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")

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

Coastal connectivity and spatial subsidy from a microbial perspective

© 2016 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. The transfer of organic material from one coastal environment to another can increase production in recipient habitats in a process known as spatial subsidy. Microorganisms drive the generation, transformation, and uptake of organic material in shallow coastal environments, but their significance in connecting coastal habitats through spatial subsidies has received limited attention. We address this by presenting a conceptual model of coastal connectivity that focuses on the flow of microbially mediated organic material in key coastal habitats. Our model suggests that it is not the difference in generation rates of organic material between coastal habitats but the amount of organic material assimilated into microbial biomass and respiration that determines the amount of material that can be exported from one coastal environment to another. Further, the flow of organic material across coastal habitats is sensitive to environmental change as this can alter microbial remineralization and respiration rates. Our model highlights microorganisms as an integral part of coastal connectivity and emphasizes the importance of including a microbial perspective in coastal connectivity studies

Viperin interacts with PEX19 to mediate peroxisomal augmentation of the innate antiviral response.

Peroxisomes are recognized as significant platforms for the activation of antiviral innate immunity where stimulation of the key adapter molecule mitochondrial antiviral signaling protein (MAVS) within the RIG-I like receptor (RLR) pathway culminates in the up-regulation of hundreds of ISGs, some of which drive augmentation of multiple innate sensing pathways. However, whether ISGs can augment peroxisome-driven RLR signaling is currently unknown. Using a proteomics-based screening approach, we identified Pex19 as a binding partner of the ISG viperin. Viperin colocalized with numerous peroxisomal proteins and its interaction with Pex19 was in close association with lipid droplets, another emerging innate signaling platform. Augmentation of the RLR pathway by viperin was lost when Pex19 expression was reduced. Expression of organelle-specific MAVS demonstrated that viperin requires both mitochondria and peroxisome MAVS for optimal induction of IFN-β. These results suggest that viperin is required to enhance the antiviral cellular response with a possible role to position the peroxisome at the mitochondrial/MAM MAVS signaling synapse, furthering our understanding of the importance of multiple organelles driving the innate immune response against viral infection

Extracting science from surveys of our Galaxy

Our knowledge of the Galaxy is being revolutionised by a series of photometric, spectroscopic and astrometric surveys. Already an enormous body of data is available from completed surveys, and data of ever increasing quality and richness will accrue at least until the end of this decade. To extract science from these surveys we need a class of models that can give probability density functions in the space of the observables of a survey -- we should not attempt to "invert" the data from the space of observables into the physical space of the Galaxy. Currently just one class of model has the required capability, so-called "torus models". A pilot application of torus models to understanding the structure of the Galaxy's thin and thick discs has already produced two significant results: a major revision of our best estimate of the Sun's velocity with respect to the Local Standard of Rest, and a successful prediction of the way in which the vertical velocity dispersion in the disc varies with distance from the Galactic plane.Comment: 13 pages. Invited review to appear in Pramana - journal of physics (Indian Academy of Sciences

Temporal dynamics of aquatic communities and implications for pond conservation

Conservation through the protection of particular habitats is predicated on the assumption that the conservation value of those habitats is stable. We test this assumption for ponds by investigating temporal variation in macroinvertebrate and macrophyte communities over a 10-year period in northwest England. We surveyed 51 ponds in northern England in 1995/6 and again in 2006, identifying all macrophytes (167 species) and all macroinvertebrates (221 species, excluding Diptera) to species. The alpha-diversity, beta-diversity and conservation value of these ponds were compared between surveys. We find that invertebrate species richness increased from an average of 29. 5 species to 39. 8 species between surveys. Invertebrate gamma-diversity also increased between the two surveys from 181 species to 201 species. However, this increase in diversity was accompanied by a decrease in beta-diversity. Plant alpha-, beta and gamma-diversity remained approximately constant between the two periods. However, increased proportions of grass species and a complete loss of charophytes suggests that the communities are undergoing succession. Conservation value was not correlated between sampling periods in either plants or invertebrates. This was confirmed by comparing ponds that had been disturbed with those that had no history of disturbance to demonstrate that levels of correlation between surveys were approximately equal in each group of ponds. This study has three important conservation implications: (i) a pond with high diversity or high conservation value may not remain that way and so it is unwise to base pond conservation measures upon protecting currently-speciose habitats; (ii) maximising pond gamma-diversity requires a combination of late and early succession ponds, especially for invertebrates; and (iii) invertebrate and plant communities in ponds may require different management strategies if succession occurs at varying rates in the two groups