Flow regulates biological NO₃¯ and N₂O production in a turbid sub-tropical stream

Streams play a critical role in attenuating the excess reactive nitrogen generated from human activities. These systems can consequently also emit significant amounts of N₂O, a potent greenhouse gas. Models and manipulative experiments now suggest that hydrology regulates the balance between nitrogen removal and N₂O production. We aimed to empirically test this hypothesis by measuring changes in the concentration and isotopic composition of NO₃¯ (δ¹⁸O, δ¹⁵N) and N₂O (δ¹⁸O, δ¹⁵N, site preference) in hyporheic sediments and surface water of a 30 m reach over eight days of falling stream discharge (2.7 to 1.8 m³ s¯¹). The stream was persistently heterotrophic (productivity/respiration: 0.005 - 0.2), while changes in conductivity, δ¹⁸O-H₂O, and ²²²Rn indicated that hyporheic mixing decreased and net groundwater inputs increased as discharge declined. The shallow groundwater had high inorganic N concentrations (2 – 10 mg 1¯¹), but increased in groundwater inputs could not fully explain the concurrent increases in NO₃¯ (1 – 3 mg N 1¯¹) and N₂O (700 to 1000% saturation) in the surface water. Biologically, rather than solely hydrologically, regulated stream nitrogen export was confirmed by changes in N₂O and NO₃¯ isotopic composition. However, isotope patterns indicated that nitrification, not denitrification, increased surface water NO₃¯ and N₂O concentrations as hyporheic exchange decreased. These findings empirically demonstrate how flow dynamics regulate biological NO₃¯ production as well as transport, with implications for predicting aquatic N₂O emissions

Method to Create Arbitrary Sidewall Geometries in 3-Dimensions Using Liga with a Stochastic Optimization Framework

Disclosed herein is a method of making a three dimensional mold comprising the steps of providing a mold substrate; exposing the substrate with an electromagnetic radiation source for a period of time sufficient to render the portion of the mold substrate susceptible to a developer to produce a modified mold substrate; and developing the modified mold with one or more developing reagents to remove the portion of the mold substrate rendered susceptible to the developer from the mold substrate, to produce the mold having a desired mold shape, wherein the electromagnetic radiation source has a fixed position, and wherein during the exposing step, the mold substrate is manipulated according to a manipulation algorithm in one or more dimensions relative to the electromagnetic radiation source; and wherein the manipulation algorithm is determined using stochastic optimization computations

Transformation and fate of microphytobenthos carbon in subtropical, intertidal sediments: potential for long-term carbon retention revealed by ¹³C-labeling

Microphytobenthos (MPB) are ubiquitous in coastal sediments, but the fate of their production (carbon biomass) is poorly defined. The processing and fate of MPB-derived carbon in subtropical intertidal sediments was investigated through in situ labeling with ¹³C-bicarbonate. Of the added ¹³C, 100% was fixed within ~ 4 h, suggesting that MPB productivity was limited by inorganic carbon availability. Although there was rapid transfer of ¹³C to bacteria (within 12 h), a relatively small fraction of ¹³C was transferred to heterotrophs (up to 12.5% of total fixed ¹³C into bacteria and 0.01% into foraminifera). MPB was the major reservoir for ¹³C throughout the study, suggesting that production of extracellular polymeric substances was limited and/or MPB recycled ¹³C. This retention of ¹³C was reflected in remarkably slow estimated turnover times for the MPB community (66–100 d). Over 31 d, ~ 70% of the ¹³C was lost from sediments. This was primarily via resuspension (~ 55%), enhanced by elevated freshwater flow following rainfall. A further ~ 13% was lost via fluxes of dissolved inorganic carbon during inundation. However, ¹³C losses via dissolved organic carbon fluxes from inundated sediments (0.5%) and carbon dioxide fluxes from exposed sediments (<0.1%) were minimal. The retention of ~ 30% of the carbon fixed by MPB within one tidal exposure after > 30 d, despite high resuspension, demonstrates the potentially substantial longer term retention of MPB-derived carbon in unvegetated sediments and suggests that MPB may contribute to carbon burial ("blue carbon")

