Pushing the boundaries: integration of multi-source digital elevation model data for seamless geological mapping of the UK's coastal zone

Recent advances in marine acoustic survey and land-based topographic monitoring technologies have resulted in increasingly cost-effective data acquisition in coastal areas. The DEFRA-funded National Network of Regional Coastal Monitoring Programmes of England are, for example, utilising swath bathymetry and airborne light detection and ranging (LiDAR) technology more routinely to survey the coastal zone around the coastline of England. The demand for data processing, visualisation and interpretation techniques to keep pace with such advances in data acquisition is clear. This study discusses collection and processing techniques for such data on the south coast of Dorset, England, which have enabled the production of a seamless, high spatial resolution digital elevation model across the coastal zone. Case studies demonstrate how this elevation model can be viewed and analysed using state-of-the-art digital techniques to allow geological mapping to be extended from onshore to offshore in unprecedented detail, effectively eliminating what is known as the ‘White Ribbon’ for coastal geological mapping. The potential for rolling out such techniques for wider surveying programmes across many environmental disciplines is significant, which could contribute towards improving the multi-disciplinary scientific evidence base in the complex coastal zone

Manipulating adenovirus hexon hypervariable loops dictates immune neutralisation and coagulation factor X-dependent cell interaction in vitro and in vivo

Adenoviruses are common pathogens, mostly targeting ocular, gastrointestinal and respiratory cells, but in some cases infection disseminates, presenting in severe clinical outcomes. Upon dissemination and contact with blood, coagulation factor X (FX) interacts directly with the adenovirus type 5 (Ad5) hexon. FX can act as a bridge to bind heparan sulphate proteoglycans, leading to substantial Ad5 hepatocyte uptake. FX “coating” also protects the virus from host IgM and complement-mediated neutralisation. However, the contribution of FX in determining Ad liver transduction whilst simultaneously shielding the virus from immune attack remains unclear. In this study, we demonstrate that the FX protection mechanism is not conserved amongst Ad types, and identify the hexon hypervariable regions (HVR) of Ad5 as the capsid proteins targeted by this host defense pathway. Using genetic and pharmacological approaches, we manipulate Ad5 HVR interactions to interrogate the interplay between viral cell transduction and immune neutralisation. We show that FX and inhibitory serum components can co-compete and virus neutralisation is influenced by both the location and extent of modifications to the Ad5 HVRs. We engineered Ad5-derived HVRs into the rare, native non FX-binding Ad26 to create Ad26.HVR5C. This enabled the virus to interact with FX at high affinity, as quantified by surface plasmon resonance, FX-mediated cell binding and transduction assays. Concomitantly, Ad26.HVR5C was also sensitised to immune attack in the absence of FX, a direct consequence of the engineered HVRs from Ad5. In both immune competent and deficient animals, Ad26.HVR5C hepatic gene transfer was mediated by FX following intravenous delivery. This study gives mechanistic insight into the pivotal role of the Ad5 HVRs in conferring sensitivity to virus neutralisation by IgM and classical complement-mediated attack. Furthermore, through this gain-of-function approach we demonstrate the dual functionality of FX in protecting Ad26.HVR5C against innate immune factors whilst determining liver targeting

Interpreting monitoring data for shoreline and geohazard mapping

The demand for marine-related spatial information has become increasingly apparent in recent years at a European and national scale, due to the increased pressures on the sea-floor environments and marine resources of UK territorial waters. The advent of economically viable swath bathymetry data acquisition in the coastal zone and effective collaborative partnerships between the Channel Coastal Observatory, Maritime and Coastguard Agency, UK Hydrographic Office, British Geological Survey and academic institutions, have opened up new opportunities to produce a robust scientific evidence base to inform integrated coastal zone management objectives and contribute to wider scientific initiatives. Interpretation of high-quality bathymetric data, acoustic backscatter and ground-truthing data allows zones of exposed bedrock, rock outcrops and pinnacles to be identified, along with areas of mobility or stability of surficial sediments. Temporal and spatial analyses of coastal and marine monitoring datasets also contribute to improved understanding of interactions between natural coastal process and coastal-defence and beach-management operations. Furthermore, developments in three-dimensional mapping techniques and visualisation technologies have enabled seamless high-resolution coastal geology maps to be re-interpreted and extended offshore, providing a more complete picture of the baseline geology, physical properties, structure and geohazards in the coastal and nearshore zone. The full paper details the methodology developed to produce a range of indicative marine mapping layers, and presents examples from eastern and southern England where marine-related spatial data has contributed to the multi-disciplinary scientific evidence base to inform development of UK marine policy and planning, coastal management and coastal zone geological mappin

Targeted nanoparticle binding & detection in petroleum hydrocarbon impacted porous media

The final publication is available at Elsevier via https://dx.doi.org/10.1016/j.chemosphere.2018.10.046 © 2019. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/Targeted nanoparticle binding has become a core feature of experimental pharmaceutical product design which enables more efficient payload delivery and enhances medical imaging by accumulating nanoparticles in specific tissues. Environmental remediation and geophysical monitoring encounter similar challenges which may be addressed in part by the adoption of targeted nanoparticle binding strategies. This study illustrates that engineered nanoparticles can bind to crude oil-impacted silica sand, a selective adsorption driven by active targeting based on an amphiphilic polymer coating. This coating strategy resulted in 2 mg/kg attachment to clean silica sand compared to 8 mg/kg attachment to oil-impacted silica sand. It was also shown that modifying the surface coating influenced the binding behaviour of the engineered nanoparticles – more hydrophobic polymers resulted in increased binding. Successful targeting of Pluronic-coated iron oxide nanoparticles to a crude oil and silica sand mixture was demonstrated through a combined quantitative Orbital Emission Spectroscopy mass analysis supported by Vibrating Scanning Magnetometer magnetometry, and a qualitative X-ray micro-computed tomography (CT) visualization approach. These non-destructive characterization techniques facilitated efficient analysis of nanoparticles in porous medium samples with minimal sample preparation, and in the case of X-Ray CT, illustrated how targeted nanoparticle binding may be used to produce 3-D images of contaminated porous media. This work demonstrated successful implementation of nanoparticle targeted binding toward viscous LNAPL such as crude oil in the presence of a porous medium, a step which opens the door to successful application of targeted delivery technology in environmental remediation and monitoring.Natural Sciences and Engineering Research Council of Canad

What's on the horizon for community-based conservation? Emerging threats and opportunities

Community-based conservation can support livelihoods and biodiversity, while reinforcing local and Indigenous values, cultures, and institutions. Its delivery can help address cross-cutting global challenges, such as climate change, conservation, poverty, and food security. Therefore, understanding trends in community-based conservation is pertinent to setting and implementing global goals. We undertook a horizon scan to prioritize 15 emerging threats and opportunities expected to impact the future effectiveness of community-based conservation. Topics relate to global biodiversity policy; human rights; shifting human geography; inclusion, diversity, equity, and access; conservation finance and income; and economic reforms. Our findings offer guidance on strengthening community-based conservation to achieve global environmental and development goals

MRE11 and RAD50, but not NBS1, are essential for gene targeting in the moss Physcomitrella patens

The moss Physcomitrella patens is unique among plant models for the high frequency with which targeted transgene insertion occurs via homologous recombination. Transgene integration is believed to utilize existing machinery for the detection and repair of DNA double-strand breaks (DSBs). We undertook targeted knockout of the Physcomitrella genes encoding components of the principal sensor of DNA DSBs, the MRN complex. Loss of function of PpMRE11 or PpRAD50 strongly and specifically inhibited gene targeting, whilst rates of untargeted transgene integration were relatively unaffected. In contrast, disruption of the PpNBS1 gene retained the wild-type capacity to integrate transforming DNA efficiently at homologous loci. Analysis of the kinetics of DNA-DSB repair in wild-type and mutant plants by single-nucleus agarose gel electrophoresis revealed that bleomycin-induced fragmentation of genomic DNA was repaired at approximately equal rates in each genotype, although both the Ppmre11 and Pprad50 mutants exhibited severely restricted growth and development and enhanced sensitivity to UV-B and bleomycin-induced DNA damage, compared with wild-type and Ppnbs1 plants. This implies that while extensive DNA repair can occur in the absence of a functional MRN complex; this is unsupervised in nature and results in the accumulation of deleterious mutations incompatible with normal growth and development

Single Molecule PCR Reveals Similar Patterns of Non-Homologous DSB Repair in Tobacco and Arabidopsis

DNA double strand breaks (DSBs) occur constantly in eukaryotes. These potentially lethal DNA lesions are repaired efficiently by two major DSB repair pathways: homologous recombination and non-homologous end joining (NHEJ). We investigated NHEJ in Arabidopsis thaliana and tobacco (Nicotiana tabacum) by introducing DNA double-strand breaks through inducible expression of I-SceI, followed by amplification of individual repair junction sequences by single-molecule PCR. Using this process over 300 NHEJ repair junctions were analysed in each species. In contrast to previously published variation in DSB repair between Arabidopsis and tobacco, the two species displayed similar DSB repair profiles in our experiments. The majority of repair events resulted in no loss of sequence and small (1–20 bp) deletions occurred at a minority (25–45%) of repair junctions. Approximately ∼1.5% of the observed repair events contained larger deletions (>20 bp) and a similar percentage contained insertions. Strikingly, insertion events in tobacco were associated with large genomic deletions at the site of the DSB that resulted in increased micro-homology at the sequence junctions suggesting the involvement of a non-classical NHEJ repair pathway. The generation of DSBs through inducible expression of I-SceI, in combination with single molecule PCR, provides an effective and efficient method for analysis of individual repair junctions and will prove a useful tool in the analysis of NHEJ

Minimal information for studies of extracellular vesicles 2018 (MISEV2018):a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points