Geochemical and mineralogical record of the impact of mining on the Teign Estuary, Devon, UK

Previous mineralogical and geochemical studies on the sediments in the Teign Estuary, Devon, UK, have shown that there are elevated levels of barium present within the surface sediments and the river catchment due to historical mining. For this investigation, 8 shallow cores (<1 m) were recovered from various locations in the estuary. These cores were subsequently logged, photographed and divided into approximately 5 cm depth intervals. The geochemistry and mineralogy of 68 samples from the cores were analysed. Bulk sediment geochemistry was determined by XRF and data for Ba, Cu, Pb and Zn are presented here. The mineralogy of the samples was determined by XRD. In addition, the samples from two cores were selected for mineralogical analysis using automated SEM-EDS (QEMSCAN®). The data show a sediment depth related geochemical trend with typically the lowest concentrations of Ba, Cu, Zn and Pb at the bases of the cores. Several of the sampling sites reveal a marked peak in the concentration of Pb and Zn mid-core; however, Cu values are low and invariant throughout. Postdating the Pb-Zn peak, there is a subsequent elevation in Ba in many of the cores studied, at a sediment depth of between 10 and 20 cm. Maximum concentrations of Ba reach 3360 ppm; Pb, 2220 ppm; Zn, 887 ppm and Cu, 258 ppm. Detrital minerals present include: barite, rutile, ilmenite, zircon, monazite, pyrite, cassiterite, sphalerite, galena and chalcopyrite. Framboidal pyrite is the only diagenetic mineral observed. The geochemical results are consistent with the historical mining records in the catchment, with barite mining postdating Pb-Zn mining. Both episodes of mining have released particulate mine waste, which has accumulated within the estuarine sediments

Chemical composition of zircons from the Cornubian Batholith of SW England and comparison with zircons from other European Variscan rare-metal granites

This is the author accepted manuscript. The final version is available from the Mineralogical Society via the DOI in this record.Zircon from 14 representative granite samples of the late-Variscan Cornubian Batholith in SW England was analyzed for W, P, As, Nb, Ta, Si, Ti, Zr, Hf, Th, U, Y, La, Ce, Pr, Nd, Sm, Gd, Dy, Er, Yb, Al, Sc, Bi, Mn, Fe, Ca, Pb, Cu, S, and F using EPMA. Zircons from the biotite and tourmaline granites are poor in minor and trace elements, usually containing 1.0–1.5 wt% HfO2, <0.5 wt% UO2 and P2O5, <0.25 wt% Y2O3, <0.2 wt% Sc203 and Bi2O3, and <0.1 wt% ThO2. Zircon from topaz granites from the St. Austell Pluton, Meldon Aplite and Megiliggar Rocks are slightly enriched in Hf (up to 4 wt% HfO2), U (1– 3.5 wt% UO2), and Sc (0.5–1 wt% Sc2O3). Scarce metamictized zircon grains are somewhat enriched in Al, Ca, Fe, and Mn. The decrease of the zircon Zr/Hf ratio, a reliable magma fractionation index, from 110-60 in the biotite granites to 30-10 in the most evolved topaz granites (Meldon Aplite and Megiliggar Rocks), supports a comagmatic origin of the biotite and topaz granites via long fractionation of common peraluminous crustal magma. In comparison with other European rare-metal provinces, the overall contents of trace elements in Cornubian zircons are low and the Zr/Hf- and U/Th-ratios show lower degrees of fractionation of the parental melt.This contribution was supported by the Czech Science Foundation, project No. GA14-13600S and RVO 67985831. Bernard Bingen and one anonymous member of the Editorial Board are thanked for careful review and inspiring comments

The Petrogenesis of the Early Permian Variscan granites of the Cornubian Batholith - lower plate post-collisional peraluminous magmatism in the Rhenohercynian Zone of SW England

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.The Early Permian Cornubian Batholith was generated during an extensional regime following Variscan convergence within the Rhenohercynian Zone of SW England. Its component granites can be classified, using mineralogical, textural and geochemical criteria, into five main types, all of which are peraluminous (A/CNK >1.1): G1 (two-mica), G2 (muscovite), G3 (biotite), G4 (tourmaline) and G5 (topaz). G1 granites formed through up to 20% muscovite and minor biotite dehydration melting of a metagreywacke source at moderate temperatures and pressures (731-806°C, >5 kbar). Younger G3 granites formed through higher temperature, lower pressure (768-847°C, <4 kbar) biotite-dominated melting of a similar source. Partial melting was strongly influenced by the progressive lower-mid crustal emplacement of mafic igneous rocks during post-Variscan extension and a minor (<5- 10%) mantle-derived component in the granites is possible. Two distinct fractionation series, G1-G2 and G3-G4, are defined using whole rock geochemical and mineral chemical data. Variations in the major elements, Ba, Sr and Rb indicate that G1 and G3 granites underwent 15-30% fractionation of an assemblage dominated by plagioclase, alkali feldspar and biotite to form, more evolved G2 and G4 granites respectively. Decreasing whole rock abundances of Zr, Th and REE support fractionation of zircon, monazite, apatite and allanite. Subsolidus alteration in G2 and G4 granites is indicated by non-primary muscovite and tourmaline and modification of major and trace element trends for G3-G4 granites, particularly for P2O5 and Rb. Topaz (G5) granites show low Zr, REE and extreme enrichment in Rb (up to 1530 ppm) and Nb (79 ppm) that cannot be related in a straightforward manner to continued differentiation of the G1-G2 or G3-G4 series. Instead, they are considered to represent partial melting, mediated by granulite facies fluids, of a biotite-rich restite following extraction of G1 and/or G3 magmas; they do not exhibit the typical geochemical characteristics of intraplate A-type granites.This study was supported by the European Regional Development Fund and European Social Fund as part of the convergence funding for Cornwall and the Isles of Scilly (Combined Universities in Cornwall project number11200NCO5), supporting a PhD for BS, and the European Union (Horizon 2020 project 641650 FAME). The Natural History Museum, London, UK are thanked for the loan of samples. We thank Richard Scrivener and Nicholas LeBoutillier for help with sampling. Steve Pendray, Sharon Uren and Joe Pickles assisted with the sample preparation and analysis. Axel Müller and Karel Breiter are thanked for discussions about topaz granites. We gratefully acknowledge Romain Tartèse and an anonymous reviewer for their constructive comments which helped to improve the manuscript

Eosinophils Are Important for Protection, Immunoregulation and Pathology during Infection with Nematode Microfilariae

Eosinophil responses typify both allergic and parasitic helminth disease. In helminthic disease, the role of eosinophils can be both protective in immune responses and destructive in pathological responses. To investigate whether eosinophils are involved in both protection and pathology during filarial nematode infection, we explored the role of eosinophils and their granule proteins, eosinophil peroxidase (EPO) and major basic protein-1 (MBP-1), during infection with Brugia malayi microfilariae. Using eosinophil-deficient mice (PHIL), we further clarify the role of eosinophils in clearance of microfilariae during primary, but not challenge infection in vivo. Deletion of EPO or MBP-1 alone was insufficient to abrogate parasite clearance suggesting that either these molecules are redundant or eosinophils act indirectly in parasite clearance via augmentation of other protective responses. Absence of eosinophils increased mast cell recruitment, but not other cell types, into the broncho-alveolar lavage fluid during challenge infection. In addition absence of eosinophils or EPO alone, augmented parasite-induced IgE responses, as measured by ELISA, demonstrating that eosinophils are involved in regulation of IgE. Whole body plethysmography indicated that nematode-induced changes in airway physiology were reduced in challenge infection in the absence of eosinophils and also during primary infection in the absence of EPO alone. However lack of eosinophils or MBP-1 actually increased goblet cell mucus production. We did not find any major differences in cytokine responses in the absence of eosinophils, EPO or MBP-1. These results reveal that eosinophils actively participate in regulation of IgE and goblet cell mucus production via granule secretion during nematode-induced pathology and highlight their importance both as effector cells, as damage-inducing cells and as supervisory cells that shape both innate and adaptive immunity

Fractionation of Li, Be, Ga, Nb, Ta, In, Sn, Sb, W and Bi in the peraluminous Early Permian Variscan granites of the Cornubian Batholith: precursor processes to magmatic-hydrothermal mineralisation

