A geological fence diagram for England and Wales

This report contains a brief description of the data and methodology used to compile the National Geological Fence Diagram (NGFD). The NGFD comprises a network of intersecting geological cross-sections covering England and Wales, to a minimum depth of 1 km and a total section length of approximately 5,500 km. It was compiled by the British Geological Survey (BGS) on behalf of the Environment Agency (EA) and is based upon lines of section agreed between both parties at the inception of the project. The model includes generalised bedrock strata based principally on the BGS 1:625 000 scale digital geological data and superficial deposits greater than 10m in thickness. Additional sources of model data were also considered, largely taken from published BGS data holdings. In total 41 cross-sections were constructed and geologically correlated within the GSI3D software

Can nuclear weapons fallout mark the beginning of the Anthropocene Epoch?

Many scientists are making the case that humanity is living in a new geological epoch, the Anthropocene, but there is no agreement yet as to when this epoch began. The start might be defined by a historical event, such as the beginning of the fossil-fueled Industrial Revolution or the first nuclear explosion in 1945. Standard stratigraphic practice, however, requires a more significant, globally widespread, and abrupt signature, and the fallout from nuclear weapons testing appears most suitable. The appearance of plutonium 239 (used in post- 1945 above-ground nuclear weapons tests) makes a good marker: This isotope is rare in nature but a significant component of fallout. It has other features to recommend it as a stable marker in layers of sedimentary rock and soil, including: long half-life, low solubility, and high particle reactivity. It may be used in conjunction with other radioactive isotopes, such as americium 241 and carbon 14, to categorize distinct fallout signatures in sediments and ice caps. On a global scale, the first appearance of plutonium 239 in sedimentary sequences corresponds to the early 1950s. While plutonium is easily detectable over the entire Earth using modern measurement techniques, a site to define the Anthropocene (known as a Ògolden spikeÓ) would ideally be located between 30 and 60 degrees north of the equator, where fallout is maximal, within undisturbed marine or lake environments

Investigating the basis of substrate recognition in the pC221 relaxosome

The nicking of the origin of transfer (oriT) is an essential initial step in the conjugative mobilization of plasmid DNA. In the case of staphylococcal plasmid pC221, nicking by the plasmid-specific MobA relaxase is facilitated by the DNA-binding accessory protein MobC; however, the role of MobC in this process is currently unknown. In this study, the site of MobC binding was determined by DNase I footprinting. MobC interacts with oriT DNA at two directly repeated 9 bp sequences, mcb1 and mcb2, upstream of the oriT nic site, and additionally at a third, degenerate repeat within the mobC gene, mcb3. The binding activity of the conserved sequences was confirmed indirectly by competitive electrophoretic mobility shift assays and directly by Surface Plasmon Resonance studies. Mutation at mcb2 abolished detectable nicking activity, suggesting that binding of this site by MobC is a prerequisite for nicking by MobA. Sequential site-directed mutagenesis of each binding site in pC221 has demonstrated that all three are required for mobilization. The MobA relaxase, while unable to bind to oriT DNA alone, was found to associate with a MobC–oriT complex and alter the MobC binding profile in a region between mcb2 and the nic site. Mutagenesis of oriT in this region defines a 7 bp sequence, sra, which was essential for nicking by MobA. Exchange of four divergent bases between the sra of pC221 and the related plasmid pC223 was sufficient to swap their substrate identity in a MobA-specific nicking assay. Based on these observations we propose a model of layered specificity in the assembly of pC221-family relaxosomes, whereby a common MobC:mcb complex presents the oriT substrate, which is then nicked only by the cognate MobA

Genetics of tension-type headache

The objective of this study was to investigate the importance of genetics in tension-type headache. A MEDLINE search from 1966 to December 2006 was performed for “tension-type headache and prevalence” and “tension-type headache and genetics” The prevalence of tensiontype headache varies from 11 to 93%, with a slight female preponderance. Co-occurrence of migraine increases the frequency of tension-type headache. A family study of chronic tension-type headache suggests that genetic factors are important. A twin study analysing tension-type headache in migraineurs found that genetic factors play a minor role in episodic tension-type headache. Another twin study analysing twin pairs without co-occurrence of migraine showed a significantly higher concordance rate among monozygotic than same-gender dizygotic twin pairs with no or frequent episodic tension-type headache, while the difference was minor in twin pairs with infrequent episodic tensiontype headache. Frequent episodic and chronic tension-type headache is caused by a combination of genetic and environmental factors, while infrequent episodic tensiontype headache is caused primarily by environmental factors

Genetic determinism: how not to interpret behavioral genetics

Recently, investigators in behavioral genetics have found loci on the genome (so-called ‘quantitative trait loci’ or QTLs) that are associated with complex mental traits, such as anxiety or novelty seeking. The interpretation of these findings raises interesting theoretical questions. At first sight, the discovery of ‘genes-for-personality’ seems to support genetic determinism and reductionism. Genetic determinism is the view that the phenotype is precoded in or determined by the genotype. However, evidence from developmental biology and neural modeling indicates that development is a result of interactive processes at many levels, not only the genome, so that geneticism must be rejected. Identifying QTLs and perhaps also the causal paths in the tangle of top-down and bottom-up influences between genome, organism and environment is best seen as a simplification. It amounts to considerably less than reduction in the classical sense of replacement via bridge laws or elimination. It is argued that higher (psychological and physiological) levels are functionally characterized and are irreducible to molecular-genetic levels. Therefore, it is to be expected that ideas about inter-level relations may be useful in clarifying the relation between loci on the genome (QTLs), gene products, the nervous system, behavior and personality, and to help identify the contribution of genetic factors in behavioral genetics. © 2000, Sage Publications. All rights reserved

Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology

The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living cells communicate genetically through transferred genes, as well as the ways in which they can reorganize their genomes in response to environmental pressure. We discuss how genome evolution can be thought of as related to the physical phenomenon of annealing, and describe the sense in which genomes can be said to exhibit an analogue of information entropy. As a direct application of these ideas, we analyze the variation with ocean depth of transposons in marine microbial genomes, predicting trends that are consistent with recent observations using metagenomic surveys.Comment: Accepted by Journal of Statistical Physic

Week 96 efficacy and safety results of the phase 3, randomized EMERALD trial to evaluate switching from boosted-protease inhibitors plus emtricitabine/tenofovir disoproxil fumarate regimens to the once daily, single-tablet regimen of darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) in treatment-experienced, virologically-suppressed adults living with HIV-1

Altres ajuts: This study was sponsored by Janssen.Darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) 800/150/200/10 mg was investigated through 96 weeks in EMERALD (NCT02269917). Virologically-suppressed, HIV-1-positive treatment-experienced adults (previous non-darunavir virologic failure [VF] allowed) were randomized (2:1) to D/C/F/TAF or boosted protease inhibitor (PI) plus emtricitabine/tenofovir-disoproxil-fumarate (F/TDF) over 48 weeks. At week 52 participants in the boosted PI arm were offered switch to D/C/F/TAF (late-switch, 44 weeks D/C/F/TAF exposure). All participants were followed on D/C/F/TAF until week 96. Efficacy endpoints were percentage cumulative protocol-defined virologic rebound (PDVR; confirmed viral load [VL] ≥50 copies/mL) and VL < 50 copies/mL (virologic suppression) and ≥50 copies/mL (VF) (FDA-snapshot analysis). Of 1141 randomized patients, 1080 continued in the extension phase. Few patients had PDVR (D/C/F/TAF: 3.1%, 24/763 cumulative through week 96; late-switch: 2.3%, 8/352 week 52-96). Week 96 virologic suppression was 90.7% (692/763) (D/C/F/TAF) and 93.8% (330/352) (late-switch). VF was 1.2% and 1.7%, respectively. No darunavir, primary PI, tenofovir or emtricitabine resistance-associated mutations were observed post-baseline. No patients discontinued for efficacy-related reasons. Few discontinued due to adverse events (2% D/C/F/TAF arm). Improved renal and bone parameters were maintained in the D/C/F/TAF arm and observed in the late-switch arm, with small increases in total cholesterol/high-density-lipoprotein-cholesterol ratio. A study limitation was the lack of a control arm in the week 96 analysis. Through 96 weeks, D/C/F/TAF resulted in low PDVR rates, high virologic suppression rates, very few VFs, and no resistance development. Late-switch results were consistent with D/C/F/TAF week 48 results. EMERALD week 96 results confirm the efficacy, high genetic barrier to resistance and safety benefits of D/C/F/TAF

From marine bands to hybrid flows: sedimentology of a Mississippian black shale

Organic‐rich mudstones have long been of interest as conventional and unconventional source rocks and are an important organic carbon sink. Yet the processes that deposited organic‐rich muds in epicontinental seaways are poorly understood, partly because few modern analogues exist. This study investigates the processes that transported and deposited sediment and organic matter through part of the Bowland Shale Formation, from the Mississippian Rheic–Tethys seaway. Field to micron‐scale sedimentological analysis reveals a heterogeneous succession of carbonate‐rich, siliceous, and siliciclastic, argillaceous muds. Deposition of these facies at basinal and slope locations was moderated by progradation of the nearby Pendle delta system, fourth‐order eustatic sea‐level fluctuation and localized block and basin tectonism. Marine transgressions deposited bioclastic ‘marine band’ (hemi)pelagic packages. These include abundant euhaline macrofaunal tests, and phosphatic concretions of organic matter and radiolarian tests interpreted as faecal pellets sourced from a productive water column. Lens‐rich (lenticular) mudstones, hybrid, debrite and turbidite beds successively overlie marine band packages and suggest reducing basin accommodation promoted sediment deposition via laminar and hybrid flows sourced from the basin margins. Mud lenses in lenticular mudstones lack organic linings and bioclasts and are equant in early‐cemented lenses and in plan‐view, and are largest and most abundant in mudstones overlying marine band packages. Thus, lenses likely represent partially consolidated mud clasts that were scoured and transported in bedload from the shelf or proximal slope, as a ‘shelf to basin’ conveyor, during periods of reduced basin accommodation. Candidate in situ microbial mats in strongly lenticular mudstones, and as rip‐up fragments in the down‐dip hybrid beds, suggest that these were potentially key biostabilizers of mud. Deltaic mud export was fast, despite the intrabasinal complexity, likely an order of magnitude higher than similar successions deposited in North America. Epicontinental basins remotely linked to delta systems were therefore capable of rapidly accumulating both sediment and organic matter