Baseline Scotland : groundwater chemistry of the Carboniferous sedimentary aquifers of the Midland Valley

This report describes the baseline groundwater chemistry of the sedimentary aquifers of Carboniferous age in the Midland Valley of Scotland. Groundwater is an important resource in the Midland Valley, largely for agriculture, but also for industry – including food and drink processing and mineral water bottling, and for domestic use. A large but unquantified volume of groundwater is also still pumped from former mine workings, largely coal mines, in order to maintain water levels and for quality treatment. Analyses for 62 groundwater samples were interpreted for the purposes of this study. Of these, 36 samples were collected for the Baseline Scotland project between September and December 2008. These were augmented with a further 25 samples collected during separate BGS projects since 2001. The sites were chosen largely to be representative of groundwater in the area, and sources that were very poorly constructed were avoided. A small number of samples were deliberately targeted from mines, either from adits, shafts or boreholes. The data were classed in one of five different hydrogeological units (or aquifer groups): four chronostratigraphic groups, which in decreasing order of age are the Inverclyde, Strathclyde, Clackmannan and Coal Measures groups; and a fifth group incorporating waters sampled from mine discharges. An estimate of the baseline groundwater chemistry conditions in the four chronostratigraphic hydrogeological units is presented, based on a statistical summary of the chemical data, which represents values between the 10th and 90th A summary of the conclusions arising from this study follows. percentiles of the full dataset range. This statistical approach to estimating baseline compositions was complemented by selecting 11 analyses of groundwater from sources where there is little or no indication of direct contamination, including likely impact from mining. The chemistry of these samples represents the typical groundwater conditions in the four non-mine hydrogeological units in the sedimentary Carboniferous aquifers of the Midland Valley

Iodine in drinking water from East African groundwater sources

Chronic deficiency has long been associated with development of iodine-deficiency disorders (IDDs). Drinking water, including groundwater, contributes to dietary iodine intake, and the prevalence of IDDs is widely reported. However, there are no minimum or maximum guideline concentrations for iodine in drinking water, and iodine is rarely analysed during traditional groundwater health studies. This study reviews the iodine content of drinking water sampled by the British Geological Survey, from groundwater sources in sixteen regions of Ethiopia, Uganda, Tanzania and Malawi. Preliminary results reveal that iodine concentration is associated with the amount of total dissolved solids, and shows the strongest relationship with sulphate, uranium, strontium, sodium and fluoride. Drinking water sourced from boreholes and hand dug wells are shown to have elevated iodine concentrations relative to local rainfall and spring sources. Work is ongoing to investigate the relationships between iodine and other solutes in the groundwater, and to build a database of groundwater in East Africa

