Nondestructive 3D Imaging and Quantification of Hydrated Biofilm-Sediment Aggregates Using X-ray Microcomputed Tomography.

Biofilm-sediment aggregate (BSA) contains a high water content, either within internal pores and channels or bound by extracellular polymeric substances (EPS) forming a highly hydrated biofilm matrix. Desiccation of BSAs alters the biofilm morphology and thus the physical characteristics of porous media, such as the binding matrix within BSA and internal pore geometry. Observing BSAs in their naturally hydrated form is essential but hampered due to the lack of techniques for imaging and discerning hydrated materials. Generally, imagery techniques (scanning electron microscopy (SEM), transmission electron microscopy (TEM), and focused ion beam nanotomography (FIB-nt)) involve the desiccation of BSAs (freeze-drying or acetone dehydration) or prevent differentiation between BSA components such as inorganic particles and pore water (confocal laser scanning microscopic (CLSM)). Here, we propose a novel methodology that simultaneously achieves the 3D visualization and quantification of BSAs and their components in their hydrated form at a submicron resolution using X-ray microcomputed tomography (μ-CT). It enables the high-resolution detection of comparable morphology of multiphase components within a hydrated aggregate: each single inorganic particle and the hydrated biofilm matrix. This allows the estimation of aggregate density and the illustration of biofilm-sediment binding matrix. This information provides valuable insights into investigations of the transport of BSAs and aggregate-associated sediment particles, contaminants (such as microplastics), organic carbon, and their impacts on aquatic biogeochemical cycling

The UK needs an open data portal dedicated to coastal flood and erosion hazard risk and resilience

In the UK, coastal flooding and erosion are two of the primary climate-related hazards to communities, businesses, and infrastructure. To better address the ramifications of those hazards, now and into the future, the UK needs to transform its scattered, fragmented coastal data resources into a systematic, integrated portal for quality-assured, publicly accessible open data. Such a portal would support analyses of coastal risk and resilience by hosting, in addition to data layers for coastal flooding and erosion, a diverse array of spatial datasets for building footprints, infrastructure networks, land use, population, and various socio-economic measures and indicators derived from survey and census data. The portal would facilitate novel combinations of spatial data layers to yield scientifically, societally, and economically beneficial insights into UK coastal systems

Understanding historical coastal spit evolution : a case study from Spurn, East Yorkshire, UK

Globally sandy coastlines are threatened by erosion driven by climatic changes and increased storminess. Understanding how they have responded to past storms is key to help manage future coastal changes. Coastal spits around the world are particularly dynamic and therefore potentially vulnerable coastal features. Therefore, how they have evolved over the last few centuries is of great importance. To illustrate this, this study focuses on the historical evolution of a spit at Spurn on the east coast of the UK, which currently provides critical protection to settlements within the Humber estuary. Through the combination of digitized historical mapping and luminescence dating, this study shows that Spurn has been a consistent coastal feature over at least the past 440 years. No significant westward migration was observed for the last 200 years. Results show a long‐term extension of the spit and a decrease in its overall area, particularly in the last 50 years. Breaches of the neck cause temporary sediment pathway changes enabling westward extension of the head. Use of digitized historical maps in GIS combined with OSL dating has allowed a more complete understanding of long‐term spit evolution and sediment transport modes at Spurn. In doing so it helps inform future possible changes linked to pressures, such as increases in storm events and sea‐level rise

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Is “Morphodynamic Equilibrium” an oxymoron?

Morphodynamic equilibrium is a widely adopted yet elusive concept in the field of geomorphology of coasts, rivers and estuaries. Based on the Exner equation, an expression of mass conservation of sediment, we distinguish three types of equilibrium defined as static and dynamic, of which two different types exist. Other expressions such as statistical and quasi-equilibrium which do not strictly satisfy the Exner conditions are also acknowledged for their practical use. The choice of a temporal scale is imperative to analyse the type of equilibrium. We discuss the difference between morphodynamic equilibrium in the "real world" (nature) and the "virtual world" (model). Modelling studies rely on simplifications of the real world and lead to understanding of process interactions. A variety of factors affect the use of virtual-world predictions in the real world (e.g., variability in environmental drivers and variability in the setting) so that the concept of morphodynamic equilibrium should be mathematically unequivocal in the virtual world and interpreted over the appropriate spatial and temporal scale in the real world. We draw examples from estuarine settings which are subject to various governing factors which broadly include hydrodynamics, sedimentology and landscape setting. Following the traditional "tide-wave-river" ternary diagram, we summarize studies todate that explore the "virtual world", discuss the type of equilibrium reached and how it relates to the real world

Is “Morphodynamic Equilibrium” an oxymoron?

Morphodynamic equilibrium is a widely adopted yet elusive concept in the field of geomorphology of coasts, rivers and estuaries. Based on the Exner equation, an expression of mass conservation of sediment, we distinguish three types of equilibrium defined as static and dynamic, of which two different types exist. Other expressions such as statistical and quasi-equilibrium which do not strictly satisfy the Exner conditions are also acknowledged for their practical use. The choice of a temporal scale is imperative to analyse the type of equilibrium. We discuss the difference between morphodynamic equilibrium in the "real world" (nature) and the "virtual world" (model). Modelling studies rely on simplifications of the real world and lead to understanding of process interactions. A variety of factors affect the use of virtual-world predictions in the real world (e.g., variability in environmental drivers and variability in the setting) so that the concept of morphodynamic equilibrium should be mathematically unequivocal in the virtual world and interpreted over the appropriate spatial and temporal scale in the real world. We draw examples from estuarine settings which are subject to various governing factors which broadly include hydrodynamics, sedimentology and landscape setting. Following the traditional "tide-wave-river" ternary diagram, we summarize studies todate that explore the "virtual world", discuss the type of equilibrium reached and how it relates to the real world.Coastal EngineeringEnvironmental Fluid Mechanic

Tidal controls on river delta morphology

River delta degradation has been caused by extraction of natural resources, sediment retention by reservoirs, and sea-level rise. Despite global concerns about these issues, human activity in the world’s largest deltas intensifies. Harbour development, construction of flood defences, sand mining and land reclamation emerge as key contemporary factors that exert an impact on delta morphology. Tides interacting with river discharge can play a crucial role in the morphodynamic development of deltas under pressure. Emerging insights into tidal controls on river delta morphology suggest that—despite the active morphodynamics in tidal channels and mouth bar regions—tidal motion acts to stabilize delta morphology at the landscape scale under the condition that sediment import during low flows largely balances sediment export during high flows. Distributary channels subject to tides show lower migration rates and are less easily flooded by the river because of opposing non-linear interactions between river discharge and the tide. These interactions lead to flow changes within channels, and a more uniform distribution of discharge across channels. Sediment depletion and rigorous human interventions in deltas, including storm surge defence works, disrupt the dynamic morphological equilibrium and can lead to erosion and severe scour at the channel bed, even decades after an intervention.Coastal Engineerin