Industrial structural geology : principles, techniques and integration : an introduction

The authors wish to acknowledge the generous financial support provided in association with this volume to the Geological Society and the Petroleum Group by Badley Geoscience Ltd, BP, CGG Robertson, Dana Petroleum Ltd, Getech Group plc, Maersk Oil North Sea UK Ltd, Midland Valley Exploration Ltd, Rock Deformation Research (Schlumberger) and Borehole Image & Core Specialists (Wildcat Geoscience, Walker Geoscience and Prolog Geoscience). We would like to thank the fine team at the Geological Society’s Publishing House for the excellent support and encouragement that they have provided to the editors and authors of this Special Publication.Peer reviewedPublisher PD

Bayesian inference of ancestral dates on bacterial phylogenetic trees

The sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated phylogeny, in which the dates of all common ancestors are estimated. Here, we propose a new Bayesian methodology to construct dated phylogenies which is specifically designed for bacterial genomics. Unlike previous Bayesian methods aimed at building dated phylogenies, we consider that the phylogenetic relationships between the genomes have been previously evaluated using a standard phylogenetic method, which makes our methodology much faster and scalable. This two-step approach also allows us to directly exploit existing phylogenetic methods that detect bacterial recombination, and therefore to account for the effect of recombination in the construction of a dated phylogeny. We analysed many simulated datasets in order to benchmark the performance of our approach in a wide range of situations. Furthermore, we present applications to three different real datasets from recent bacterial genomic studies. Our methodology is implemented in a R package called BactDating which is freely available for download at https://github.com/xavierdidelot/BactDating

The design, implementation, and assessment of software for use in the teaching of history

(1) In recent years nine arts-related departments at Glasgow University have been successful in winning funds for the creation of large databases. Although these data are being extensively exploited for research, the great potential they offer for undergraduate teaching remains largely untapped due to the lack of suitably tailored software and hardware provision. (2) Our objective is to give arts-based students access to these complex highly structured data in the classroom without requiring them to master difficult operating systems. In this way they would gain valuable transferable skills in information technology. These will enhance the historians' traditional skills of evaluating, interpreting and presenting evidence, long recognized as useful by employers. (3) The scheme will require the establishment of a centrally sited teaching laboratory comprising sixteen micro-computers and fileserver linked to the mainframe through a communications PAD. Chosen to ensure a maximum degree of compatability, the micro-computers (with the appropriate operating system) will be capable of acting as terminals, as a local area network or as single workstations. A facility technician will be employed to supervise the lab's day-to-day running, leaving a programmer/analyst to concentrate exclusively on applying and developing software for the three designated courses. (4) The software will enable students to access and scan files with ease and submit complex search, correlative, and quantitative requests by means of a friendly user interface. It will be possible to generate output in alphanumeric and graphic format either online or in hard copy. Throughout, priority will be given to transferability and portability, particularly in relation to the complementary project at the University of Edinburgh. (5) The project will be directed by Dr. R.H. Trainor consulting with a committee representing the participants - the departments of Modern History, Scottish History and Economic History, the University Archives, the Wellcome Unit for the History of Medicine - and the Computing Service. The latter will provide overall technical supervision. The department of Computing Science will co-operate in formulating an academic staff development programme. With the help of the University adviser on teaching methods the designated courses will be closely monitored in order to assess the value of the particular software, hardware and teaching methods in the project

Visualizing electrostatic gating effects in two-dimensional heterostructures

The ability to directly observe electronic band structure in modern nanoscale field-effect devices could transform understanding of their physics and function. One could, for example, visualize local changes in the electrical and chemical potentials as a gate voltage is applied. One could also study intriguing physical phenomena such as electrically induced topological transitions and many-body spectral reconstructions. Here we show that submicron angle-resolved photoemission (micro-ARPES) applied to two-dimensional (2D) van der Waals heterostructures affords this ability. In graphene devices, we observe a shift of the chemical potential by 0.6 eV across the Dirac point as a gate voltage is applied. In several 2D semiconductors we see the conduction band edge appear as electrons accumulate, establishing its energy and momentum, and observe significant band-gap renormalization at low densities. We also show that micro-ARPES and optical spectroscopy can be applied to a single device, allowing rigorous study of the relationship between gate-controlled electronic and excitonic properties.Comment: Original manuscript with 9 pages with 4 figures in main text, 5 pages with 4 figures in supplement. Substantially edited manuscript accepted at Natur

