Comparison of CpG- and UpA-mediated restriction of RNA virus replication in mammalian and avian cells and investigation of potential ZAP-mediated shaping of host transcriptome compositions

The ability of zinc finger antiviral protein (ZAP) to recognize and respond to RNA virus sequences with elevated frequencies of CpG dinucleotides has been proposed as a functional part of the vertebrate innate immune antiviral response. It has been further proposed that ZAP activity shapes compositions of cytoplasmic mRNA sequences to avoid self-recognition, particularly mRNAs for interferons (IFNs) and IFN-stimulated genes (ISGs) expressed during the antiviral state. We investigated whether restriction of the replication of mutants of influenza A virus (IAV) and the echovirus 7 (E7) replicon with high CpG and UpA frequencies varied in different species of mammals and birds. Cell lines from different bird orders showed substantial variability in restriction of CpG-high mutants of IAV and E7 replicons, whereas none restricted UpA-high mutants, in marked contrast to universal restriction of both mutants in mammalian cells. Dinucleotide representation in ISGs and IFN genes was compared with those of cellular transcriptomes to determine whether potential differences in inferred ZAP activity between species shaped dinucleotide compositions of highly expressed genes during the antiviral state. While mammalian type 1 IFN genes typically showed often profound suppression of CpG and UpA frequencies, there was no oversuppression of either in ISGs in any species, irrespective of their ability to restrict CpG- or UpA-high mutants. Similarly, genome sequences of mammalian and avian RNA viruses were compositionally equivalent, as were IAV strains recovered from ducks, chickens and humans. Overall, we found no evidence for host variability in inferred ZAP function shaping host or viral transcriptome compositions.

Consistent concentrations of critically endangered Balearic shearwaters in UK waters revealed by at-sea surveys

AIM

Europe's only globally critically endangered seabird, the Balearic shearwater (Puffinus mauretanicus), is thought to have expanded its postbreeding range northwards into UK waters, though its at sea distribution there is not yet well understood. This study aims to identify environmental factors associated with the species' presence, map the probability of presence of the species across the western English Channel and southern Celtic Sea, and estimate the number of individuals in this area.

LOCATION

The western English Channel and southern Celtic Sea.

METHODS

This study analyses strip transect data collected between 2013 and 2017 from vessel-based surveys in the western English Channel and southern Celtic Sea during the Balearic shearwater's postbreeding period. Using environmental data collected directly and from remote sensors both Generalized Additive Models and the Random Forest machine learning model were used to determine shearwater presence at different locations. Abundance was estimated separately using a density multiplication approach.

RESULTS

Both models indicated that oceanographic features were better predictors of shearwater presence than fish abundance. Seafloor aspect, sea surface temperature, depth, salinity, and maximum current speed were the most important predictors. The estimated number of Balearic shearwaters in the prediction area ranged from 652 birds in 2017 to 6,904 birds in 2014.

MAIN CONCLUSIONS

Areas with consistently high probabilities of shearwater presence were identified at the Celtic Sea front. Our estimates suggest that the study area in southwest Britain supports between 2% and 23% of the global population of Balearic shearwaters. Based on the timing of the surveys (mainly in October), it is probable that most of the sighted shearwaters were immatures. This study provides the most complete understanding of Balearic shearwater distribution in UK waters available to date, information that will help inform any future conservation actions concerning this endangered species.

Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C4 rhizomatous grasses Miscanthus and switchgrass

Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter-binding protein-Like, MADS-box SEPELLATA2 and gibberellin-responsive bHLH137. The former is emerging as a key component of the age-related flowering time pathway.

Relating characteristics of global biodiversity targets to reported progress

To inform governmental discussions on the nature of a revised Strategic Plan for Biodiversity of the Convention on Biological Diversity (CBD), we reviewed the relevant literature and assessed the framing of the 20 Aichi Biodiversity Targets in the current strategic plan. We asked international experts from nongovernmental organizations, academia, government agencies, international organizations, research institutes, and the CBD to score the Aichi Targets and their constituent elements against a set of specific, measurable, ambitious, realistic, unambiguous, scalable, and comprehensive criteria (SMART based, excluding time bound because all targets are bound to 2015 or 2020). We then investigated the relationship between these expert scores and reported progress toward the target elements by using the findings from 2 global progress assessments (Global Biodiversity Outlook and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services). We analyzed the data with ordinal logistic regressions. We found significant positive relationships (p < 0.05) between progress and the extent to which the target elements were perceived to be measurable, realistic, unambiguous, and scalable. There was some evidence of a relationship between progress and specificity of the target elements, but no relationship between progress and ambition. We are the first to show associations between progress and the extent to which the Aichi Targets meet certain SMART criteria. As negotiations around the post-2020 biodiversity framework proceed, decision makers should strive to ensure that new or revised targets are effectively structured and clearly worded to allow the translation of targets into actionable policies that can be successfully implemented nationally, regionally, and globally.