Protocol for a process-oriented qualitative evaluation of the Waltham Forest and East London Collaborative (WELC) integrated care pioneer programme using the Researcher-in-Residence model

INTRODUCTION: The integration of health and social care in England is widely accepted as the answer to fragmentation, financial concerns and system inefficiencies, in the context of growing and ageing populations with increasingly complex needs. Despite an expanding body of literature, there is little evidence yet to suggest that integrated care can achieve the benefits that its advocates claim for it. Researchers have often adopted rationalist and technocratic approaches to evaluation, treating integration as an intervention rather than a process. Results have usually been of limited use to practitioners responsible for health and social care integration. There is, therefore, a need to broaden the evidence base, exploring not only what works but also how integrated care can most successfully be implemented and delivered. For this reason, we are carrying out a formative evaluation of the Waltham Forest and East London Collaborative (WELC) integrated care pioneer programme. Our expectation is that this will add value to the literature by focusing on the processes by which the vision and objectives of integrated care are translated through phases of development, implementation and delivery from a central to a local perspective, and from a strategic to an operational perspective. METHODS AND ANALYSIS: The qualitative and process-oriented evaluation uses an innovative participative approach-the Researcher-in-Residence model. The evaluation is underpinned by a critical ontology, an interpretive epistemology and a critical discourse analysis methodology. Data will be generated using interviews, observations and documentary gathering. ETHICS AND DISSEMINATION: Emerging findings will be interpreted and disseminated collaboratively with stakeholders, to enable the research to influence and optimise the effective implementation of integrated care across WELC. Presentations and publications will ensure that learning is shared as widely as possible. The study has received ethical approval from University College London's Research Ethics Committee and has all appropriate NHS governance clearances

Evidence for variation in the effective population size of animal mitochondrial DNA

Background: It has recently been shown that levels of diversity in mitochondrial DNA are remarkably constant across animals of diverse census population sizes and ecologies, which has led to the suggestion that the effective population of mitochondrial DNA may be relatively constant. Results: Here we present several lines of evidence that suggest, to the contrary, that the effective population size of mtDNA does vary, and that the variation can be substantial. First, we show that levels of mitochondrial and nuclear diversity are correlated within all groups of animals we surveyed. Second, we show that the effectiveness of selection on non-synonymous mutations, as measured by the ratio of the numbers of non-synonymous and synonymous polymorphisms, is negatively correlated to levels of mitochondrial diversity. Finally, we estimate the effective population size of mitochondrial DNA in selected mammalian groups and show that it varies by at least an order of magnitude. Conclusions: We conclude that there is variation in the effective population size of mitochondria. Furthermore we suggest that the relative constancy of DNA diversity may be due to a negative correlation between the effective population size and the mutation rate per generation

A non-linear optimal estimation inverse method for radio occultation measurements of temperature, humidity and surface pressure

An optimal estimation inverse method is presented which can be used to retrieve simultaneously vertical profiles of temperature and specific humidity, in addition to surface pressure, from satellite-to-satellite radio occultation observations of the Earth's atmosphere. The method is a non-linear, maximum {\it a posteriori} technique which can accommodate most aspects of the real radio occultation problem and is found to be stable and to converge rapidly in most cases. The optimal estimation inverse method has two distinct advantages over the analytic inverse method in that it accounts for some of the effects of horizontal gradients and is able to retrieve optimally temperature and humidity simultaneously from the observations. It is also able to account for observation noise and other sources of error. Combined, these advantages ensure a realistic retrieval of atmospheric quantities. A complete error analysis emerges naturally from the optimal estimation theory, allowing a full characterisation of the solution. Using this analysis a quality control scheme is implemented which allows anomalous retrieval conditions to be recognised and removed, thus preventing gross retrieval errors. The inverse method presented in this paper has been implemented for bending angle measurements derived from GPS/MET radio occultation observations of the Earth. Preliminary results from simulated data suggest that these observations have the potential to improve NWP model analyses significantly throughout their vertical range.Comment: 18 (jgr journal) pages, 7 figure

