Conodont biostratigraphy of the Crawford Group, Southern Uplands, Scotland

Extensive new conodont collections from the Crawford Group, the oldest succession in the Southern Uplands of Scotland, support the previously documented biostratigraphical ages for the included formations. The Raven Gill Formation is lower Whitlandian, Arenig (comparable in age to the Dounans Limestone in the Highland Border Complex) and the Kirkton Formation is latest Llandeilian-Aurelucian, Llanvirn to Caradoc in age. It is concluded that there is a significant stratigraphical gap within the Crawford Group. The restricted and probably fault-bounded nature of the Raven Gill outcrops suggests that these may represent olistoliths within a mélange of Llandeilian-Aurelucian age. The chert-bearing succession of the Northern Belt of the Southern Uplands thus represents the juxtaposed sedimentary records of two entirely separate basins – the oldest pre-dates the Grampian assembly of the Laurentian margin, and the younger, the Northern Belt Basin sensu stricto, entirely post-dates this event

Estimating organic surface horizon depth for peat and peaty soils across a Scottish upland catchment using linear mixed models with topographic and geological covariates

In order to evaluate and protect ecosystem services provided by peat and peaty soils, accurate estimations for the depth of the surface organic horizon are required. This study uses linear mixed models (LMMs) to test how topographic (elevation, slope, aspect) and superficial geology parameters can contribute to improved depth estimates across a Scottish upland catchment. Mean (n = 5) depth data from 283 sites (representing full covariate ranges) were used to calibrate LMMs, which were tested against a validation dataset. Models were estimated using maximum likelihood, and the Akaike Information Criterion was used to test whether the iterative addition of covariates to a model with constant fixed effects was beneficial. Elevation, slope and certain geology classes were all identified as useful covariates. Upon addition of the random effects (i.e. spatial modelling of residuals), the RMSE for the model with constant‐only fixed effects reduced by 24%. Addition of random effects to a model with topographic covariates (fixed effects = constant, slope, elevation) reduced the RMSE by 13%, whereas the addition of random effects to a model with topographic and geological covariates (fixed effects = constant, slope, elevation, certain geology classes) reduced the RMSE by only 3%. Therefore, much of the spatial pattern in depth was explained by the fixed effects in the latter model. The study contributes to a growing research base demonstrating that widely available topographic (and also here geological) datasets, which have national coverage, can be included in spatial models to improve organic horizon depth estimations

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

Correlation between infectivity and disease associated prion protein in the nervous system and selected edible tissues of naturally affected scrapie sheep

<div><p>The transmissible spongiform encephalopathies (TSEs) or prion diseases are a group of fatal neurodegenerative disorders characterised by the accumulation of a pathological form of a host protein known as prion protein (PrP). The validation of abnormal PrP detection techniques is fundamental to allow the use of high-throughput laboratory based tests, avoiding the limitations of bioassays. We used scrapie, a prototype TSE, to examine the relationship between infectivity and laboratory based diagnostic tools. The data may help to optimise strategies to prevent exposure of humans to small ruminant TSE material via the food chain. Abnormal PrP distribution/accumulation was assessed by immunohistochemistry (IHC), Western blot (WB) and ELISA in samples from four animals. In addition, infectivity was detected using a sensitive bank vole bioassay with selected samples from two of the four sheep and protein misfolding cyclic amplification using bank vole brain as substrate (vPMCA) was also carried out in selected samples from one animal. Lymph nodes, oculomotor muscles, sciatic nerve and kidney were positive by IHC, WB and ELISA, although at levels 100–1000 fold lower than the brain, and contained detectable infectivity by bioassay. Tissues not infectious by bioassay were also negative by all laboratory tests including PMCA. Although discrepancies were observed in tissues with very low levels of abnormal PrP, there was an overall good correlation between IHC, WB, ELISA and bioassay results. Most importantly, there was a good correlation between the detection of abnormal PrP in tissues using laboratory tests and the levels of infectivity even when the titre was low. These findings provide useful information for risk modellers and represent a first step toward the validation of laboratory tests used to quantify prion infectivity, which would greatly aid TSE risk assessment policies.</p></div

The geology of the central Pentland Hills : 1:10000 sheets NT16SE (Scald Law) and 1:10560 sheets NT15NW (Baddinsgill) and part of NT15NE (Carlops) : part of 1:50000 sheets 32W (Livingston), 32E (Edinburgh) and 24W (Biggar)

This report describes the geology of 1:10 000 sheet NT16SE (Scald Law), and the 1:10 560 sheets NT15NW (Baddinsgill) and the area NW of the Pentland Fault on NT15NE (Carlops). These are included in 1:50 000 geological sheets 32W (Livingston), 32E (Edinburgh) and 24W (Biggar). Sheet boundaries are depicted on Figure 1. The area resurveyed falls within the City of Edinburgh, Midlothian, Borders and West Lothian unitary authority areas (Figure 1). It straddles the central part of the south-west to north-east chain of the Pentland Hills, including the highest summits of Scald Law (579m), West Kip (551m), East Cairn Hill (567m) and West Cairn Hill (562m). The north-west side of the range is drained by the Water of Leith via the Harperrig, Threipmuir and Harlaw reservoirs. Cutting north-west to south-east between Black Hill and Scald Law is the major glacial meltwater channel of Green Cleugh. To the south the basins of the Baddinsgill and North Esk Reservoirs are drained by the Lyne Water and River North Esk respectively (Figure 2). Most of the upland area is used for grazing sheep and to a lesser extent for hill cattle. Some grouse shooting takes place though this is in decline. Mixed farming predominates to the north-west of Threipmuir Reservoir and on the low ground immediately north-west of the Pentland Fault. The Pentlands are also extensively used for recreation, particularly walking and mountain-biking. Much of the resurveyed area on NT16SE and NT15NE is managed, in partnership with the owners, by the Pentland Hills Regional Park. The Edinburgh to New Galloway road, the A702, follows the Pentland Fault in the south-east of the area (Figure 1). The area was first geologically surveyed on the 1:10 560-scale by A Geikie and H H Howell in 1856–1866 and published on the 1:63 360-scale in 1859. Sheet NT16SE was revised in 1902–1903 by B N Peach, J S Grant-Wilson and E H Cunningham Craig. A second revision was carried out during 1949–1952 by H E Wilson and W Mykura and the sheet was resurveyed by H F Barron and A D McAdam in 1993–1996. Sheet NT15NE was revised by E H Cunningham Craig, L W Hinxman and B N Peach, and resurveyed by W Mykura, T Robertson and H E Wilson in 1938–1952. A second resurvey was carried out by H F Barron (north of the Pentland Fault) and A D McAdam (south of the Pentland Fault) in 1994–1996. Sheet NT15NW was revised by B N Peach and partly published in 1907; W Q Kennedy, W Mykura and H H Read resurveyed the sheet in 1928–1952. A second resurvey was carried out by H F Barron in 1994–1996. A new 1:63 360-scale edition (solid) of sheet 32 was published in 1967 and accompanying memoir published in 1962 (Mitchell and Mykura, 1962). The sheet was reprinted at 1:50 000-scale in 1977 without geological revision as Sheet 32W (Livingston) and 32E (Edinburgh). All grid references used in this report refer to National Grid 100 km square NT. This report is an interim statement and lithostratigraphical nomenclature may require revision as mapping proceeds in the contiguous areas

Moyeria cabottii from the Ordovician of Wales, United Kingdom

Recent work by Gray and Boucot suggests that Moyeria occurs abundantly only in the nonmarine and nearshore environments. Further supportive evidence has been lound in North Wales where Moyeria cabottii has been found in abundance in the I-ate Ordovician (Caradoc) Capel Curig Volcanic Formation at Capel Curi

Scotland’s geodiversity : development of the basis for a national framework

Geodiversity is the variety of rocks, minerals, fossils, landforms sediments and soils, together with the natural processes which form and alter them. It delivers important ecosystem services through its influence on landscape, habitats and species, economic activities, historical and cultural heritage and people’s health and well-being. Understanding of geodiversity also has a key part to play in climate change adaptation and in sustainable management of the land, river catchments and the coast. The aim of this study was to undertake an assessment of the value and status of geodiversity in Scotland and to develop the basis for a national framework to enable better integration of geodiversity within relevant policy areas, including helping to deliver the Scottish Government’s Strategic Objectives. Main findings The geological development of Scotland has given rise to a remarkable geodiversity for a country of its size. Many sites in Scotland are of great importance to geoscience for their rocks, fossils and landforms, demonstrating important geological processes or events. Scotland’s marine geodiversity is less well known, but also includes outstanding features. Geodiversity is important both as an intrinsic part of the natural heritage and because it provides ecosystem services and functions for the benefit of Scotland’s people and environment. In doing so, it contributes to the delivery of the Scottish Government’s 5 Strategic Objectives, National Outcomes and the 5 key themes for a Greener Scotland. The ‘ecosystem approach’ provides a potentially powerful framework for developing better integration of geodiversity and biodiversity, as well as a means of demonstrating the wider values and benefits of geodiversity through its contribution to delivering ecosystem services. Understanding geodiversity has a key part to play in adapting to climate change and sea-level rise. Changes in geomorphological processes are likely to have significant implications for most ecosystems. Effective conservation strategies for managing ecosystem responses will need to work in sympathy with natural processes. The iv concepts of working with nature and making space for natural processes have broader value to society as a whole. Pressures on geodiversity arise principally from planning developments and land-use changes. These may damage key features, impair their visibility and accessibility or fragment the interest. Sites located on the coast, adjacent to rivers or on active slopes are most likely to be impacted by climate change, sea-level rise and increased erosion or flooding. The human responses to these changes, in the form of ‘hard’ coastal protection or river and slope engineering are, however, likely to have the greatest impact on geodiversity. A separate commissioned review of the current Scottish policy environment concluded that there was limited recognition of the value of geodiversity in a range of relevant key areas such as economic development, landscape, climate change adaptation, health, recreation and education. The following conclusions were reached: There is a responsibility to ensure that the best geodiversity sites and features continue to be protected not only as part of our geoheritage, but also as an essential resource for field education, training and lifelong learning. The concept of biodiversity and our need to protect this component of the natural heritage at local, national and global scales is relatively well developed and understood at a strategic level. It forms the basis for much of the effort and activities in nature conservation and is relatively well integrated into the wider policy framework. Conversely, the concept and values of geodiversity are less well appreciated and, by comparison, relatively undervalued and poorly integrated. Proposals for the vision, aim and outcomes for a ‘Scottish Geodiversity Framework’ are set out for discussion. Such a framework would help to ensure that geodiversity is recognised as an integral and vital part of our environment, economy and heritage to be safeguarded for existing and future generations. It would instigate a process through which key stakeholders would work together to identify strategic priorities for geodiversity action, in a similar way to ‘The Scottish Soil Framework’. It would help to achieve an environment in which the rich geodiversity of Scotland can be understood, valued and conserved, and make geodiversity relevant to the way we work and live, as well as the decisions we make about a sustainable future for our environment, for both people and nature. In doing so, it should contribute to delivering the Scottish Government’s National Outcome on Natural Resource Protection and Enhancement. It is proposed that a ‘Scottish Geodiversity Framework’ covers the following areas of activity: 1. ‘Future-proofing’ ecosystem services, particularly in a context of climate change and sea-level rise. 2. Integration of geodiversity into all relevant policies. 3. Sustainable management of geodiversity for the wider benefit of Scotland’s people, environment and economy. 4. Conservation of geodiversity. 5. Raising awareness of the values and benefits of geodiversity and their contribution to ecosystem services. 6. Improving understanding of geodiversity and key knowledge gaps. Promoting wider awareness, understanding and involvement is also crucial. At policy, planning and decision-making levels, there is a need to make understanding v of the way the Earth works one of the cornerstones of sustainable development. Improving public awareness and engagement at a community level is also essential. In the present economic climate there is a need to strengthen links with the business community to generate financial returns as well as real benefits for geodiversity from geoconservation and use of the Earth’s resources in a sustainable way. It is recommended that the framework outlined in this report provides a starting point and should be developed and formalised through the mechanism of a ‘Scottish Geodiversity Forum’ or Working Group, set up with the support of the Scottish Government with clear leadership and appropriate convening power and involving appropriate partners and stakeholders. This should also be tasked with preparing a prioritised implementation plan, targets and actions

Acritarchs from the Ashgill Series (Ordovician) of the UK

Recent and continuing investigations on the acritarch biostratigraphy of the Ashgill Series of the {.IK is yielding encouraging results