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.The Early Permian Variscan Cornubian Batholith is a peraluminous, composite pluton intruded into Devonian and Carboniferous metamorphosed sedimentary and volcanic rocks. Within the batholith there are: G1 (two-mica), G2 (muscovite), G3 (biotite), G4 (tourmaline) and G5 (topaz) granites. G1-G2 and G3-G4 are derived from greywacke sources and linked through fractionation of assemblages dominated by feldspars and biotite, with minor mantle involvement in G3. G5 formed though flux-induced biotite-dominate melting in the lower crust during granulite facies metamorphism. Fractionation enriched G2 granites in Li (average 315 ppm), Be (12 ppm), Ta (4.4 ppm), In (74 ppb), Sn (18 ppm) and W (12 ppm) relative to crustal abundances and G1 granites. Gallium (24 ppm), Nb (16 ppm) and Bi (0.46 ppm) are not significantly enriched during fractionation, implying they are more compatible in the fractionating assemblage. Sb (0.16 ppm) is depleted in G1-G2 relative to the average upper and lower continental crust. Muscovite, a late-stage magmatic/subsolidus mineral, is the major host of Li, Nb, In, Sn and W in G2 granites. G2 granites are spatially associated with W-Sn greisen mineralisation. Fractionation within the younger G3-G4 granite system enriched Li (average 364 ppm), Ga (28 ppm), In (80 ppb), Sn (14 ppm), Nb (27 ppm), Ta (4.6 ppm), W (6.3 ppm) and Bi (0.61 ppm) in the G4 granites with retention of Be in G3 granites due to partitioning of Be into cordierite during fractionation. The distribution of Nb and Ta is controlled by accessory phases such as rutile within the G4 granites, facilitated by high F and lowering the melt temperature, leading to disseminated Nb and Ta mineralisation. Lithium, In, Sn and W are hosted in biotite micas which may prove favourable for breakdown on ingress of hydrothermal fluids. Higher degrees of scattering on trace element plots may be attributable to fluid–rock interactions or variability within the magma chamber. The G3-G4 system is more boron-rich, evidenced by a higher modal abundance of tourmaline. In this system, there is a stronger increase of Sn compared to G1-G2 granites, implying Sn in tourmaline-dominated mineral lodes may represent exsolution from G4 granites. G1-G4 granite abundances can be accounted for by 20–30% partial melting and 10–40% fractionation of a greywacke source. G5 granites are analogues of Rare Metal Granites described in France and Germany. These granites are enriched in Li (average 1363 ppm), Ga (38 ppm), Sn (21 ppm), W (24 ppm), Nb (52 ppm) and Ta (15 ppm). Within G5 granites, the metals partition into accessory minerals such as rutile, columbite-tantalite and cassiterite, forming disseminated magmatic mineralisation. High observed concentrations of Li, In, Sn, W, Nb and Ta in G4 and G5 granites are likely facilitated by high F, Li and P, which lower melt temperature and promote retention of these elements in the melt, prior to crystallisation of disseminated magmatic mineralisation.This study was supported by the European Regional Development Fund and European Social Fund as part of the convergence funding for Cornwall and the Isles of Scilly supporting a PhD for BS (Combined Universities in Cornwall project number11200NCO5) and the European Union (Horizon 2020 project 641650 FAME). The LA-ICP-MS work was supported by a grant from the Natural Environment Research Council (NERC, NE/L001896/1). The Cornwall Heritage Trust are thanked for providing additional funds for analysis. The Natural History Museum, London, UK are thanked for loan of samples from collection BM.2004,P14, specimen numbers 1, 7, 8, 10, 21, 23, 24, 30 and 31 and thin sections P11849, P11851, P11864, P12400 and P12399. Samples GG6, GG15, GG28, and GG44 from the study of Darbyshire and Shepherd (1994) came from Peter Floyd, University of Keele. Steve Pendray, Sharon Uren and Joe Pickles assisted with the sample preparation and analysis at Camborne School of Mines. Sam Hammond assisted with LA-ICP-MS analysis at the Open University. De Lank, Carnsew and Castle-an-Dinas quarries, Richard Scrivener, Nick LeBoutillier and Ben Thompson (Imerys) are thanked for help with sampling. Karel Breiter and one anonymous reviewer are thanked for their generous and constructive comments which have helped to improve the manuscript

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita

© The Author(s). 2018Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle. Conclusions: Here we provide evidence of an early transcriptional response by the nematode upon infection by Pasteuria prior to root invasion. We found that adhesion of Pasteuria endospores to the cuticle induced a down-regulated protein response in the nematode. In addition, we show that fructose bisphosphate aldolase, glucosyl transferase, aspartic protease and ubiquitin coding transcripts are involved in modulating the endospore attachment on the nematode cuticle. Our results add new and significant information to the existing knowledge on early molecular interaction between M. incognita and P. penetrans.Peer reviewedFinal Published versio

Attempts to Image the Early Inflammatory Response during Infection with the Lymphatic Filarial Nematode Brugia pahangi in a Mouse Model

Helminth parasites remain a major constraint upon human health and well-being in many parts of the world. Treatment of these infections relies upon a very small number of therapeutics, most of which were originally developed for use in animal health. A lack of high throughput screening systems, together with limitations of available animal models, has restricted the development of novel chemotherapeutics. This is particularly so for filarial nematodes, which are long-lived parasites with a complex cycle of development. In this paper, we describe attempts to visualise the immune response elicited by filarial parasites in infected mice using a non-invasive bioluminescence imaging reagent, luminol, our aim being to determine whether such a model could be developed to discriminate between live and dead worms for in vivo compound screening. We show that while imaging can detect the immune response elicited by early stages of infection with L3, it was unable to detect the presence of adult worms or, indeed, later stages of infection with L3, despite the presence of worms within the lymphatic system of infected animals. In the future, more specific reagents that detect secreted products of adult worms may be required for developing screens based upon live imaging of infected animals