Reduced performance of native infauna following recruitment to a habitat-forming invasive marine alga

Despite well-documented negative impacts of invasive species on native biota, evidence for the facilitation of native organisms, particularly by habitat-forming invasive species, is increasing. However, most of these studies are conducted at the population or community level, and we know little about the individual fitness consequences of recruitment to habitat-forming invasive species and, consequently, whether recruitment to these habitats is adaptive. We determined the consequences of recruitment to the invasive green alga Caulerpa taxifolia on the native soft-sediment bivalve Anadara trapezia and nearby unvegetated sediment. Initially, we documented the growth and survivorship of A. trapezia following a natural recruitment event, to which recruitment to C. taxifolia was very high. After 12 months, few clams remained in either habitat, and those that remained showed little growth. Experimental manipulations of recruits demonstrated that all performance measures (survivorship, growth and condition) were significantly reduced in C. taxifolia sediments compared to unvegetated sediments. Exploration of potential mechanisms responsible for the reduced performance in C. taxifolia sediments showed that water flow and water column dissolved oxygen (DO) were significantly reduced under the canopy of C. taxifolia and that sediment anoxia was significantly higher and sediment sulphides greater in C. taxifolia sediments. However, phytoplankton abundance (an indicator of food supply) was significantly higher in C. taxifolia sediments than in unvegetated ones. Our results demonstrate that recruitment of native species to habitat-forming invasive species can reduce growth, condition and survivorship and that studies conducted at the community level may lead to erroneous conclusions about the impacts of invaders and should include studies on life-history traits, particularly juveniles. © 2008 Springer-Verlag

The role of mutation rate variation and genetic diversity in the architecture of human disease

Background We have investigated the role that the mutation rate and the structure of genetic variation at a locus play in determining whether a gene is involved in disease. We predict that the mutation rate and its genetic diversity should be higher in genes associated with disease, unless all genes that could cause disease have already been identified. Results Consistent with our predictions we find that genes associated with Mendelian and complex disease are substantially longer than non-disease genes. However, we find that both Mendelian and complex disease genes are found in regions of the genome with relatively low mutation rates, as inferred from intron divergence between humans and chimpanzees, and they are predicted to have similar rates of non-synonymous mutation as other genes. Finally, we find that disease genes are in regions of significantly elevated genetic diversity, even when variation in the rate of mutation is controlled for. The effect is small nevertheless. Conclusions Our results suggest that gene length contributes to whether a gene is associated with disease. However, the mutation rate and the genetic architecture of the locus appear to play only a minor role in determining whether a gene is associated with disease

Treating depression and depression-like behavior with physical activity: An immune perspective

The increasing burden of major depressive disorder makes the search for an extended understanding of etiology, and for the development of additional treatments highly significant. Biological factors may be useful biomarkers for treatment with physical activity (PA), and neurobiological effects of PA may herald new therapeutic development in the future. This paper provides a thorough and up-to-date review of studies examining the neuroimmunomodulatory effects of PA on the brain in depression and depression-like behaviors. From a neuroimmune perspective, evidence suggests PA does enhance the beneficial and reduce the detrimental effects of the neuroimmune system. PA appears to increase the following factors: interleukin (IL)-10, IL-6 (acutely), macrophage migration inhibitory factor, central nervous system-specific autoreactive CD4+ T cells, M2 microglia, quiescent astrocytes, CX3CL1, and insulin-like growth factor-1. On the other hand, PA appears to reduce detrimental neuroimmune factors such as: Th1/Th2 balance, pro-inflammatory cytokines, C-reactive protein, M1 microglia, and reactive astrocytes. The effect of other mechanisms is unknown, such as: CD4+CD25+ T regulatory cells (T regs), CD200, chemokines, miRNA, M2-type blood-derived macrophages, and tumor necrosis factor (TNF)-α [via receptor 2 (R2)]. The beneficial effects of PA are likely to occur centrally and peripherally (e.g., in visceral fat reduction). The investigation of the neuroimmune effects of PA on depression and depression-like behavior is a rapidly developing and important field.Harris A. Eyre, Evan Papps and Bernhard T. Baun

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans