9,094 research outputs found

    Benthic algae control sediment-water column fluxes of organic and inorganic nitrogen compounds in a temperate lagoon

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    Coastal lagoons are a common land-margin feature worldwide and function as an important filter for nutrients entering from the watershed. The shallow nature of lagoons leads to dominance by benthic autotrophs, which can regulate benthic-pelagic coupling. Here we demonstrate that both microalgae and macroalgae are important in controlling dissolved inorganic as well as organic nitrogen (DIN and DON) fluxes between the sediments and the water column. Fluxes of nitrogen (NH4+, NO3-, DON, urea, and dissolved free and combined amino acids [DFAA, DCAA]) and O-2 were measured from October 1998 through August 1999 in sediment cores collected from Hog Island Bay, Virginia. Cores were collected from four sites representing the range of environmental conditions across this shallow lagoon: muddy, high-nutrient and sandy, low-nutrient sites that were both dominated by benthic microalgae, and a mid-lagoon site with fine sands covered by dense macroalgal mats. Sediment-water column DON fluxes were highly variable and comparable in magnitude to DIN fluxes; fluxes of individual compounds (urea, DFAA, DCAA) often proceeded simultaneously in different directions. Where sediment metabolism was net autotrophic because of microalgal activity, TDN (total dissolved nitrogen) fluxes, mostly comprised of DIN, urea, and DFAA, were directed into the sediments. Heterotrophic sediments, including those underlying macroalgal mats, were a net source of TDN, mostly as DIN. Macroalgae intercepted sediment-water column fluxes of DIN, urea, and DFAA, which accounted for 27-75% of calculated N demand. DON uptake was important in satisfying macroalgal N demand seasonally and where DIN concentrations were low. Up to 22% of total N uptake was released to the water column as DCAA. Overall, macroalgae assimilated, transformed, and rereleased to the water column both organic and inorganic N on short (minutes-hours) and long (months) time scales. Microalgae and macroalgae clearly regulate benthic-pelagic coupling and thereby influence transformations and retention of N moving across the land-sea interface

    Microbial mediation of \u27reactive\u27 nitrogen transformations in a temperate lagoon

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    Coastal lagoons positioned along the land margin may play an important role in removing or transforming \u27reactive\u27 nitrogen during its transport from land to the ocean. Hog Island Bay is a shallow, coastal lagoon located on the ocean-side of the Delmarva Peninsula in Virginia (USA). External nitrogen inputs are derived primarily from agriculturally enriched groundwater, and these support, in part, the high production of benthic macroalgae and microalgae as the dominant primary producers. This study focuses on processes in the water column (phytoplankton and bacterial) and in the sediments (microalgal and bacterial) responsible for transformations of dissolved inorganic and organic nitrogen (N). Sediment-water exchanges of dissolved inorganic and organic N were measured as well as sediment gross and net mineralization of organic N. Net changes in dissolved inorganic nitrogen concentrations were greater in the water-column incubations than in the incubations including sediment and water. In the water column, metabolism resulted in net uptake of NH4+ during all seasons and in net uptake of NO3- during most seasons. In the sediments, gross mineralization, which ranged from 0.9 to 6.5 mmol N m(-2) d(-1), resulted in short turnover times (\u3c 1 d) for the sediment NH4+ pool; however, sediment-water fluxes of both NH4+ and NO3- were either negligible or directed into the sediments. The NH4+ produced by gross mineralization was rapidly consumed in the dark. Biological processes potentially responsible for removal of sediment NH4+ and NO3- include coupled nitrification-denitrification, dark uptake by benthic microalgae, and immobilization by heterotrophic bacteria. In the absence of dark uptake of NH4+ by benthic microalgae, potential nitrification calculated as the difference between gross mineralization and NH4+ fluxes, would range from 1.5 to 6.4 mmol N m(-2) d(-1), similar to rates observed in a range of other systems. Similarly, potential denitrification rates estimated as the difference between calculated nitrification rates and measured NO3- fluxes would vary from 1.88 to 5.16 mol N m(-2) d(-1) and fall within the range of rates reported for similar systems. However, since calculated benthic microalgal N demand (2.51 to 16.11 mmol N m(-2) d(-1)) exceeded NH4+ release by gross mineralization at all sites and during all seasons, this suggests that dark benthic microalgal uptake was likely to be an important sink for mineralized N. Finally, sediment bacterial N immobilization may also be important given the relatively high C/N of sediment organic matter. These estimates of the potential consumptive processes for mineralized sediment N indicate that the lagoon is likely to retard and or remove \u27reactive\u27 N during its transport to the coastal ocean

