuary wide effects of the proposed potential uses identified in this study on the environmental, hydrographical, sediment transport and economic aspects. This study is time and site specific for the identified potential uses on the Humber Estuary however the criteria used can be applied to future projects and on other estuaries

Integrating management tools and concepts to develop an estuarine planning support system: A case study of the Humber Estuary, Eastern England

© 2015. Estuaries are important because of their multiple uses and users which often makes them challenging to manage since management must strike a balance between the needs of users, the estuaries' ecological and economic value and the context of multiple legislative drivers. To facilitate management we have therefore developed an Estuarine Planning Support System (EPSS) framework using the Humber Estuary, Eastern England, as a case study which integrates the current legislation tools and concepts. This integrated EPSS framework is an improvement on previous approaches for assessing cumulative impacts as it takes into account legislative drivers, management tools and other mechanisms for controlling plans/projects specific to the estuary. It therefore enables managers and users to assess and address both the current state and the way in which a new industrial, port or urban development could impact an estuary in an accessible and understandable framework

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

The potential alternative uses of dredged material in the Humber Estuary

The Humber Estuary handles around 16% of the UK’s maritime trade. It is important for Economic reasons with a number ports and wharves as well as for the environment, with local, national and international designations applied to numerous species and habitats. Associated British Ports (ABP) (as well as other port operators) routinely dredges parts of the estuary for the safe navigation of vessels. Occasionally developer’s capitals dredge new areas to create new or deeper channels or berth pockets in order to remain economically competitive. This study has investigated the alternative uses of the maintenance and capital dredged material which is usually disposed of within the estuary, to alternative suitable locations within the Humber Estuary whilst taking into account the sediment composition and hydrodynamics, as well as the local need, economics and adherence to the 7 tenets of sustainable development. The potential use locations were based primarily on the sites that have been identified by the Environment Agency (EA) has having flood defences in less than favourable condition. These locations were characterised by the sediment type, quantity of material needed to ensure protection, average flow velocities at the sites and distance from the dredge site. By disposing of this sediment within the estuary, it keeps it available to maintain the equilibrium; however this material could potentially be used as a resource to reduce erosion and protect the flood defences behind along the banks of the Humber. Maintenance dredging involves the removal of the recently settled sediment that contributes to the sediment budget (sediment within a system at one time including the sources, sinks and processes). Therefore only those options that allow the sediment to remain part of the budget have been considered. After taking into account the considerations identified above, this study has indicated that the maintenance dredge arisings could potentially be used for the creation of berm breakwaters within the estuary in order to protect the shore and flood defences behind from erosion and the continuation of disposal within the estuary. Capital dredging occurs rarely in order to create new channels or berths for new or expanding ports. As capital dredge arisings do not contribute to the sediment budget more options were available to investigate. Dependant on the material type, quantity and distance between the dredge and disposal sites, the alternative uses include the construction of berm breakwaters, intertidal enhancement and also the continuation of disposal within the estuary. Potential alternative uses for the maintenance and the proposed capital dredge arisings from the Humber Estuary have been identified taking the considerations above into account. The organisations that carry out the dredging operations however are different to those who would require the material for the potential uses identified; therefore there would be difficulties in combining the projects. From this study it appears that due to the designations of the estuary and the characteristics of the dredged material, the continuation of within estuary disposal is the most suitable method of disposal at this time. As it has fewer constraints associated with it, requires less monitoring and also appears to have more neutral than detrimental effects on the estuary than other identified potential uses. From monitoring past published charts and the dynamics of the estuary, historically there is no evidence to prove that this method of disposal negatively affects the estuary’s functioning. Further work including a detailed field investigation to determine the local and estuary wide effects of the proposed potential uses identified in this study on the environmental, hydrographical, sediment transport and economic aspects. This study is time and site specific for the identified potential uses on the Humber Estuary however the criteria used can be applied to future projects and on other estuaries

Managing estuaries under a changing climate: A case study of the Humber Estuary, UK

Estuaries are globally important zones for urban, recreational and commercial activities as well as supporting a range of habitats and species of significant ecological importance. The role of estuaries is recognised by the legislative framework that has been developed to protect and manage these areas as well as those species and resources in adjoining habitats. However, estuaries worldwide are subject to a number of major threats, including increasing industrialisation and urbanisation, increasing resource scarcity notably for space and energy, and the impacts of climate change, sea-level rise and related increases in vulnerability and decreases in resilience. In addition to local pressures, climate change is now increasingly recognised as having a range of severe impacts on estuarine ecosystem functions and services, but current legislation and associated management may not necessarily be wholly appropriate to deal with these longer-term changes. Here we consider how the current legislation and management addresses the potential impacts of climate change on a large estuarine system. Alongside a set of recommendations, we emphasise that the implementation of governance instruments needs to be underpinned by continued monitoring, improved modelling and enhanced predictive capabilities and integration and collaboration across management levels

Reviewing the UK’s Action Levels for the Management of Dredged Material

Action Levels (ALs) are thresholds which are used to determine whether dredged material is suitable for disposal at sea by providing a proxy risk assessment for potential impacts to biological features such as fish and benthos. This project tested proposed scenarios for changes to the UK Action Levels to determine the likely implications for navigational dredge licensing in England and Wales. Approximately 3000 sample data records from 2009 to 2018 were collated with varying numbers of concentrations for contaminant parameters including trace metals, organotins, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and polybrominated diphenyl ethers (PBDEs). Initially, these data were assessed using current ALs to determine the percentages of the samples with levels below AL1 (generally acceptable for disposal), between AL1 and AL2 and those showing levels above AL2 (generally unacceptable for disposal). These results were then used to compare with the results of the proposed new AL scenarios for each contaminant type derived from literature reviews and historic data. The results indicate that there are changes to the ALs which could be made such as updating the current ALs with the revised ALs, as well as the introduction of ALs where there are currently none set. The benefits of changing the ALs include reducing contaminant disposal to the marine environment and increased transparency in decision making. Any proposed scenarios will need to be phased in carefully in full liaison with stakeholders

Reviewing the UK’s Action Levels for the Management of Dredged Material

Action Levels (ALs) are thresholds which are used to determine whether dredged material is suitable for disposal at sea by providing a proxy risk assessment for potential impacts to biological features such as fish and benthos. This project tested proposed scenarios for changes to the UK Action Levels to determine the likely implications for navigational dredge licensing in England and Wales. Approximately 3000 sample data records from 2009 to 2018 were collated with varying numbers of concentrations for contaminant parameters including trace metals, organotins, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and polybrominated diphenyl ethers (PBDEs). Initially, these data were assessed using current ALs to determine the percentages of the samples with levels below AL1 (generally acceptable for disposal), between AL1 and AL2 and those showing levels above AL2 (generally unacceptable for disposal). These results were then used to compare with the results of the proposed new AL scenarios for each contaminant type derived from literature reviews and historic data. The results indicate that there are changes to the ALs which could be made such as updating the current ALs with the revised ALs, as well as the introduction of ALs where there are currently none set. The benefits of changing the ALs include reducing contaminant disposal to the marine environment and increased transparency in decision making. Any proposed scenarios will need to be phased in carefully in full liaison with stakeholders

Dynamic landscape and regulation of RNA editing in mammals

Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules1. Although many editing sites have recently been discovered2,3,4,5,6,7, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood8,9,10. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing