Harmonising topographic & remotely sensed datasets, a reference dataset for shoreline and beach change analysis.

This paper presents a novel reference dataset for North Norfolk, UK, that demonstrates the value of harmonising coastal field-based topographic and remotely sensed datasets at local scales. It is hoped that this reference dataset and the associated methodologies will facilitate the use of topographic and remotely sensed coastal datasets, as demonstrated here using open-access UK Environment Agency datasets. Two core methodologies, used to generate the novel reference dataset, are presented. Firstly, we establish a robust approach to extracting shorelines from vertical aerial photography, validated against LiDAR (Light Detection and Ranging) and coastal topography surveys. Secondly, we present a standard methodology for quantifying sediment volume change from spatially continuous LiDAR elevation datasets. As coastal systems are monitored at greater spatial resolution and temporal frequency there is an unprecedented opportunity to determine how and why coastal systems have changed in the past with a view to informing future forecasting. With revelation of trends that suggest increasing coastal risk, coastal change research is needed to inform the management and protection of coasts

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

Will nature work with us? Erosion and flooding impacts on a UK barrier

‘Barrier island’ refers to a diverse collection of coastal landforms that often support substantial human populations, critical infrastructures, and ecosystems. Globally, many coastal barriers are experiencing climatically altered environmental forcing coupled with increasing anthropogenic pressures. This paper undertakes high resolution shoreline change analysis to reveal how Blakeney Point, a mixed sandy-gravel barrier located on the UK’s East Coast, has evolved over centennial, decadal and event timescales. We seek to establish the implications of barrier evolution, under contrasting management regimes, for present erosion and flooding hazards. Interrogating a series of alternative shoreline proxies reveals a series of interdependent behaviors. Over the 130-year period of study, Blakeney Point is shown to be rolling landward at a mean rate of 0.60 m a-1. Assuming continued landward retreat over the coming decades, future flood-generating storm events will encounter more landward shoreline positions than today. Superimposed on this trend, we observe the presence of alongshore migrating erosional hotspots which give rise to unpredictable morphologies at any given location on the spit. Finally, we find that instances of barrier setback are driven by individual storm events, which makes barrier retreat both highly variable and discontinuous in time and space. This is illustrated by the presence of overwash, particularly along stretches of the barrier that have experienced a recent shift in management regime towards a non-interventionist approach.This work was funded by the NERC/ESRC Data, Risk and Environmental Analytical Methods (DREAM) Centre, Grant/Award Number: NE/M009009/1. It is also a contribution to the NERC-funded project “Physical and Biological dynamic coastal processes and their role in coastal recovery” (BLUEcoast), Grant Award Number: NE/N015924/1

Indices of Body Composition and Repeatability of Residual Feed Intake in Growing Columbia Ewes Fed the Same Diet

Residual feed intake (RFI), an efficiency measurement based upon the difference in expected and actual feed intake, is used to improve production efficiency of livestock. The purpose of this study was to evaluate the repeatability of ewe RFI measured for two consecutive years, and to investigate the relationship between indices of body composition in yearling ewes and RFI. Two trials, using the same Columbia ewe lambs (n = 17) were conducted in consecutive years (2014, 2015) using the same diet. RFI was calculated for each ewe each year. RFI did not differ (P = 0.77) between years. Each year, ewes were separated into RFI classes (LOW (efficient); MOD (average); HIGH (inefficient)). In 2014, ewe lamb performance did not differ among classes (P > 0.3). In 2015, dry matter intake was greater for HIGH ewes (P < 0.0002). Ribeye area (REA; cm2) and backfat thickness (BF; cm) were measured by ultrasound on day 0 (start of trial), 17, and 45 (end of trial) in 2015 and used to calculate estimates of final body composition. RFI classification did not affect REA or BF (P > 0.25). There was a trend for whole-body muscle mass to differ among RFI classes (P = 0.09), but no other body composition estimates were affected. Results suggest that RFI is repeatable; however, indices of body composition seem to be independent of RFI in Columbia ewes fed the same diet under similar conditions

Recent Decisions

Comments on recent decisions by Richard M. Di Valerio, James A. Uhl, Donald J. Prebenda, Wilbur L. Pollard, William N. Antonis, Richard E. Shipman, Richard D. Heman, Thomas P. Meaney, Jr., John A. Pietrykowski, and Richard F. Welter

Evaluating the viability of coastal wet grassland to a changing management regime through flood hazard modelling

The high-risk nature of low-lying coastal areas means that many are characterised by protective dikes, sea walls, and earthen embankments. Across Europe, such structures are employed to limit landward sea flooding and have been used historically to reclaim wetlands, many of which have since gained international protected habitat status. Sea level rise and storms threaten the future viability of fixed flood defences which will be overtopped with increasing frequency and, in extreme cases, breached. This raises questions surrounding defence maintenance and the fate of the reclaimed wetlands they encircle and support. One approach is to design defences with the expectation that they will be overtopped during extreme events, but that catastrophic failure as a result of breaching will be prevented. Such an approach was recently implemented at Blakeney Freshes, North Norfolk Coast, UK, an embanked area of reedbeds and coastal wet grassland. Lowering and widening of the Freshes embankment was undertaken following extensive breaching during the 5 December 2013 storm surge. In this paper we develop and apply a numerical model chain, comprising storm surge water levels, waves, and overtopping, to explore inundation extent, depth, and duration resulting from storm surge induced flooding under several sea level rise scenarios. Modelling results revealed that 99.5% of the flood volume of the 2013 event resulted from embankment breaching. Simulating the same storm event after embankment reprofiling shows that flooding of the Freshes is reduced by 97%, largely because the lower, wider embankments preclude breaching. However, under future sea level rise scenarios, storm surge induced overtopping results in increased inundation depths and drainage times, raising questions regarding the resilience of vegetation communities within the Freshes. By 2100 under the lowest SLR scenario, and by 2050 under the mid SLR scenario, over half of the Freshes will be inundated for >10 days, a potentially critical threshold for current wet grassland survival. Our findings suggest that while effective defence redesign may increase the viability of reclaimed wetland habitats in the short term, as sea levels rise, lengthened inundation durations may render these habitats increasingly vulnerable to ecosystem change under extreme events

Twelve years of SAMtools and BCFtools.

BACKGROUND: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org

Common cancer-associated imbalances in the DNA damage response confer sensitivity to single agent ATR inhibition

ATR is an attractive target in cancer therapy because it signals replication stress and DNA lesions for repair and to S/G2 checkpoints. Cancer-specific defects in the DNA damage response (DDR) may render cancer cells vulnerable to ATR inhibition alone. We determined the cytotoxicity of the ATR inhibitor VE-821 in isogenically matched cells with DDR imbalance. Cell cycle arrest, DNA damage accumulation and repair were determined following VE-821 exposure. Defects in homologous recombination repair (HRR: ATM, BRCA2 and XRCC3) and base excision repair (BER: XRCC1) conferred sensitivity to VE-821. Surprisingly, the loss of different components of the trimeric non-homologous end-joining (NHEJ) protein DNA-PK had opposing effects. Loss of the DNA-binding component, Ku80, caused hypersensitivity to VE-821, but loss of its partner catalytic subunit, DNA-PKcs, did not. Unexpectedly, VE-821 was particularly cytotoxic to human and hamster cells expressing high levels of DNA-PKcs. High DNA-PKcs was associated with replicative stress and activation of the DDR. VE-821 suppressed HRR, determined by RAD51 focus formation, to a greater extent in cells with high DNA-PKcs. Defects in HRR and BER and high DNA-PKcs expression, that are common in cancer, confer sensitivity to ATR inhibitor monotherapy and may be developed as predictive biomarkers for personalised medicine