Cognitive and psychological science insights to improve climate change data visualization

Visualization of climate data plays an integral role in the communication of climate change findings to both expert and non-expert audiences. The cognitive and psychological sciences can provide valuable insights into how to improve visualization of climate data based on knowledge of how the human brain processes visual and linguistic information. We review four key research areas to demonstrate their potential to make data more accessible to diverse audiences: directing visual attention, visual complexity, making inferences from visuals, and the mapping between visuals and language. We present evidence-informed guidelines to help climate scientists increase the accessibility of graphics to non-experts, and illustrate how the guidelines can work in practice in the context of Intergovernmental Panel on Climate Change graphics

Increasing the Depth of Current Understanding: Sensitivity Testing of Deep-Sea Larval Dispersal Models for Ecologists

Larval dispersal is an important ecological process of great interest to conservation and the establishment of marine protected areas. Increasing numbers of studies are turning to biophysical models to simulate dispersal patterns, including in the deep-sea, but for many ecologists unassisted by a physical oceanographer, a model can present as a black box. Sensitivity testing offers a means to test the models' abilities and limitations and is a starting point for all modelling efforts. The aim of this study is to illustrate a sensitivity testing process for the unassisted ecologist, through a deep-sea case study example, and demonstrate how sensitivity testing can be used to determine optimal model settings, assess model adequacy, and inform ecological interpretation of model outputs. Five input parameters are tested (timestep of particle simulator (TS), horizontal (HS) and vertical separation (VS) of release points, release frequency (RF), and temporal range (TR) of simulations) using a commonly employed pairing of models. The procedures used are relevant to all marine larval dispersal models. It is shown how the results of these tests can inform the future set up and interpretation of ecological studies in this area. For example, an optimal arrangement of release locations spanning a release area could be deduced; the increased depth range spanned in deep-sea studies may necessitate the stratification of dispersal simulations with different numbers of release locations at different depths; no fewer than 52 releases per year should be used unless biologically informed; three years of simulations chosen based on climatic extremes may provide results with 90% similarity to five years of simulation; and this model setup is not appropriate for simulating rare dispersal events. A step-by-step process, summarising advice on the sensitivity testing procedure, is provided to inform all future unassisted ecologists looking to run a larval dispersal simulation

The transition from granite to banded aplite-pegmatite sheet complexes: An example from Megiliggar rocks, Tregonning topaz granite, Cornwall

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.The genetic relationship between a granite pluton and adjacent complex of rare-metal pegmatite-aplite-banded sheets (Megiliggar Sheet Complex - MSC) has been studied at the border of the Tregonning topaz granite at Megiliggar Rocks, Cornwall, SW England. Similarities in whole-rock chemical and mineralogical compositions, together with a gradual change in textures away from the granite margin, provide strong evidence for a genetic link between the Tregonning Granite and MSC. The sheets are likely to represent apophyses of residual melt which escaped from the largely crystallised roof of the granite pluton. The escaping melt was peraluminous, had a composition near the F, B, Li slightly enriched granite minimum, and, in comparison with other Cornish granites, was enriched in F, Li, Rb, Cs, Sn, W, Nb, Ta, and U, and depleted in Fe, Mg, Ca, Sr, Th, Zr, and REE. With increasing distance from the Tregonning Granite, the silicate melt crystallised as homogeneous leucogranite sheets and banded complex sheets (i.e. combinations of bands with granitic, aplitic and pegmatitic textures), then layered aplite-pegmatites; this sequence becoming progressively more depleted in the fluxing and volatile elements F, Li, Rb, and Cs, but showing no change in Zr/Hf ratios. The fixed Zr/Hf ratio is interpreted as indicating a direct genetic link (parental melt) between all rock types, however the melt progressively lost fluxing and volatile elements with distance from the granite pluton, probably due to wall-rock reaction or fluid exsolution and migration via fractures. Differentiation of the primary melt into Na-Li-F-rich and separate K-B-rich domains was the dominant chemical process responsible for the textural and mineral diversity of the MSC. On a large (cliff-section) scale, the proximal Na-Li-F-rich leucogranite passes through complex sheets into K-B-rich aplite-pegmatites, whilst at a smaller (< 1 m) scale, the K-B-rich bands are interspersed (largely overlain) by Na-Li-F-rich segregations. The grain size differences between the aplite and pegmatite could be related to pressure fluctuations and/or undercooling.Laser-ablation ICP-MS analyses of micas and tourmaline in Masaryk University Brno were supported by the Czech Science Foundation project No. GA14-13600S. All other analytical work for this contribution was supported by the RVO 67985831 in the Institute of Geology of the Czech Academy of Sciences, Praha. We are grateful to P. Davidson and an anonymous referee for their reviews