Monitoring mosaic biotopes in a marine conservation zone by autonomous underwater vehicle

The number of marine protected areas (MPAs) has increased dramatically in the last decade and poses a major logistic challenge for conservation practitioners in terms of spatial extent and the multiplicity of habitats and biotopes that now require assessment. Photographic assessment by autonomous underwater vehicle (AUV) enables the consistent description of multiple habitats, in our case including mosaics of rock and sediment. As a case study, we used this method to survey the Greater Haig Fras marine conservation zone (Celtic Sea, northeast Atlantic). We distinguished 7 biotopes, detected statistically significant variations in standing stocks, species density, species diversity, and faunal composition, and identified significant indicator species for each habitat. Our results demonstrate that AUV-based photography can produce robust data for ecological research and practical marine conservation. Standardizing to a minimum number of individuals per sampling unit, rather than to a fixed seafloor area, may be a valuable means of defining an ecologically appropriate sampling unit. Although composite sampling represents a change in standard practice, other users should consider the potential benefits of this approach in conservation studies. It is broadly applicable in the marine environment and has been successfully implemented in deep-sea conservation and environmental impact studies. Without a cost-effective method, applicable across habitats, it will be difficult to further a coherent classification of biotopes or to routinely assess their conservation status in the rapidly expanding global extent of MPAs.

Current state of the global operational aerosol multi-model ensemble: An update from the International Cooperative for Aerosol Prediction (ICAP)

Since the first International Cooperative for Aerosol Prediction (ICAP) multi-model ensemble (MME) study, the number of ICAP global operational aerosol models has increased from five to nine. An update of the current ICAP status is provided, along with an evaluation of the performance of ICAP-MME over 2012-2017, with a focus on June 2016-May 2017. Evaluated with ground-based Aerosol Robotic Network (AERONET) aerosol optical depth (AOD) and data assimilation quality MODerate-resolution Imaging Spectroradiometer (MODIS) retrieval products, the ICAP-MME AOD consensus remains the overall top-scoring and most consistent performer among all models in terms of root-mean-square error (RMSE), bias and correlation for total, fine- and coarse-mode AODs as well as dust AOD; this is similar to the first ICAP-MME study. Further, over the years, the performance of ICAP-MME is relatively stable and reliable compared to more variability in the individual models. The extent to which the AOD forecast error of ICAP-MME can be predicted is also examined. Leading predictors are found to be the consensus mean and spread. Regression models of absolute forecast errors were built for AOD forecasts of different lengths for potential applications. ICAP-MME performance in terms of modal AOD RMSEs of the 21 regionally representative sites over 2012-2017 suggests a general tendency for model improvements in fine-mode AOD, especially over Asia. No significant improvement in coarse-mode AOD is found overall for this time period.

What Works? the Influence of Changing Wastewater Treatment Type, Including Tertiary Granular Activated Charcoal, on Downstream Macroinvertebrate Biodiversity Over Time

The present study reviewed the impacts of wastewater on macroinvertebrates over 4 decades in a United Kingdom lowland river. This involved examining changes in chemicals, temperature, flow, and macroinvertebrate diversity from the 1970s until 2017 for a wastewater-dominated river downstream of Swindon in the United Kingdom (population ~ 220 000). When the wastewater treatment process changed from trickling filter to activated sludge in 1991, biological oxygen demand was nearly halved (90th percentile from 8.1 to 4.6 mg/L), ammonia peaks dropped more than 7-fold (90th percentile from 3.9 to 0.53 mg/L), whereas dissolved oxygen climbed consistently above 60% saturation (10th percentile from 49 to 64%) at a sampling point 2 km downstream of the wastewater treatment plant. A sustained increase in the number of macroinvertebrate species was evident from that point. River flow did not change, temperature rose slightly, and the major metal concentrations declined steadily over most of the monitoring period. Neither the introduction of phosphate stripping in 1999 nor the use of tertiary granular activated charcoal from 2008 to 2014 had strong positive effects on subsequent macroinvertebrate diversity. That the diversity still had not reached the ideal status by 2016 may be related to the modest habitat quality, agricultural pesticides, and limited recolonization potential in the catchment. The results indicate that urban wastewaters, with their chemical pollutants, are today probably not the biggest threat to the macroinvertebrate diversity of multiply stressed lowland rivers in the United Kingdom. Environ Toxicol Chem 2019;38:1820-1832. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

Cryptic diets of forage fish: jellyfish consumption observed in the Celtic Sea and western English Channel

To establish if fishes' consumption of jellyfish changes through the year, we conducted a molecular gut-content assessment on opportunistically sampled species from the Celtic Sea in October and compared these with samples previously collected in February and March from the Irish Sea. Mackerel Scomber scombrus were found to feed on hydrozoan jellyfish relatively frequently in autumn, with rare consumption also detected in sardine Sardina pilchardus and sprat Sprattus sprattus. By October, moon jellyfish Aurelia aurita appeared to have escaped predation, potentially through somatic growth and the development of stinging tentacles. This is in contrast with sampling in February and March where A. aurita ephyrae were heavily preyed upon. No significant change in predation rate was observed in S. sprattus, but jellyfish predation by S. scombrus feeding in autumn was significantly higher than that seen during winter. This increase in consumption appears to be driven by the consumption of different, smaller jellyfish species than were targeted during the winter.

What is multispecies MSY? A worked example from the North Sea

The concept of an optimum yield at intermediate levels of fishing (the so called maximum sustainable yield or MSY) has been with us since the 1930s and is now enshrined in legislation as a key objective of fisheries management. The concept seems intuitively reasonable and is readily applicable to a single stock treated in isolation and assuming a constant environment. However, translating this concept into a mixed and multispecies fishery, where there are complex trade-offs between fleets and stocks and in general no simple optimum solution, has been problematic. Here I introduce a framework for thinking about multispecies MSY in terms of an integrated risk of stock depletion and expected long-term yield. Within this framework I consider the performance of a set of simple harvest control rules based upon a single-limit fishing mortality rate (F) which is common to all stocks and a target biomass which is a set fraction of a stock's virgin biomass. Using a multispecies management strategy evaluation, I compare expected outcomes for a set of these harvest control rules with alternative scenarios, in which each stock has its own F based on the assessment process. I find that the simple framework can produce outcomes that are similar to those from the more sophisticated estimates of F. I therefore conclude that achieving multispecies MSY may depend more upon setting reasonable biomass targets and faithfully applying a harvest control rule approach rather than determining the best possible Fs for each stock.

Unraveling past impacts of climate change and land management on historic peatland development using proxy-based reconstruction, monitoring data and process modeling

Peatlands represent globally significant soil carbon stores that have been accumulating for millennia under water-logged conditions. However, deepening water-table depths (WTD) from climate change or human-induced drainage could stimulate decomposition resulting in peatlands turning from carbon sinks to carbon sources. Contemporary WTD ranges of testate amoebae (TA) are commonly used to predict past WTD in peatlands using quantitative transfer function models. Here we present, for the first time, a study comparing TA-based WTD reconstructions to instrumentally monitored WTD and hydrological model predictions using the MILLENNIA peatland model to examine past peatland responses to climate change and land management. Although there was very good agreement between monitored and modeled WTD, TA-reconstructed water table was consistently deeper. Predictions from a larger European TA transfer function data set were wetter, but the overall directional fit to observed WTD was better for a TA transfer function based on data from northern England. We applied a regression-based offset correction to the reconstructed WTD for the validation period (1931-2010). We then predicted WTD using available climate records as MILLENNIA model input and compared the offset-corrected TA reconstruction to MILLENNIA WTD predictions over an extended period (1750-1931) with available climate reconstructions. Although the comparison revealed striking similarities in predicted overall WTD patterns, particularly for a recent drier period (1965-1995), there were clear periods when TA-based WTD predictions underestimated (i.e. drier during 1830-1930) and overestimated (i.e. wetter during 1760-1830) past WTD compared to MILLENNIA model predictions. Importantly, simulated grouse moor management scenarios may explain the drier TA WTD predictions, resulting in considerable model predicted carbon losses and reduced methane emissions, mainly due to drainage. This study demonstrates the value of a site-specific and combined data-model validation step toward using TA-derived moisture conditions to understand past climate-driven peatland development and carbon budgets alongside modeling likely management impacts.