An NADPH-Dependent Genetic Switch Regulates Plant Infection by the Rice Blast Fungus

To cause rice blast disease, the fungus Magnaporthe oryzae breaches the tough outer cuticle of the rice leaf by using specialized infection structures called appressoria. These cells allow the fungus to invade the host plant and proliferate rapidly within leaf tissue. Here, we show that a unique NADPH-dependent genetic switch regulates plant infection in response to the changing nutritional and redox conditions encountered by the pathogen. The biosynthetic enzyme trehalose-6-phosphate synthase (Tps1) integrates control of glucose-6-phosphate metabolism and nitrogen source utilization by regulating the oxidative pentose phosphate pathway, the generation of NADPH, and the activity of nitrate reductase. We report that Tps1 directly binds to NADPH and, thereby, regulates a set of related transcriptional corepressors, comprising three proteins, Nmr1, Nmr2, and Nmr3, which can each bind NADP. Targeted deletion of any of the Nmr-encoding genes partially suppresses the nonpathogenic phenotype of a Δtps1 mutant. Tps1-dependentNmr corepressors control the expression of a set of virulence-associated genes that are derepressed during appressorium-mediated plant infection. When considered together, these results suggest that initiation of rice blast disease by M. oryzae requires a regulatory mechanism involving an NADPH sensor protein, Tps1, a set of NADP-dependent transcriptional corepressors, and the nonconsuming interconversion ofNADPHandNADPacting as signal transducer

Nitrogen enrichment in macroalgae following mass coral mortality

Scleractinian corals are engineers on coral reefs that provide both structural complexity as habitat and sustenance for other reef-associated organisms via the release of organic and inorganic matter. However, coral reefs are facing multiple pressures from climate change and other stressors, which can result in mass coral bleaching and mortality events. Mass mortality of corals results in enhanced release of organic matter, which can cause significant alterations to reef biochemical and recycling processes. There is little known about how long these nutrients are retained within the system, for instance, within the tissues of other benthic organisms. We investigated changes in nitrogen isotopic signatures (δ15N) of macroalgal tissues (a) ~ 1 year after a bleaching event in the Seychelles and (b) ~ 3 months after the peak of a bleaching event in Mo’orea, French Polynesia. In the Seychelles, there was a strong association between absolute loss in both total coral cover and branching coral cover and absolute increase in macroalgal δ15N between 2014 and 2017 (adjusted r2 = 0.79, p = 0.004 and adjusted r2 = 0.86, p = 0.002, respectively). In Mo’orea, a short-term transplant experiment found a significant increase in δ15N in Sargassum mangarevense after specimens were deployed on a reef with high coral mortality for ~ 3 weeks (p < 0.05). We suggest that coral-derived nutrients can be retained within reef nutrient cycles, and that this can affect other reef-associated organisms over both short- and long-term periods, especially opportunistic species such as macroalgae. These species could therefore proliferate on reefs that have experienced mass mortality events, because they have been provided with both space and nutrient subsidies by the death and decay of corals. © 2021, The Author(s)

The effect of decoupling on marginal agricultural systems: implications for farm incomes, land use and upland ecology

In many parts of Europe, decades of production subsidies led to the steady intensification of agriculture in marginal areas, but the recent decoupling of subsidies from production decisions means that the future of farming in these areas is uncertain. For example, in the uplands of the United Kingdom, an area important both for biodiversity conservation and ecosystem service provision, hill farmers steadily increased stocking densities in response to headage payments but must now reconfigure farm businesses to account for the shift to the Single Farm Payment scheme. We examined hill farming in the Peak District National Park as a case study into the future of marginal agriculture after decoupling. We surveyed 44 farm businesses and from this identified six representative farm types based on enterprise mix and land holdings. We developed linear programming models of production decisions for each farm type to examine the impacts of policy changes, comparing the effects of decoupling with and without agri-environment and hill farm support, and evaluating the effects of removal of the Single Farm Payment. The main effects of decoupling are to reduce stocking rates, and to change the mix of livestock activities. Agri-environmental schemes mediate the income losses from decoupling, and farmers are predicted to maximise take up of new Environmental Stewardship programmes, which have both positive and negative feedback effects on livestock numbers. Finally, removal of the Single Farm Payment would lead to negative net farm incomes, and some land abandonment. These changes have important implications for ongoing debates about how ecological service flows can be maintained from upland areas, and how marginal upland farming communities can be sustained