Humanising and dehumanising pigs in genomic and transplantation research

Biologists who work on the pig (Sus scrofa) take advantage of its similarity to humans by constructing the inferential and material means to traffic data, information and knowledge across the species barrier. Their research has been funded due to its perceived value for agriculture and medicine. Improving selective breeding practices, for instance, has been a driver of genomics research. The pig is also an animal model for biomedical research and practice, and is proposed as a source of organs for cross-species transplantation: xenotransplantation. Genomics research has informed transplantation biology, which has itself motivated developments in genomics. Both have generated models of correspondences between the genomes of pigs and humans. Concerning genomics, I detail how researchers traverse species boundaries to develop representations of the pig genome, alongside ensuring that such representations are sufficiently porcine. In transplantation biology, the representations of the genomes of humans and pigs are used to detect and investigate immunologically-pertinent differences between the two species. These key differences can then be removed, to ‘humanise’ donor pigs so that they can become a safe and effective source of organs. In both of these endeavours, there is a tension between practices that ‘humanise’ the pig (or representations thereof) through using resources from human genomics, and the need to ‘dehumanise’ the pig to maintain distinctions for legal, ethical and scientific reasons. This paper assesses the ways in which this tension has been managed, observing the differences between its realisations across comparative pig genomics and transplantation biology, and considering the consequences of this

Quantifying measures to limit wind driven resuspension of sediments for improvement of the ecological quality in some shallow Dutch lakes

Although phosphorus loadings are considered the main pressure for most shallow lakes, wind-driven resuspension can cause additional problems for these aquatic ecosystems. We quantified the potential effectiveness of measures to reduce the contribution of resuspended sediments, resulting from wind action, to the overall light attenuation for three comparable shallow peat lakes with poor ecological status in the Netherlands: Loosdrecht, Nieuwkoop, and Reeuwijk (1.8–2.7 m depth, 1.6–2.5 km fetch). These measures are: 1. wave reducing barriers, 2. water level fluctuations, 3. capping of the sediment with sand, and 4. combinations of above. Critical shear stress of the sediments for resuspension (Vcrit), size distribution, and optical properties of the suspended material were quantified in the field (June 2009) and laboratory. Water quality monitoring data (2002–2009) showed that light attenuation by organic suspended matter in all lakes is high. Spatial modeling of the impact of these measures showed that in Lake Loosdrecht limiting wave action can have significant effects (reductions from 6% exceedance to 2% exceedance of Vcrit), whereas in Lake Nieuwkoop and Lake Reeuwijk this is less effective. The depth distribution and shape of Lake Nieuwkoop and Lake Reeuwijk limit the role of wind-driven resuspension in the total suspended matter concentration. Although the lakes are similar in general appearance (origin, size, and depth range) measures suitable to improve their ecological status differ. This calls for care when defining the programme of measures to improve the ecological status of a specific lake based on experience from other lakes.

Modelling chemistry in the nocturnal boundary layer above tropical rainforest and a generalised effective nocturnal ozone deposition velocity for sub-ppbv NOx conditions

Measurements of atmospheric composition have been made over a remote rainforest landscape. A box model has previously been demonstrated to model the observed daytime chemistry well. However the box model is unable to explain the nocturnal measurements of relatively high [NO] and [O3], but relatively low observed [NO2]. It is shown that a one-dimensional (1-D) column model with simple O3 -NOx chemistry and a simple representation of vertical transport is able to explain the observed nocturnal concentrations and predict the likely vertical profiles of these species in the nocturnal boundary layer (NBL). Concentrations of tracers carried over from the end of the night can affect the atmospheric chemistry of the following day. To ascertain the anomaly introduced by using the box model to represent the NBL, vertically-averaged NBL concentrations at the end of the night are compared between the 1-D model and the box model. It is found that, under low to medium [NOx] conditions (NOx <1 ppbv), a simple parametrisation can be used to modify the box model deposition velocity of ozone, in order to achieve good agreement between the box and 1-D models for these end-of-night concentrations of NOx and O3. This parametrisation would could also be used in global climate-chemistry models with limited vertical resolution near the surface. Box-model results for the following day differ significantly if this effective nocturnal deposition velocity for ozone is implemented; for instance, there is a 9% increase in the following day’s peak ozone concentration. However under medium to high [NOx] conditions (NOx > 1 ppbv), the effect on the chemistry due to the vertical distribution of the species means no box model can adequately represent chemistry in the NBL without modifying reaction rate constants

Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon

Background: Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN) challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools. Results: Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified. Conclusions: We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data in a large complex genome, and its possible utility in farmed animal selection programs

Advanced Preparation Makes Research in Emergencies and Isolation Care Possible: The Case of Novel Coronavirus Disease (COVID-19)

The optimal time to initiate research on emergencies is before they occur. However, timely initiation of high-quality research may launch during an emergency under the right conditions. These include an appropriate context, clarity in scientific aims, preexisting resources, strong operational and research structures that are facile, and good governance. Here, Nebraskan rapid research efforts early during the 2020 coronavirus disease pandemic, while participating in the first use of U.S. federal quarantine in 50 years, are described from these aspects, as the global experience with this severe emerging infection grew apace. The experience has lessons in purpose, structure, function, and performance of research in any emergency, when facing any threat

Tropospheric modeling of acetic acid in the UK for summer, winter and spring seasons using a mesoscale 3-dimensional chemistry and transport model, WRF-Chem-CRI

The measurement of acetic acid during the ClearfLo campaign for Winter 2012 and Summer 2012 in London and at the Weybourne Research Station (East Anglia), UK for Spring 2013 gives the average ± 1σ mixing ratios of 45.9 ± 31.5, 25.7 ± 14.3 and 55.1 ± 32.0 ppt, respectively. The WRF-Chem-CRI model was run over these three seasons and within uncertainty reproduced the data from London, with mixing ratios during Winter (32.3 ± 25.3 ppt) and Summer (55.1 ± 22.6 ppt). The model's seasonality was opposite to that observed and although within the combined uncertainty of the measurement and model data it underpredicted the levels observed at Weybourne during Spring (28.9 ± 19.3 ppt). The model-measurement correlations of the meteorological parameters (e.g. temperature, wind direction, wind speed) were good with a correlation of R > 0.7. The predicted diurnal trend of acetic acid resembled measurement data with a small negative bias during winter but performed less well during summer with a large positive bias and in spring with a large negative bias. The reasonable correlation of acetic acid mixing ratios with temperature was found to be similar for both measurement and model (Rmeasurement = 0.5, Rmodel = 0.6) during Summer suggesting the importance of the photochemical secondary source of acetic acid which was reflected both in the measurement and the model. The key processes identified from the model results were a) missing direct anthropogenic sources of acetic acid (accounting for the lower model winter values) and b) not including its loss process by Criegee intermediates (accounting for the higher model values in summer). Comparing the weekend data with weekday data revealed a likely underpredicted source of acetic acid from vehicles. The wet deposition removal process of acetic acid was found not to be as significant in the UK as anticipated

Fatty acid profiles and stable isotope composition of Antarctic macroalgae: a baseline for a combined biomarker approach in food web studies

The Western Antarctic Peninsula supports a diverse assemblage of > 100 described macroalgal species that contribute to the base of coastal food webs, but their contribution to local nearshore food webs is still uncertain across larger spatial scales. The analysis of biomarkers, specifically fatty acids and stable isotopes, offers a tool to clarify the trophic role of Antarctic macroalgae. The aim of this study was to describe the fatty acid profiles and stable isotope values of 31 algal species from three divisions (Chlorophyta—1, Ochrophyta—8, Rhodophyta—22) collected at the same sites for both biomarkers. Of these, 13 species had no previously published fatty acid profiles. Most species were rich in polyunsaturated fatty acids (PUFAs), suggesting they are highly nutritious and could be a resource of essential fatty acids for consumers. This was specifically noticeable in the overall low PUFA ratio (∑ω6/∑ω3 ratio), with low ratios being an indicator of high nutritional quality for consumers. Fatty acid profiles of macroalgae grouped strongly by phylogeny (at the levels of division, order, and family), while stable isotope groupings were more driven by the physiological properties of the species. Specifically, some closely related red algal species exhibited very different stable isotope values based on their carbon concentrating mechanisms, with highly 13C-depleted values in several Rhodophyta species. The fact that the two biomarker approaches created different groupings of Antarctic macroalgae collected at the same locations emphasizes that their combined application can be a powerful tool in Antarctic coastal food web studies.National Science Foundation. Antarctic Organisms and Ecosystems Program. National Science Foundation Graduate Research Fellowship. University of Oregon's Raymund Fellowship.Abstract -- Introduction -- Methods -- Results -- Discussion -- Data availability -- References -- Acknowledgements -- Author information -- Ethics declarations -- Additional information -- Supplementary information -- Rights and permissions -- About this articleYe