    Movement of feeder-using songbirds: the influence of urban features

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    Private gardens provide vital opportunities for people to interact with nature. The most popular form of interaction is through garden bird feeding. Understanding how landscape features and seasons determine patterns of movement of feeder-using songbirds is key to maximising the well-being benefits they provide. To determine these patterns we established three networks of automated data loggers along a gradient of greenspace fragmentation. Over a 12-month period we tracked 452 tagged blue tits Cyantistes caeruleus and great tits Parus major moving between feeder pairs 9,848 times, to address two questions: (i) Do urban features within different forms, and season, influence structural (presence-absence of connections between feeders by birds) and functional (frequency of these connections) connectivity? (ii) Are there general patterns of structural and functional connectivity across forms? Vegetation cover increased connectivity in all three networks, whereas the presence of road gaps negatively affected functional but not structural connectivity. Across networks structural connectivity was lowest in the summer when birds maintain breeding territories, however patterns of functional connectivity appeared to vary with habitat fragmentation. Using empirical data this study shows how key urban features and season influence movement of feeder-using songbirds, and we provide evidence that this is related to greenspace fragmentation.This work was funded under the NERC Biodiversity and Ecosystem Services Sustainability (BESS) thematic programme for the “Fragments Functions and Flows in Urban Ecosystems” project (Reference: NE/J015237/1; http://bess-urban.group.shef.ac.u

    Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

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    GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

    Skewed contributions of individual trees to indirect nature experiences

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    This is the author accepted manuscript. Final version available from Elsevier via the DOI in this record.Exposure to nature is associated with a broad range of benefits to human health. Whilst there has been exploration of how these experiences vary amongst people, the converse – how different individual organisms contribute to human nature experiences – has largely been overlooked. The most common way that people experience nature occurs indirectly, when they are in a room with a natural view. Here, we estimate variation in how individual trees provide indirect nature experiences in an urban human population. As a proxy for its contribution towards indirect nature experiences, within an extended urban area in southern England, UK (n = 612,920) we calculated the number of buildings with line of sight to each tree. We then modelled each tree’s contribution towards these experiences against potential predictors, namely tree height, land ownership, social deprivation, while controlling for human population density. We demonstrate that a small number of trees contribute disproportionately towards indirect nature experiences, with individual trees in socio-economically deprived high density housing falling within the viewscape of significantly more buildings. Further, trees in private gardens were generally more important for providing indirect nature experiences than those in public green spaces. This novel study demonstrates the skewed contribution of different organisms to human population indirect nature experiences. This approach can be applied more broadly to understand how individual organisms provide indirect, incidental and intentional nature experiences. Understanding the ecology behind human nature experiences is an important step towards linking urban design and policy for maximising the health benefits from nature.Natural Environment Research Council (NERC

    Characterisation of spin-incoherent transport in one dimension

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    Spin-incoherent transport in quantum wires, whereby exchange coupling between neighbouring electrons is overcome by thermal energy, leading to the suppression of spin modes of transport expected in a Luttinger liquid, has been observed in the form of a conductance plateau at e(2)/h in the absence of a magnetic field. We present here further characterisation of this spin-incoherent plateau in a source-drain bias, which causes it to evolves to 0.85 x 2e(2)/h. Laterally shifting the channel and illuminating the sample allows us to verify its origin

    HIRA contributes to zygote formation in mice and is implicated in human 1PN zygote phenotype

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    Elucidating the mechanisms underpinning fertilisation is essential to optimising IVF procedures. One of the critical steps involves paternal chromatin reprogramming, in which compacted sperm chromatin packed by protamines is removed by oocyte factors and new histones, including histone H3.3, are incorporated. HIRA is the main H3.3 chaperone governing this protamine-to-histone exchange. Failure of this step results in abnormally fertilised zygotes containing only one pronucleus (1PN), in contrast to normal two-pronuclei (2PN) zygotes. 1PN zygotes are frequently observed in IVF treatments, but the genotype-phenotype correlation remains elusive. We investigated the maternal functions of two other molecules of the HIRA complex, Cabin1 and Ubn1, in mouse. Loss-of-function Cabin1 and Ubn1 mouse models were developed: their zygotes displayed an abnormal 1PN zygote phenotype. We then studied human 1PN zygotes and found that the HIRA complex was absent in 1PN zygotes that lacked the male pronucleus. This shows that the role of the HIRA complex in male pronucleus formation potentially has coherence from mice to humans. Furthermore, rescue experiments in mouse showed that the abnormal 1PN phenotype derived from Hira mutants could be resolved by overexpression of HIRA. We have demonstrated that HIRA complex regulates male pronucleus formation in mice and is implicated in humans, that both CABIN1 and UBN1 components of the HIRA complex are equally essential for male pronucleus formation, and that rescue is feasible

    An identification and brief advice programme for low-risk alcohol consumption in an acute medical setting: an implementation study.

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    OBJECTIVES: To implement an identification and brief advice (IBA) intervention to detect low-risk/hazardous alcohol consumption. DESIGN: Implementation was guided through the use of quality improvement tools and training. SETTING: This study was conducted over an 18-month period from April 2010 to September 2011 on a 42-bed acute medical unit at a central London acute hospital. PARTICIPANTS: All medical patients over the age of 18 admitted to the acute assessment unit were eligible; any patient unable to provide a medical history either through language barriers or due to illness was excluded. MAIN OUTCOME MEASURES: Percentage of medical patients admitted each week to the acute assessment unit who were screened for low-risk/hazardous alcohol consumption. RESULTS: Weekly data were analysed in time series run charts and cross-referenced to the date of educational sessions and their effect on the uptake of screening monitored. A demonstrable change in the mean percentage number of patients screened was observed in different time periods, 67.3-80.1%, following targeted teaching on the AAU. CONCLUSIONS: Our study demonstrates the successful use of quality improvement methodology to guide the implementation of Alcohol Use Disorders Identification Test-Consumption (AUDIT-C), an IBA intervention, in the acute medical setting. The incorporation of the AUDIT-C into an admission document has been well accepted by the junior doctors, attaining an average (mean) of 80% of patients being screened using the tool. Targeted teaching of clinical staff involved in admitting patients appears to be the most effective method in improving uptake of IBA by junior doctors

    Doses of neighborhood nature: the benefits for mental health of living with nature

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    This is the author accepted manuscript. The final version is available from OUP via the DOI in this record.Experiences of nature provide many mental health benefits, particularly for people living in urban areas. The natural characteristics of city residents’ neighborhoods are likely to be critical determinants of the daily nature dose that they receive, however which characteristics are important remains unclear. One possibility is that the greatest benefits are provided by characteristics that are most visible during the day and so most likely to be experienced by people. We demonstrate that of five neighborhood nature characteristics tested, vegetation cover and afternoon bird abundances were positively associated with a lower prevalence of depression, anxiety and stress. Further, dose-response modelling shows a threshold response where the population prevalence of mental health issues is significantly lower beyond minimum limits of neighborhood vegetation cover (depression >20% cover, anxiety >30% cover, stress >20% cover). Our findings demonstrate quantifiable associations of mental health with the characteristics of nearby nature that people actually experience

    Mesenchymal stem cell-based therapy for ischemic stroke

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    Ischemic stroke represents a major, worldwide health burden with increasing incidence. Patients affected by ischemic strokes currently have few clinically approved treatment options available. Most currently approved treatments for ischemic stroke have narrow therapeutic windows, severely limiting the number of patients able to be treated. Mesenchymal stem cells represent a promising novel treatment for ischemic stroke. Numerous studies have demonstrated that mesenchymal stem cells functionally improve outcomes in rodent models of ischemic stroke. Recent studies have also shown that exosomes secreted by mesenchymal stem cells mediate much of this effect. In the present review, we summarize the current literature on the use of mesenchymal stem cells to treat ischemic stroke. Further studies investigating the mechanisms underlying mesenchymal stem cells tissue healing effects are warranted and would be of benefit to the field