Baseline groundwater chemistry in Scotland's aquifers

This report is an output from the Baseline Scotland project, which ran from 2005 to 2014. It provides a summary of data on the chemistry of groundwater from the eleven main bedrock aquifer groups in Scotland. Groundwater is an important natural resource for Scotland. It provides drinking water, supports agriculture, and is fundamental to the nation’s mineral water and whisky industries. Groundwater also plays a vital role in sustaining the flow of rivers and supporting many of Scotland’s fragile ecosystems. The naturally high quality of groundwater in Scotland is an important part of why it provides so many benefits. However, groundwater is not invulnerable, and it needs to be protected and managed to preserve it. This report presents a synthesis of the results of the Baseline Scotland project, which mapped the natural chemistry of groundwater in Scotland’s aquifers. The project ran from 2005 to 2014, funded mainly by the British Geological Survey with additional support from the Scottish Environment Protection Agency, and included ten regional surveys that covered much of Scotland. In this overview, the results of the surveys are combined to produce a summary of the baseline chemistry of groundwater in the eleven main bedrock aquifer groups of Scotland. These aquifer groups represent a range of hydrogeological environments with differing geological controls on both physical aquifer properties and natural groundwater chemistry. They were primarily divided according to rock type: sedimentary (indurated sedimentary or calcareous), metamorphic or igneous; and secondarily according to geological age. The aquifers are: Permo-Triassic; Carboniferous sedimentary rocks (not extensively mined for coal); Carboniferous sedimentary rocks (extensively mined for coal); Old Red Sandstone North; Old Red Sandstone South; Silurian- Ordovician; Precambrian North, Precambrian South; Igneous Volcanics; Igneous Intrusive rocks; and Highland Calcareous rocks. The chemistry of groundwater in Scotland’s bedrock aquifers is highly variable, reflecting a combination of lithology, mineral reactions, redox conditions, groundwater flow paths and residence times. Major ion water types include Ca-HCO 3 , Na-HCO 3 , Na-SO 4 and Na-Cl, with no single type dominating across Scotland. Total dissolved solid (TDS) concentrations in groundwater are typically between 54 and 520 mg/L (10–90th percentile; median 150 mg/L). Some of the highest values of TDS (up to 5000 mg/L) are seen in Carboniferous sedimentary aquifers in central Scotland, particularly where mining has occurred. Elevated TDS also affects some groundwaters in coastal areas. Mineralised springs (e.g. Na-Cl, Na-SO 4 types) occur rarely. Median pH values for each of the aquifers are near neutral, in the range 6.5 to 7.5 (overall median 7.2). However, acidic groundwater (pH<6) occurs in most of the aquifers, reflecting an absence of carbonate minerals and/or oxidation of pyrite and other metal sulphides. More strongly acidic conditions can give rise to the presence of dissolved Al, Fe, Mn and REE in some groundwaters. Oxic groundwater conditions dominate in most aquifers in Scotland, consistent with dominantly shallow groundwater flowlines in fractured bedrock. Local exceptions occur with mildly reducing zones in several aquifers, but the only regionally extensive reducing conditions are in the Old Red Sandstone North aquifer, particularly in Moray. Within the Carboniferous sedimentary aquifers, and in localised mineralised springs in the Ordovician–Silurian aquifer, conditions can be more strongly reducing, causing SO 4 and NH 4 reduction and even methanogenesis at some locations. The main impact of land use on groundwater chemistry is the common occurrence of high concentrations of NO3 in groundwater, which correlate reasonably well with the areal extent of agricultural land use. Occurrences of high P and K are also seen, but are more sporadic in distribution, reflecting the more complex transport properties of these elements in soils and aquifers. Not all the groundwaters sampled are used for drinking water, and it is not appropriate to assess the state of drinking water quality in Scotland on the basis of the data presented here. These data nonetheless show the typical chemical compositions of raw groundwaters from the sampled aquifers, and indicate the general state of groundwater quality and any potential problems that may be encountered within each aquifer. On this basis, the most frequent exceedances of drinking water limits in the groundwaters are for Fe and Mn (21% and 27% of samples respectively). These elements, together with NH 4 (6.7% exceedance), are largely naturally derived, linked to reducing aquifer conditions. Exceedances for NO 3 (11%) occur in oxic aquifer conditions, and are linked to pollutant inputs, particularly from agriculture. Exceedances for trace elements are less common but do occur locally. In this report the study methodology is described along with some of the main factors controlling groundwater chemistry. The inorganic chemistry of Scotland’s groundwater is then summarised and put in context, before the baseline chemistry for each aquifer is presented

Baseline Scotland : the Lower Devonian aquifer of Strathmore

This report presents a summary of the groundwater chemistry of the Devonian sedimentary aquifer in Strathmore, eastern Scotland. The area covered by this study extends from Perth in the southwest to Stonehaven in the northeast. The survey forms part of the ongoing Baseline Scotland project. The Devonian sedimentary rocks of Strathmore form an important regional aquifer in an area of some of the most fertile agricultural land in Scotland, with a number of major urban settlements. The aquifer provides water for agriculture, industry, recreation and domestic use. The aquifer can be divided into six main geological units, largely sandstones but with significant conglomerates and, less commonly, mudstones. All of these units are classed as moderately or highly productive aquifers, but too few data are available to allow a detailed analysis of the hydrogeological variations between the formations. A total of 35 new groundwater samples were collected during this project, and the resulting chemistry data combined with data from 13 additional samples collected during a BGS sampling programme in 2001. The samples were analysed at BGS laboratories for a wide range of chemical constituents. The collection and interpretation of new groundwater chemistry data for the Strathmore area has led to the following conclusions. • The groundwaters of the Devonian aquifer in Strathmore are mainly weakly mineralised, with TDS concentrations mostly less than 400 mg l–1. Groundwaters have near-neutral to slightly alkaline pH values and are for the most part oxygenated, with detectable dissolved oxygen and high redox potentials. As a result, dissolved iron, manganese and ammonium (NH4-N) concentrations are usually low. Water from shallow boreholes and springs is often undersaturated with calcite, but in deeper boreholes, reaction with carbonate minerals in the aquifer is more usual and most of these are saturated with respect to calcite. • Nitrate concentrations are often high, with an interquartile range of 2.6 mg l–1 to 11.7 mg l–1 as NO3-N. Nearly one third of the samples exceeded the EC drinkingwater limit for nitrate of 11.4 mg l-1 as NO3-N. An anomalously high nitrate concentration of 81 mg l–1 as NO3-N was observed in one sample, and appears to result from direct downhole contamination by nitrogen fertiliser. Under the oxidising conditions, nitrate is a stable solute species across the aquifer and is found at depths in excess of 100 m. • Concentrations of phosphorous in groundwater across the aquifer are typically less than 0.1 mg l-1 (the 90th percentile), with a median of 0.03 mg l-1. Given the importance of P in controlling eutrophication in surface water, these concentrations in groundwater may be significant. • Increased salinity occurs in groundwater in some near-coastal boreholes, most likely as a result of mixing with seawater. • Most cationic trace elements have low concentrations, in accordance with the neutralpH groundwater conditions. Concentrations of arsenic are relatively high in some groundwaters (up to 8.8 μg l-1) though none exceeds the EC maximum permissible value for drinking water of 10 μg l-1. Concentrations of uranium reach up to 15.4 μg l–1, with the highest concentration just exceeding the WHO provisional guideline value for drinking water of 15 μg l–1. Two other exceedances above maximum permissible values for drinking were observed, for nitrite (highest concentration 0.194 mg l-1) and fluoride (highest concentration 3.7 mg l-1). The chemistry and residence time indicators (CFC and stable isotopes) indicate that the groundwaters are largely of young age, being mostly recharged within the last 40 years, with mixing throughout the top 100 m of the aqufier. The samples show little evidence of the presence of palaeowaters. The young age of the groundwaters means they are vulnerable to contamination. • A first estimate of the baseline groundwater chemistry conditions in the Strathmore Lower Devonian aquifer can be given by the statistical summary of the data collected in this study (with the exception of nitrogen (N) and phosphorous (P), where the influence of anthropogenic activity is likely to have affected concentrations across the aquifer). To compliment this approach, six good quality sites have been chosen which represent the majority of groundwaters found in Strathmore. • The most significant groundwater-quality problems identified by this survey are: o the widespread presence of elevated nitrate concentrations in groundwater, which is strongly linked to agricultural activity; o elevated phosphate concentrations which may affect the quality of surface water when discharged to rivers as baseflow. o the presence of saline water in some near-coastal boreholes, indicating localised saline intrusion. It is not clear to what degree the saline intrusion is natural and to what degree it has been enhanced by over-pumping

Baseline Scotland : groundwater chemistry of the Old Red Sandstone aquifers of the Moray Firth area

The groundwater chemistry of Old Red Sandstone aquifers in the Moray Firth area has been characterised based on new chemistry analyses generated during the Baseline Scotland project, combined with existing analyses from earlier projects. A total of 39 groundwater sample analyses were interpreted for the purposes of this study. Of these, 17 were collected in 2007 specifically for the Baseline Scotland project. These were augmented with a further 22 samples collected during separate BGS projects since 2001. The sites were chosen to be representative of groundwater in the area, and sources that were poorly constructed were avoided. A summary of the conclusions arising from this study follows. 1. Groundwater in the Old Red Sandstone aquifers of the Moray Firth is generally moderately mineralised, with a median SEC of 469 μS/cm (interquartile range 341–591 μS/cm). The pH is variable: median pH is slightly alkaline (7.31), but values range from 5.33 to 8.06. The major ion chemistry appears to be dominated by the dissolution of carbonate cements within the aquifer and overlying deposits, and the variable influence of seawater (either directly as saline intrusion or as aerosols). 2. The dominant cation is Ca, with a median concentration of 54.8 mg/L (interquartile range 42.5 – 74 mg/L). Mg and K concentrations are generally low (median 4.21 and 3.7 mg/L respectively). The median Na is 20.6 mg/L (interquartile range 12.6–28 mg/L); however, a few samples have been affected by proximity to the sea and have much higher concentrations, as illustrated by the 95th percentile (68 mg/L) and maximum concentration (153 mg/L). 3. The dominant anion is bicarbonate, with a median concentration of 183 mg/L (interquartile range 183–230 mg/L). Around one third of the samples are saturated with respect to calcite. Sulphate concentrations are generally low (median 14.6 mg/L, interquartile range 7.7–36.4 mg/L), although higher concentrations are encountered in samples affected by seawater, and/or possibly by gypsum bands within the aquifer. Chloride concentrations follow broadly the same distribution as Na and have a median of 38.8 mg/L and interquartile range of 19.5–49.5 mg/L; the same few samples show high Cl concentrations as do Na. 4. Concentrations of minor and trace elements in the groundwater are dominated by the redox conditions. Measured values of dissolved oxygen indicate a large range in redox conditions across the aquifer. Concentrations of DO close to 10 mg/L indicate fully oxic conditions. By contrast, groundwaters with DO concentrations <1 mg/L are indicative of sub-oxic or mildly reducing conditions, and appear to be prevalent in much of the Upper Old Red Sandstone outcrop, and parts of the Middle Old Red Sandstone. Reducing conditions may reflect the presence of low permeability layers (often marine in origin) within the thick superficial deposits overlying the Old Red Sandstone aquifer. The effect of reducing conditions is to increase concentrations of Fe and Mn, which show median concentrations of 38 and 43 μg/L respectively, and 75th percentile values of 354 and 227 μg/L respectively. 5. The majority of samples (21) were collected from the Upper Old Red Sandstone aquifer; 14 samples were collected from the Middle Old Red Sandstone and only 4 samples from the Lower Old Red Sandstone. The samples show broadly similar chemistry across the three aquifer units; however, there are several notable differences. Samples from the Upper Old Sandstone aquifer show very similar cation distribution, dominated by Ca, while the Lower and Middle Old Red Sandstone aquifers show a wider cation distribution and appear less affected by calcite dissolution. The pH of the Lower and Middle Old Red Sandstone aquifers is slightly lower (more acidic), generally less than 7.0. Groundwaters within the Upper Old Red Sandstone aquifer are generally more reducing, probably reflecting their location close to the coast and hence the influence of the sea and/or overlying marine superficial deposits. 6. Nitrate concentrations are variable across the aquifer units, although median concentrations are low (1.45 mg/L TON-N or less in each aquifer). The prevalence of low oxygen conditions in the sampled groundwaters has led to denitrification, which means the relationship between land use and nitrate concentrations is less obvious than for other parts of Scotland (MacDonald et al., 2005a). However, there is a clear relationship between nitrate concentrations and the Nitrate Vulnerable Zone (NVZ) that covers much of the study area, with the seven highest groundwater nitrate concentrations, ranging from 5.98 to 22.1 mg/L TON-N, all from samples taken within the NVZ. The highest median concentrations were from samples collected on land known to be used for dairy, pig or poultry farming. 7. Phosphorus concentrations in Moray Firth groundwaters range from less than detection limit up to 172 μg P/L, with an overall median of 36 μg P/L, which is in the eutrophic range for surface waters. Concentrations are generally low in the western part of the study area, and an observed relationship with the spatial pattern of F suggests that both elements may be in part derived from the dissolution of phosphate minerals, such as apatite, from the aquifer rocks. Concentrations in the eastern part of the study area are generally higher, usually in the mesotrophic or eutrophic range for surface waters. The higher values may be related to land use, with P inputs from agricultural activity. 8. An estimate of the baseline groundwater chemistry conditions in the Old Red Sandstone aquifers has been presented, based on a statistical summary of the chemical data. This represents data between the 10th and 90th percentiles, with the exception of NO3-N and P, where the influence of anthropogenic activity is likely to have distorted baseline conditions throughout much of the study area. This statistical approach to estimating baseline was complemented by selecting ten analyses of groundwater samples collected from high quality groundwater sources, which are unlikely to have been impacted by any agricultural contamination, and which represent the general the groundwater conditions in the Old Red Sandstone aquifers in the Moray Firth area

Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism

ANKRD17 is an ankyrin repeat-containing protein thought to play a role in cell cycle progression, whose ortholog in Drosophila functions in the Hippo pathway as a co-factor of Yorkie. Here, we delineate a neurodevelopmental disorder caused by de novo heterozygous ANKRD17 variants. The mutational spectrum of this cohort of 34 individuals from 32 families is highly suggestive of haploinsufficiency as the underlying mechanism of disease, with 21 truncating or essential splice site variants, 9 missense variants, 1 in-frame insertion-deletion, and 1 microdeletion (1.16 Mb). Consequently, our data indicate that loss of ANKRD17 is likely the main cause of phenotypes previously associated with large multi-gene chromosomal aberrations of the 4q13.3 region. Protein modeling suggests that most of the missense variants disrupt the stability of the ankyrin repeats through alteration of core structural residues. The major phenotypic characteristic of our cohort is a variable degree of developmental delay/intellectual disability, particularly affecting speech, while additional features include growth failure, feeding difficulties, non-specific MRI abnormalities, epilepsy and/or abnormal EEG, predisposition to recurrent infections (mostly bacterial), ophthalmological abnormalities, gait/balance disturbance, and joint hypermobility. Moreover, many individuals shared similar dysmorphic facial features. Analysis of single-cell RNA-seq data from the developing human telencephalon indicated ANKRD17 expression at multiple stages of neurogenesis, adding further evidence to the assertion that damaging ANKRD17 variants cause a neurodevelopmental disorder.Neurolog

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Baseline Scotland : groundwater chemistry of Aberdeenshire

This report describes the baseline groundwater chemistry of Precambrian and igneous bedrock aquifers in the northeast of Scotland

Distribution of natural radioactivity in the environment

This report describes our current knowledge of the distribution of natural radioactivity in rocks, groundwater and soils of the United Kingdom. Elements of interest include Uranium (U), Thorium (Th) and Potassium (K), along with radon (Rn) and radium (Ra) in groundwater. This information is then used to describe the likely background conditions at each of the U.K.’s nuclear sites, particularly in relation to the geology